+++ /dev/null
-#include <stdio.h>
-#include <stdlib.h>
-#include <math.h>
-#include <stdarg.h>
-#include <string.h>
-#include <ctype.h>
-#include "io_lib_header.h"
-#include "util_lib_header.h"
-#include "dp_lib_header.h"
-#include "define_header.h"
-
-int aln_has_stockholm_structure (Alignment *A)
-{
- return name_is_in_list ("#=GC SS_cons", A->name, A->nseq, 100);
-}
-
-int get_aln_stockholm_structure (Alignment *A)
-{
- int i;
- if ((i=aln_has_stockholm_structure(A))==-1)
- A=add_alifold2aln (A, NULL);
- return aln_has_stockholm_structure(A);
-}
-int ** update_RNAfold_list (Alignment *A, int **pos, int s, int **l)
-{
- int a=0;
- while (l[a])
- {
- if (!is_gap(A->seq_al[s][l[a][0]]) && !is_gap (A->seq_al[s][l[a][1]]))
- {
- l[a][2]=pos[s][l[a][0]];
- l[a][3]=pos[s][l[a][1]];
- }
- else
- {
- l[a][2]=l[a][3]=-1;
- }
- a++;
- }
- return l;
-}
-
-Alignment *compare_RNA_fold ( Alignment *A, Alignment *B)
-{
- int i1, i2, i;
- int **l1, **l2;
- int **pos1, **pos2;
- int a, b;
- int tot_ol=0, tot_l=0;
-
- i1=get_aln_stockholm_structure (A);
- i2=get_aln_stockholm_structure (B);
-
- l1=vienna2list (A->seq_al[i1]);
- l2=vienna2list (B->seq_al[i2]);
-
- pos1=aln2pos_simple(A, A->nseq);
- pos2=aln2pos_simple(B, B->nseq);
-
-
-
- for (a=0; a< A->nseq; a++)
- {
- char **lu;
- int ol=0, ll1=0, ll2=0;
- if ( A->name[a][0]=='#')continue;
- i=name_is_in_list (A->name[a], B->name, B->nseq, 100);
- if (i!=-1)
- {
- l1=update_RNAfold_list (A,pos1,a, l1);
- l2=update_RNAfold_list (B,pos2,i, l2);
- lu=declare_char (A->len_aln, B->len_aln);
-
- b=0;
- while (l2[b])
- {
-
- if (l2[b][2]==-1 || l2[b][3]==-1);
- else
- {
- ll2++;
- lu[l2[b][2]][l2[b][3]]=1;
-
- }
- b++;
- }
- b=0;
-
- while (l1[b])
- {
-
- if (l1[b][2]==-1 || l1[b][3]==-1);
- else
- {
- ll1++;
- if (lu[l1[b][2]][l1[b][3]]==1)
- {
- A->seq_al[a][l1[b][0]]='6';
- A->seq_al[a][l1[b][1]]='6';
- ol++;
- }
- else
- {
- A->seq_al[a][l1[b][0]]='0';
- A->seq_al[a][l1[b][1]]='0';
- }
- }
- b++;
- }
-
- free_char (lu, -1);
- }
- tot_ol+=ol;
- tot_l+=ll1;
- tot_l+=ll2;
- fprintf ( stdout, "@@ Seq: %s Overalp: %.2f Al1: %.2f Al2: %.2f \n", A->name[a], (float)(ol*200)/(ll1+ll2), (float)(ol*100)/ll1,(float)(ol*100)/ll2);
- }
-
- fprintf ( stdout, "@@ Seq: Tot Overalp: %.2f \n", (float)(tot_ol*200)/(tot_l));
-
- return A;
-}
-int is_neutral(char c1, char c2);
-int is_watson (char c1, char c2);
-int is_watson2 (char c1, char c2);
-int is_watson (char c1, char c2)
-{
- c1=tolower (c1);
- c2=tolower (c2);
- if ( is_watson2 (c1, c2)) return 1;
- else return is_watson2 (c2, c1);
-}
-int is_watson2 (char c1, char c2)
-{
-
- if ( c1=='g' && c2=='c')return 1;
- else if (c1=='a' && (c2=='t' || c2=='u'))return 1;
- return 0;
-}
-int is_neutral (char c1, char c2)
-{
-
- c1=tolower (c1);
- c2=tolower (c2);
- if (is_watson (c1, c2)) return 1;
- else if (c1=='g' && (c2=='t' || c2=='u'))return 1;
- else if ((c1=='t' || c1=='u') && c2=='g')return 1;
- return 0;
-}
-
-int ** vienna2list ( char *seq)
-{
- int a, b, i, i2,l;
- int **list;
- l=strlen (seq);
- list=declare_int (l+1, 8);
- for (i=0,a=0; a<l; a++)
- {
- if ( seq[a]=='(')
- {
- list[i][0]=a;
- for (i2=0,b=a+1; b<l && i2>=0; b++)
- {
- if (seq[b]=='(')i2++;
- else if (seq[b]==')')i2--;
- }
- list[i][1]=b-1;
- i++;
- }
- }
-
- list[i]=NULL;
- return list;
-}
-Alignment *aln2alifold(Alignment *A)
-{
- char *tmp1;
- char *tmp2;
-
- print_aln (A);
- tmp1=vtmpnam (NULL);
- tmp2=vtmpnam (NULL);
- output_clustal_aln (tmp1,A);
- printf_system ("RNAalifold %s >%s 2>/dev/null", tmp1, tmp2);
- return alifold2aln (tmp2);
-}
-
-Alignment *add_alifold2aln (Alignment *A, Alignment *ST)
-{
- int a,b,c,d,p1,p2;
- int r1, rr1, r2, rr2;
- int watson, comp,tot;
- int **compmat;
- int max, p,k;
- int minseq=3;
- int **list;
- int ncomp=0, nwatson=0;
- int cons_l, fold_l;
- int i,l;
-
- if (!ST)
- {
- char *tmp1, *tmp2;
- int f;
- Alignment *T;
- T=copy_aln (A, NULL);
- tmp1=vtmpnam (NULL);
- tmp2=vtmpnam (NULL);
- cons_l=A->len_aln;
- for (a=0; a<A->len_aln; a++)
- {
- for (f=0,b=0; b<A->nseq && f==0; b++)
- {
- if (is_gap (A->seq_al[b][a]))f=1;
-
- }
- if (f)
- {
- cons_l--;
- for (b=0; b<A->nseq; b++)T->seq_al[b][a]='-';
- }
- }
- ST=aln2alifold (T);
- }
- //add or Replace the structure
- l=strlen (ST->seq_al[1]);
- for (a=0; a< l; a++)if (ST->seq_al[1][a]==STOCKHOLM_CHAR)ST->seq_al[1][a]='.';
- if ((i=name_is_in_list ("#=GC SS_cons", A->name, A->nseq, 100))!=-1)
- {
- sprintf (A->seq_al[i], "%s", ST->seq_al[1]);
- }
- else
- {
- A=realloc_aln2 ( A, A->nseq+1, A->len_aln+1);
- sprintf (A->name[A->nseq], "#=GC SS_cons");
- sprintf (A->seq_al[A->nseq], "%s", ST->seq_al[1]);
- A->nseq++;
- }
- return A;
-}
-Alignment * alifold2analyze (Alignment *A, Alignment *ST, char *mode)
-{
- int s;
- int **list;
- int usegap;
-
- s=name_is_in_list ("#=GC SS_cons", A->name,A->nseq, 100);
-
- if (s==-1)
- {
- A=add_alifold2aln (A,ST);
- s=name_is_in_list ("#=GC SS_cons", A->name,A->nseq, 100);
- }
-
- list=vienna2list (A->seq_al[s]);
- list=alifold_list2cov_list (A, list);
-
- usegap=0; //do not use gaped positions by default
- if (mode && strstr (mode, "usegap"))usegap=1;//count positions with gaps
-
- if (!mode)
- {
- A=alifold2cov_stat (A, list,usegap);
- }
- else
- {
- if ( strstr (mode, "stat")) A=alifold2cov_stat (A, list, usegap);
- if ( strstr (mode, "list")) A=alifold2cov_list (A, list, usegap);
- if ( strstr (mode, "aln")) A=alifold2cov_aln (A, list, usegap);
- if ( strstr (mode, "color") )
- {
- Alignment *C;
- C=copy_aln (A, NULL);
- C=alifold2cov_cache (C, list, usegap);
- A=alifold2cov_aln (A, list, usegap);
- if ( strstr ( mode, "ps"))
- output_color_ps (A, C, "stdout");
- else
- output_color_html (A, C, "stdout");
- myexit (EXIT_SUCCESS);
- }
- }
- return A;
-}
-
-
-int ** alifold_list2cov_list (Alignment *A, int **list)
-{
- int a,b,c,d,p1,p2,s;
- int r1, rr1, r2, rr2;
- int neutral,watson, comp,tot, occupancy;
- int **compmat;
- int max, p,k;
- int minseq=3;
-
- int ncomp=0, nwatson=0, nneutral=0, ncomp_wc=0;
- int cons_l, fold_l;
- int nseq;
-
-
- for (nseq=0,a=0; a< A->nseq; a++)if ( A->name[a][0]!='#')nseq++;
- max=((nseq*(nseq-1))/2);
- a=0;
- while (list[a])
- {
- p1=list[a][0];
- p2=list[a][1];
- watson=0;
- comp=0;
- neutral=0;
- tot=0;
- occupancy=0;
- for (c=0; c<A->nseq-1; c++)
- {
- if (A->name[c][0]=='#')continue;
- r1=tolower(A->seq_al[c][p1]);
- r2=tolower(A->seq_al[c][p2]);
- if (is_gap(r1) || is_gap(r2))continue;
- for (d=c+1; d<A->nseq; d++)
- {
- if (A->name[d][0]=='#')continue;
- rr1=tolower(A->seq_al[d][p1]);
- rr2=tolower(A->seq_al[d][p2]);
- if (is_gap(rr1) || is_gap(rr2))continue;
- if (is_watson (r1, r2))watson++;
- if (is_watson (rr1, rr2))watson++;
- if (is_neutral (r1, r2))neutral++;
- if (is_neutral (rr1, rr2))neutral++;
- if (r1!=rr1 && r2!=rr2)comp++;
- occupancy++;
- }
- }
- if (occupancy==0)
- {
- a++;
- continue;
- }
- watson=(watson*100)/(occupancy*2);
- comp=(comp*100)/occupancy;
- neutral=(neutral*100)/(occupancy*2);
- occupancy=(occupancy*100)/max;
- list[a][3]=neutral;
- list[a][4]=watson;
- list[a][5]=comp;
- list[a][6]=occupancy;
-
- if (list[a][3]<100)list[a][7]='I';//incompatible pair
- else
- {
- list[a][7]='N';//Neutral pair
- if (list[a][4]==100)
- {
- list[a][7]='W';//Watson and Crick
- if ( list[a][5]>0)list[a][7]='C'; //Watson and crick compensated
- }
- else if ( list[a][5]>0)
- {
- list[a][7]='c';//compensated
- }
- }
- a++;
- }
-
- return list;
-}
-Alignment *alifold2cov_aln (Alignment *inA,int **list, int ug)
-{
- int a=0;
- a=0;
- Alignment *A;
-
- A=copy_aln (inA, NULL);
- A=realloc_aln2 ( A, A->nseq+1, A->len_aln+1);
- sprintf (A->name[A->nseq], "#=GC SS_analyze");
- sprintf (A->seq_al[A->nseq], "%s", A->seq_al[A->nseq-1]);
- A->nseq++;
- while (list[a])
- {
- char s;
- if (list[a][6]<100 && !ug);
- else
- {
- s=list[a][7];
- A->seq_al[A->nseq-1][list[a][0]]=s;
- A->seq_al[A->nseq-1][list[a][1]]=s;
- }
- a++;
- }
- return A;
-}
-Alignment *alifold2cov_stat (Alignment *A,int **list, int ug)
-{
- int fold=0,watson=0, comp=0, compwc=0, incomp=0, neutral=0;
- int a;
-
- a=0;
- while (list[a])
- {
- int s;
- fold++;
- if (list[a][6]<100 && !ug);
- else
- {
- s=list[a][7];
- watson +=(s=='W')?1:0;
- compwc +=(s=='C')?1:0;
- comp +=(s=='c')?1:0;
- neutral+=(s=='N')?1:0;
- incomp +=(s=='I')?1:0;
- }
- a++;
- }
- fprintf ( stdout, "@@ TOT Nseq:%d tot_len: %d fold: %d neutral: %d watson: %d CorWC: %d cor: %d Incompatible: %d\n",A->nseq-1, A->len_aln,fold, neutral,watson, compwc,comp,incomp);
- return A;
-}
-Alignment *alifold2cov_cache (Alignment *inA, int **list, int ug)
-{
- int a,b, c;
- Alignment *A;
-
- A=copy_aln (inA, NULL);
- a=0;
- while (list[a])
- {
- int v, s;
- if (list[a][6]<100 && !ug);
- else
- {
- s=list[a][7];
- if (s=='C')v=9; //red
- else if ( s=='c')v=7; //orange
- else if ( s=='W')v=5; //Yellow
- else if ( s=='N')v=2; //green
- else if ( s=='I')v=0; //blue;
- for (b=0;b<A->nseq; b++)
- {
- if (A->name[b][0]=='#');
- else
- {
- for (c=0; c<2; c++)
- {
- A->seq_al[b][list[a][c]]='0'+v;
- }
- }
- }
- }
- a++;
- }
- return A;
-}
-
-Alignment *alifold2cov_list (Alignment *A,int **list, int ug)
-{
- int a,b, s;
-
- a=0;
- while (list[a])
- {
- s=list[a][7];
- if (list[a][6]<100 && !ug);
- else if (s=='C')
- {
- fprintf ( stdout, "@@ WC Compensated pair: %4d %4d =>", list[a][0]+1, list [a][1]+1);
- for (b=0; b<A->nseq; b++)if (A->name[b][0]!='#')fprintf ( stdout, "[%c%c]", toupper (A->seq_al[b][list[a][0]]), toupper(A->seq_al[b][list[a][1]]));
- fprintf (stdout,"\n");
- }
- else if (s=='c')
- {
- fprintf ( stdout, "@@ Neural Compensated pair: %4d %4d =>", list[a][0]+1, list [a][1]+1);
- for (b=0; b<A->nseq; b++)if (A->name[b][0]!='#')fprintf ( stdout, "[%c%c]", toupper (A->seq_al[b][list[a][0]]), toupper(A->seq_al[b][list[a][1]]));
- fprintf (stdout,"\n");
- }
- else if (s=='W')
- {
- fprintf ( stdout, "@@ WC pair: %4d %4d =>", list[a][0]+1, list [a][1]+1);
- for (b=0; b<A->nseq; b++)if (A->name[b][0]!='#')fprintf ( stdout, "[%c%c]", toupper (A->seq_al[b][list[a][0]]), toupper(A->seq_al[b][list[a][1]]));
- fprintf (stdout,"\n");
- }
- else if (s=='N')
- {
- fprintf ( stdout, "@@ Neutral pair: %4d %4d =>", list[a][0]+1, list [a][1]+1);
- for (b=0; b<A->nseq; b++)if (A->name[b][0]!='#')fprintf ( stdout, "[%c%c]", toupper (A->seq_al[b][list[a][0]]), toupper(A->seq_al[b][list[a][1]]));
- fprintf (stdout,"\n");
- }
- else if (s=='I')
- {
- fprintf ( stdout, "@@ incompatible pair: %4d %4d =>", list[a][0]+1, list [a][1]+1);
- for (b=0; b<A->nseq; b++)if (A->name[b][0]!='#')fprintf ( stdout, "[%c%c]", toupper (A->seq_al[b][list[a][0]]), toupper(A->seq_al[b][list[a][1]]));
- fprintf (stdout,"\n");
- }
- a++;
- }
-
- return A;
-}
-
-
-Alignment *aln2sample (Alignment *A, int n)
-{
- Alignment *B;
- int a, b, p;
- int **pos;
-
- B=copy_aln (A, NULL);
-
- vsrand(0);
-
- pos=declare_int (A->len_aln, 2);
- for (a=0; a<A->len_aln; a++){pos[a][0]=a;pos[a][1]=rand()%(1000*A->len_aln);}
-
- sort_int (pos, 2, 1, 0, A->len_aln-1);
-
- n=(n==0)?A->len_aln:(MIN (n, (A->len_aln)));
- for (a=0; a<n; a++)
- for (b=0; b<A->nseq; b++)
- A->seq_al[b][a]=B->seq_al[b][pos[a][0]];
- for (b=0; b<A->nseq; b++)
- A->seq_al[b][n]='\0';
- A->len_aln=n;
-
- free_aln (B);
- free_int (pos, -1);
- return A;
-}
-Alignment *aln2bootstrap (Alignment *A, int n)
-{
- Alignment *B;
- int a, b, p;
-
- if (n==0)n=A->len_aln;
- else A=realloc_aln (A, n+1);
- vsrand(0);
- B=copy_aln (A, NULL);
- for (a=0; a<n; a++)
- {
- p=rand ()%A->len_aln;
- for (b=0; b<A->nseq; b++)
- A->seq_al[b][a]=B->seq_al[b][p];
- }
- for ( b=0; b<A->nseq; b++)A->seq_al[b][n]='\0';
- A->len_aln=n;
-
- free_aln (B);
- return A;
-
-}
-
-
-Alignment * aln2random_aln (Alignment *A, char *smode)
-
-{
- int a, b, n, **res;
- int max;
-
-
-
- if ( smode==NULL)
- {
- smode=vcalloc (4, sizeof (char));
- sprintf ( smode, "SCR");//Sequences, Column Residues
- }
- else if ( strm (smode, "NO"))return A;
-
- vsrand(0);
- max=A->nseq*1000;
-
- if ( strstr ( smode, "S"))
- {
- A=aln2scramble_seq (A);
- }
- if ( strstr ( smode, "C"))
- {
-
- res=declare_int (A->nseq, 2);
- for (a=0; a< A->len_aln; a++)
- {
- for (n=0,b=0;b<A->nseq; b++)
- {
- if ( !is_gap(A->seq_al[b][a]))
- {
- res[n][0]=A->seq_al[b][a];
- res[n][1]=rand()%max;
- n++;
- }
- sort_int (res, 2, 1, 0, n-1);
- }
- for (n=0,b=0;b<A->nseq; b++)
- {
- if ( !is_gap(A->seq_al[b][a]))A->seq_al[b][a]=res[n++][0];
- }
- }
- free_int (res, -a);
- }
-
-
- //Redistributes the residues randomly without changing the gap pattern
- if ( strstr ( smode, "R"))
- {
- max=A->len_aln*A->nseq;
- res=declare_int (max, 2);
-
- for (n=0,a=0; a< A->len_aln; a++)
- {
- for (b=0;b<A->nseq; b++)
- {
- if ( !is_gap(A->seq_al[b][a]))
- {
- res[n][0]=A->seq_al[b][a];
- res[n][1]=rand()%max;
- n++;
- }
-
- }
- }
- sort_int (res, 2, 1, 0, n-1);
- for (n=0,a=0; a< A->len_aln; a++)
- {
- for (b=0;b<A->nseq; b++)
- {
- if ( !is_gap(A->seq_al[b][a]))
- {
- A->seq_al[b][a]=res[n++][0];
- }
-
- }
- }
-
- free_int (res, -1);
- }
-
- return A;
-}
-Alignment *score_aln2score_ascii_aln (Alignment *A, Alignment *C)
-{
- //Convert the output of T-Coffee evaluate into a printable score_ascii alignment*/
- //A and C must be sorted
- //sets to 0 lone residues
- int a, b;
-
- for (a=0; a<A->nseq; a++)
- for (b=0; b<A->len_aln; b++)
- {
-
- int rC=C->seq_al[a][b];
- int rA=A->seq_al[a][b];
- if ( !strm (A->name[a], C->name[a])){HERE ("Unsorted aln in score_aln2score_ascii"); myexit (EXIT_FAILURE);}
-
- if ( rA=='x' || rA=='X')C->seq_al[a][b]='9';
- else if ( rC >='0' && rC<='9');
- else if ( rC<10)C->seq_al[a][b]='0'+rC;
- else if ( rC==NO_COLOR_RESIDUE && !is_gap(rA)) C->seq_al[a][b]='0';
- else if ( rC==NO_COLOR_RESIDUE && is_gap(rA))C->seq_al[a][b]='-';
- }
- return C;
-}
-Alignment*aln2gap_cache (Alignment *A, int val)
-{
- Alignment *B;
- int a, b, c, nr;
-
- B=copy_aln (A, NULL);
- for (b=0; b<A->len_aln; b++)
- {
- for (nr=0,a=0; a<A->nseq; a++)nr+=!is_gap (A->seq_al[a][b]);
- for (a=0; a<A->nseq; a++)if (!is_gap(A->seq_al[a][b]))B->seq_al[a][b]=(nr==1)?'0'+val:'1';
- }
- return B;
-}
-
-Alignment* aln2case_aln (Alignment *B, char *upper, char *lower)
-{
- int a, b, c, up, lo;
- Alignment *A;
-
- A=copy_aln (B, NULL);
-
- up=(upper)?upper[0]:'u';
- lo=(lower)?lower[0]:'l';
-
- for (a=0; a<A->nseq; a++)
- for (b=0; b<A->len_aln; b++)
- {
- c=A->seq_al[a][b];
-
- if ( is_gap(c));
- else A->seq_al[a][b]=(isupper (c))?up:lo;
- }
- return A;
-}
-Alignment *aln2scale (Alignment *A, char *coffset)
-{
- int a, b, t, v, n;
- char *s1, *s2;
- char s[1000];
- int offset;
-
- if (coffset)offset=atoi(coffset);
- else offset=0;
-
- sprintf (s, "%d", A->len_aln+offset);
- n=strlen (s);
-
- A=realloc_aln2 (A, A->nseq+n, A->len_aln+1);
- s1=vcalloc ( n+1, sizeof (char));
- s2=vcalloc ( n+1, sizeof (char));
-
- for (a=0; a<n; a++)
- {
- if (a==0)s2[a]='1';
- else strcat (s2, "0");
- sprintf (A->name[A->nseq+a], "%s", s2);
- }
-
- for (a=0; a<A->len_aln; a++)
- {
- sprintf (s1, "%d", a+1+offset);
- s2=invert_string (s1);
- t=strlen (s2);
-
- for (b=0; b<=n; b++)
- {
- if (b>=t) v='0';
- else v=s2[b];
-
- A->seq_al[A->nseq+b][a]=v;
- }
- }
-
- A->nseq+=n;
- return A;
-}
-
-
-
-
-int * pos2list (int * pos, int len, int *nl)
-{
- int *list;
- int a;
- nl[0]=0;
- list=vcalloc (len, sizeof (int));
- for (a=0; a<len; a++)if (pos[a])list[nl[0]++]=a;
- return list;
-}
-int *list2pos (int *list, int nl, int len)
-{
- int *pos, a;
- pos=vcalloc (len, sizeof (int));
- for (a=0; a<nl; a++)pos[list[a]]=1;
- return pos;
-}
-
-int **aln2resindex ( Alignment *A, Alignment *B, FILE *fp)
-{
- int *list, **pos;
- int a, b, n, s;
-
-
- list=vcalloc (A->nseq+((B)?B->nseq:0), sizeof (int));
- pos=aln2pos_simple_2 (A);
- if (B)
- {
- n=B->nseq;
- for ( a=0; a<B->nseq; a++)
- {
- list[a]=name_is_in_list(B->name[a], A->name, A->nseq, 100);
- }
- }
- else
- {
- for ( a=0; a<A->nseq; a++)
- list[a]=a;
- n=A->nseq;
- }
-
-
- fprintf ( fp, "#");
- for ( b=0; b<n; b++)
- {
- s=list[b];
- if ( s!=-1)fprintf (fp, " %s",A->name[s]);
- }
- fprintf (fp, "\n");
-
- for ( a=0; a<A->len_aln; a++)
- {
- for ( b=0; b<n; b++)
- {
- s=list[b];
- if ( s==-1);
- else if (pos[s][a]<0)
- fprintf (fp, "%4d", -1);
- else
- fprintf (fp, "%4d", pos[s][a]);
- }
- fprintf (fp, "\n");
- }
- return pos;
-}
-
-int **index_seq_res ( Sequence *S1, Sequence *S2, int **name_index)
-{
- /*Index the residues of S1 according to S2
- index[seq1 of S1][z]->x, where x is the position of residue z of seq1/S1 in S2->seq[index[Seq1/S1]]
- */
- int a;
- int **index;
- char *seq1=NULL, *seq2=NULL;
- Alignment *Profile;
-
- index=vcalloc ( S1->nseq, sizeof (int*));
-
- for (a=0; a< S1->nseq; a++)
- {
- int len1, len2, b, c;
-
- seq1=S1->seq[a];
-
- if (name_index[a][0]==-1)
- seq2=NULL;
- else if (name_index[a][1]==-1)
- {
- seq2=S2->seq[name_index[a][0]];
- }
- else if ((Profile=seq2R_template_profile (S2, name_index[a][0])) !=NULL)
- {
- seq2=Profile->seq_al[name_index[a][1]];
- }
-
- len1=(seq1)?strlen (seq1):0;
- len2=(seq2)?strlen (seq2):0;
- index[a]=vcalloc (len2, sizeof(int));
-
-
- for (c=0,b=0; b<len2; b++)if( !is_gap(seq2[b]))index[a][c++]=b;
- //index[a]=get_res_index ( seq1, seq2);
- }
- return index;
-}
-
-int **index_seq_name ( Sequence *S1, Sequence *S2)
-{
- /*Index the names of S1 according to S2
- index[seq1 of S1][0]->x if seq1 is the xth sequence of S2
- ->-1 if seq1 is nowhere to be found
- index[seq1 of S1][1]->z if seq1 is the zth sequence within the xth profile of S2
- */
- int **index;
- int a, b, x, z;
- Alignment *Profile;
- index=declare_int (S1->nseq, 2);
-
-
- for ( a=0; a<S1->nseq; a++)
- {
- index[a][0]=index[a][1]=-1;
- x=name_is_in_list (S1->name[a],S2->name,S2->nseq,100);
- if ( x!=-1){index[a][0]=x;index[a][1]=-1;}
- for ( b=0; b<S2->nseq; b++)
- {
- if ((Profile=seq2R_template_profile (S2,b)))
- {
- z=name_is_in_list (S1->name[a],Profile->name,Profile->nseq,100);
- if ( z!=-1){index[a][0]=b;index[a][1]=z;b=S2->nseq;}
- }
- }
- }
- return index;
-}
-
-
-
-
-int *get_name_index (char **l1, int n1, char **l2, int n2)
-{
- int *r;
- int a;
- /*return Array[Index_L1]=Index_L2 */
- r=vcalloc ( n1, sizeof (int));
- for ( a=0; a< n1; a++)
- r[a]=name_is_in_list (l1[a],l2,n2,100);
- return r;
-}
-
-int* get_res_index (char *seq0, char *seq1)
-{
- int *coor, a;
-
- if ( !seq0 || !seq1) return NULL;
-
-
- coor=vcalloc ( strlen (seq0)+1, sizeof (int));
- if (!strm (seq0, seq1))
- {
- int r0, r1 , isr0, isr1;
- int l0=0, l1=0;
- Alignment *A;
- A=align_two_sequences (seq0,seq1,"pam250mt",-5,-1, "myers_miller_pair_wise");
-
- for ( a=0; a< A->len_aln; a++)
- {
- r0=A->seq_al[0][a];r1=A->seq_al[1][a];
- isr0=!is_gap(r0);
- isr1=!is_gap(r1);
- l0+= isr0;
- l1+= isr1;
- if (isr0 && isr1)coor[l0-1]=l1-1;
- else if (isr0) coor[l0-1]=-1;
- }
- free_aln (A);
- }
- else
- {
- int l0;
-
- l0=strlen (seq0);
- for ( a=0;a< l0; a++)
- coor[a]=a;
- }
-
- return coor;
-}
-
-int change_residue_coordinate ( char *in_seq1, char *in_seq2, int v)
-{
- /*Expresses the coordinate of a residue in seq1, in the coordinate system of seq2*/
-
-
- static char *seq1, *seq2;
- static int *coor;
-
-
- if ( seq1 !=in_seq1 || seq2 !=in_seq2)
- {
- int r0, r1 , isr0, isr1;
- int l0=0, l1=0;
- Alignment *A;
- int a;
-
- vfree (coor);
- seq1=in_seq1, seq2=in_seq2;
- A=align_two_sequences (seq1,seq2,"pam250mt", -14, -2, "myers_miller_pair_wise");
-
- coor=vcalloc ( A->len_aln, sizeof (int));
- for ( a=0; a< A->len_aln; a++)
- {
- r0=A->seq_al[0][a];r1=A->seq_al[1][a];
-
- isr0=!is_gap(r0);
- isr1=!is_gap(r1);
- l0+= isr0;
- l1+= isr1;
-
- if (isr0 && isr1)coor[l0-1]=l1-1;
- else if (isr0) coor[l0-1]=-1;
- }
- free_aln (A);
- }
- return coor[v];
-}
-
-
-int ** minimise_repeat_coor (int **coor, int nseq, Sequence *S)
- {
- int **new_coor;
- int a, min;
- new_coor=declare_int ( nseq, 3);
- min=return_min_int (coor, nseq, 2);
- for ( a=0; a< nseq; a++)
- {
- new_coor[a][0]=coor[a][0];
- new_coor[a][1]=coor[a][1];
- new_coor[a][2]=min;
- }
- return new_coor;
- }
-int ** get_nol_seq ( Constraint_list *CL, int **coor, int nseq, Sequence *S)
- {
- int a, s, p, l, nl;
- int **buf;
- int **new_coor;
-
- new_coor=declare_int ( nseq+1, 3);
-
-
- buf=get_undefined_list ( CL);
-
-
-
- for ( a=0; a< nseq; a++)buf[coor[a][0]][coor[a][1]]=1;
-
-
- for ( a=0; a< nseq; a++)
- {
- s=coor[a][0];
- p=coor[a][1]+1;
- l=strlen(S->seq[s]);
- nl=0;
- while ( p<=l && !buf[s][p++])nl++;
- new_coor[a][0]=s;
- new_coor[a][1]=coor[a][1];
- new_coor[a][2]=nl;
- }
- free_int ( buf, -1);
- return new_coor;
- }
-
-
-
-int compare_pos_column( int **pos1,int p1, int **pos2,int p2, int nseq)
- {
- int a,v1, v2;
- int identical=0;
-
- for ( a=0; a< nseq; a++)
- {
-
- v1=pos1[a][p1];
- v2=pos2[a][p2];
-
- if (v1>0 || v2>0)
- {
- if ( v1!=v2)return 0;
- else identical=1;
- }
- }
-
- return identical;
- }
-
-char *seq2alphabet (Sequence *S)
-{
- return array2alphabet (S->seq, S->nseq, "");
-}
-
-char *aln2alphabet (Alignment *A)
-{
- return array2alphabet (A->seq_al, A->nseq, "");
-}
-
-char *array2alphabet (char **array, int n, char *forbiden)
-{
- int a, b, l;
- int *hasch;
- char *alphabet;
-
- hasch=vcalloc (256, sizeof (int));
- alphabet=vcalloc ( 257, sizeof (char));
-
-
- for ( a=0; a<n; a++)
- {
- l=strlen (array[a]);
- for ( b=0; b<l; b++)
- hasch[tolower(array[a][b])]++;
- }
-
- for ( a=0, b=0; a< 256; a++)
- {
- if (hasch[a] && !strrchr(forbiden,a))alphabet[b++]=a;
- }
-
- alphabet[b]='\0';
- vfree (hasch);
- return alphabet;
-}
-
-
-//***************************************************************
-//
- // TM PRED
-//***************************************************************
-
-char* alnpos2hmmtop_pred (Alignment *A,Alignment *Pred, int pos, int mode)
-{
- static char *result;
- static Alignment *Cache;
- static int *score;
- int a, tot, cons;
-
- if (!score)
- {
- score=vcalloc (256, sizeof (int));
- result=vcalloc (100, sizeof (char));
- }
-
- if (!Pred && !Cache)
- {
- Cache=aln2hmmtop_pred (A);
- }
- if (!Pred) Pred=Cache;
-
-
- for (tot=0,a=0; a<A->nseq; a++)
- {
- char s;
- s=Pred->seq_al[a][pos];
- if (!is_gap(s))
- {
- score[tolower(s)]++;
- tot++;
- }
- }
-
- if ( score['h']>score['i'] && score['h']>score['o'])cons='h';
-
- else if ( score['i']>score['o'])cons='i';
- else cons='o';
- if (tot==0) return "";
-
-
- if (mode==VERBOSE)sprintf (result, " H: %3d I: %3d O: %3d P: %c", (score['h']*100)/tot, (score['i']*100)/tot, (score['o']*100)/tot, cons);
- else if (mode == SHORT)sprintf ( result, "%c", cons);
- score['h']=score['o']=score['i']=0;
- return result;
-}
-
-
-Alignment * aln2hmmtop_pred (Alignment *A)
- {
- int a, b, c;
- char *buf, *pred;
- Alignment *PA;
-
- PA=copy_aln (A, NULL);
- buf=vcalloc ( A->len_aln+1, sizeof (char));
-
- for ( a=0; a< A->nseq; a++)
- {
- sprintf (buf, "%s", A->seq_al[a]);
- pred=seq2tmstruc (buf);
- for (c=0,b=0; b<A->len_aln; b++)
- {
- if (!is_gap (PA->seq_al[a][b]))PA->seq_al[a][b]=pred[c++];
- }
- vfree (pred);
- }
- vfree (buf);
- return PA;
- }
-
-char * seq2tmstruc ( char *seq)
- {
- static Sequence *S;
- char *seqfile, *predfile, *buf;
- FILE *fp;
-
- seqfile=vtmpnam (NULL);
- predfile=vtmpnam (NULL);
-
- fp=vfopen (seqfile, "w");
- fprintf ( fp, ">seq1\n%s", seq);
- vfclose (fp);
-
-
- printf_system ( "fasta_seq2hmmtop_fasta.pl -in=%s -out=%s -arch=%s/%s -psv=%s/%s", seqfile, predfile, get_mcoffee_4_tcoffee(), "hmmtop.arch", get_mcoffee_4_tcoffee(), "hmmtop.psv");
- S=get_fasta_sequence (predfile, NULL);
- buf=vcalloc ( strlen (S->seq[0])+1, sizeof (char));
- sprintf ( buf, "%s", S->seq[0]);
-
- free_sequence (S, S->nseq);
-
- return buf;
- }
-
-char * set_blast_default_values()
-{
- set_string_variable ("blast_server", (getenv ("blast_server_4_TCOFFEE"))?getenv ("blast_server_4_TCOFFEE"):"EBI");
- set_string_variable ("pdb_db", (getenv ("pdb_db_4_TCOFFEE"))?getenv ("pdb_db_4_TCOFFEE"):"pdb");
- set_string_variable ("prot_db", (getenv ("prot_db_4_TCOFFEE"))?getenv ("prot_db_4_TCOFFEE"):"uniprot");
- set_int_variable ("prot_min_sim", 0);
- set_int_variable ("prot_max_sim", 100);
-
- set_int_variable ("prot_min_cov", 0);
- set_int_variable ("prot_max_cov", 100);
-
- set_int_variable ("pdb_min_sim", 0);
- set_int_variable ("pdb_max_sim", 100);
- set_int_variable ("pdb_min_cov", 0);
- set_int_variable ("pdb_max_cov", 100);
-
- return;
-}
-
-char * seq2pdb (Sequence *S)
-{
- set_blast_default_values();
- S->nseq=1;
- S=seq2template_seq (S, "PDB", NULL);
- return seq2P_pdb_id(S,0);
-}
-
-Alignment * seq2blast ( Sequence *S)
-{
- Alignment *A;
- set_blast_default_values();
-
- if (S->nseq==1)
- {
- S=seq2template_seq (S, "BLAST", NULL);
- A=seq2R_template_profile(S,0);
- sprintf ( A->name[0], "%s", S->name[0]);
- }
- else
- {
- int a;
- for (a=0; a< S->nseq; a++)
- {
- Sequence *NS;
- char name[1000];
- NS=fill_sequence_struc(1, &(S->seq[a]), &(S->name[a]));
- NS=seq2template_seq (NS, "BLAST", NULL);
- A=seq2R_template_profile(NS,0);
- sprintf ( name, "%s.prf", S->name[a]);
-
- output_fasta_aln (name,A);
- fprintf (stdout, "\nOUTPUT %s\n", name);
- }
- myexit (EXIT_SUCCESS);
- }
- return A;
-}
-
-
-
-
-Sequence * seq2unique_name_seq ( Sequence *S)
-{
- int a;
- if ((a=name_list2unique_name_list (S->nseq, S->name)))
- {
- add_warning ( stderr, "\nWarning: Sequence %s is duplicated in file %s. The sequence will be renamed", S->name[a-1], S->file[a-1]);
- }
- return S;
-}
-Alignment * aln2unique_name_aln ( Alignment *S)
-{
- int a;
- if ((a=name_list2unique_name_list (S->nseq, S->name)))
- {
- add_warning ( stderr, "\nWarning: Sequence %s is duplicated in file %s. The sequence will be renamed", S->name[a-1], S->file[a-1]);
- }
- return S;
-}
-
-
-int name_list2unique_name_list (int n, char **name)
-{
- int duplicate=0;
- int a, b;
-
- for (a=0; a<n-1; a++)
- for (b=a+1; b<n; b++)
- {
- if ( strm (name[a], name[b]))
- {duplicate=a+1;b=a=n;}
- }
-
- if (duplicate)
- {
- char *tmp1, *tmp2;
- Sequence *S;
- FILE *fp;
-
- tmp1=vtmpnam (NULL);
- tmp2=vtmpnam (NULL);
- fp=vfopen (tmp1, "w");
- for (a=0; a< n; a++)fprintf ( fp, ">%s\naggggg\n", name[a]);
- vfclose (fp);
- printf_system ("fasta_aln2fasta_aln_unique_name.pl %s > %s", tmp1, tmp2);
- S=get_fasta_sequence (tmp2, NULL);
- for (a=0; a<n; a++)
- {
- name[a]=vrealloc (name [a], sizeof (int)*(strlen (S->name[a])+1));
- sprintf ( name[a], "%s", S->name [a]);
- }
- free_sequence(S, -1);
- }
- return duplicate;
-}
-char**gene2exons (char **seq, int nseq)
-{
-
- int a, b, c,r;
- for (a=0; a<nseq; a++)
- {
- int in_exon=0, flag=0,l;
- l=strlen (seq[a]);
- for ( b=0; b<l; b++)
- {
- r=seq[a][b];
- if (isupper (r))
- {
- in_exon=1;
- seq[a][b]=(flag)?r:tolower(r);
- }
- else if (in_exon)
- {
- in_exon=0;
- flag=1-flag;
- seq[a][b]='-';
- }
- else seq[a][b]='-';
- }
- }
- return seq;
-}
-Sequence* seq2clean_seq (Sequence *S, char *alp)
-{
- int a, b, c, d, l;
-
- for (a=0; a< S->nseq; a++)
- {
- l=strlen (S->seq[a]);
- for (d=0,b=0; b<l; b++)
- {
- c=S->seq[a][b];
- if ( alp==NULL && !strchr (AA_ALPHABET, c) && !strchr (DNA_ALPHABET, c));
- else if (alp && strchr (alp, c));
- else S->seq[a][d++]=c;
- }
- S->seq[a][d]='\0';
- S->len[a]=strlen (S->seq[a]);
- }
- return S;
-}
-int ** seq2aln_pos (Alignment *A, int *ns, int **l_s)
- {
- int **code;
- int a, b,c, d,l, p , g;
-
-
- l=MAX(strlen (A->seq_al[l_s[0][0]]), strlen (A->seq_al[l_s[1][0]]));
- code=declare_int ((A->S)->nseq,l+1);
-
- for (c=0; c<2; c++)
- {
- l=strlen (A->seq_al[l_s[c][0]]);
- for (d=0; d<ns[c]; d++)
- {
- a=A->order[l_s[c][d]][0];
- for (p=0, b=0; b<l; b++)
- {
- g=is_gap (A->seq_al[l_s[c][d]][b]);
- if (!g){p++; code[a][p]=b+1;}
- }
- }
- }
- return code;
- }
-
-Alignment *local_maln2global_maln (char *seq, Alignment *A)
- {
- /*inputs a BLAST alignmnent where the master sequence may be partila
- outputs the same alignment, while amkeing sure the profile is perfectly in sink with its master sequence
- */
-
- int a, b, c;
- int start, end, rend;
- char qname[100], *p;
- Alignment *B=NULL;
-
- sprintf ( qname, "%s", A->name[0]);
- p=strtok (qname, "_");
- if ( !strm (p, "QUERY"))
- {
- fprintf ( stderr, "\nUnappropriate format for the alignment [%s:FATAL]", PROGRAM);
- myexit (EXIT_FAILURE);
- }
-
- start=atoi(strtok (NULL, "_"));
- end=atoi(strtok (NULL, "_"));
- rend=strlen (seq);
-
- B=copy_aln (A,NULL);
- if ( start>1 || end<rend )A=realloc_aln (A,rend+1);
-
- for (a=0; a<start-1; a++)
- {
- A->seq_al[0][a]=seq[a];
- for ( b=1; b< A->nseq; b++)A->seq_al[b][a]='-';
- }
-
- for (c=0,a=start-1; a< end; a++, c++)
- {
- A->seq_al[0][a]=seq[a];
- for ( b=1; b< A->nseq; b++)
- {
- A->seq_al[b][a]=B->seq_al[b][c];
- }
- }
- for ( a=end; a<rend; a++)
- {
- A->seq_al[0][a]=seq[a];
- for ( b=1; b< A->nseq; b++)A->seq_al[b][a]='-';
- }
- for ( a=0; a< A->nseq; a++) A->seq_al[a][rend]='\0';
- free_aln (B);
-
- A->len_aln=rend;
- return A;
- }
-
-int ** aln2inv_pos ( Alignment *A)
-{
- int **pos,a;
- pos=vcalloc (A->nseq, sizeof (char*));
- for (a=0; a< A->nseq; a++)pos[a]=seq2inv_pos (A->seq_al[a]);
- return pos;
-}
-int * seq2inv_pos ( char *seq)
-{
- /*returns a list where each value gives the index of the corresponding residue in seq*/
- /*Numbering: 1 to L : Analogy to the aln2pos*/
-
- int a,l1, l2;
- int *pos;
-
- l1=strlen ( seq);
- for ( l2=a=0; a< l1; a++)l2+=1-is_gap(seq[a]);
- pos=vcalloc (l2+1, sizeof (int));
- for ( l2=a=0; a< l1; a++)if (!is_gap(seq[a]))pos[++l2]=a+1;
- return pos;
-}
-
-
-int ** aln2pos_simple_2 (Alignment *A)
- {
- int **pos1;
- int **pos2;
- pos1=aln2pos_simple (A, A->nseq);
- pos2=duplicate_int (pos1, A->nseq,read_size_int (pos1[0],sizeof (int)));
- pos1=aln2pos_simple (NULL, 0);
- return pos2;
- }
-int ** aln2pos_simple (Alignment *A, int n_nseq, ...)
- {
- /*
- function documentation: start
- int ** aln2pos_simple (Alignment *A, int n_nseq, ...)
-
-####with two parameter only: Alignment *A, int n_nseq
-
- this function turns A into pos, a matrix where each residue is replace by its index according to the complete sequence.
- the indices in pos are computed using A->order[x][1] that contains the indice of the first residue of seq x of A
-
- n_nseq MUST not be null
-
-####with more than two param:
- int ** aln2pos_simple (Alignment *A, int n_nseq, int *ns, int **ls)
- n_nseq must be set to 0 for the param 3 and four to be read
-
- ns[x]=number seq in group
- ls[x]=list of the sequences in group x ( size=ns[x])
-
- The computation of the indices is only carried out on the scpecified residues
-
-####IMPORTANT
- in pos, the numbering of the residues goes from 1 to L:
- pos[0][0]=3, means that the first position of the first sequence
- in the alignmnet contains residue #3 from sequence A->order[0][0];
-
- function documentation: end
- */
-
- int a, b,c, p, g,l;
- int **T;
-
- int max_nseq;
- int n_len=0;
-
- int *list=NULL;
- int *ns=NULL;
- int **ls=NULL;
-
-
-
- va_list ap;
-
-
- if ( A==NULL)
- {
- return NULL;
- }
- else
- {
- if ( n_nseq>0)
- {
- list=vcalloc(n_nseq, sizeof (int));
- for ( a=0; a< n_nseq; a++)list[a]=a;
- }
- else
- {
- va_start (ap, n_nseq);
- ns=va_arg(ap, int * );
- ls=va_arg(ap, int **);
- va_end(ap);
- list=vcalloc ( ns[0]+ns[1], sizeof (int));
- n_nseq=0;
- for ( a=0; a< ns[0]; a++)list[n_nseq++]=ls[0][a];
- for ( a=0; a< ns[1]; a++)list[n_nseq++]=ls[1][a];
-
- }
- max_nseq=MAX(read_size_int(A->order,sizeof (int*)),return_max_int (A->order, read_size_int(A->order,sizeof (int*)),0))+1;
- n_len=get_longest_string ( A->seq_al,A->max_n_seq, NULL, NULL)+1;
-
-
- T=declare_int (max_nseq, n_len);
- for ( c=0; c< n_nseq; c++)
- {
- a=list[c];
- l=strlen ( A->seq_al[a]);
-
- for ( p=A->order[a][1],b=0; b<l; b++)
- {
- g=1-is_gap(A->seq_al[a][b]);
- p+=g;
- T[a][b]=(g==1)?p:-(1+p);
- if ( A->seq_al[a][b]==UNDEFINED_RESIDUE)T[a][b]=0;
- if ( A->seq_cache && T[a][b]>0)T[a][b]=A->seq_cache[A->order[a][0]][T[a][b]];
- }
- }
- vfree (list);
- }
-
- return T;
- }
-Alignment ** split_seq_in_aln_list ( Alignment **aln, Sequence *S, int n_seq, char **seq_list)
- {
- int a, b, c;
- char * long_seq=NULL;
- int len,l;
- int **translation;
- int **table;
-
-
-
-
- if ( aln==NULL)return NULL;
- translation=declare_int ( S->nseq,2);
-
- for (len=0,a=0; a< S->nseq; a++)
- {
- if((b=name_is_in_list (S->name[a],seq_list, n_seq, 100))!=-1)
- {
- l=strlen(S->seq[a])+1;
- long_seq=vrealloc(long_seq,(len+l+1)*sizeof(char));
- long_seq=strcat(long_seq, S->seq[a]);
- long_seq=strcat(long_seq, "*");
-
- translation[a][0]=b;
- translation[a][1]=len;
- len+=l;
- }
- else translation[a][0]=-1;
- }
-
- long_seq[len-1]='\0';
- len--;
-
- table=declare_int ( len+1, 2);
-
- for ( b=0,a=0; a< S->nseq; a++)
- {
- if ( translation[a][0]!=-1)
- {
- c=1;
- while (long_seq[b]!='\0' && long_seq[b]!='*')
- {
- table[b+1][1]=c++;
- table[b+1][0]=translation[a][0];
- b++;
- }
- table[b][1]=c++;
- table[b][0]=translation[a][0];
- b++;
- }
- }
-
- for ( a=0; a< (aln[-1])->nseq; a++)
- {
- for ( b=0; b< (aln[a])->nseq; b++)
- {
-
- (aln[a])->order[b][0]=table[(aln[a])->order[b][1]][0];
- (aln[a])->order[b][1]=table[(aln[a])->order[b][1]][1];
- sprintf ( (aln[a])->name[b],"%s_%d_%d", S->name[(aln[a])->order[b][0]],a+1,b+1);
- }
- }
- free_int (translation, -1);
- free_int (table, -1);
- return aln;
- }
-
-
-
-Sequence * fill_sequence_struc ( int nseq, char **sequences, char **seq_name)
- {
- int a;
- Sequence *S;
- int shortest, longuest;
-
- if (!sequences)
- {
- shortest=longuest=0;
- }
- else if ( nseq>1)
- {
- shortest=get_shortest_string( sequences, nseq, NULL, NULL);
- longuest=get_longest_string (sequences, nseq, NULL, NULL);
- }
- else if ( nseq==1)
- {
- shortest=longuest=strlen (sequences[0]);
- }
- else
- {
- return NULL;
- }
-
-
- S=declare_sequence (shortest, longuest,nseq);
- S->nseq=nseq;
-
- if (sequences)S->seq=copy_char ( sequences, S->seq, nseq, -1);
- else S->seq=declare_char (S->nseq, 1);
-
- S->name=copy_char ( seq_name, S->name,nseq, -1);
-
- ungap_array (S->seq,nseq);
- for ( a=0; a< S->nseq; a++)S->len[a]=strlen(S->seq[a]);
- return S;
- }
-
-
-Alignment * thread_profile_files2aln (Alignment *A, char *template_file, Fname *F)
-{
-
- Alignment *P;
- int a;
-
- if (!A->S)A->S=aln2seq (A);
- if (template_file)A->S=seq2template_seq (A->S, template_file,F);
- for ( a=0; a< A->nseq; a++)
- {
- P=seq2R_template_profile (A->S, a);
- if ( P)
- {
- P->expand=1;
- sprintf ( P->name[0], "%s", A->name[a]);
- }
- }
-
- return expand_aln (A);
-}
-
-
-
-
-Alignment * expand_aln (Alignment *A)
- {
- /*This function expands the profiles within an alignment*/
-
-
- int a, b, d, e;
- Alignment *MAIN=NULL, *SUB=NULL;
- int n_sub_seq=0;
- int new_nseq=0;
- int *list;
- Alignment *Profile;
-
- if ( !A)return A;
-
-
-
- list=vcalloc (A->nseq, sizeof (int));
- for ( a=0; a< A->nseq; a++)
- {
- Profile=seq2R_template_profile (A->S, A->order[a][0]);
- if (Profile && Profile->expand)
- {
- new_nseq+=Profile->nseq;
- }
- else
- {
- new_nseq++;
- list[n_sub_seq++]=a;
- }
- }
-
- if ( n_sub_seq==A->nseq){vfree(list);return A;}
- else if (n_sub_seq==0){MAIN=copy_aln (A, MAIN);MAIN->nseq=0;}
- else
- {
- MAIN=extract_sub_aln (A, n_sub_seq, list);
- }
- vfree(list);
-
-
- for ( a=0; a< A->nseq; a++)
- {
- Profile=seq2R_template_profile (A->S, A->order[a][0]);
- if ( Profile && Profile->expand)
- {
-
- SUB=copy_aln (Profile,SUB);
-
- SUB=realloc_aln2(SUB, SUB->nseq, A->len_aln+1);
-
- for ( e=0,b=0; b< A->len_aln; b++)
- {
- if ( is_gap(A->seq_al[a][b]))
- {for (d=0; d< SUB->nseq; d++)SUB->seq_al[d][b]='-';}
- else
- {
- for(d=0; d<SUB->nseq; d++)SUB->seq_al[d][b]=Profile->seq_al[d][e];
- e++;
- }
-
- }
- MAIN=stack_aln(MAIN, SUB);
- }
- }
- free_aln (A);
- free_aln (SUB);
- return MAIN;
- }
-Alignment * expand_number_aln (Alignment *A,Alignment *EA)
- {
- /*This function expands the profiles within an alignment*/
-
-
- int a, b, d, e;
- Alignment *MAIN=NULL, *SUB=NULL, *C=NULL;
- int n_sub_seq=0;
- int new_nseq=0;
- int *list;
- Alignment *Profile;
-
- if ( !EA || !A)return EA;
-
- if ( EA->nseq<A->nseq)
- {
- fprintf (stderr, "\n[ERROR:expand_number_aln] Using as a master an expanded aln (%d %d) [FATAL:%s]", EA->nseq, A->nseq,PROGRAM);
- EA->A=A->A=NULL;
- print_aln (EA);
- print_aln (A);
- myexit (EXIT_FAILURE);
- }
-
-
- list=vcalloc (EA->nseq, sizeof (int));
- for ( a=0; a< EA->nseq; a++)
- {
- Profile=seq2R_template_profile (EA->S, EA->order[a][0]);
- if (Profile && Profile->expand)new_nseq+=Profile->nseq;
- else
- {
- new_nseq++;
- list[n_sub_seq++]=a;
- }
- }
-
- if ( n_sub_seq==EA->nseq){vfree(list);return EA;}
- else if (n_sub_seq==0){MAIN=copy_aln (EA, MAIN);MAIN->nseq=0;}
- else
- {
- MAIN=extract_sub_aln (EA, n_sub_seq, list);
- }
-
-
- list[0]=EA->nseq;
- C=extract_sub_aln (EA,1, list);
- vfree(list);
-
-
-
- for ( a=0; a< EA->nseq; a++)
- {
- Profile=seq2R_template_profile (EA->S, EA->order[a][0]);
- if ( Profile && Profile->expand)
- {
- SUB=copy_aln (Profile,SUB);
- SUB=realloc_aln2(SUB, SUB->nseq, EA->len_aln+1);
-
- for ( e=0,b=0; b<= EA->len_aln; b++)
- {
- if (is_gap(A->seq_al[a][b]))
- {
- for ( d=0; d<SUB->nseq; d++)
- SUB->seq_al[d][b]=NO_COLOR_RESIDUE;
- }
- else
- {
- for ( d=0; d<SUB->nseq; d++)
- {
-
- if ( is_gap (Profile->seq_al[d][e]))
- {
- SUB->seq_al[d][b]=NO_COLOR_RESIDUE;
- }
- else SUB->seq_al[d][b]=EA->seq_al[a][b];
- }
- e++;
- }
- }
- for (d=0; d< SUB->nseq; d++)SUB->score_seq[d]=EA->score_seq[a];
-
- MAIN=stack_aln(MAIN, SUB);
- }
- }
-
- MAIN=stack_aln(MAIN, C);
- MAIN->nseq--;
- MAIN->score=MAIN->score_aln=EA->score_aln;
-
- free_aln (SUB);
- free_aln (EA);
-
- free_aln (C);
-
- return MAIN;
- }
-
-Alignment * probabilistic_rm_aa ( Alignment *A, int pos, int len)
-{
- int random_len=0;
- int a, b;
- int left, right;
-
- if ( len<0)
- {
- random_len=1;
- len=-len;
- }
-
- vsrand(0);
-
- if (pos==0)pos= (rand()%(A->len_aln-(2*len+len))) +len;
-
-
- for ( a=0; a< A->nseq; a++)
- {
- if (random_len)left =rand()%len;
- else left=len;
- if (random_len)right=rand()%len;
- else right=len;
- if ( (pos-right)<0 || (pos+left)>A->len_aln)
- {
- add_warning ( stderr, "\nWarning: probabilistic_rm_aa, pos out of range [%s]\n", PROGRAM);
- }
- else
- for ( b=pos-right; b<pos+left; b++)A->seq_al[a][b]=(b==pos)?'~':'*';
- }
-
- ungap_aln (A);
- free_sequence ( A->S, A->nseq);
- A->S=aln2seq (A);
- return A;
-
-}
-
-Alignment * remove_gap_column ( Alignment *A, char *mode)
- {
- int a, b;
- char *p;
- int *seq_list;
- int nseq=0;
- int keep_col, cl;
-
-
- seq_list =vcalloc ( A->nseq, sizeof (int));
- while ( (p=strtok(mode, ":")))
- {
- mode=NULL;
- if (p[0]=='#')
- {
- seq_list[nseq++]=atoi(p+1)-1;
- }
- else if ( (a=name_is_in_list (p, A->name, A->nseq, 100))!=-1)
- {
- seq_list[nseq++]=a;
- }
- }
-
- if ( nseq==0)
- {
- for ( a=0; a< A->nseq; a++)seq_list[a]=a;
- nseq=A->nseq;
- }
-
- for ( cl=0,a=0; a<=A->len_aln; a++)
- {
- for (keep_col=1, b=0; b< nseq && keep_col; b++)
- {
- keep_col=(is_gap(A->seq_al[seq_list[b]][a]))?0:keep_col;
- }
-
- if ( keep_col)
- {
- for ( b=0; b< A->nseq; b++)
- {
- A->seq_al[b][cl]=A->seq_al[b][a];
- }
- cl++;
- }
- else
- {
- for ( b=0; b< A->nseq; b++)
- {
- A->seq_al[b][cl]='-';
- }
- cl++;
- }
- }
- A->len_aln=cl;
- vfree (seq_list);
-
- return A;
- }
-
-
-Alignment * ungap_sub_aln (Alignment *A, int ns, int *ls)
- {
-
- int a, b, c,t;
- int len;
-
- len=strlen ( A->seq_al[ls[0]]);
-
- for ( c=0,a=0; a<len; a++)
- {
- for ( t=0,b=0; b<ns; b++)
- t+=is_gap(A->seq_al[ls[b]][a]);
- if (t==ns);
- else
- {
- for ( b=0; b<ns; b++)
- A->seq_al[ls[b]][c]=A->seq_al[ls[b]][a];
- c++;
- }
- }
- for ( b=0; b<ns; b++)A->seq_al[ls[b]][c]='\0';
- return A;
- }
-
-Sequence * ungap_seq ( Sequence *S)
- {
- int a;
-
- if ( !S)return NULL;
- ungap(S->seq[0]);
- S->max_len=S->min_len=strlen (S->seq[0]);
- for ( a=0; a< S->nseq; a++)
- {
- ungap(S->seq[a]);
- S->len[a]=strlen (S->seq[a]);
- S->max_len=MAX(S->max_len,S->len[a]);
- S->min_len=MAX(S->min_len,S->len[a]);
- }
- return S;
-
- }
-Alignment* shift_column (Alignment *A, int from, int to);
-int max_shift (Alignment *A, int p);
-int column_is_lower (Alignment *A, int p);
-
-Alignment * unalign_aln_2 (Alignment *A, Alignment *C, int t)
-{
- int a, b, pos, len;
- Sequence *S;
- int n, insert;
- if (C)
- {
- for (a=0; a<A->nseq; a++)
- for (b=0; b<A->len_aln; b++)
- {
- int res=C->seq_al[a][b];
- A->seq_al[a][b]=toupper(A->seq_al[a][b]);
- if ((isdigit (res) && (res-'0')<=t))
- A->seq_al[a][b]=tolower(A->seq_al[a][b]);
- }
- }
-
- n=0;
- while ( A->seq_al[0][n])
- {
- insert=0;
- for (b=0; b<A->nseq; b++)if (islower (A->seq_al[b][n]))insert=1;
- if (insert)
- {
- insert_gap_col (A,n,1);
- for (b=0; b<A->nseq; b++)
- {
- if ( islower (A->seq_al[b][n+1]))
- {
- A->seq_al[b][n]=A->seq_al[b][n+1];
- A->seq_al[b][n+1]='-';
- }
- }
- }
- n++;
- }
- for (a=A->len_aln-1; a>=0; a--)
- {
- if (column_is_lower (A,a))
- {
- int s;
- s=max_shift (A,a);
- shift_column (A,a, a+s);
- }
- }
- return A;
-}
-Alignment* shift_column (Alignment *A, int from, int to)
-{
- char *buf;
- int a;
-
- buf=vcalloc (A->nseq, sizeof (char));
- for (a=0; a<A->nseq; a++)
- {
- buf[a]=A->seq_al[a][from];
- A->seq_al[a][from]='-';
- }
- to++;
- insert_gap_col (A, to, 1);
- for ( a=0; a<A->nseq; a++)A->seq_al[a][to]=buf[a];
- vfree (buf);
- ungap_aln (A);
- return A;
-}
-int max_shift (Alignment *A, int p)
-{
- int shift, max_shift, a;
- for (max_shift=A->len_aln,a=0; a< A->nseq; a++)
- {
- shift=0;
-
- if (!islower (A->seq_al[a][p]) || A->seq_al[a][p]=='-')continue;
- while (A->seq_al[a][p+shift+1]=='-')shift++;
- max_shift=MIN(shift,max_shift);
- }
- return max_shift;
-}
-int column_is_lower (Alignment *A, int p)
-{
- int a;
-
- for ( a=0; a<A->nseq; a++)
- if ( !is_gap (A->seq_al[a][p]) && !islower(A->seq_al[a][p]))return 0;
- return 1;
-}
-
-Alignment * unalign_aln (Alignment *A, Alignment *C, int t)
-{
- int a, b, pos, len;
- Sequence *S;
-
- for (a=0; a<A->nseq; a++)
- for (b=0; b<A->len_aln; b++)
- {
- int res=C->seq_al[a][b];
- A->seq_al[a][b]=toupper(A->seq_al[a][b]);
- if ((isdigit (res) && (res-'0')<=t))
- A->seq_al[a][b]=tolower(A->seq_al[a][b]);
- }
-
-
- for (pos=-1, a=0; a<C->nseq; a++)
- {
- b=0;
- while ( C->seq_al[a][b])
- {
- int res=C->seq_al[a][b];
- if ((isdigit (res) && (res-'0')<=t))
- {
- if (pos==-1){pos=b;len=1;}
- else len++;
- }
- else if (pos!=-1)
- {
-
- C=unalign_aln_pos(C,a,pos, len);
- pos=-1;
- }
- b++;
- }
- if ( pos!=-1){C=unalign_aln_pos(C,a,pos, len);pos=-1;}
- }
- S=aln2seq (A);
- thread_seq_struc2aln (C, S);
- A=realloc_aln2 (A, A->nseq, C->len_aln+1);
- A->len_aln=C->len_aln;
- for (a=0; a<A->nseq; a++)sprintf ( A->seq_al[a], "%s", C->seq_al[a]);
- ungap_aln (A);
-
- free_sequence (S, -1);
- return A;
-}
-Alignment * unalign_aln_pos (Alignment *A, int s, int p, int l)
-{
- int a;
- char *buf;
- int unalign=0;
-
-
- buf=vcalloc (l+1, sizeof (char));
- for (a=0; a<l; a++)
- {
- buf[a]=A->seq_al[s][p+a];
- A->seq_al[s][p+a]='-';
- }
-
-
- A=insert_gap_col (A,p, l);
- for (a=0; a<l; a++)
- {
- A->seq_al[s][p+a]=buf[a];
- }
- vfree (buf);
- return A;
-}
-Alignment * insert_gap_col (Alignment *A, int p, int l)
-{
- int a, c;
- char *buf;
- char *gap;
-
- gap=generate_null(l);
- if ( !A || p>=A->len_aln || p<0)return A;
-
- buf=vcalloc (A->len_aln+l+1, sizeof (char));
- A=realloc_aln2(A,A->nseq, A->len_aln+l+1);
- for (a=0; a<A->nseq; a++)
- {
- c=A->seq_al[a][p];
- A->seq_al[a][p]='\0';
- sprintf ( buf, "%s%s%c%s", A->seq_al[a],gap,c,A->seq_al[a]+p+1);
- sprintf (A->seq_al[a], "%s", buf);
- }
- vfree (buf);
- A->len_aln+=l;
- return A;
-}
-Alignment * unalign_residues (Alignment *A, int si1, int si2)
-{
- char *s1, *s2, *ns1, *ns2;
- int l, a, b,r1, r2;
-
- s1=A->seq_al[si1];s2=A->seq_al[si2];
- l=strlen (s1);
-
- ns1=vcalloc (2*l+1, sizeof (char));
- ns2=vcalloc (2*l+1, sizeof (char));
-
- for (b=a=0; a< l; a++)
- {
- r1=s1[a]; r2=s2[a];
- if (is_gap(r1) || is_gap(r2) || isupper (r1) || isupper(r2))
- {
- ns1[b]=(r1=='.')?'-':r1;
- ns2[b]=(r2=='.')?'-':r2;
- b++;
- }
- else
- {
- ns1[b]=r1;
- ns2[b]='-';
- b++;
- ns2[b]=r2;
- ns1[b]='-';
- b++;
- }
- }
- ns1[b]='\0';
- ns2[b]='\0';
- A->seq_al[si1]=ns1;
- A->seq_al[si2]=ns2;
-
-
- A->len_aln=strlen (ns1);
- return A;
-}
-Alignment *degap_aln (Alignment *A)
-{
- //Reomove all the gaps
- int a;
- for ( a=0; a< A->nseq; a++)ungap (A->seq_al[a]);
- return A;
-}
-
-Alignment *ungap_aln_n ( Alignment *A, int p)
- {
-/*remove all the columns of gap-only within an alignment*/
- int a, b, c;
- int t;
- int gp;
-
- if ( A->nseq==0)return A;
-
- for ( c=0,a=0; a< A->len_aln; a++)
- {
- for ( t=0,b=0; b<A->nseq; b++)
- t+=is_gap(A->seq_al[b][a]);
- gp=(t*100)/A->nseq;
- if (p>0 && (gp>=p || (t==A->nseq && p==100) || (t && p==1)));//Remove columns containing more than p% gaps
- else if (p<0 && (gp<=p || (t==0 && p==-100) ||(t && p==-1)));//remove columns containing less than p% gaps
- else
- {
- for ( b=0; b<A->nseq; b++)
- A->seq_al[b][c]=A->seq_al[b][a];
- c++;
- }
- }
- for ( b=0; b<A->nseq; b++)A->seq_al[b][c]='\0';
- A->len_aln=c;
- return A;
- }
-
-Alignment *ungap_aln ( Alignment *A)
-{
- return ungap_aln_n (A, 100);
-}
-/*
-Alignment *ungap_aln ( Alignment *A)
- {
- int a, b, c,t;
-
- for ( c=0,a=0; a< A->len_aln; a++)
- {
- for ( t=0,b=0; b<A->nseq; b++)
- t+=is_gap(A->seq_al[b][a]);
- if (t==A->nseq);
- else
- {
- for ( b=0; b<A->nseq; b++)
- A->seq_al[b][c]=A->seq_al[b][a];
- c++;
- }
- }
- for ( b=0; b<A->nseq; b++)A->seq_al[b][c]='\0';
- A->len_aln=c;
- return A;
-
- }
-*/
-
-
-Alignment *remove_end (Alignment *A)
- {
- int a, b, d;
- int left, right;
-
- for (a=0; a< A->len_aln; a++)
- {
- for ( b=0, d=0; b< A->nseq; b++)
- if ( !is_gap(A->seq_al[b][a]))d++;
- if ( d>1)break;
- }
- left=a;
- for (a=A->len_aln-1; a>0; a--)
- {
- for ( b=0, d=0; b< A->nseq; b++)
- if ( !is_gap(A->seq_al[b][a]))d++;
- if ( d>1)break;
- }
- right=a;
-
- return extract_aln(A, left, right+1);
- }
-
-Alignment* condense_aln (Alignment *A)
-{
- /* condense complementarz columns:
- X- X
- -X ....>X
- X- X
-
- */
- int a, b, plen, n,m, r1, r2;
-
- plen=0;
- while ( A->len_aln !=plen)
- {
- plen=A->len_aln;
- for ( a=0; a< A->len_aln-1; a++)
- {
- for ( n=m=b=0; b< A->nseq; b++)
- {
- r1=is_gap(A->seq_al[b][a]);
- r2=is_gap(A->seq_al[b][a+1]);
- n+=(r1 || r2);
- m+=r1;
- }
-
- if ( n==A->nseq && m!=A->nseq)
- {
- for (b=0; b< A->nseq; b++)
- {
- if (!is_gap(A->seq_al[b][a+1]))
- {
- A->seq_al[b][a]=A->seq_al[b][a+1];
- A->seq_al[b][a+1]='-';
- }
- }
- a++;
- }
- }
- }
- A=ungap_aln(A);
- return A;
-}
-
-
-
-
-void compress_aln ( Alignment *A)
- {
-
- /*remove all the columns of gap-only within an alignment*/
- int a, b, c, d;
-
-
-
- for (c=0, a=0; a< A->len_aln; a++)
- {
- for ( b=0, d=0; b< A->nseq; b++)
- if ( A->seq_al[b][a]!='-'){d=1; break;}
- if ( d==0);
- else
- {
- for (b=0; b< A->nseq; b++)
- A->seq_al[b][c]=A->seq_al[b][a];
- c++;
- }
- }
- A->len_aln=c;
-
- for ( a=0; a< A->nseq; a++)
- A->seq_al[a][c]='\0';
- }
-
-Alignment *seq_coor2aln ( Sequence *S, Alignment *A, int **coor, int nseq)
- {
- int a;
- char *buf;
-
- A=realloc_alignment2(A, nseq, return_maxlen ( S->seq, S->nseq)+1);
- for ( a=0; a< S->nseq; a++)sprintf ( A->file[a], "%s", S->file[a]);
- for ( a=0; a< nseq; a++)
- {
- sprintf (A->name[a], "Repeat_%d_%d", a, coor[a][0]);
- buf=extract_char ( S->seq[coor[a][0]], coor[a][1]-1, coor[a][2]);
- sprintf ( A->seq_al[a],"%s", buf);
- vfree(buf);
- A->order[a][0]=0;
- A->order[a][1]=coor[a][1]-1;
- }
- A->nseq=nseq;
- return A;
- }
-
-Alignment *strings2aln (int nseq,...)
- {
- /*strings2aln(nseq, <name1>, <seq1>, <name2>, <seq2>....)*/
- va_list ap;
- char **list, **list2;
- char **name, **name2;
- Sequence *S;
- Alignment *A;
- int a, max;
-
- va_start(ap, nseq);
- list=vcalloc (nseq, sizeof (char*));
- name=vcalloc (nseq, sizeof (char*));
- for ( a=0; a< nseq; a++)
- {
- name[a]=va_arg(ap,char*);
- list[a]=va_arg(ap,char*);
-
- }
- va_end(ap);
-
- for ( max=0,a=0; a< nseq; a++)
- {
- max=(strlen (list[a])>max)?strlen(list[a]):max;
- }
- list2=declare_char (nseq, max+1);
- name2=declare_char (nseq, MAXNAMES+1);
-
- for ( a=0; a< nseq; a++)
- {
- sprintf ( list2[a], "%s", list[a]);
- sprintf ( name2[a], "%s", name[a]);
- }
-
-
- S=fill_sequence_struc(nseq,list2,name2);
-
- free_char (list2, -1);
- free_char (name2, -1);
- vfree (list);
- vfree(name);
- A=seq2aln(S,NULL, 1);
- return A;
- }
-Alignment *seq2aln ( Sequence *S, Alignment *A,int rm_gap)
- {
- int a;
-
- A=realloc_alignment2(A, S->nseq, S->max_len+1);
- for ( a=0; a< S->nseq; a++)sprintf ( A->file[a], "%s", S->file[a]);
- A->nseq=S->nseq;
- A->max_len=S->max_len;
- A->min_len=S->min_len;
-
- for ( a=0; a< S->nseq; a++)
- {
- A->order[a][0]=a;
- A->order[a][1]=0;
-
- sprintf ( A->seq_comment[a], "%s", S->seq_comment[a]);
- sprintf ( A->aln_comment[a], "%s", S->aln_comment[a]);
-
- sprintf ( A->name[a], "%s", S->name[a]);
- sprintf ( A->seq_al[a], "%s", S->seq[a]);
-
- ungap ( A->seq_al[a]);
- A->len[a]=strlen ( A->seq_al[a]);
-
- if ( rm_gap==0 || rm_gap==NO_PAD)sprintf ( A->seq_al[a], "%s", S->seq[a]);
-
- }
- if (rm_gap!=NO_PAD)padd_aln (A);
- A->S=S;
- return A;
- }
-
-Alignment *padd_aln ( Alignment *A)
-{
- A->seq_al=padd_string (A->seq_al, A->nseq, '-');
- A->len_aln=strlen (A->seq_al[0]);
- return A;
-}
-
-char **padd_string ( char **string, int n,char pad)
-{
- /*Pads a the strings so that they all have the same length*/
-
- int max_len, a;
- char *buf;
-
- max_len=get_longest_string (string,n, NULL, NULL);
- for (a=0; a<n; a++)
- {
- buf=generate_null (max_len-strlen (string[a]));
- strcat ( string[a], buf);
- vfree (buf);
- }
- return string;
-}
-
-Alignment * trim_aln_with_seq ( Alignment *S, Alignment *P)
-{
- Alignment *A, *R;
- int a, b, c;
- static int seqindex;
- P=aln2profile (P);
- S=aln2profile (S);
-
- A=align_two_aln (S,P, "blosum62mt",-8,-1, "myers_miller_pair_wise");
- for (a=0; a<A->nseq; a++) sprintf (A->name[a], "tmpname_%d", seqindex++);
-
- R=copy_aln (A, NULL);
- for (c=0, a=0; a< A->len_aln; a++)
- {
- if ( is_gap (A->seq_al[0][a]));
- else
- {
- for ( b=0; b<A->nseq; b++)
- R->seq_al[b][c]=A->seq_al[b][a];
- c++;
- }
- }
- for ( a=0; a< A->nseq; a++)R->seq_al[a][c]='\0';
- R->len_aln=c;
- R->S=aln2seq (R);
-
- free_aln (S);
- free_aln (P);
- free_aln (A);
-
- return R;
-}
-
-Alignment * add_align_seq2aln ( Alignment *A, char *seq, char *seq_name)
- {
- if ( !A)
- {
- A=declare_aln (NULL);
- A=realloc_aln2 ( A, 1, strlen (seq)+1);
- A->nseq=0;
- sprintf ( A->name[A->nseq], "%s", seq_name);
- sprintf ( A->seq_al[A->nseq], "%s", seq);
- A->nseq++;
-
- }
- else if ( strlen (seq)!=A->len_aln)
- {
- fprintf ( stderr, "\nError: Attempt to stack incompatible aln and aligned sequence[FATAL]\n");
- myexit (EXIT_FAILURE);
- A=NULL;
- }
- else
- {
-
- A=realloc_aln2 ( A, A->nseq+1, A->len_aln+1);
- sprintf ( A->name[A->nseq], "%s", seq_name);
- sprintf ( A->seq_al[A->nseq], "%s", seq);
- A->nseq++;
- }
- return A;
- }
-
-
-Alignment *aln2number (Alignment *A)
- {
- A->seq_al=char_array2number(A->seq_al, A->nseq);
- return A;
- }
-Sequence *seq2number (Sequence *A)
- {
- A->seq=char_array2number(A->seq, A->nseq);
- return A;
- }
-
-Sequence * aln2seq (Alignment *A)
-{
- return aln2seq_main(A, RM_GAP);
-}
-Sequence * aln2seq_main (Alignment *A, int mode)
- {
- Sequence *LS;
- int a;
- int maxlen;
-
- if ( !A) return NULL;
- else if ( A->nseq==0)return NULL;
- for (maxlen=0,a=0; a<A->nseq; a++)maxlen=MAX(maxlen, strlen (A->seq_al[a]));
-
-
- LS=declare_sequence ( maxlen+1, maxlen+1, A->nseq);
- LS->nseq=A->nseq;
- for ( a=0; a< LS->nseq; a++)
- {
- sprintf (LS->file[a],"%s", A->file[a]);
-
- sprintf ( LS->seq[a], "%s", A->seq_al[a]);
-
- if (mode==RM_GAP)ungap ( LS->seq[a]);
-
- LS->len[a]=strlen ( LS->seq[a]);
-
- sprintf ( LS->seq_comment[a], "%s",A->seq_comment[a]);
- sprintf ( LS->aln_comment[a], "%s",A->aln_comment[a]);
- sprintf ( LS->name[a], "%s", A->name[a]);
- }
- return LS;
- }
-
-Sequence *keep_residues_in_seq ( Sequence *S, char *list, char replacement)
-{
- Alignment *A=NULL;
- int a;
-
- A=seq2aln (S, A,1);
- A=keep_residues_in_aln ( A, list, replacement);
- for ( a=0; a< A->nseq; a++)
- {
- ungap (A->seq_al[a]);
- sprintf ( S->seq[a], "%s", A->seq_al[a]);
- }
- free_aln (A);
- return S;
-}
-
-
-Alignment *aln2short_aln ( Alignment *A, char *list, char *new, int spacer)
-{
- int a, b, r, cl, l;
- char *buf;
-
- for ( a=0; a< A->nseq; a++)
- {
- buf=vcalloc ( strlen (A->seq_al[a])+1, sizeof (char));
-
- for (l=0,cl=0, b=0; b< A->len_aln; b++)
- {
- r=A->seq_al[a][b];
- if ( is_gap(r));
- else if ( is_in_set (r, list))
- {
- if (cl){cl=0; buf[l++]=new[0];}
- buf[l++]=r;
- }
- else
- {
- if ( cl==spacer){buf[l++]=new[0];cl=0;}
- cl++;
- }
-
- }
-
- buf[l]='\0';
- sprintf (A->seq_al[a], "%s", buf);
- vfree (buf);
- }
- return A;
-}
-
-Alignment *keep_residues_in_aln ( Alignment *A, char *list, char replacement)
-{
- return filter_keep_residues_in_aln (A,NULL, 0, -1, list, replacement);
-}
-Alignment *filter_keep_residues_in_aln ( Alignment *A,Alignment *ST, int use_cons, int value, char *list, char replacement)
-{
- char **sl;
- int n, a;
-
- n=strlen (list);
- sl=declare_char (n+1, 256);
- for (a=0; a< n; a++)
- sprintf ( sl[a], "%c%c", list[a], list[a]);
- sprintf ( sl[a],"#%c", replacement);
- A=filter_aln_convert (A, ST,use_cons,value, n+1, sl);
- free_char (sl, -1);
- return A;
-}
-
-
-Alignment *filter_convert_aln ( Alignment *A,Alignment *ST, int use_cons, int value, int n, ...)
-{
- va_list ap;
- char **sl;
- int a;
- va_start (ap, n);
- sl=vcalloc ( n,sizeof(char*));
- for ( a=0; a< n; a++)
- {
- sl[a]=va_arg(ap, char * );
- }
- va_end(ap);
- A=filter_aln_convert (A,ST,use_cons,value, n,sl);
- vfree(sl);
- return A;
-}
-
-Alignment * filter_aln ( Alignment *A, Alignment *ST, int value)
- {
- return filter_aln_convert (A, ST,0,value,DELETE, NULL);
- }
-Alignment * filter_aln_switchcase ( Alignment *A, Alignment *ST,int use_cons, int value)
- {
- return filter_aln_convert (A, ST,0,value,SWITCHCASE, NULL);
- }
-Alignment * filter_aln_upper_lower ( Alignment *A, Alignment *ST,int use_cons, int value)
- {
- return filter_aln_convert (A, ST,use_cons,value, LOWER, NULL);
- }
-Alignment * filter_aln_lower_upper ( Alignment *A, Alignment *ST,int use_cons, int value)
- {
-
- return filter_aln_convert (A, ST,use_cons,value, UPPER, NULL);
- }
-Alignment * STseq2STaln ( Alignment *A, Alignment *ST)
- {
- int a, i=0;
-
- if (ST && ST->len_aln !=A->len_aln)
- {
- Sequence *S_T, *S_A;
-
- S_T=aln2seq (ST);
- S_A=aln2seq (A);
-
- for (a=0; a< A->nseq; a++)
- {
- i=name_is_in_list (A->name[a], S_T->name,S_T->nseq, 100);
- if (i!=-1)
- {
- char *s1, *s2;
- s1=(S_T)->seq[i];ungap(s1);
- s2=(S_A)->seq[a];ungap(s2);
-
- if ( strlen (s1)!=strlen(s2))
- {
- fprintf ( stderr, "%s\n%s\n", s1, s2);
- printf_exit (EXIT_FAILURE, stderr, "ERROR: Sequence %s has different length in the alignment and in the structure Alignment [FATAL:%s]\n", A->name[a], PROGRAM);
- }
- }
- }
- ST=copy_aln (A, ST);
- thread_seq_struc2aln (ST,S_T);
- }
-
- return ST;
- }
-Alignment * merge_annotation ( Alignment *A, Alignment *ST, char *seq)
-{
- int s, a, b;
-
- ST=STseq2STaln (A, ST);
- if ( seq==NULL)s=0;
- else
- s=name_is_in_list ( seq, A->name, A->nseq, 100);
-
- if (s==-1)
- {
- add_warning ( stderr, "\nERROR: %s is not in your MSA [FATAL: %s]", PROGRAM);
- myexit (EXIT_FAILURE);
- }
-
- for (a=0; a<A->len_aln; a++)
- {
- int t, r;
-
- t=A->seq_al[s][a];
- if (is_gap (t))continue;
- for (b=0; b<A->nseq; b++)
- {
- t=A->seq_al[s][a];
- r=ST->seq_al[b][a];
- if ( isdigit (r))
- {
- if (!isdigit(t) || (isdigit (t) && t<r))
- A->seq_al[s][a]=r;
- }
- }
- }
- return A;
-}
-
-
-
-Alignment * filter_aln_convert ( Alignment *A, Alignment *ST,int use_cons, int value, int n_symbol,char **symbol_list)
- {
- int a, b, c;
- int st;
- int cons=0;
-
-
- ST=STseq2STaln (A, ST);
- if ( ST && use_cons)
- {
- cons=name_is_in_list ("con", ST->name,ST->nseq+1, 100);
- if ( cons==-1)cons=name_is_in_list ("cons", ST->name,ST->nseq+1, 100);
- if ( cons==-1)cons=name_is_in_list ("Cons", ST->name,ST->nseq+1, 100);
- if ( cons==-1)
- {
- use_cons=0;
- fprintf (stderr, "WARNING: Could Not Use the Consensus Sequence [WARNING:%s]\n", PROGRAM);
- }
- }
-
- A->residue_case=KEEP_CASE;
- for ( a=0; a< A->nseq; a++)
- {
- if(value!=10 && ST && !use_cons)
- {
- c=name_is_in_list (A->name[a], ST->name, ST->nseq,100);
- if (c==-1)st=11;
- }
-
- for ( b=0; b< A->len_aln; b++)
- {
- if ( value==10 || !ST)st=11;
- else if ( ST && use_cons)
- {
- st=(isdigit(ST->seq_al[cons][b]))?ST->seq_al[cons][b]-'0':ST->seq_al[cons][b];
- }
- else st=(isdigit(ST->seq_al[c][b]))?ST->seq_al[c][b]-'0':ST->seq_al[c][b];
-
-
- if ( st==value || value==-1 || st==NO_COLOR_RESIDUE)
- {
- if ( n_symbol==UPPER && !symbol_list)A->seq_al[a][b]=toupper (A->seq_al[a][b]);
- else if ( n_symbol==LOWER && !symbol_list)A->seq_al[a][b]=tolower (A->seq_al[a][b]);
- else if ( n_symbol==SWITCHCASE && !symbol_list)
- {
- if ( !isalpha(A->seq_al[a][b]));
- else if (isupper (A->seq_al[a][b]))A->seq_al[a][b]=tolower (A->seq_al[a][b]);
- else if (islower (A->seq_al[a][b]))A->seq_al[a][b]=toupper (A->seq_al[a][b]);
- }
- else if ( n_symbol==DELETE && !symbol_list)A->seq_al[a][b]='-';
- else
- {
- A->seq_al[a][b]=convert(A->seq_al[a][b],n_symbol,symbol_list);
- }
- }
-
- }
- }
- return A;
- }
-
-
-char ** sar_aln2motif (Alignment *A, Alignment *B, int *pos, int c);
-char ** sar_aln2motif (Alignment *A, Alignment *B, int *pos, int c)
-{
- static Alignment *I;
- static Alignment *O;
- int a, b, o, i;
-
- float tp,tn,fp,fn,best, sp, sn, sen2;
- float best_pred=-1;
- int best_motif=0;
-
-
- int n1;
- static char ***alp;
- static int *alp_size;
-
- char ***motif_list;
- int n;
-
-
- if (!I)
- {
- I=copy_aln(A, NULL);
- O=copy_aln(A, NULL);
- }
-
-
-
- I->nseq=O->nseq=I->len_aln=O->len_aln=0;
- for (a=0; a<A->len_aln; a++)
- {
- if (pos[a])
- {
- for (i=o=0,b=0; b<A->nseq; b++)
- {
-
- if ( is_gap(A->seq_al[b][a]))return 0;
- if (B->seq_al[b][c]=='I')I->seq_al[i++][I->len_aln]=A->seq_al[b][a];
- else O->seq_al[o++][O->len_aln]=A->seq_al[b][a];
- }
- I->len_aln++;
- O->len_aln++;
- }
- }
-
- if (O->len_aln==0 || I->len_aln==0) return 0;
- O->nseq=o;
- I->nseq=i;
- for (a=0; a<o; a++)O->seq_al[a][O->len_aln]='\0';
- for (a=0; a<i; a++)I->seq_al[a][I->len_aln]='\0';
-
- alp=vcalloc ( sizeof (char**), I->len_aln);
- alp_size= vcalloc ( I->len_aln, sizeof (int));
- for (a=0; a<I->len_aln; a++)
- {
- char *col;
- alp[a]=string2alphabet ( (col=aln_column2string (I,a)),2, &alp_size[a]);
- vfree (col);
- }
-
-
-
- motif_list=generate_array_string_list (I->len_aln, alp, alp_size, &n, NULL, OVERLAP);
- best_pred=best_motif=0;
- for (a=0; a<n; a++)
- {
-
- tp=tn=fp=fn=0;
-
- for (b=0; b<I->nseq; b++)
- {
- if (match_motif (I->seq_al[b], motif_list[a]))tp++;
- else fn++;
- }
- for (b=0; b<O->nseq; b++)
- {
- if (match_motif (O->seq_al[b], motif_list[a]))fp++;
- else tn++;
- }
- rates2sensitivity (tp, tn, fp, fn, &sp, &sn, &sen2, &best);
-
- if (best> best_pred)
- {
- best_pred=best;
- best_motif=a;
- }
- }
-
- output_Alignment_without_header ( I, stdout);
- fprintf ( stdout, "\n");
- output_Alignment_without_header ( O, stdout);
-
-
- fprintf ( stdout, "\nMotifCompound %d pred: %.2f motif: ", c, best_pred);
- for (n1=0, a=0; a<I->len_aln; a++)
- {
- char *m;
- int l;
- m=motif_list[best_motif][a];
- fprintf ( stdout, "[%s]-", m);
- l=strlen (m);
- n1+=(l==1 && !strm ("*",m) )?1:0;
- }
- fprintf (stdout, "SCORE: %d", n1);
-
- for (a=0; a<n; a++)vfree (motif_list[a]);
- vfree (motif_list);
- free_arrayN((void ***) alp, 3);
- vfree (alp_size);
-
- return NULL;
-}
-
-
-
-
-void explore_weight_matrix (Alignment *A, Alignment *B, int range, int n, int *array);
-void explore_weight_matrix (Alignment *A, Alignment *B, int range, int n, int *array)
-{
- int a;
- if ( n==A->len_aln)
- {
- fprintf ( stdout, "\n W:");
- for (a=0; a<A->len_aln; a++)fprintf ( stdout, "%d", array[a]);
- fprintf ( stdout, " %.4f",(float)sar_aln2r(A,B,array,0));
- return;
- }
- else
- {
- for ( a=0; a<range; a++)
- {
- array[n]=a;
- explore_weight_matrix (A, B, range, n+1, array);
- }
- }
-}
-float search_best_combo(Alignment *A, Alignment *B);
-void search_best_combo_sar_aln(Alignment *A, Alignment *B);
-void search_best_combo_sar_aln(Alignment *A, Alignment *B)
-{
- int a,b,c;
- Alignment *S;
- float s;
- int w=5;
-
- S=copy_aln (B, NULL);
- S->len_aln=w;
- for ( a=0; a<B->len_aln-w;a++)
- {
- for (b=0; b<B->nseq; b++)
- {
- for (c=0; c<w; c++)
- {
- S->seq_al[b][c]=B->seq_al[b][a+c];
- }
- S->seq_al[b][c]='\0';
- }
-
- s=search_best_combo (A, S);
- fprintf ( stdout,"\nP: XXXX \nP: XXXXX A=%d / %d", a, B->len_aln);
-
- }
-
-}
-
-float search_best_combo(Alignment *A, Alignment *B)
-{
- int a, b, c, d, best_pos,nl, max;
- float best_score, score;
- int *list, *pos;
-
- int w;
- int combo_mode=1; //1: greedy 2: consider all thw w combinations;
- FILE *fp2;
- static int **M;
- max=2;
- int delta=0;
- w=1;
-
- pos=vcalloc ( A->len_aln, sizeof (int));
- list=vcalloc (A->len_aln, sizeof (int));
- nl=0;
-
- if ( combo_mode==1)
- {
- for (a=0; a< max; a++)
- {
- for (best_score=-9999,best_pos=0,b=0; b< A->len_aln-w; b++)
- {
- for (c=0; c<nl; c++)pos[list[c]]=1;
- for (c=0; c<w; c++)pos[b+c]=1;
- score=sar_aln2r(A,B,pos,0);
- if ( score>best_score)
- {
- best_score=score;
- best_pos=b;
- }
- for (c=0; c<w; c++)pos[b+c]=0;
- }
- if (best_pos==list[nl-1])break;
- list[nl++]=best_pos;
- for (b=0; b<nl; b++) pos[list[b]]=1;
- fprintf ( stdout, "\n%2d P: %d S:%.3f Delta= %d", nl,best_pos, best_score, (int)sar_aln2delta(A,B, pos,0));
- for (b=0; b<nl; b++) pos[list[b]]=0;
-
-
- }
- for (a=0; a<nl; a++) pos[list[a]]=1;
- fprintf ( stdout, "\nR: %3f " ,(float)sar_aln2r(A,B,pos,1));
-
- }
- else if ( combo_mode==2)
- {
- int *array;
- char *tmpf;
- FILE *fp;
- char *buf=NULL;
- int *preset, n_preset;
-
- tmpf=vtmpnam (NULL);
- max=1;
- generate_array_int_list (max, 0,A->len_aln-1, 1,NULL, tmpf);
- printf_system ( "cp %s testfile", tmpf);
- buf=vcalloc ( 1000, sizeof (char));
- fp=vfopen (tmpf, "r");
- best_score=-99999;
-
- n_preset=0;
- preset=vcalloc (A->len_aln, sizeof (int));
- preset[n_preset++]=353;
- preset[n_preset++]=361;
- //preset[n_preset++]=365;
- //preset[n_preset++]=187;
- //preset[n_preset++]=397;
- //preset[n_preset++]=492;
-
-
- while ( (buf=vfgets ( buf, fp))!=NULL)
- {
-
- array=string2num_list (buf);
-
- for (a=1; a<=max; a++)
- {
- pos[array[a]]=1;
- }
- for ( a=0; a<n_preset; a++)pos[preset[a]]=1;
-
- score=sar_aln2r(A,B,pos,0);
-
- if ( score>best_score)
- {
- best_score=score;
- fprintf ( stdout, "\n");
- for (a=0; a<n_preset; a++)fprintf (stdout, "%2d ", preset[a]);
- for (a=1; a<=max; a++)fprintf (stdout, "%2d ", array[a]);
- fprintf ( stdout, " R: %.3f", best_score);
- for (nl=0,a=0; a<n_preset; a++)list[nl++]=preset[a];
- for (a=1; a<=max; a++)list[nl++]=array[a];
- }
- //if ( score!=0)HERE ("R=%.2f", score);
- for (b=1; b<=max; b++)
- pos[array[b]]=0;
- vfree (array);
- }
- fprintf ( stdout, "\n");
- vfclose (fp);
- //for (a=0; a<max; a++)fprintf (stdout, "%2d ", array[best_pos][a]);
- //fprintf ( stdout, " R: %.3f", best_score);
- }
- for (c=0; c<B->len_aln; c++)
- {
- sar_aln2motif (A,B,pos, c);
-
- }
- myexit (EXIT_FAILURE);
- HERE ("***************");
- fp2=vfopen ("aln.aln", "w");
- for (a=0; a<A->nseq; a++)
- {
- fprintf (fp2, ">%s\n", A->name[a]);
- for ( b=0; b<nl; b++)fprintf (fp2, "%c", A->seq_al[a][list[b]]);
- fprintf ( fp2, "\n");
- }
- vfclose (fp2);
- HERE ("Output aln.aln");
- if (1)
- {
- float tp=0, tn=0, fp=0, fn=0, pp2=0,pp=0, sn,sn2, sp;
- int **result,**result2,**compound_score, *ref_score,n2,n, s, p, c;
- Alignment *AI, *AO;
- int simI, simO;
-
- compound_score=declare_int (B->len_aln, 2);
- ref_score=vcalloc (nl, sizeof (int));
-
- result=declare_int (B->len_aln*A->nseq*A->nseq, 2);
- result2=declare_int (B->len_aln*A->nseq*A->nseq, 2);
-
- for (n2=c=0; c< B->len_aln; c++)
- {
-
- int sar1, sar2;
- pp=tp=tn=fp=fn=0;
- if (!M)M=read_matrice ("blosum62mt");
- for (n=0,a=0; a<A->nseq-1; a++)
- {
- for (b=a+1; b<A->nseq;b++)
- {
- for (s=0,p=0; p<nl; p++)
- {
- char r1, r2;
-
- r1=A->seq_al[a][list[p]];
- r2=A->seq_al[b][list[p]];
- if ( !is_gap (r1) && !is_gap(r2))s+=M[r1-'A'][r2-'A'];
- }
- result2[n2][0]=result[n][0]=s;
-
- sar1=B->seq_al[a][c];sar2=B->seq_al[b][c];
-
- if (sar1=='I' && sar1==sar2)
- {
- result2[n2][1]=result[n][1]=1;
- pp++;pp2++;
- n++;n2++;
- }
- else if ( sar1==sar2 && sar1=='O')
- {
- ;
- }
- else
- {
- result2[n2][1]=result[n][1]=0;
- n++;n2++;
- }
- //else if ( s1==s2=='O')result[n][1]=-1;
- }
- }
-
- if (pp==0)continue;
- sort_int_inv (result, 2, 0, 0, n-1);
-
-
- for (tp=0,a=0; a<n; a++)
- {
- tp+=result[a][1];
- if ((pp-tp) == (a-tp))break;
- }
- fp=a-tp;
- fn=pp-tp;
- tn=n-pp;
-
- sn=(tp/(tp+fn));
- sn2=(tp/(tp+fp));
- sp=(tn/(tn+fp));
- fprintf ( stdout, "\nCompound %3d sn: %.3f sn2: %.3f sp: %.3f MIN: %.3f",c,sn, sn2,sp, MIN((MIN(sn,sn2)),sp));
- compound_score[c][0]=c;
- compound_score[c][1]=1000*MIN((MIN(sn,sn2)),sp);
- }
-
- sort_int_inv (compound_score,2, 1, 0, B->len_aln-1);
-
- fp2=vfopen ("compound.fasta", "w");
- for (d=0; d<nl; d++)
- {
- int r1, r2;
- for (n=0,a=0;a<A->nseq; a++)
- for (b=0; b<A->nseq; b++)
- {
- r1= A->seq_al[b][list[d]];
- r2= A->seq_al[b][list[d]];
- if (is_gap(r1) || is_gap(r2))continue;
- else
- {
- ref_score[d]+=M[r1-'A'][r2-'A'];
- n++;
- }
- }
- ref_score[d]/=n;
- }
- AO=copy_aln (A, NULL);
- AI=copy_aln (A,NULL);
- AO->len_aln=AI->len_aln=nl;
- for (a=0; a<A->nseq; a++)AO->seq_al[a][nl]=AI->seq_al[a][nl]='\0';
-
- for (a=0; a<B->len_aln; a++)
- {
- fprintf (stdout, "\n>%4d %4d ", compound_score[a][0], compound_score[a][1]);
- for (b=0; b<B->nseq; b++) fprintf (stdout, "%c", B->seq_al[b][compound_score[a][0]]);
- fprintf ( stdout, "\n");
-
- for (AI->nseq=0,b=0; b<B->nseq; b++)
- {
- if (B->seq_al[b][compound_score[a][0]]=='O')continue;
- fprintf ( stdout, "\n\t");
- for (c=0; c<nl; c++)
- {
- fprintf ( stdout, "%c", A->seq_al[b][list[c]]);
- AI->seq_al[AI->nseq][c]=A->seq_al[b][list[c]];
- }
- AI->nseq++;
- }
- fprintf ( stdout, "\n\t");
- for (d=0; d<nl; d++)
- {
- for (score=0,n=0,b=0; b<B->nseq; b++)
- {
- if (B->seq_al[b][compound_score[a][0]]=='O')continue;
- for (c=0; c<B->nseq; c++)
- {
- if (B->seq_al[c][compound_score[a][0]]=='O')continue;
- {
- int r1, r2;
-
- r1= A->seq_al[b][list[d]];
- r2= A->seq_al[b][list[d]];
- if (is_gap(r1) || is_gap(r2))continue;
- else score+=M[r1-'A'][r2-'A'];
- n++;
- }
- }
- }
- score/=n;
- if ((float)score/(float)ref_score[d]>1.2)fprintf ( stdout, "*");
- else fprintf ( stdout, " ");
- }
- for (AO->nseq=0,b=0; b<B->nseq; b++)
- {
- if (B->seq_al[b][compound_score[a][0]]=='I')continue;
- fprintf ( stdout, "\n\t");
- for (c=0; c<nl; c++)
- {
- AO->seq_al[AO->nseq][c]=A->seq_al[b][list[c]];
- fprintf ( stdout, "%c", A->seq_al[b][list[c]]);
- }
- AO->nseq++;
- }
- simI=aln2sim (AI, "blosum62mt"); simO=aln2sim (AO, "blosum62mt");
- fprintf ( stdout, "\nDELTA: I: %d O: %d %d",simI,simO, simI-simO);
- delta+=simI-simO;
- }
-
- for ( a=0; a<B->nseq; a++)
- {
-
- fprintf ( fp2, ">%s\n", B->name[a]);
- for (b=0; b<B->len_aln/2; b++)
- fprintf ( fp2, "%c", B->seq_al[a][compound_score[b][0]]);
- fprintf (fp2, "\n");
- }
- vfclose (fp2);
- HERE ("OUTPUT compound.fasta");
- result=result2;
- n=n2;
- pp=pp2;
-
- sort_int_inv (result, 2, 0, 0, n-1);
-
-
- for (tp=0,a=0; a<n; a++)
- {
- tp+=result[a][1];
- if ((pp-tp) == (a-tp))break;
- }
- fp=a-tp;
- fn=pp-tp;
- tn=n-pp;
-
- sn=(tp/(tp+fn));
- sn2=(tp/(tp+fp));
- sp=(tn/(tn+fp));
- fprintf ( stdout, "\nTOT: sn: %.3f sn2: %.3f sp: %.3f MIN: %.3f",sn, sn2,sp, MIN((MIN(sn,sn2)),sp));
-
- }
- HERE ("Delta= %d", delta);
-
-
- /*
- C=copy_aln(A, NULL);
- for (a=0; a< nl; a++)
- for (b=0; b<A->nseq; b++)
- C->seq_al[b][a]=A->seq_al[b][list[a]];
- C->len_aln=nl;
- array=vcalloc (C->len_aln, sizeof (int));
- explore_weight_matrix (C, B, 6,0, array);
- */
-
- return best_score;
-}
-
-
-void count_misc (Alignment *A, Alignment *B)
-{
- int **done, a, b, c, d, e,f, g, *list, n, score;
- double **slist, *r;
- int *pos;
- int w=1;
-
- search_best_combo (A,B);
- myexit (EXIT_FAILURE);
- pos=vcalloc (A->len_aln+1, sizeof (int));
- /*
- pos[354]=1;
- pos[362]=1;
- pos[366]=1;
- pos[398]=1;
- pos[476]=1;
-
-
- fprintf ( stdout, "\nR: %3f " ,(float)sar_aln2r(A,B,pos,1));myexit (EXIT_FAILURE);
- */
- for (a=0; a< A->len_aln-w; a++)
- {
- for (c=0; c<w; c++)
- {
- pos[a+c]=1;
- }
- pos[398]=1;
- pos[362]=1;
- pos[354]=1;
- pos[366]=1;
- pos[419]=1;
- pos[494]=1;
- pos[476]=1;
- pos[337]=1;
- fprintf ( stdout, "\nP: %3d W:2 R: %3f ",a+1, (float)sar_aln2r(A,B,pos,0));
- for (c=0; c<w; c++)
- {
- pos[a+c]=0;
- }
- }
-
- myexit (EXIT_FAILURE);
- for (a=0; a<w; a++) pos[a]=1;
- for (a=w; a< A->len_aln-1; a++)
- {
- pos[a-w]=0;
- pos[a]=1;
- fprintf ( stdout, "\nP: %3d W:2 R: %3f ",a, (float)sar_aln2r(A,B,pos,0));
- }
-
- myexit (EXIT_FAILURE);
- pos[2]=1;
- pos[3]=1;
-
-
-
- explore_weight_matrix (A, B,3, 0,pos);
- myexit (EXIT_FAILURE);
-
- for (a=0; a<A->len_aln; a++)
- for ( b=0; b<A->len_aln; b++)
- for (c=0; c<A->len_aln; c++)
- for (d=0; d<A->len_aln; d++)
- for (f=0; f<A->len_aln; f++)
- for (g=0; g<A->len_aln; g++)
- {
- e=0;
- pos[e++]=a;
- pos[e++]=b;
- pos[e++]=c;
- pos[e++]=d;
- pos[e++]=f;
- pos[e++]=g;
- pos[e++]=-1;
- fprintf ( stdout, "\n%d %d %d %d %d %d %.3f", a, b,c,d,f, g, sar_aln2r(A,B, pos,0));
-
- }
-
- myexit (EXIT_FAILURE);
-
-
- slist=declare_double (A->nseq*A->nseq*10, 2);
- done=declare_int (256, 256);
- list=vcalloc ( A->nseq, sizeof (int));
-
- for (a=0; a<A->len_aln-1; a++)
- {
- for (b =0; b<256; b++)for (c=0; c<256; c++)done[b][c]=0;
-
- for (b=0; b<A->nseq-1; b++)
- {
- int r1, r2;
- r1=A->seq_al[b][a];
- r2=A->seq_al[b][a+1];
- if (done[r1][r2])continue;
- n=0;
- done[r1][r2]=1;
- list[n++]=b;
- fprintf ( stdout, "\n%3d %c%c: %s ",a+1, r1, r2, A->name[b]);
- for ( c=b+1; c<A->nseq; c++)
- {
- if (r1==A->seq_al[c][a] && r2==A->seq_al[c][a+1])
- {
- fprintf ( stdout, "%s ", A->name[c]);
- list[n++]=c;
- }
-
- }
- if (B && n>1)
- {
- for (e=0,score=0,c=0; c<n-1; c++)
- for (d=c+1; d<n; d++,e++)
- score+=get_sar_sim2(B->seq_al[list[c]], B->seq_al[list[d]]);
- fprintf ( stdout, " Score=%d", score/e);
- }
- }
- }
- for (score=0,e=0,a=0; a<A->nseq-1; a++)
- for (b=a+1; b<A->nseq; b++,e++)
- {
- score+=get_sar_sim2(B->seq_al[a], B->seq_al[b]);
- }
- fprintf (stdout,"AVG=%d", score/e);
- for (n=0,a=0; a< A->nseq-1; a++)
- {
- static int **M;
- int sim;
- if (!M)M=read_matrice ("blosum62mt");
-
-
- for (b=a+1; b<A->nseq; b++)
- {
- int n11, n01, n10, n00, n1;
-
- for (sim=d=0;d<A->len_aln; d++)
- {
- int r1, r2;
- r1=A->seq_al[a][d];
- r2=A->seq_al[b][d];
- sim+=(r1==r2)?1:0;
- //sim +=(M[r1-'A'][r2-'A']>0)?1:0;
- }
-
- sim=(100*sim)/(A->len_aln);//+rand()%10;
- for (n1=n00=n11=n10=n01=score=0, d=0; d<B->len_aln; d++)
- {
- int r1, r2;
- r1=B->seq_al[a][d];
- r2=B->seq_al[b][d];
- n11+=(r1=='I' && r2=='I');
- n00+=(r1=='O' && r2=='O');
- n10+=(r1=='I' && r2=='0');
- n01+=(r1=='O' && r2=='I');
- n1+=(r1=='I' || r2=='I');
- }
- score =((n11+n00)*100)/B->len_aln;
-
- //score=get_sar_sim2(B->seq_al[a], B->seq_al[b]);
-
- fprintf ( stdout, "\nSIM: %d SC: %d", sim, score);
- slist[n][0]=(double)sim;
- slist[n][1]=(double)score;
- n++;
- }
- }
- r=return_r(slist, n);
- fprintf ( stdout, "\nR= %.4f", (float)r[0]);
- myexit (EXIT_FAILURE);
-}
-
-int aln2ngap ( Alignment *A)
-{
- int ngap=0, a, b;
- for (a=0; a< A->len_aln; a++)
- for (b=0; b<A->nseq; b++) ngap+=is_gap (A->seq_al[b][a]);
- return ngap;
-}
-int * count_in_aln ( Alignment *A, Alignment *ST, int value, int n_symbol,char **symbol_list, int *table)
- {
- int a, b, c=0, d;
- int st;
-
- if (!table)table=vcalloc (n_symbol, sizeof (int));
-
- A->residue_case=KEEP_CASE;
- for ( a=0; a< A->nseq; a++)
- {
- if(value!=10 && ST)for ( c=0; c< ST->nseq; c++)if ( strm(ST->name[c], A->name[a]))break;
- for ( b=0; b< A->len_aln; b++)
- {
- if ( value==10 || !ST)st=11;
- else st=(isdigit(ST->seq_al[c][b]))?ST->seq_al[c][b]-'0':ST->seq_al[c][b];
- if ( st==value || value==-1)
- {
- for ( d=0; d<n_symbol; d++)table[d]+=is_in_set ( A->seq_al[a][b], symbol_list[d]);
- }
- }
- }
- return table;
- }
-
-char *dna_aln2cons_seq ( Alignment *A)
- {
- int a, b, best;
- static int **column_count;
- static int **old_tot_count;
- static int **new_tot_count;
- static char *string1, *string2;
- int **count_buf;
- char r1, r2,*seq;
- int NA=0, NG=1, NC=2, NT=3, IGAP=4;
- static int MAX_EST_SIZE=10000;
- static int size_increment=1000;
- static int first;
- int overlap=0, best_overlap=0;
-
-
- seq=vcalloc ( A->len_aln+1, sizeof (char));
-
- if (!column_count )
- {
- column_count=vcalloc(MAX_EST_SIZE, sizeof (int*));
- for ( a=0; a< MAX_EST_SIZE; a++)
- column_count[a]=vcalloc (5, sizeof (int));
-
- old_tot_count=vcalloc(MAX_EST_SIZE, sizeof (int*));
- new_tot_count=vcalloc(MAX_EST_SIZE, sizeof (int*));
- A->P=declare_profile( "agct-",MAX_EST_SIZE);
- string1=vcalloc (MAX_EST_SIZE, sizeof (char));
- string2=vcalloc (MAX_EST_SIZE, sizeof (char));
- }
- else if (A->len_aln>MAX_EST_SIZE)
- {
- if ( column_count)
- {
- for ( a=0; a< MAX_EST_SIZE; a++)
- vfree(column_count[a]);
- vfree(column_count);
- vfree(old_tot_count);
- vfree(new_tot_count);
- vfree(string1);
- vfree(string2);
- }
-
- column_count=vcalloc(MAX_EST_SIZE+ size_increment, sizeof (int*));
- for ( a=0; a< MAX_EST_SIZE+ size_increment; a++)
- column_count[a]=vcalloc (5, sizeof (int));
-
- old_tot_count=vcalloc(MAX_EST_SIZE+ size_increment, sizeof (int*));
- new_tot_count=vcalloc(MAX_EST_SIZE+ size_increment, sizeof (int*));
-
- for (a=0; a< MAX_EST_SIZE; a++)
- {
- old_tot_count[a]=*(column_count++);
- for ( b=0; b<5; b++)old_tot_count[a][b]=(A->P)->count[b][a];
- }
- free_int ( (A->P)->count, -1);
-
- (A->P)->count=declare_int (5, MAX_EST_SIZE+ size_increment);
- (A->P)->max_len=MAX_EST_SIZE+ size_increment;
- MAX_EST_SIZE+= size_increment;
- string1=vcalloc (MAX_EST_SIZE, sizeof (char));
- string2=vcalloc (MAX_EST_SIZE, sizeof (char));
- }
-
-
- sprintf ( string1, "%s",A->seq_al[0]);
- sprintf ( string2, "%s",A->seq_al[1]);
-
-
- string1=mark_internal_gaps(string1,'.');
- string2=mark_internal_gaps(string2,'.');
-
-
-
- for (b=0,a=0; a< A->len_aln; a++)
- {
- r1=string1[a];
- r2=string2[a];
-
- if ( r1==r2)
- {
- overlap++;
- }
- else
- {
- best_overlap=MAX(overlap, best_overlap);
- overlap=0;
- }
-
-
- if (!is_gap(r1) && first==1)new_tot_count[a]=old_tot_count[b++];
- else if (is_gap(r1) || first==0){new_tot_count[a]=*column_count;column_count++;};
-
- if ( first==0)
- {
- if(r1=='a') new_tot_count[a][NA]++;
- else if ( r1=='g')new_tot_count[a][NG]++;
- else if ( r1=='c')new_tot_count[a][NC]++;
- else if ( r1=='t')new_tot_count[a][NT]++;
- else if (is_gap(r1));
- else
- {
- new_tot_count[a][NA]++;
- new_tot_count[a][NG]++;
- new_tot_count[a][NC]++;
- new_tot_count[a][NT]++;
- }
- }
- if ( a> 0 && a<A->len_aln-1 && r1=='.')
- {
- new_tot_count[a][IGAP]+=((new_tot_count[a-1][NA]+new_tot_count[a-1][NG]+new_tot_count[a-1][NC]+new_tot_count[a-1][NT]));
- }
-
-
- if(r2=='a') new_tot_count[a][NA]++;
- else if ( r2=='g')new_tot_count[a][NG]++;
- else if ( r2=='c')new_tot_count[a][NC]++;
- else if ( r2=='t')new_tot_count[a][NT]++;
- else if ( r2=='.')new_tot_count[a][IGAP]++;
- else if ( r2=='-');
- else
- {
- new_tot_count[a][NA]++;
- new_tot_count[a][NG]++;
- new_tot_count[a][NC]++;
- new_tot_count[a][NT]++;
- }
- (A->P)->count[0][a]=new_tot_count[a][NA];
- (A->P)->count[1][a]=new_tot_count[a][NG];
- (A->P)->count[2][a]=new_tot_count[a][NC];
- (A->P)->count[3][a]=new_tot_count[a][NT];
- (A->P)->count[4][a]=new_tot_count[a][IGAP];
-
- best_int(4,1, &best,new_tot_count[a][NA], new_tot_count[a][NG],new_tot_count[a][NC],new_tot_count[a][NT]);
- if( best==0) seq[a]='a';
- else if ( best==1)seq[a]='g';
- else if ( best==2)seq[a]='c';
- else if ( best==3)seq[a]='t';
- }
-
- first=1;
-
- seq[a]='\0';
- fprintf ( stderr, "[Best Overlap: %d Residues]", best_overlap);
- count_buf=old_tot_count;
- old_tot_count=new_tot_count;
- new_tot_count=count_buf;
-
- return seq;
-
- }
-
-char *aln2cons_maj ( Alignment *A, int ns, int *ls, int n_groups, char **group_list)
- {
- char *seq;
- int a, b;
- int len;
- int clean_ls=0;
- static int *aa;
-
- if ( !aa) aa=vcalloc (1000, sizeof (int));
-
- len=strlen (A->seq_al[ls[0]]);
- seq=vcalloc (len+1, sizeof (char));
-
- if ( ns==0)
- {
- ns=A->nseq;
- ls=vcalloc ( A->nseq, sizeof (int));
- for ( a=0; a< A->nseq; a++)ls[a]=a;
- clean_ls=1;
- }
-
- for ( a=0; a<len; a++)
- {
- int best_s=0, best_aa=0, r;
- for (b=0; b< ns; b++)
- {
- r=tolower(A->seq_al[ls[b]][a]);
- aa[r]++;
- if (!is_gap(r) && aa[r]>best_s)
- {
- best_s=aa[r];
- best_aa=r;
- }
- seq[a]=best_aa;
- }
- for (best_s=0, best_aa=0,b=0; b< ns; b++)
- {
- aa[tolower(A->seq_al[ls[b]][a])]=0;
- }
- }
- if ( clean_ls)vfree(ls);
- seq[a]='\0';
-
- return seq;
- }
-
-char *aln2cons_seq ( Alignment *A, int ns, int *ls, int n_groups, char **group_list)
- {
- char *seq;
- int a, b, c;
- int best_group=0;
- int aa_group=0;
- int *group;
- int len;
- int clean_ls=0;
-
- len=strlen (A->seq_al[ls[0]]);
- seq=vcalloc (len+1, sizeof (char));
-
- if ( ns==0)
- {
- ns=A->nseq;
- ls=vcalloc ( A->nseq, sizeof (int));
- for ( a=0; a< A->nseq; a++)ls[a]=a;
- clean_ls=1;
- }
-
-
- if ( !group_list)
- {
- group_list=declare_char ( 26, 2);
- for ( a=0; a<26; a++)group_list[a][0]=a+'a';
- n_groups=26;
- aa_group=1;
- }
-
-
- for ( a=0; a<len; a++)
- {
- group=vcalloc (n_groups+1, sizeof (int));
- for (best_group=0,b=0; b< ns; b++)
- {
- if ( !is_gap(A->seq_al[ls[b]][a]))
- {
- for (c=0; c< n_groups; c++)
- if ( is_in_set (tolower(A->seq_al[ls[b]][a]), group_list[c]))
- {group[c]++;
- best_group=(group[c]>group[best_group])?c:best_group;
- }
- }
- seq[a]=group_list[best_group][0];
- }
- vfree (group);
- }
- seq[a]='\0';
- if ( aa_group) free_char (group_list, -1);
-
- if ( clean_ls)vfree(ls);
-
- return seq;
- }
-
-Alignment *aln2conservation ( Alignment *A, int threshold,char *seq)
-{
- int a, b, c, d, i, c1, c2;
- int *pos;
- float *eval;
- float tot=0;
- float tn=0;
- int **sim;
- int w=0;
-
- pos =vcalloc (A->len_aln, sizeof (int));
- eval=vcalloc (A->len_aln, sizeof (int));
- sim=aln2sim_mat (A, "idmat");
- if (seq)i=name_is_in_list (seq, A->name, A->nseq, 100);
- else i=0;
-
- if ( i==-1) {HERE ("%s is an unknown:sequence [FATAL]"); myexit (EXIT_FAILURE);}
-
- for (a=0; a<A->len_aln; a++)
- {
- double s;
- int e;
- for (c=0,e=a-w; e<=a+w; e++)
- {
- if (e<0 || e==A->len_aln)continue;
- c1=toupper (A->seq_al[i][e]);
- for (b=0; b<A->nseq; b++)
- {
- c2=toupper (A->seq_al[b][a]);
- if (c1==c2)
- {
- c++;
- s=(double)((double)sim[i][b]/(double)(100));
-
- }
- else
- {
- s=(double)(((double)100-(double)sim[i][b])/(double)(100));
- }
- eval[a]+=(s==0)?0:log(s);
- }
- }
- pos[a]=(c*100)/A->nseq;
- if (!is_gap(c1)){tot+=pos[a]; tn++;}
-
- if (pos[a]>=threshold)A->seq_al[i][a]=toupper (A->seq_al[i][a]);
- else A->seq_al[i][a]=tolower (A->seq_al[i][a]);
- }
- fprintf (stdout, ">%s %s [i=%d]\n%s\n", A->name[i],A->aln_comment[i],i, A->seq_al[i]);
- tot=(tn>0)?(float)tot/(float)tn:0;
-
- for (d=0,a=0; a<A->len_aln; a++)
- {
- fprintf (stdout, "# %c %4d", A->seq_al[i][a],pos[a]);
-
-
- if ( !is_gap (A->seq_al[i][a]))
- {
- fprintf (stdout, " LogOdd: %6.2f ", (tot==0 || pos[a]==0)?0:(float)log((float)pos[a]/tot));
- fprintf ( stdout, " Pos: %5d E-Val: %9.2f", ++d, eval[a]/(A->nseq));
- }
- fprintf ( stdout, "\n");
- }
- fprintf ( stdout, "#average conservation: %.2f", tot);
- myexit (EXIT_SUCCESS);
-}
-char *aln2cons_seq_mat ( Alignment *A, char *mat_name)
-{
- return sub_aln2cons_seq_mat (A, A->nseq, NULL, mat_name);
-}
-char *sub_aln2cons_seq_mat2 ( Alignment *A,int ns, char **ls, char *mat_name)
-{
- char *cons;
- int *list;
- list=name_array2index_array(ls, ns, A->name, A->nseq);
- cons=sub_aln2cons_seq_mat ( A,ns, list, mat_name);
- vfree (list);
- return cons;
-}
-
-char *sub_aln2cons_seq_mat ( Alignment *A,int ns, int *ls, char *mat_name)
-{
- int a, b, c, s;
- char *seq, r1, r2;
- int **mat;
- int score=0, best_score=0, best_r=0;
- int len;
- int naa;
-
- mat=read_matrice (mat_name);
- len=strlen ( A->seq_al[(ls==NULL)?0:ls[0]]);
- seq=vcalloc (len+1, sizeof (char));
- for ( a=0; a<len; a++)
- {
- for (b=0; b<20; b++)
- {
- r1=AA_ALPHABET[b];
- for ( naa=0,score=0,c=0; c<ns; c++)
- {
- s=(ls==NULL)?c:ls[c];
- if ( ls && ls[c]==-1) continue;
- else if (is_gap(A->seq_al[s][a]))continue;
- else
- {
- naa++;
- r2=A->seq_al[s][a];
- score+=mat[r1-'A'][r2-'A'];
- }
- }
- if (naa==0)best_r='-';
- if ( b==0 || score>best_score){best_score=score; best_r=r1;}
- }
- seq[a]=best_r;
- }
- free_int (mat, -1);
- return seq;
-}
-
-int seq_list2in_file ( TC_method *M, Sequence *S, char *list, char *file)
-{
- X_template *T=NULL;
-
- if ( !S)return 0;
- else
- {
- int t;
- t=tolower(M->seq_type[0]);
-
- if ( t=='s')
- {
- return seq_list2fasta_file ( S, list, file, M->out_mode);
-
- }
- else
- {
- FILE *fp, *fp2;
- int a, n, s, c;
- int *slist;
-
-
-
- fp=vfopen ( file, "w");
- slist=string2num_list (list);
- n=slist[0];
-
- if (strlen (M->seq_type) >1)
- {
- add_warning( stderr, "\nERROR: Mixed seq_type not supported for external methods\n[FATAL:%s]", PROGRAM);
- }
-
- for ( a=2; a<n; a++)
- {
- s=slist[a];
- if (t=='p')T=(S->T[s])->P;
- else if (t=='r')T=(S->T[s])->R;
- else if (t=='g')T=(S->T[s])->G;
-
- if (!T && t=='r')
- {
- fprintf ( fp, ">%s\n%s%s", S->name[s], S->seq[s], LINE_SEPARATOR);
- }
- else if ( T && T->template_file && T->template_file[0])
- {
- fp2=vfopen (T->template_file, "r");
- while ( (c=fgetc (fp2))!=EOF)
- {
- fprintf ( fp, "%c", c);
- }
- fprintf (fp, "%s", LINE_SEPARATOR);
- vfclose (fp2);
- }
- }
-
- fprintf (fp, "TARGET_SEQ_NAME: ");
- for (a=2; a<n; a++)fprintf ( fp, "%s ", (S->name[slist[a]]));
- fprintf ( fp, "%s", LINE_SEPARATOR);
-
- vfclose (fp); vfree (slist);
-
- }
-
- return 1;
- }
-}
-
-int seq_list2fasta_file( Sequence *S, char *list, char *file, char *outmode)
- {
- FILE *fp;
- int n, a, s;
- static char *buf;
- static int blen;
- int l;
- //out_mode: names can only be re-converted when out mode is aln
-
- /*Buf is used because cmalloced functions cannot go through strtok*/
- if ( !S)return 0;
- else
- {
- fp=vfopen ( file, "w");
- if ( !list)
- {
- for ( a=0; a<S->nseq; a++)
- {
- if (outmode && strm (outmode, "aln"))fprintf ( fp, ">%s %s\n%s\n", decode_name (S->name[a], CODE),S->name[a], S->seq[a]);
- else fprintf ( fp, ">%s %s\n%s\n", S->name[a],S->name[a], S->seq[a]);
- }
- }
- else
- {
- int **list2;
- int max;
-
- l=strlen (list);
- if ( l>blen)
- {
- if (buf)vfree(buf);
- buf=vcalloc ( strlen (list)+1, sizeof (char));
- sprintf ( buf, "%s", list);
- blen=l;
- }
- n=atoi(strtok (list,SEPARATORS));
-
- list2=declare_int (n, 2);
- max=n*1000;
- for ( a=0; a<n; a++)
- {
- list2[a][0]=atoi(strtok (NULL, SEPARATORS));
- list2[a][1]=rand()%max;
- }
- if ( atoigetenv ("HoT_4_TCOFFEE"))sort_int ( list2,2, 1, 0, n-1);
- for ( a=0; a< n; a++)
- {
- int i=list2[a][0];
- if (outmode && strm (outmode, "aln"))fprintf ( fp, ">%s %s\n%s\n", decode_name (S->name[i], CODE), S->name[a],S->seq[i]);
- else fprintf ( fp, ">%s %s\n%s\n", S->name[a], S->name[a],S->seq[i]);
- }
- }
- vfclose (fp);
- }
- return 1;
- }
-Structure * seq2struc ( Sequence *S, Structure *ST)
- {
- int a, b;
-
- for ( a=0; a< S->nseq; a++)
- for ( b=0; b< S->len[a]; b++)
- ST->struc[a][b+1][ST->n_fields-1]=S->seq[a][b];
- return ST;
- }
-
-void aln2struc (Alignment *A, Structure *ST)
- {
- int a, b, c;
-
- for ( a=0; a< A->nseq; a++)
- for (c=0, b=0; b< A->len_aln; b++)
- {
- if ( !is_gap (A->seq_al[a][b]))
- {
- ST->struc[a][c][ST->n_fields-1]=A->seq_al[a][b];
- c++;
- }
- }
- }
-Alignment *stack_aln (Alignment *A, Alignment *B)
- {
- int a,b;
- int max_len=0, max_nseq=0;
- if ( B==NULL)return A;
- if ( A==NULL)return B;
-
- max_nseq=A->nseq+B->nseq;
- for (a=0; a< A->nseq; a++)max_len=MAX(strlen(A->seq_al[a]),max_len);
- for (a=0; a< B->nseq; a++)max_len=MAX(strlen(B->seq_al[a]),max_len);
-
- A=realloc_aln2 ( A,max_nseq,max_len+1);
-
- for (a=A->nseq,b=0; b< B->nseq; b++, a++)
- {
- sprintf ( A->seq_comment[a] , "%s", B->seq_comment[b]);
- sprintf ( A->aln_comment[a] , "%s", B->aln_comment[b]);
-
- sprintf ( A->seq_al [a] , "%s", B->seq_al [b]);
- sprintf ( A->name [a] , "%s", B->name[b]);
- sprintf ( A->file [a], "%s" , B->file[b]);
- A->order[a][0]=B->order[b][0];
- A->order[a][1]=B->order[b][1];
- A->score_seq[a]=B->score_seq[b];
- A->len[a]=B->len[b];
- }
-
- A->len_aln=MAX(A->len_aln, B->len_aln);
- A->nseq=A->nseq+B->nseq;
- A->score_aln=A->score_aln+B->score_aln;
-
- A->finished=A->finished+B->finished;
- return A;
- }
-
-Alignment *chseqIaln(char *name, int seq_n, int start,int len,Sequence *S, int seqIaln, Alignment *A)
- {
- char *seq;
-
- seq=extract_char ( S->seq[seq_n], start, len);
- A=realloc_aln2 (A, (A==NULL)?(seqIaln+1):MAX(A->nseq,seqIaln+1), ((A==NULL)?(strlen (seq)):MAX(strlen (seq),A->len_aln))+1);
-
-
- sprintf ( A->seq_al[seqIaln], "%s",seq);
-
-
- A->order[seqIaln][0]=seq_n;
- A->order[seqIaln][1]=start;
- sprintf ( A->name[seqIaln], "%s", name);
- A->nseq=MAX(A->nseq, seqIaln+1);
- A->len_aln=return_maxlen(A->seq_al, A->nseq);
- A->S=S;
- vfree (seq);
- return A;
- }
-
-Alignment * aln_gap2random_aa(Alignment *A)
- {
- int a, b,l;
- char alp[200];
-
- if (strm ( (A->S)->type, "PROTEIN"))
- sprintf ( alp, "acefghiklmnpqrstuvwy");
- else if ( strm ( (A->S)->type, "DNA") ||strm ( (A->S)->type, "RNA") )
- sprintf ( alp, "agct");
- l=strlen (alp);
-
-
- for (a=0; a<A->nseq; a++)
- for ( b=0; b<A->len_aln; b++)
- if ( is_gap (A->seq_al[a][b]))A->seq_al[a][b]=alp[(int)rand()%(l)];
- return A;
- }
-
-Alignment * make_random_aln(Alignment *A,int nseq, int len, char *alphabet)
- {
- int a;
-
-
- A=realloc_aln2(A, nseq, len+1);
-
- A->nseq=0;
- A->len_aln=len;
- for ( a=0; a< A->nseq; a++)sprintf ( A->file[a], "random alignment");
- for ( a=0; a< nseq; a++)
- A=add_random_sequence2aln(A,alphabet);
- return A;
- }
-Alignment * add_random_sequence2aln( Alignment *A, char *alphabet)
- {
- int a, n;
-
- vsrand(0);
-
- n=strlen(alphabet);
- A=realloc_alignment2 (A, A->nseq+1, A->len_aln+1);
-
- for ( a=0; a< A->len_aln; a++)A->seq_al[A->nseq][a]=alphabet[rand()%n];
- if (! A->name[A->nseq][0])
- {
- for ( a=0; a<10; a++)A->name[A->nseq][a]=alphabet[rand()%n];
- A->name[A->nseq][a]='\0';
- }
-
- A->nseq++;
- return A;
- }
-
-Sequence *get_defined_residues( Alignment *A)
- {
- char *buf;
- Sequence *S;
- int a, b, s, l, r;
- if ( !A || !A->S) return NULL;
-
- S=duplicate_sequence (A->S);
- for ( a=0; a< S->nseq; a++)
- for ( b=0; b< S->len[a]; b++)S->seq[a][b]=UNDEFINED_RESIDUE;
- buf=vcalloc(A->len_aln+1,sizeof (char));
- for ( a=0; a< A->nseq; a++)
- {
- sprintf ( buf, "%s",A->seq_al[a]);
- ungap(buf);
- l=strlen (buf);
- s=A->order[a][0];
-
- for ( b=1; b<= l; b++)
- {
- r=A->seq_cache[s][b];
-
- if ( r>=0)S->seq[s][r-1]=(A->S)->seq[s][r-1];
- }
- }
- vfree(buf);
- return S;
- }
-Alignment *thread_defined_residues_on_aln ( Alignment *A, Sequence *S1)
- {
- int a, b;
- int gap, r,s, r2;
- for ( a=0; a< A->nseq; a++)
- {
- s=A->order[a][0];
- r=A->order[a][1];
- for (b=0;b< A->len_aln; b++)
- {
- gap=is_gap(A->seq_al[a][b]);
-
- if (!gap)
- {
- r+=!gap;
- r2=A->seq_cache[s][r]-1;
-
- if (r2>=0 && S1->seq[s][r2]==UNDEFINED_RESIDUE)
- A->seq_al[a][b]=UNDEFINED_RESIDUE;
- }
- }
- }
- return A;
- }
-
-int ** trim_aln_borders (char **seq1, char **seq2, int nseq)
- {
- int a, b, c,l1,l2;
- char *buf1;
- char *buf2;
- int max;
-
-
-
-
- max=MAX(get_longest_string (seq1,-1, NULL, NULL),get_longest_string (seq2,-1, NULL, NULL))+1;
- buf1=vcalloc ( max, sizeof(char));
- buf2=vcalloc ( max, sizeof(char));
-
- for ( a=0; a< nseq; a++)
- {
- sprintf ( buf1, "%s", seq1[a]);
- sprintf ( buf2, "%s", seq2[a]);
-
-
-
- ungap (buf1);
- ungap (buf2);
-
- if (str_overlap ( buf1, buf2,'*')!=0)
- {
- l1=strlen ( seq1[a]);
- l2=strlen ( seq2[a]);
- for ( b=0,c=0; c< l1; c++)
- if ( !is_gap(seq1[a][c]))seq1[a][c]=buf1[b++];
- seq1[a][c]='\0';
- for ( b=0,c=0; c< l2; c++)
- if ( !is_gap(seq2[a][c]))seq2[a][c]=buf2[b++];
- seq2[a][c]='\0';
- }
- }
- vfree (buf1);
- vfree (buf2);
- return NULL;
-
- }
-Sequence * merge_seq ( Sequence *IN, Sequence *OUT)
- {
- int a;
-
- if ( OUT==NULL)return duplicate_sequence (IN);
- else
- {
- if ( IN && check_list_for_dup( IN->name, IN->nseq))
- {
- fprintf ( stderr, "\nERROR: %s is duplicated in file %s[FATAL]\n", check_list_for_dup( IN->name, IN->nseq), IN->file[0]);
- myexit (EXIT_FAILURE);
- }
- for ( a=0; a< IN->nseq; a++)
- if ((OUT=add_sequence ( IN, OUT, a))==NULL)return NULL;
- return OUT;
- }
- }
-
-Alignment *seq_name2removed_seq_name(Sequence *S, Alignment *NA, float **diff)
-{
- int a, b, rb, s;
- float min_diff;
- for (a=0; a< S->nseq; a++)
- {
- if (name_is_in_list( S->name[a], NA->name, NA->nseq, 100)!=-1) continue;
- for ( min_diff=100, s=0, b=0; b< NA->nseq; b++)
- {
- rb=name_is_in_list ( NA->name[b], S->name, S->nseq, 100);
- if ( diff[a][rb]<min_diff)
- {
- s=b;
- min_diff=diff[a][rb];
-
- }
- }
- strcat ( NA->seq_comment[s], " ");
- strcat ( NA->seq_comment[s], S->name[a]);
- }
- return NA;
-}
-
-
-
-
-int seq_name2index (char *name, Sequence *S)
-{
- if ( !S) return -1;
- else return name_is_in_list ( name, S->name, S->nseq, MAXNAMES+1);
-}
-char * seq_name2coor ( char *s, int *start, int *end, char sep)
-{
- /*name|start|end */
- char n1[100], n2[100];
- int a=0, b=0, c=0;
-
- n1[0]=n2[0]='\0';
- start[0]=end[0]=0;
-
- while ( s[a]!=sep && s[a]!='\0')a++;
- if ( s[a]=='\0')return s;
- else
- s[a++]='\0';
-
-
-
- while ( s[a]!=sep && s[a]!='\0')n1[b++]=s[a++];
-
- if ( s[a]=='\0'){n1[b]='\0';if ( n1[0])start[0]=atoi(n1);return s;}
- else s[a++]=n1[b]='\0';
-
-
- while ( s[a]!=sep && s[a]!='\0')n2[c++]=s[a++];
- n2[c]='\0';
-
-
- if ( n1[0])start[0]=atoi(n1);
- if ( n2[0])end[0]=atoi(n2);
-
-
- return s;
-}
-
-Sequence *extract_one_seq(char *n,int start, int end, Alignment *S, int keep_name)
- {
-
- int seq, a;
- FILE*fp;
- char *name;
- Sequence *OUT_S;
-
-
- if ( n[0]=='#')seq=S->nseq;
- else if ( (seq=name_is_in_list (n, S->name, S->nseq, 100)+1)!=0);
- else if (is_number (n) && (seq=atoi(n))!=0) seq=atoi(n);
- else
- {
- fprintf ( stderr, "\nCould not find Sequence %s [FATAL]", n);
- myexit (EXIT_FAILURE);
- }
- seq--;
-
- name=vtmpnam ( NULL);
- fp=vfopen ( name, "w");
- if ( start && end &&!keep_name)fprintf (fp, ">%s_%d_%d\n",S->name[seq],start, end);
- else if ( start && end==0 && !keep_name)fprintf (fp, ">%s_%d_%d\n",S->name[seq],start,(int)strlen ( S->seq_al[seq]));
- else fprintf (fp, ">%s\n", S->name[seq]);
-
- if ( start==0 && end==0){fprintf (fp, "%s\n", S->seq_al[seq]);}
- else if (end==0){fprintf (fp, "%s\n", S->seq_al[seq]+start-1);}
- else
- {
- for ( a=start-1; a<end; a++){fprintf ( fp, "%c", S->seq_al[seq][a]);}
- fprintf ( fp, "\n");
- }
-
-
- vfclose (fp);
- OUT_S=get_fasta_sequence_num (name, NULL);
-
- return OUT_S;
- }
-
-
-
-Sequence * extract_sub_seq( Sequence *COOR, Sequence *S)
- {
- int a, b, c,s;
- int start, end;
-
- for ( a=0; a< S->nseq; a++)
- {
- if ( (s=name_is_in_list ( S->name[a], COOR->name, COOR->nseq, 100))!=-1)
- {
-
- sscanf ( COOR->seq_comment[s], "%d %d", &start, &end);
- for (c=0,b=start-1; b< end; b++, c++)S->seq[a][c]=S->seq[a][b];
- S->seq[a][c]='\0';
- sprintf ( S->seq_comment[a], "%s",COOR->seq_comment[s]);
-
- }
- }
- S=reorder_seq ( S, COOR->name, COOR->nseq);
- return S;
- }
-
-
-
-char * aln_column2string (Alignment *A, int p)
- {
- char *s;
- int a;
- if (p>=A->len_aln)
- {
- HERE ("ERROR: index (p=%d) loger than aln (l=%d) [FATAL]", p, A->len_aln);
- myexit (EXIT_FAILURE);
- }
- else
- {
- s=vcalloc (A->nseq+1, sizeof (char));
- for (a=0; a< A->nseq; a++)s[a]=A->seq_al[a][p];
- }
- return s;
- }
-
-
-int **fix_seq_aln (Sequence *S, Alignment*A, int **cache)
-{
- int s, b,i,nr;
-
- if (!cache)cache=vcalloc (S->nseq, sizeof (int*));
-
- for (s=0; s<A->nseq; s++)
- {
- if ((i=name_is_in_list (A->name[s], S->name, S->nseq, 100)==-1))continue;
- for (nr=0,b=0; b<A->len_aln; b++)
- {
- if (!is_gap(A->seq_al[s][b]))
- cache[i][++nr]=b+1;
- }
- }
- return cache;
-}
-
-int **fix_seq_seq (Sequence *S0, Sequence *Sx)
-{
- //Expresses seq1 in terms of s2
- //sequences 0-N
- //residues 1-N+1
- int s0, r0,i;
- int **index;
-
- index=vcalloc ( S0->nseq, sizeof (int*));
- for (s0=0; s0<S0->nseq; s0++)
- {
- int l=S0->len[s0];
- index[s0]=vcalloc (l+1, sizeof (int));
- i=index[s0][0]=name_is_in_list (S0->name[s0], Sx->name, Sx->nseq, 100);
- if (i==-1);
- else if (strm (S0->seq[s0], Sx->seq[i]))
- {
- for (r0=1; r0<=l; r0++)
- {
- index [s0][r0]=r0;
- }
- }
- else
- {
- int c;
- int nr0=0;
- int nr1=0;
-
- Alignment *B=align_two_sequences (S0->seq[s0],Sx->seq[i],(strm(S0->type, "PROTEIN"))?"blosum62mt":"idmat",-4,-1, "myers_miller_pair_wise");
- for (c=0; c<B->len_aln; c++)
- {
-
- int g0=is_gap(B->seq_al[0][c]);
- int g1=is_gap(B->seq_al[1][c]);
- nr0+=1-g0;
- nr1+=1-g1;
- if (!g0 && !g1)index[s0][nr0]=nr1;
- }
- if (aln2sim(B, "idmat")<20) add_warning (stderr,"Unreliable reconciliation for sequence %s. If it a PDB, check source file", S0->name[s0]);
- free_aln (B);B=NULL;
- }
- }
- return index;
-}
-int **fix_aln_seq_new (Alignment *A, Sequence *Sx)
-{
- Sequence *S;
- int **f;
-
- S=aln2seq (A);
- f=fix_seq_seq(S, Sx);
- free_sequence (S, S->nseq);
- return f;
-}
-Alignment * fix_aln_seq ( Alignment *A, Sequence *S)
- {
- int a, b, c;
- char *buf1, *buf2;
- int g0, g1, nr0, nr1;
- int id, tot;
- Alignment *B;
-
-
- /*This function establishes the correspondance between every (1..N+1) residue of each aligned sequence
- and its correspondance in S:
- A->seq_cache[a][b]=x means that residue b of aligned sequence a corresponds to residue x of the sequence with tye same index in S
- A->seq_cache[a][b]=0 means there is no correspondance.
- a is the index of the sequence
- Applying this function is needed for turning an alignment into a constraint list
- */
-
-
- if ( S==NULL)return A;
- reorder_aln (A, S->name,S->nseq);
- if (A->seq_cache)free_int (A->seq_cache, -1);
- A->seq_cache=declare_int ( S->nseq, MAX((A->len_aln+1), S->max_len+1));
-
- for (a=0; a< S->nseq; a++)
- for ( b=0; b< A->len_aln; b++)A->seq_cache[a][b]=-1;
-
- buf1=buf2=NULL;
- for ( a=0; a< S->nseq; a++)
- {
- for (b=0; b< A->nseq; b++)
- {
- if (strm ( S->name[a], A->name[b]))
- {
- A->order[b][0]=a;
-
- vfree (buf1);
- buf1=vcalloc ( A->len_aln+1, sizeof (char));
- sprintf (buf1, "%s", A->seq_al[b]);
- ungap (buf1);
- upper_string (buf1);
-
- vfree(buf2);
- buf2=vcalloc (strlen(S->seq[a])+1, sizeof (char));
- sprintf (buf2, "%s",S->seq[a]);
- ungap (buf2);
- upper_string (buf2);
-
-
-
- if ( strm (buf1,buf2))
- {
-
- for ( c=0; c<S->len[a]; c++)A->seq_cache[a][c+1]=c+1;
- }
- else
- {
-
- B=align_two_sequences (buf2,buf1,"blosum62mt",-4,-1, "myers_miller_pair_wise");
- if ( getenv ("DEBUG_RECONCILIATION"))
- {
- fprintf (stderr, "\n[DEBUG_RECONCILIATION:fix_aln_seq]\nReconciliation of %s\nA=Ref_sequence\nB=New_seq", S->name[a]);
- print_aln (B);
- }
-
- for (id=0, tot=0,nr0=0,nr1=0,c=0; c<B->len_aln; c++)
- {
- g0=is_gap(B->seq_al[0][c]);
- g1=is_gap(B->seq_al[1][c]);
- nr0+=1-g0;
- nr1+=1-g1;
- if ( !g0 && !g1)
- {
- tot++;
- id+=(B->seq_al[0][c]==B->seq_al[1][c])?1:0;
- A->seq_cache[a][nr1]=nr0;
- }
- else if (g0 && !g1)
- {
- A->seq_cache[a][nr1]=0;
- }
- }
- if ( ((id*100)/tot)<20)
- {
- print_aln (B);
- fprintf ( stderr, "\nTwo different sequences have the same name: %s", S->name[a]);
- fprintf ( stderr, "\nIf %s is a PDBID, Make sure it identifies the right chain (A, B, 1, 2...)", S->name[a]);
- fprintf ( stderr, "\nChain number or index must be added to the PDB id (i.e. 1gowA)");
- fprintf ( stderr, "\nIf You want to use %s anyway, rename it with a non-PDB identifier such as seq_%s\n",S->name[a],S->name[a]);
- myexit (EXIT_FAILURE);
- }
-
- free_sequence ( B->S, -1);
- free_aln (B);
- }
-
- }
- }
- }
- vfree(buf1);vfree(buf2);
- return A;
- }
-
-Sequence * add_prf2seq ( char *file, Sequence *S)
- {
- char **new_seq;
- Sequence *NS;
-
- if ( !is_aln (file)&& !is_seq (file))return S;
- else
- {
- X_template *R;
- Alignment *A;
-
-
- R=fill_R_template(file,file, S);
-
- A=(R->VR)->A;
- ((R->VR)->A)->expand=1;
- new_seq=declare_char (1,A->len_aln+1);
- sprintf ( new_seq[0], "%s",aln2cons_seq_mat(A, "blosum62mt"));
-
- NS=fill_sequence_struc(1, new_seq,A->file);
- S=add_sequence (NS, S, 0);
- (S->T[S->nseq-1])->R=R;
-
- free_sequence (NS, NS->nseq);
- free_char( new_seq, -1);
-
- return S;
- }
- }
-int prf_in_seq ( Sequence *S)
-{
- int a;
-
- if ( !S) return 0;
- else
- {
- for ( a=0; a< S->nseq; a++)
- if (seq2R_template_profile(S, a)) return 1;
- }
- return 0;
-}
-Sequence * add_sequence ( Sequence *IN, Sequence *OUT, int i)
- {
- int s, a;
-
- char *buf;
- if (OUT==NULL)
- {
-
- OUT=duplicate_sequence (IN);
- return OUT;
- }
- for (a=0; a<OUT->nseq; a++)
- {
- Alignment *P;
- P=seq2R_template_profile (OUT, a);
- if (!P) continue;
- else if (name_is_in_list (IN->name[i], P->name, P->nseq, 100)!=-1) return OUT;
- }
-
- /*Adds sequence i of IN at the end of OUT*/
-
- if ((s=name_is_in_list ( IN->name[i], OUT->name, OUT->nseq,STRING))==-1 )
- {
- OUT=realloc_sequence (OUT, OUT->nseq+1, IN->len[i]);
- sprintf ( OUT->name[OUT->nseq],"%s",IN->name[i]);
- sprintf ( OUT->file[OUT->nseq],"%s",IN->file[i]);
- sprintf ( OUT->seq_comment[OUT->nseq],"%s",IN->seq_comment[i]);
- sprintf ( OUT->aln_comment[OUT->nseq],"%s",IN->aln_comment[i]);
-
- sprintf ( OUT->seq[OUT->nseq],"%s",IN->seq[i]);
- OUT->len[OUT->nseq]=IN->len[i];
- OUT->T[OUT->nseq][0]=IN->T[i][0];
- OUT->nseq++;
- return OUT;
- }
- else if ( s!=-1 && !case_insensitive_strcmp ( IN->seq[i], OUT->seq[s]))
- {
-
- if ( getenv4debug("DEBUG_RECONCILIATION"))fprintf ( stderr,"[DEBUG_RECONCILIATION:add_sequence]\n%s\n%s\n", IN->seq[i], OUT->seq[s]);
-
- add_warning (stderr, "DISCREPANCY:%s in [%s] and [%s]\n", IN->name[i], IN->file[i], OUT->file[s]);
-
-
- if (((buf=build_consensus(IN->seq[i], OUT->seq[s],"cfasta_pair_wise" ))!=NULL)||((buf=build_consensus(IN->seq[i], OUT->seq[s],"myers_miller_pair_wise" ))!=NULL))
- {
-
- OUT->max_len=MAX(OUT->max_len, strlen(buf));
- OUT->min_len=MIN(OUT->min_len, strlen(buf));
- OUT->seq =realloc_char ( OUT->seq, -1, -1,OUT->nseq,OUT->max_len+1);
-
- sprintf ( OUT->seq[s],"%s",buf);
- OUT->len[s]=strlen (buf);
- vfree (buf);
- return OUT;
- }
- else
- {
- fprintf ( stderr, "IMPOSSIBLE TO RECONCILIATE SOME SEQUENCES[FATAL:%s]\n", PROGRAM);
- print_aln ( align_two_sequences (IN->seq[i], OUT->seq[s], "idmat", 0, 0, "fasta_pair_wise"));
- myexit (EXIT_FAILURE);
- return NULL;
- }
-
- }
- else
- {
- return OUT;
- }
- }
-
-
-Sequence * trim_seq ( Sequence *A, Sequence *B)
- {
- int a;
- Sequence *R;
-
- if (A->nseq>B->nseq)
- {
- Sequence *I;
- I=A;A=B;B=I;
- }
-
- R=declare_sequence (MIN(A->min_len,B->min_len), MAX(A->max_len, B->max_len), MIN(A->nseq, B->nseq));
- R->nseq=0;
-
- for (a=0; a< A->nseq; a++)
- {
- if ( name_is_in_list ( A->name[a], B->name, B->nseq,STRING+1)!=-1)
- {
- sprintf ( R->name[R->nseq], "%s", A->name[a]);
- sprintf ( R->seq[R->nseq], "%s", A->seq[a]);
- sprintf ( R->file[R->nseq], "%s", A->file[a]);
- sprintf ( R->aln_comment[R->nseq], "%s", A->aln_comment[a]);
- sprintf ( R->seq_comment[R->nseq], "%s", A->seq_comment[a]);
-
- R->len[R->nseq]=A->len[a];
- R->nseq++;
- }
- }
- return R;
- }
-
-Sequence * trim_aln_seq ( Alignment *A, Alignment *B)
- {
- int a;
- static char **name_list;
- int n=0;
- Sequence *SA, *SB;
- int **cache_A=NULL;
- int **cache_B=NULL;
- int * p;
-
- /*This function inputs two alignments A and B
- It removes sequences that are not common to both of them
- It rearange the sequences so that they are in the same order
- A decides on the order
- The Sequences (A->S) and (B->S) are treated the same way
- Sequences are also merged in order to detects discrepencies.
- A pointer to S is returned
- */
- if (name_list)free_char (name_list, -1);
- name_list=declare_char (MAX(A->nseq, B->nseq), STRING+1);
-
- for ( a=0; a< A->nseq; a++)
- {
- if ( name_is_in_list ( A->name[a], B->name, B->nseq,STRING)!=-1)
- {
- sprintf ( name_list[n++], "%s", A->name[a]);
- }
- }
-
-
-
- reorder_aln ( A, name_list, n);
- if (A->seq_cache)cache_A=duplicate_int (A->seq_cache, -1, -1);
- if (B->seq_cache)cache_B=duplicate_int (B->seq_cache, -1, -1);
- reorder_aln ( B, name_list, n);
- for ( a=0; a< n; a++)
- {
- if ( cache_A)
- {
- p=A->seq_cache[A->order[a][0]];
- A->seq_cache[A->order[a][0]]=cache_A[a];
- cache_A[a]=p;
- }
- if ( cache_B)
- {
- p=B->seq_cache[B->order[a][0]];
- B->seq_cache[B->order[a][0]]=cache_B[a];
- cache_B[a]=p;
- }
- A->order[a][0]=B->order[a][0]=a;
- }
- free_int(A->seq_cache, -1);
- free_int(B->seq_cache, -1);
-
- A->seq_cache=cache_A;
- B->seq_cache=cache_B;
-
-
-
- SA=aln2seq(A);
- SB=aln2seq(B);
-
- A->S=B->S=merge_seq (SA, SB);
- return A->S;
- }
-Sequence * trim_aln_seq_name ( Alignment *A, Alignment *B)
- {
- int a;
- Sequence *S;
-
- /*This function inputs two alignments A and B
- It removes sequences that are not common to both of them
- It rearange the sequences so that they are in the same order
- A decides on the order
- */
- S=declare_sequence ( 1, 1, A->nseq+B->nseq);
- S->nseq=0;
- for ( a=0; a< A->nseq; a++)
- {
- if ( name_is_in_list ( A->name[a], B->name, B->nseq,STRING)!=-1)
- {
- sprintf ( S->name[S->nseq++], "%s", A->name[a]);
- }
- }
- return S;
- }
-
-
-
-char ** rm_name_tag (char **name, int nseq, char *tag)
-{
- int a , b, ntag;
- char **tag_list;
- char *s;
- char **template_list;
- if ( !name )return NULL;
-
- tag_list=declare_char (10, 4);
-
- if ( tag)
- {
- ntag=1; sprintf ( tag_list[0], "%s", tag);
- }
- else
- {
- ntag=0;
- sprintf ( tag_list[ntag++], "_S_");
- sprintf ( tag_list[ntag++], "_G_");
- }
- template_list=declare_char (nseq, 100);
- for ( a=0; a<nseq ; a++)
- {
- for ( b=0; b<ntag; b++)
- {
- s=strstr(name[a], tag_list[b]);
- if ( s)
- {
- s[0]='\0';
- s[2]='\0';
- sprintf ( template_list[a], ">%s _%s_ %s", name[a], s+1, s+3);
- break;
- }
- }
- }
-
- free_char (tag_list, -1);
- return template_list;
-}
-Sequence * swap_header ( Sequence *S, Sequence *H)
-{
- int a, b, n;
-
- for ( a=0; a< S->nseq; a++)
- {
- if ( (n=name_is_in_list (S->name[a],H->name, H->nseq, 1000))!=-1)
- {
- char **list;
-
-
- list=string2list (H->seq_comment[n]);
- if ( list==NULL || atoi(list[0])==1)continue;
- S->seq_comment[a]='\0';
- sprintf (S->name[a], "%s%s%s",H->name[n], list[1], list[2]);
- vfree ( S->seq_comment[a]);S->seq_comment[a]=vcalloc ( strlen (H->seq_comment[n])+1, sizeof (char));
- for (b=3; b< atoi(list[0]); b++)S->seq_comment[a]=strcat (S->seq_comment[a], list[b]);
- free_char (list, -1);
- }
- }
- return S;
-}
-
-
-Sequence * profile_seq2template_seq ( Sequence *S, char *template_file, Fname *F)
-{
- /*This function fetches potential templates associated with sequences within a profile*/
- int i;
- Alignment *A;
-
- for ( i=0; i< S->nseq; i++)
- {
-
- if ( (A=seq2R_template_profile (S, i)))
- {
-
- A->S=aln2seq (A);
- A->S=seq2template_seq (A->S, template_file, F);
- if (!A->S)return NULL;
- }
- }
-
- return S;
-}
-
-Sequence * seq2template_type(Sequence *Seq)
-{
- //add template
- int a, e;
- int s;
- struct X_template *S=NULL;
- struct X_template *P=NULL;
- struct X_template *R=NULL;
- struct X_template *G=NULL;
- struct X_template *F=NULL;
- struct X_template *T=NULL;
- struct X_template *E=NULL;
- struct X_template *U=NULL;
- Alignment *A;
-
-
- e=' ';
- for (a=0; a< Seq->nseq; a++)
- {
- if (!Seq->T[a])continue;
- //HERE ADD a Template
- P=seq_has_template (Seq, a, "_P_");
- S=seq_has_template (Seq, a, "_S_");
- R=seq_has_template (Seq, a, "_R_");
- G=seq_has_template (Seq, a, "_G_");
- F=seq_has_template (Seq, a, "_F_");
- T=seq_has_template (Seq, a, "_T_");
- E=seq_has_template (Seq, a, "_E_");
- U=seq_has_template (Seq, a, "_U_");
-
- s=(!P)?1:0;
- sprintf ( (Seq->T[a])->seq_type, "%c%c%c%c%c%c%c%c", (P)?'P':e, (S)?'S':e, (S &&!P)?'s':e,(R)?'R':e, (G)?'G':e,(T)?'T':e,(E)?'E':e,(U)?'U':e);
-
- if (R && (A=seq2R_template_profile (Seq,a)) && A->S)
- {
-
- A->S=seq2template_type ( A->S);
- }
- }
- return Seq;
-}
-
-char * string_contains_template_tag (char *string_in)
-{
- char string[100];
-
- if ( strstr (string, "_P_"))return "_P_";
- if ( strstr (string, "_S_"))return "_S_";
- if ( strstr (string, "_R_"))return "_R_";
- if ( strstr (string, "_G_"))return "_G_";
- if ( strstr (string, "_F_"))return "_F_";
- if ( strstr (string, "_T_"))return "_T_";
- if ( strstr (string, "_E_"))return "_E_";
- if ( strstr (string, "_U_"))return "_U_";
-
- return NULL;
-}
-static int check_blast_is_installed (char *server);
-
-
-
-static int check_blast_is_installed (char *server)
-{
- if (strm (server, "EBI"));
- else if ( strm (server, "NCBI"))
- return check_program_is_installed (NCBIWEBBLAST_4_TCOFFEE,NULL, NULL,NCBIWEBBLAST_ADDRESS, INSTALL_OR_DIE);
- else if ( strm (server, "LOCAL"))
- return check_program_is_installed (NCBIBLAST_4_TCOFFEE,NULL, NULL,NCBIBLAST_ADDRESS, INSTALL_OR_DIE);
- return 1;
-}
-
-
-Sequence * vremove_seq_template_files(Sequence *S)
-{
- return handle_seq_template_file (S, "remove");
-}
-Sequence * display_seq_template_files(Sequence *S)
-{
- return handle_seq_template_file (S, "display");
-}
-Sequence * handle_seq_template_file (Sequence *S, char *mode)
-{
- int a;
- Template *T;
-
- for (a=0; a< S->nseq; a++)
- {
- T=S->T[a];
- if (T)
- {
- handle_X_template_files (T->P, mode);
- handle_X_template_files (T->F, mode);
- handle_X_template_files (T->R, mode);
- handle_X_template_files (T->T, mode);
- handle_X_template_files (T->E, mode);
- }
- }
-
- return S;
-}
-int handle_X_template_files ( X_template *T, char *mode)
- {
- if (!T)return 0;
-
- if ( strm (mode, "remove"))
- {
- vremove (T->template_file);
- vremove (T->template_name);
- }
- else if (strm (mode, "display"))
- {
- char buf[100];
- sprintf ( buf, "Template %s", template_type2type_name (T->template_type));
- if (check_file_exists (T->template_name))display_output_filename ( stdout,buf,T->template_format,T->template_name, STORE);
- }
- else
- {
- printf_exit (EXIT_FAILURE, stderr, "\nUnkonwn mode %s for template handling [FATAL:%s]", mode, PROGRAM);
- }
- return 1;
- }
-Sequence * seq2template_seq ( Sequence *S, char *template_list, Fname *F)
-{
- /*Expected format for the template file:
- >seq_name _X_ Target_template
- X: S for Structures
- G for genomes (Exoset)
- When alternative templates are given for a sequence, the first one superseeds all the others
- */
-
- /*Fill the sequences*/
- /*1: No template*/
- char buf[1000];
-
- int PmC,PmI,PMI;
- int BmC,BmI,BMI;
- char *server;
- char *pdb_db,*prot_db;
- char pdb_type[100];
- char *p;
- int remove_template_file=0;
-
-
- remove_template_file=get_int_variable ("remove_template_file");
- server=get_string_variable ("blast_server");
- pdb_db=get_string_variable ("pdb_db");
- prot_db=get_string_variable ("prot_db");
-
- PmI=get_int_variable ("pdb_min_sim");
- PMI=get_int_variable ("pdb_max_sim");
- PmC=get_int_variable ("pdb_min_cov");
-
- BmI=get_int_variable ("prot_min_sim");
- BMI=get_int_variable ("prot_max_sim");
- BmC=get_int_variable ("prot_min_cov");
-
- //Set the type of the PDB structure
- if ((p=get_string_variable ("pdb_type")))
- {
- sprintf ( pdb_type, "%s",p);
- }
- else
- {
- sprintf (pdb_type, "dmn");
- }
-
- if ( (template_list && template_list[0]=='\0') || strm ( template_list, "no_template"))
- {
- return S;
- }
- else if ( strstr (template_list, "MODE_"))//pre_set mode
- {
- return seq2template_seq ( S,template_list+strlen ("MODE_"),F);
- }
- else if ( strm ( template_list, "SSP")|| strm ( template_list, "GOR"))
- {
-
- /*use GOR to Predict the secondary structure*/
- check_program_is_installed (GOR4_4_TCOFFEE,NULL, NULL,GOR4_ADDRESS, INSTALL_OR_DIE);
- sprintf ( buf, "SCRIPT_tc_generic_method.pl@mode#ssp_template@seq#%s/%s@obs#%s/%s@cache#%s@type#_E_",get_mcoffee_4_tcoffee(), "New_KS.267.seq", get_mcoffee_4_tcoffee(), "New_KS.267.obs", get_cache_dir());
- S=seq2template_seq (S,buf, F);
- return S;
- }
- else if ( strm ( template_list, "PSISSP") || strm (template_list, "PSIGOR"))
- {
-
- /*Computes a GOR consensus on a psi-blast output*/
- check_program_is_installed (GOR4_4_TCOFFEE,NULL, NULL,GOR4_ADDRESS, INSTALL_OR_DIE);
- check_blast_is_installed(server);
-
- sprintf ( buf, "SCRIPT_tc_generic_method.pl@mode#psissp_template@seq#%s/%s@obs#%s/%s@cache#%s@minid#%d@maxid#%d@mincov#%d@server#%s@type#_E_",get_mcoffee_4_tcoffee(), "New_KS.267.seq", get_mcoffee_4_tcoffee(), "New_KS.267.obs", get_cache_dir(), BmI,BMI,BmC,server);
- S=seq2template_seq (S,buf, F);
- return S;
- }
- else if ( strm ( template_list, "TM"))
- {
-
- /*predict transmembrane structure*/
- check_program_is_installed (HMMTOP_4_TCOFFEE,NULL, NULL,HMMTOP_ADDRESS, INSTALL_OR_DIE);
- sprintf ( buf, "SCRIPT_tc_generic_method.pl@mode#tm_template@arch#%s/%s@psv#%s/%s@type#_T_",get_mcoffee_4_tcoffee(), "hmmtop.arch", get_mcoffee_4_tcoffee(), "hmmtop.psv");
- S=seq2template_seq (S,buf, F);
- return S;
- }
- else if ( strm ( template_list, "PSITM"))
- {
-
- /*predict transmembrane structure*/
- check_program_is_installed (HMMTOP_4_TCOFFEE,NULL, NULL,HMMTOP_ADDRESS, INSTALL_OR_DIE);
- check_blast_is_installed(server);
-
- sprintf ( buf, "SCRIPT_tc_generic_method.pl@mode#psitm_template@database#%s@arch#%s/%s@psv#%s/%s@cache#%s@minid#%d@maxid#%d@mincov#%d@server#%s@type#_T_", prot_db, get_mcoffee_4_tcoffee(), "hmmtop.arch", get_mcoffee_4_tcoffee(), "hmmtop.psv",get_cache_dir(), BmI,BMI,BmC,server);
- S=seq2template_seq (S,buf, F);
- return S;
- }
-
- else if (strm ( template_list, "PSIBLAST"))
- {
-
- check_blast_is_installed(server);
- sprintf ( buf, "SCRIPT_tc_generic_method.pl@mode#psiprofile_template@database#%s@method#psiblast@cache#%s@minid#%d@maxid#%d@mincov#%d@server#%s@type#_R_", prot_db,get_cache_dir(),BmI,BMI,BmC,server);
- S=seq2template_seq (S,buf, F);
-
- return S;
- }
- else if (strm ( template_list, "BLAST") )
- {
- check_blast_is_installed(server);
- sprintf ( buf, "SCRIPT_tc_generic_method.pl@mode#profile_template@database#%s@method#blastp@cache#%s@minid#%d@maxid#%d@mincov#%d@server#%s@type#_R_", prot_db,get_cache_dir(),BmI,BMI,BmC,server);
- S=seq2template_seq (S,buf, F);
-
- return S;
- }
- else if ( strm ( template_list, "EXPRESSO") || strm (template_list, "PDB"))
- {
- check_blast_is_installed(server);
-
- int isRNA = 0;
- int i;
- for (i= 0; i < S->len[0]; ++i)
- {
- isRNA = (isRNA || is_rna(S->seq[0][i]));
- }
-
- if (isRNA)
- {
- sprintf ( buf, "SCRIPT_tc_generic_method.pl@mode#pdb_template@database#%s@method#blastn@cache#%s@minid#%d@maxid#%d@mincov#%d@server#%s@type#_P_@pdb_type#%s",pdb_db, get_cache_dir(),PmI,PMI,PmC, server,pdb_type);
- }
- else
- {
- sprintf ( buf, "SCRIPT_tc_generic_method.pl@mode#pdb_template@database#%s@method#blastp@cache#%s@minid#%d@maxid#%d@mincov#%d@server#%s@type#_P_@pdb_type#%s",pdb_db, get_cache_dir(),PmI,PMI,PmC, server,pdb_type);
- }
- return seq2template_seq (S,buf, F);
- }
-
- else if ( strm (template_list, "RCOFFEE") || strm (template_list, "RNA"))
- {
- char *file_struc_clac = vtmpnam (NULL);
- FILE* struc_calc_f =vfopen(file_struc_clac,"w");
- int i;
- int j=0;
- for (i = 0; i< S->nseq; ++i)
- {
- if (S->T[i]->P)
- {
- ++j;
- fprintf(struc_calc_f,"%s %s\n",S->name[i],S->T[i]->P->template_file);
- }
- }
- vfclose(struc_calc_f);
- if (j == S->nseq)
- {
-// S = seq2template_seq (S,buf,F);
- sprintf ( buf, "SCRIPT_tc_generic_method.pl@mode#calc_rna_template@pdbfile#%s@cache#%s@type#_F_", file_struc_clac,get_cache_dir());
- }
- else
- {
- check_program_is_installed (RNAPLFOLD_4_TCOFFEE,NULL, NULL,RNAPLFOLD_ADDRESS, IS_FATAL);
- sprintf ( buf, "SCRIPT_tc_generic_method.pl@mode#RNA_template@type#_F_");
- if (j > 0)
- {
- S = seq2template_seq (S,buf,F);
- sprintf ( buf, "SCRIPT_tc_generic_method.pl@mode#calc_rna_template@pdbfile#%s@cache#%s@type#_F_", file_struc_clac,get_cache_dir());
- }
- }
-// printf("IN T_\n");
- return seq2template_seq (S,buf,F);
- }
-
-
- /*2: Templates from seqnames (SELF) or named like the sequences (SEQFILE)*/
- else if ( strstr (template_list, "SELF_") ||strstr (template_list, "SEQFILE_") )
- {
- int a;
- char *p;
-
- //add template
- for (a=0; a< S->nseq; a++)
- {
-
- if ( (p=strstr (template_list,"SELF_")))p=S->name[a];
- else if ( strstr (template_list, "SEQFILE_"))p=template_list;
- else
- {
- fprintf ( stderr, "\nUnkown mode for Template [FATAL:%s]\n", PROGRAM);
- myexit (EXIT_FAILURE);
- }
-
- if ( strstr (template_list, "_P_") && !(S->T[a])->P)(S->T[a])->P =fill_P_template ( S->name[a], p,S);//PDB
- else if ( strstr (template_list, "_S_") && !(S->T[a])->S)(S->T[a])->S =fill_S_template ( S->name[a], p,S);//Sequence
- else if ( strstr (template_list, "_R_" )&& !(S->T[a])->R)(S->T[a])->R =fill_R_template ( S->name[a], p,S);//pRofile
- else if ( strstr (template_list, "_G_" )&& !(S->T[a])->G)(S->T[a])->G =fill_G_template ( S->name[a], p,S);//Genomic
- else if ( strstr (template_list, "_F_" )&& !(S->T[a])->F)(S->T[a])->F =fill_F_template ( S->name[a], p,S);//Fold
- else if ( strstr (template_list, "_T_" )&& !(S->T[a])->T)(S->T[a])->T =fill_T_template ( S->name[a], p,S);//Trans Membrane
- else if ( strstr (template_list, "_E_" )&& !(S->T[a])->E)(S->T[a])->E =fill_E_template ( S->name[a], p,S);//Secondary Structure
- else if ( strstr (template_list, "_U_" )&& !(S->T[a])->U)(S->T[a])->U =fill_U_template ( S->name[a], p,S);//unicode, list template
-
- }
- return S;
- }
-
- /*2: Templates comes in a template_file*/
- else if ( template_list==NULL || format_is_fasta (template_list))
- {
- Sequence *T;
- int a, i;
- int ntemp=0;
- T=(template_list!=NULL)?get_fasta_sequence (template_list, NULL):S;
- for (a=0; a< T->nseq; a++)
- {
-
- char *p;
- if ((i=name_is_in_list(T->name[a], S->name, S->nseq, MAXNAMES))!=-1)
- {
-
- if ( (p=strstr (T->seq_comment[a], " _P_ ")) && !(S->T[i])->P &&( (S->T[i])->P=fill_P_template (S->name[i],p,S)))ntemp++;
- else if ( (p=strstr (T->seq_comment[a], " _F_ ")) && !(S->T[i])->F &&( (S->T[i])->F=fill_F_template (S->name[i],p,S)))ntemp++;
- else if ( (p=strstr (T->seq_comment[a], " _S_ ")) && !(S->T[i])->S &&( (S->T[i])->S=fill_S_template (S->name[i],p,S)))ntemp++;
-
- else if ( (p=strstr (T->seq_comment[a], " _R_ ")) && !(S->T[i])->R &&( (S->T[i])->R=fill_R_template (S->name[i],p,S)))ntemp++;
- else if ( (p=strstr (T->seq_comment[a], " _G_ ")) && !(S->T[i])->G &&( (S->T[i])->G=fill_G_template (S->name[i],p,S)))ntemp++;
- else if ( (p=strstr (T->seq_comment[a], " _T_ ")) && !(S->T[i])->T &&( (S->T[i])->T=fill_T_template (S->name[i],p,S)))ntemp++;
- else if ( (p=strstr (T->seq_comment[a], " _E_ ")) && !(S->T[i])->E &&( (S->T[i])->E=fill_E_template (S->name[i],p,S)))ntemp++;
- else if ( (p=strstr (T->seq_comment[a], " _U_ ")) && !(S->T[i])->U &&( (S->T[i])->E=fill_U_template (S->name[i],p,S)))ntemp++;
-
- if (T!=S)strcat (S->seq_comment[i], T->seq_comment[a]);
-
- }
- }
-
- if (T!=S)free_sequence (T, -1);
-
- if ( remove_template_file==2)
- {
- vremove (template_list);
- }
- else
- if (template_list)display_output_filename ( stdout, "Template_List","fasta_seq", template_list, STORE);
- return S;
- }
-
- /*3 Templates are generated with a script*/
- else if (strstr (template_list, "SCRIPT_") && get_string_variable ("multi_core") && strstr (get_string_variable ("multi_core"), "templates") && get_nproc()>1)
- {
- char *tmp1,*command;
- Alignment *A;
- char **temp_file,**seq_file;
- int * pid_list, pid, npid, submited;
- int nproc, max_nproc;
- int num=0;
-
- char outfile[1000];
- static char *script;
- static int ntemp;
- char *p;
- int z, i;
- int freeF=0;
-
- if (!script)script=vcalloc ( 1000, sizeof(char));
-
- ntemp++;
-
- command=vcalloc ( 1000, sizeof (char));
- tmp1=vtmpnam (NULL);
-
- A=seq2aln (S,NULL, 0);
- string_array_upper(A->seq_al, A->nseq);
- output_fasta_seq (tmp1, A);
- sprintf ( script, "%s", after_strstr (template_list, "SCRIPT_"));
-
- if ((p=strstr (template_list, "@type#")))
- p+=strlen ("@type#");
-
- if (!F){F=parse_fname (S->file[0]);freeF=1;}
- sprintf (outfile, "%s%s_%s%d.template_list", F->path,F->name,template_type2short_type_name(p),ntemp);
- while ( check_file_exists (outfile))
- {
- sprintf (outfile, "%s%s_%s%d.%d.template_list",F->path, F->name,template_type2short_type_name(p),ntemp, ++num);
- }
- if (freeF)free_fname(F);
-
- nproc=get_nproc();
- //max_nproc=2*nproc;
- max_nproc=20; //EBI recommended maximum
- script=substitute(script, "@", " -");
- script=substitute(script, "#", "=");
-
- temp_file=vcalloc ( A->nseq, sizeof (char*));
- seq_file =vcalloc (A->nseq, sizeof (char*));
- pid_list =vcalloc (MAX_N_PID, sizeof (int *));
-
- fprintf ( stderr, "\n\t------ Fetch Templates [Multi Core Mode %d CPUs]\n",get_nproc());
- for (npid=0, submited=0,i=0; i<S->nseq; i++)
- {
- FILE *fp2;
- seq_file[i]=vtmpnam (NULL);
- temp_file[i]=vtmpnam (NULL);
- fp2=vfopen (seq_file[i], "w");
- fprintf ( fp2, ">%s\n%s\n", S->name[i], S->seq[i]);
- vfclose (fp2);
-
- pid=vvfork(NULL);
- if (pid==0)
- {
- initiate_vtmpnam (NULL);
- if ( strstr (script, "tc_generic_method"))
- {
- //sprintf ( command, "%s -other_pg %s -infile=%s -outfile=%s -tmpdir=%s",get_string_variable ("t_coffee"),script,seq_file[i],temp_file[i],get_tmp_4_tcoffee());
- sprintf ( command, "%s -infile=%s -outfile=%s -tmpdir=%s",script,seq_file[i],temp_file[i],get_tmp_4_tcoffee());
- }
- else
- //sprintf ( command, "%s -other_pg %s -infile=%s -outfile=%s",get_string_variable("t_coffee"),script,seq_file[i],temp_file[i]);
- sprintf ( command, "%s -infile=%s -outfile=%s",script,seq_file[i],temp_file[i]);
- command=substitute(command, "@", " ");
- //my_system ( command);
- myexit (my_system(command));
- }
- else
- {
- pid_list[pid]=npid;
- //set_pid(pid);
- npid++;
- submited++;
- submited=vwait_npid(submited,max_nproc,nproc);
- }
- }
-
- submited=vwait_npid(submited,0,0);
- //Concatenate all the files
- vremove (outfile);
- for (i=0; i<npid; i++) file_cat (temp_file[i],outfile);
-
- //Free the process table
- vfree (temp_file);
- vfree (pid_list);
- vfree (seq_file);
-
- free_aln (A);
- if ( check_file_exists (outfile) && format_is_fasta(outfile))
- {
- S=seq2template_seq (S, outfile, F);
- }
- else if (strstr (command, "webblast.pl"))return S;
- else
- {
-
- add_warning (stderr, "Could not Run %s to find templates[%s](Forked mode)\n",command, PROGRAM);
- return NULL;
- }
-
- vfree (command);
- return S;
- }
-
- else if (strstr (template_list, "SCRIPT_"))
- {
- char x[299];
- char *tmp1,*command;
- Alignment *A;
- char outfile[1000];
- static char *script;
- static int ntemp;
- char *p;
- int z;
- if (!script)script=vcalloc ( 1000, sizeof(char));
-
- ntemp++;
-
- command=vcalloc ( 1000, sizeof (char));
- tmp1=vtmpnam (NULL);
-
- A=seq2aln (S,NULL, 0);
- string_array_upper(A->seq_al, A->nseq);
- output_fasta_seq (tmp1, A);
- sprintf ( script, "%s", after_strstr (template_list, "SCRIPT_"));
- fprintf ( stderr, "\n");
- if ((p=strstr (template_list, "@type#")))
- p+=strlen ("@type#");
- if (F)
- {
- sprintf (outfile, "%s%s_%s%d.template_list", F->path,F->name,template_type2short_type_name(p),ntemp);
- }
- else
- {
- F=parse_fname (S->file[0]);
- sprintf (outfile, "%s%s_%s%d.template_list",F->path, F->name,template_type2short_type_name(p),ntemp);
- free_fname (F);
- }
-
- script=substitute(script, "@", " -");
- script=substitute(script, "#", "=");
-
- if ( strstr (script, "tc_generic_method"))
- {
- sprintf ( command, "%s -other_pg %s -infile=%s -outfile=%s -tmpdir=%s",get_string_variable ("t_coffee"),script, tmp1,outfile,get_tmp_4_tcoffee());
- }
- else sprintf ( command, "%s -other_pg %s -infile=%s -outfile=%s",get_string_variable("t_coffee"),script, tmp1, outfile);
-
- vremove (outfile);
- command=substitute(command, "@", " ");
-
- my_system ( command);
-
- free_aln (A);
-
- if ( check_file_exists (outfile) && format_is_fasta(outfile))
- {
- S=seq2template_seq (S, outfile, F);
- }
- else if (strstr (command, "webblast.pl"))return S;
- else
- {
-
- add_warning (stderr, "Could not Run %s to find templates[%s](unforked mode)\n",command, PROGRAM);
- return NULL;
- }
-
- vfree (command);
- return S;
- }
-
- return S;
-}
-
-char* seq2template_file (Sequence *S, char *file)
-{
- Alignment *A;
- int i;
- if (!S)return file;
- if (file==NULL)file=vtmpnam (NULL);
-
- seq2template_file2 (S, file, "w");
-
- for (i=0; i<S->nseq; i++)
- {
- if ( (A=seq2R_template_profile (S, i)))
- {
- Sequence *S;
- S=A->S;
- if (S)seq2template_file2 (A->S, file, "a");
- }
- }
- return file;
-}
-
-int seq2template_file2 (Sequence *S, char *file, char *mode)
-{
- FILE *fp;
- int i;
- char buf1[10000];
- char buf2[10000];
- struct X_template *X;
-
- fp=vfopen ( file, mode);
- for ( i=0; i< S-> nseq; i++)
- {
- buf1[0]=0;
- if ( S->T)
- {
- if (S->T[i])
- {
- if ( (X=(S->T[i])->P)){sprintf (buf2, " %s %s ", X->template_type, X->template_file);strcat (buf1, buf2);}
- /*if ( (X=(S->T[i])->S)){sprintf (buf2, " %s %s ", X->template_type, X->template_file);strcat (buf1, buf2);}*/
- if ( (X=(S->T[i])->R)){sprintf (buf2, " %s %s ", X->template_type, X->template_file);strcat (buf1, buf2);}
- if ( (X=(S->T[i])->G)){sprintf (buf2, " %s %s ", X->template_type, X->template_file);strcat (buf1, buf2);}
- if (buf1[0])fprintf ( fp, ">%s %s\n", S->name[i], buf1);
- }
- }
- }
- vfclose (fp);
- return EXIT_SUCCESS;
-}
-
-
-
-
-int seq2n_X_template ( Sequence *S, char *type)
-{
- int a, n;
-
- for (n=0,a=0; a< S->nseq; a++)
- {
- if ( strm2 (type, "_P_","_*_") && (S->T[a])->P)n++;
- if ( strm2 (type, "_F_","_*_") && (S->T[a])->F)n++;
- if ( strm2 (type, "_S_","_*_") && (S->T[a])->S)n++;
- if ( strm2 (type, "_R_","_*_") && (S->T[a])->R)n++;
- if ( strm2 (type, "_G_","_*_") && (S->T[a])->G)n++;
- }
- return n;
-}
-struct X_template *fill_X_template ( char *name, char *p, char *token)
-{
- struct X_template *X;
-
-
-
-
- char *k;
-
- X=vcalloc (1, sizeof (X_template));
- sprintf ( X->seq_name, "%s", name);
- if ( (k=strstr (p, token)))sscanf (k+strlen(token), "%s",X->template_name);
- else sprintf (X->template_name, "%s", p);
-
-
- /*Add a Structure HERE*/
- sprintf ( X->template_type, "%s", token);
- if ( strm (token, "_P_"))X->VP=vcalloc (1, sizeof (P_template));
- if ( strm (token, "_F_"))X->VF=vcalloc (1, sizeof (F_template));
-
- if ( strm (token, "_S_"))X->VS=vcalloc (1, sizeof (S_template));
- if ( strm (token, "_R_"))X->VR=vcalloc (1, sizeof (R_template));
- if ( strm (token, "_G_"))X->VG=vcalloc (1, sizeof (G_template));
- if ( strm (token, "_T_"))X->VT=vcalloc (1, sizeof (T_template));
- if ( strm (token, "_E_"))X->VE=vcalloc (1, sizeof (E_template));
- if ( strm (token, "_U_"))X->VU=vcalloc (1, sizeof (U_template));
-
- return X;
-}
-
-struct X_template* free_X_template ( struct X_template *X)
-{
- if (X->VP)
- {
- vfree (X->VP);
- }
- if (X->VF)
- {
- vfree (X->VF);
- }
- if ( X->VS)
- {
- free_sequence ((X->VS)->S, -1);
- vfree (X->VS);
- }
- if ( X->VR)
- {
- free_aln ((X->VR)->A);
- vfree (X->VR);
- }
- if ( X->VG)
- {
- free_sequence ((X->VG)->S, -1);
- vfree (X->VG);
- }
-
- vfree (X);
- return NULL;
-}
-
-FILE * display_sequence_templates (Sequence *S,int i, FILE *io)
-{
-
-
- io=display_X_template ( (S->T[i])->P, io);
-
- io=display_X_template ( (S->T[i])->F, io);
-
- io=display_X_template ( (S->T[i])->S, io);
-
- io=display_X_template ( (S->T[i])->R, io);
- io=display_X_template ( (S->T[i])->G, io);
- io=display_X_template ( (S->T[i])->T, io);
- io=display_X_template ( (S->T[i])->E, io);
-
- return io;
-}
-
-FILE * display_X_template (struct X_template *X, FILE *io)
-{
-
- if ( !X) return io;
- if ( !strm (X->template_type, "_S_"))fprintf (io, "\n\t%s: Template=%s, File=%s",template_type2type_name (X->template_type), X->template_name,X->template_file);
- return io;
-}
-char *template_type2short_type_name (char *type)
-{
- //add_template
- if (!type)return "";
- else if ( strstr (type, "_P_")) return "pdb";
- else if ( strstr (type, "_F_")) return "rfold";
- else if ( strstr (type, "_S_")) return "seq";
- else if ( strstr (type, "_R_")) return "prf";
- else if ( strstr (type, "_G_")) return "genome";
- else if ( strstr (type, "_E_")) return "ssp";
- else if ( strstr (type, "_T_")) return "tmp";
- else if ( strstr (type, "_U_")) return "unicode";
- else return type;
-}
-char *template_type2type_name (char *type)
-{
- //add_template
- if ( strstr (type, "_P_")) return "PDB struc";
- else if ( strstr (type, "_F_")) return "RNA Fold";
- else if ( strstr (type, "_S_")) return "Sequeence";
- else if ( strstr (type, "_R_")) return "Profile";
- else if ( strstr (type, "_G_")) return "Genomic";
- else if ( strstr (type, "_E_")) return "Protein Secondary Structure";
- else if ( strstr (type, "_T_")) return "Protein Trans Membrane Structure ";
- else if ( strstr (type, "_U_")) return "Unicode and strings";
-
- else return type;
-}
-struct X_template *fill_F_template ( char *name,char *p, Sequence *S)
-{
- /*Profile template*/
- struct X_template *F;
-
- F=fill_X_template ( name, p, "_F_");
- sprintf (F->template_format , "TCOFFEE_LIBRARY");
- if (!F || !check_file_exists (F->template_name))
- {
- fprintf ( stderr, "Could Not Fill _F_ (Fold) template for sequence |%s|", name);
- free_X_template (F);
- return NULL;
- }
- else if ( check_file_exists (F->template_name))
- {
- sprintf ( F->template_file, "%s", F->template_name);
- }
-
- return F;
-
-}
-
-
-struct X_template *fill_P_template ( char *name,char *p, Sequence *S)
-{
- struct X_template *P;
- Sequence *PS;
- Alignment *A;
- int sim, cov, i;
- char *buf;
-
-
- P=fill_X_template ( name, p, "_P_");
- sprintf (P->template_format , "pdb");
-
- if (!P ||(check_file_exists (P->template_name) && !is_pdb_file (P->template_name) ))
- {
- //fprintf ( stderr, "Could Not Fill _P_ template for sequence |%s|", name);
- free_X_template (P);
- return NULL;
- }
- else if ( check_file_exists (P->template_name))
- {
- sprintf ( P->template_file, "%s", P->template_name);
- buf=path2filename (P->template_name);
- if (P->template_name!=buf)
- {
- sprintf ( P->template_name, "%s",buf );
- vfree (buf);
- }
- }
- else
- {
- char *st;
-
- st=is_pdb_struc (P->template_name);
- if (st)
- {
- if (st!=P->template_file)sprintf ( P->template_file, "%s", st);
- }
- }
-
- /*Make a first run to fix relaxed PDB files*/
- buf=fix_pdb_file (P->template_file);
-
- if ( buf!=P->template_file)
- {
-
- sprintf ( P->template_file, "%s",buf);
- vfree (buf);
- }
-
- /*Check the PDB FILE EXISTS*/
-
- if (!is_pdb_file (P->template_file))
- {
-
- if (p)add_warning(stderr, "_P_ Template | %s | Could Not Be Found\n",p);
- else if (name)add_warning(stderr, "_P_ Template | %s | Could Not Be Found\n",name);
- free_X_template (P);
- return NULL;
- }
- else
- {
- buf= get_pdb_id (P->template_file);
- if (buf!=(P->VP)->pdb_id)
- {
- sprintf ((P->VP)->pdb_id, "%s", buf);
- vfree (buf);
- }
- }
-
- /*Check the target sequence is similar enough*/
-
- PS=get_pdb_sequence (P->template_file);
-
-
-
- if ( PS==NULL)
- {
- add_warning( stderr, "_P_ Template |%s| Could Not be Used for Sequence |%s|: Structure Not Found", P->template_name, name);
- free_X_template (P);P=NULL;
- }
- else
- {
- int minsim=get_int_variable ("pdb_min_sim");
- int mincov=get_int_variable ("pdb_min_cov");
-
-
- i=name_is_in_list (name, S->name, S->nseq, 100);
-
- A=align_two_sequences (S->seq[i], PS->seq[0],"idmat",-3,0, "fasta_pair_wise");
-
- sprintf ( A->name[0], "seq");
- sprintf ( A->name[1], "pdb");
- cov=aln2coverage (A, 0);
- sim=aln2sim (A, "idmat");
-
- if (sim<=minsim)
- {
- add_information( stderr, "_P_ Template %s Could Not be Used for Sequence %s: Similarity too low [%d, Min=%d]",P->template_name,name,sim,minsim);
- add_information( stderr, "If you want to include %s in anycase,add -pdb_min_sim=%d to the command line",name,sim);
- print_aln (A);
- free_X_template (P);
- P=NULL;
- }
- else if ( cov<=mincov)
- {
- add_information(stderr, "_P_ Template |%s| Could Not be Used for Sequence |%s|: Coverage too low [%d, Min=%d]",P->template_name,name, cov, mincov);
- add_information( stderr, "If you want to include this sequence in anycase add -pdb_min_cov=%d to the command line", cov);
- print_aln (A);
- free_X_template (P);P=NULL;
- }
- free_aln(A);
- free_sequence (PS, -1);
- }
-
- return P;
-}
-
-struct X_template *fill_S_template ( char *name,char *p, Sequence *Seq)
-{
- struct X_template *S;
- S=fill_X_template ( name, p, "_S_");
- if ( strm (name, p))sprintf ( S->template_file, "%s",output_fasta_seqX (NULL,"w",Seq,NULL, seq_name2index (name, Seq)));
- (S->VS)->S=get_fasta_sequence (S->template_file, NULL);
- return S;
-}
-struct X_template *fill_R_template ( char *name,char *p, Sequence *S)
-{
- /*Profile template*/
- struct X_template *R;
-
-
- R=fill_X_template ( name, p, "_R_");
- sprintf (R->template_format , "fasta_aln");
-
-
- if (!is_aln(R->template_name) && !is_seq (R->template_name))
- {
-
- add_information ( stderr, "_R_ Template %s Could Not Be Found\n",R->template_name);
- free_X_template (R);
- return NULL;
- }
- else
- {
- int s;
- Sequence *S1;
- Alignment *A1;
-
- (R->VR)->A=main_read_aln (R->template_name, NULL);
-
- if ( !S)
- sprintf ( R->template_file, "%s", R->template_name);
- else
- {
- s=name_is_in_list(name, S->name, S->nseq, 100);
- if ( s!=-1)
- {
- S1=fill_sequence_struc (1, &S->seq[s], &S->name[s]);
- A1=seq2aln (S1,NULL, RM_GAP);
-
- (R->VR)->A=trim_aln_with_seq (A1, (R->VR)->A);
-
- sprintf ( R->template_file, "%s", vtmpnam (NULL));
- output_clustal_aln (R->template_file, (R->VR)->A);
- }
- else
- sprintf ( R->template_file, "%s", R->template_name);
- }
- (R->VR)->A=aln2profile ((R->VR)->A);
-
- //free_data_in_aln ((R->VR)->A);
-
- }
- return R;
-}
-
-struct X_template *fill_T_template ( char *name,char *p, Sequence *S)
-{
- /*Profile template*/
- struct X_template *T;
-
- T=fill_X_template ( name, p, "_T_");
- sprintf (T->template_format , "fasta_seq");
-
- if (!is_aln(T->template_name) && !is_seq (T->template_name))
- {
-
- add_information ( stderr, "_T_ Template %s Could Not Be Found\n",T->template_name);
- free_X_template (T);
- return NULL;
- }
- else
- {
-
- (T->VT)->S=main_read_seq(T->template_name);
- sprintf ( T->template_file, "%s", T->template_name);
- }
- return T;
-}
-//add template
-struct X_template *fill_U_template ( char *name,char *p, Sequence *S)
-{
- /*Profile template*/
- struct X_template *U;
-
- U=fill_X_template ( name, p, "_U_");
- sprintf (U->template_format , "string list");
-
- if (!check_file_exists(U->template_name))
- {
- add_information ( stderr, "_U_ Template %s Could Not Be Found\n",U->template_name);
- free_X_template (U);
- return NULL;
- }
- else
- {
- //(U->VU)->list=file2string(U->template_name);
- sprintf ( U->template_file, "%s", U->template_name);
- }
- return U;
-}
-struct X_template *fill_E_template ( char *name,char *p, Sequence *S)
-{
- /*Profile template*/
- struct X_template *E;
-
-
- E=fill_X_template ( name, p, "_E_");
- sprintf (E->template_format , "fasta_seq");
-
- if (!is_aln(E->template_name) && !is_seq (E->template_name))
- {
-
- add_information ( stderr, "_E_ Template %s Could Not Be Found\n",E->template_name);
- free_X_template (E);
- return NULL;
- }
- else
- {
- (E->VE)->S=main_read_seq (E->template_name);
- sprintf ( E->template_file, "%s", E->template_name);
- }
- return E;
-}
-struct X_template *fill_G_template ( char *name,char *p, Sequence *S)
-{
- struct X_template *G;
- G=fill_X_template ( name, p, "_G_");
- sprintf (G->template_format , "fasta_seq");
-
- /*1: Get the sequence from another file if needed*/
- if ( strm (name, p))sprintf ( G->template_file, "%s",output_fasta_seqX (NULL,"w",S,NULL, seq_name2index (name, S)));
- else if ( strstr (p, "SEQFILE_"))
- {
- Sequence *ST;
- int i2;
-
-
- ST=main_read_seq (after_strstr ( p,"SEQFILE_G_"));
-
- i2=seq_name2index (name, ST);
- if ( i2!=-1)
- {
- sprintf ( G->template_file, "%s",output_fasta_seqX (NULL,"w",ST,NULL, i2));
- sprintf ( G->template_name, "%s", name);
- }
- free_sequence (ST, -1);
- }
- else sprintf (G->template_file, "%s", G->template_name);
-
-
- /*2: Put the template in VG->S*/
- if (!is_seq (G->template_file))
- {
- add_information ( stderr, "_G_ Template %s Could Not Be Found \n",p);
-
- free_X_template (G);
- return NULL;
- }
- else
- {
- (G->VG)->S=get_fasta_sequence (G->template_file, NULL);
- }
- return G;
-}
-
-
-char *seq2T_value ( Sequence *S, int n, char *value, char *type)
-{
- static char *rv_buf;
- X_template *X;
-
- if ( !rv_buf)rv_buf=vcalloc (100, sizeof(char));
- if (!(X=seq_has_template (S, n, type)))return NULL;
- else
- {
- if (strm (value, "template_file"))return X->template_file;
- else if ( strm (value, "template_name"))return X->template_name;
- else if ( strm (value, "seq_name"))return X->seq_name;
- else if (strm (type, "_P_"))
- {
- if ( strm (value, "pdb_id"))return (X->VP)->pdb_id;
- }
- else if ( strm (type, "_R_"))
- {
- if ( strm (value, "A"))
- {
- if ((X->VR)->A)
- {sprintf ( rv_buf, "%ld", (long)(X->VR)->A);return rv_buf;}
- else return NULL;
- }
- }
-
- }
- return NULL;
-}
-char *seq2P_pdb_id (Sequence *S, int n)
-{
- if (!S->T || !S->T[n] || !(S->T[n])->P ) return NULL;
- else return ((S->T[n])->P)->template_name;
-}
-
-
-char *seq2P_template_file(Sequence *S, int n)
-{
-
- return seq2T_value (S, n, "template_file", "_P_");
-}
-
-char *profile2P_template_file (Sequence *S, int n)
-{
- Alignment *A;
- int a;
- char *p;
-
- if ( !(A=seq2R_template_profile (S, n)))return NULL;
- for (a=0; a<A->nseq; a++)
- {
- if ((p=seq2P_template_file (A->S, a))!=NULL)return p;
- }
- return NULL;
-}
-Alignment * seq2R_template_profile (Sequence *S, int n)
-{
- X_template *X;
-
- return (Alignment *)atop(seq2T_value (S, n, "A", "_R_"));
-
- if (!(X=seq_has_template (S, n, "_R_")))return NULL;
- else
- {
- if (!(X->VR))return NULL;
- else return (X->VR)->A;
- }
- return NULL;
-
-
-
-}
-char * seq2E_template_string (Sequence *S, int n)
-{
- struct X_template *T;
-
- if ( (T=seq_has_template (S, n, "_E_"))!=NULL)
- return ((T->VE)->S)->seq[0];
- else
- return NULL;
-}
-//add template
-int* seq2U_template (Sequence *S, int n)
-{
- struct X_template *T;
-
- if ( (T=seq_has_template (S, n, "_U_"))!=NULL)
- return (T->VU)->list;
- else
- return NULL;
-}
-char * seq2T_template_string (Sequence *S, int n)
-{
- struct X_template *T;
-
- if ( (T=seq_has_template (S, n, "_T_"))!=NULL)
- return ((T->VT)->S)->seq[0];
- else
- return NULL;
-}
-
-struct X_template* seq_has_template ( Sequence *S, int n, char *mode)
-{
- Template *T;
-
- if ( !S || !mode) return NULL;
- else if ( n<0 || n>=S->nseq)return NULL;
- else if ( !(S->T)) return NULL;
- else if ( !(S->T[n]))return NULL;
-
- T=S->T[n];
- //ADD STRUCTURE
- //add template
- if ( strm (mode, "_P_"))return T->P;
- else if ( strm (mode, "_F_"))return T->F;
- else if ( strm (mode, "_S_"))return T->S;
- else if ( strm (mode, "_R_"))return T->R;
- else if ( strm (mode, "_T_"))return T->T;
- else if ( strm (mode, "_E_"))return T->E;
- else if ( strm (mode, "_U_"))return T->U;
- else if ( strm (mode, "_G_"))return T->G;
- else return NULL;
-}
-
-char ** name2random_subset (char **in_name, int n_in, int n_out)
-{
- char **out_name;
-
- int **list;
- int a,max;
-
-
- vsrand (0);
- max=n_in*10000;
- out_name=declare_char (n_out,MAXNAMES+1 );
- list=declare_int (n_in, 2);
-
- for (a=0; a<n_in; a++)
- {
- list[a][0]=a;
- list[a][1]=rand ()%max;
- }
- sort_int ( list,2, 1, 0, n_in-1);
-
- for ( a=0; a<n_in; a++)
- {
- sprintf ( out_name[a], "%s", in_name[list[a][0]]);
- }
- free_int (list, -1);
- return out_name;
-}
-
-Alignment * aln2random_order (Alignment *A)
-{
-
- char **name_list;
-
- name_list=name2random_subset (A->name, A->nseq, A->nseq);
- A=reorder_aln (A, name_list, A->nseq);
- free_char (name_list, -1);
- return A;
-}
-Alignment *aln2jacknife (Alignment *A, int nseq, int len)
-{
- int a, b;
-
- if (nseq!=0 && nseq<A->nseq)
- {
- char **name;
-
- name=name2random_subset (A->name, A->nseq, nseq);
- A=reorder_aln (A, name, nseq);
- free_char (name, -1);
- }
-
- if (len!=0 && len<A->len_aln)
- {
- int **l;
- Alignment *B;
-
- l=declare_int (A->len_aln, 2);
- for (a=0; a< A->len_aln; a++)
- {
- l[a][0]=a;
- l[a][1]=rand()%(A->len_aln*1000);
- }
- sort_int ( l,2, 1, 0, A->len_aln-1);
- B=copy_aln (A, NULL);
- for ( a=0; a< len; a++)
- {
- for ( b=0; b<A->nseq; b++)
- {
- A->seq_al[b][a]=B->seq_al[b][l[a][0]];
- }
- }
- for (b=0; b<A->nseq; b++)A->seq_al[b][len]='\0';
- free_aln (B);
- free_int (l, -1);
- }
- return A;
-}
-Alignment * aln2scramble_seq (Alignment *A)
-{
- int **list;
- char **name_list;
- int a,max;
-
- max=100*A->nseq;
- vsrand (0);
-
- list=declare_int (A->nseq, 2);
- name_list=vcalloc (A->nseq, sizeof (char*));
-
-
- for (a=0; a<A->nseq; a++)
- {
- list[a][0]=a;
- list[a][1]=rand ()%max;
- }
- sort_int ( list,2, 1, 0, A->nseq-1);
-
- for ( a=0; a< A->nseq; a++)
- name_list[a]=A->seq_al[a];
- for (a=0; a<A->nseq; a++)
- {
- A->seq_al[a]=name_list[list[a][0]];
- }
- vfree (name_list);
- free_int (list, -1);
- return aln2random_order (A);
-}
-
-
-
-Alignment * reorder_aln ( Alignment *A, char **name, int nseq)
- {
- int a,sn;
- Alignment *BUF;
- int n=0;
- int *tpp_int;
-
- if ( name==NULL)return aln2random_order(A);
-
-
- BUF=copy_aln ( A,NULL);
- for ( a=0; a<nseq; a++)
- {
- sn =name_is_in_list ( name[a],BUF->name, A->nseq,STRING);
- if ( sn==-1)
- {
- ;
- }
- else
- {
-
-
- SWAPP(A->order[n], BUF->order[sn], tpp_int);
- sprintf ( A->name[n], "%s", BUF->name[sn]);
- sprintf ( A->seq_al[n], "%s",BUF->seq_al[sn]);
- sprintf ( A->seq_comment[n], "%s", BUF->seq_comment[sn]);
-
- n++;
-
- }
- }
-
- for ( a=n; a< A->nseq; a++)A->name[a][0]=A->seq_al[a][0]='\0';
- A->nseq=n;
-
- if ( A->A)A->A=reorder_aln(A->A, name, nseq);
- free_aln (BUF);
- return A;
- }
-Sequence * reorder_seq_2 ( Sequence *A, int **order,int field, int nseq)
- {
- char **name;
- int a;
-
- if (!A || !order) return A;
- name=declare_char (A->nseq, 100);
- for (a=0; a<nseq; a++)
- sprintf ( name[a], "%s", A->name[order[a][field]]);
- A=reorder_seq (A, name,nseq);
- free_char (name, -1);
- return A;
- }
-Sequence * reorder_seq ( Sequence *A, char **name, int nseq)
- {
- int a,sn;
- Sequence *nA;
-
-
- nA=duplicate_sequence (A);
-
-
- for ( a=0; a< nseq; a++)
- {
- sn=name_is_in_list (name[a] ,nA->name, nA->nseq, 100);
- if (sn==-1)continue;
-
- if ( nA->file) sprintf ( A->file[a], "%s", nA->file[sn]);
-
- if ( nA->seq_comment)sprintf ( A->seq_comment[a], "%s", nA->seq_comment[sn]);
- if ( nA->aln_comment)sprintf ( A->aln_comment[a], "%s", nA->aln_comment[sn]);
- sprintf ( A->seq[a], "%s", nA->seq[sn]);
- A->len[a]=nA->len[sn];
- sprintf ( A->name[a], "%s", nA->name[sn]);
- A->T[a][0]=nA->T[sn][0];
- }
- A->nseq=nseq;
- free_sequence (nA, nA->nseq);
-
- return A;
-}
-
-char * concatenate_seq ( Sequence *S, char *conc, int *order)
- {
- int a;
-
- vfree (conc);
- conc=vcalloc ( S->nseq*S->max_len, sizeof (char));
-
- for ( a=0; a< S->nseq; a++)
- {
- conc=strcat ( conc, S->seq[order[a]]);
- }
- return conc;
-
- }
-
-
-
-
-Alignment * rotate_aln ( Alignment *A, char *name)
-{
- Alignment *B;
- int a, b;
-
- B=declare_aln2 (A->len_aln, A->nseq+1);
- for ( a=0; a< A->nseq; a++)
- for ( b=0; b< A->len_aln; b++)
- {
- B->seq_al[b][a]=A->seq_al[a][b];
- }
- for (a=0; a< A->len_aln; a++)
- if (name && name[0])sprintf ( B->name[a], "%s_%s%d", name, (a<9)?"0":"",a+1);
- else
- sprintf ( B->name[a], "%d", a+1);
-
-
- for (a=0; a< A->len_aln; a++)B->seq_al[a][A->nseq]='\0';
- B->len_aln=A->nseq;
- B->nseq=A->len_aln;
- /*free_aln (A);*/
- return B;
-}
-
-Alignment * invert_aln ( Alignment *A)
-{
- char *buf;
- int l, a, b, c;
-
- for ( a=0; a< A->nseq; a++)
- {
- l=strlen ( A->seq_al[a]);
- buf=vcalloc ( l+1,sizeof (char) );
-
- for ( c=l-1,b=0; b< l; b++, c--)
- {
- buf[c]=A->seq_al[a][b];
- }
- buf[l]='\0';
- sprintf ( A->seq_al[a], "%s", buf);
- }
- vfree(buf);
- return A;
-}
-char * complement_string (char *s)
-{
- char *buf;
- int l, a, b, c;
-
- l=strlen (s);
- for ( b=0; b< l; b++)
- {
- char r;
- r=s[b];
- if ( r=='a')r='t';
- else if (r=='A')r='T';
- else if (r=='t')r='a';
- else if (r=='T')r='A';
- else if (r=='g')r='c';
- else if (r=='G')r='C';
- else if (r=='c')r='g';
- else if (r=='C')r='G';
- s[b]=r;
- }
-
- return invert_string (s);
-}
-Alignment * complement_aln ( Alignment *A)
-{
- char *buf;
- int l, a, b, c;
-
- for ( a=0; a< A->nseq; a++)
- {
- A->seq_al[a]=complement_string (A->seq_al[a]);
- }
-
- return A;
-}
-
-Alignment * extract_nol_local_aln(Alignment *A, int start, int max_end)
- {
- A=extract_aln ( A, start, max_end);
- A=trunkate_local_aln (A);
- return A;
- }
-
-Alignment * alnpos_list2block (Alignment *A, int n, char **in_list)
-{
- int *pos;
- int a;
- char **list;
- int list_declared=0;
- Alignment *B;
-
- if (check_file_exists (in_list[0]))
- {
- int mn;
- char ***tmp_list;
-
- mn=count_n_line_in_file (in_list[0]);
- list=declare_char (mn, 100);
- list_declared=1;
- tmp_list=file2list (in_list[0], " ");
- a=0;
- n=0;
- while (tmp_list[a])
- {
- if (tmp_list[a][1][0]!='!')
- {
- sprintf (list[n++], "%s", tmp_list[a][1]);
- }
- a++;
- }
- free_arrayN ((void **)tmp_list, 3);
- }
- else
- {
- list=in_list;
- }
-
-
- pos=vcalloc (A->len_aln, sizeof (int));
- for (a=0; a<n; a++)
- {
-
- if (strstr (list[a], "-"))
- {
- int start, end, x;
- x=sscanf (list[a], "%d-%d", &start, &end);
- if (x!=2 || !A || start<=0 || start>=end || end>A->len_aln+1)
- {
- add_warning ( stderr, "Illegal coordinates in extract_pos_list [%s]", list[a]);
- return A;
- }
- start--; end--;
- for (a=start; a<end; a++)pos[a]=1;
- }
- else
- {
- int p;
- p=atoi (list[a]);
- if (p<1 || p>A->len_aln)
- {
- add_warning ( stderr, "Illegal coordinates in extract_pos_list [%s]", list[a]);
- }
- p--;
- pos[p]=1;
- }
- }
- B=alnpos2block(A, pos, NULL);
- vfree (pos);
- if ( list_declared)free_char (list, -1);
-
- return B;
-}
-Alignment * aln2block (Alignment *A, int start, int end, Alignment *B)
-{
- if ( !A || start<=0 || start>=end || end>A->len_aln+1)
- {
- add_warning ( stderr, "Illegal coordinates in extract_block start=%d end=%d len=%d [Note : [start-end[, with [1...n] ** Block Ingored", start, end, A->len_aln);
- return A;
- }
- else
- {
- int *pos, p;
- start--;
- end--;
- pos=vcalloc (A->len_aln, sizeof (int));
- for (p=start;p<end;p++)
- {
- pos[p]=1;
- }
- B=alnpos2block (A, pos, B);
- vfree (pos);
- return B;
- }
-}
-Alignment * alnpos2block (Alignment *A, int *pos, Alignment *B)
-{
-
- //extract a subset of B without over-writing A
- int a, b;
-
- B=copy_aln (A, B);
- B->len_aln=0;
- for (a=0; a<=A->len_aln; a++)
- {
- if ( pos[a]!=0 || a==A->len_aln)
- {
- for ( b=0; b<A->nseq; b++)
- B->seq_al[b][B->len_aln]=A->seq_al[b][a];
- if ( a!=A->len_aln)B->len_aln++;
- }
- }
-
- return B;
-}
-Alignment * extract_aln ( Alignment *A, int start, int end)
-{
- return extract_aln2 ( A, start, end, "cons");
-}
-
-Alignment * extract_aln2 ( Alignment *A, int in_start, int in_end, char *seq)
- {
- char *tmp;
- FILE *fp;
-
-
- tmp=vtmpnam (NULL);
- fp=vfopen (tmp, "w");
- fprintf ( fp, "%s %d %d\n", seq, in_start, in_end);
- vfclose (fp);
- return extract_aln3 (A,tmp);
- }
-Alignment * extract_aln3 ( Alignment *B, char *file)
- {
- int a, b, c;
- int start, end;
- int n, i, s, nline=0;
- FILE *fp;
- Alignment *A=NULL;
- int *col;
- char name[MAXNAMES];
- char line[VERY_LONG_STRING];
- int *offset;
-
- /*Reads in a file
- #comment
- ! seq_name offset
- seqname pos
- OR
- seqname start end[
- modifies the incoming alignment
- */
-
- offset=vcalloc ( B->nseq+1, sizeof (int));
- fp=vfopen (file,"r");
- while ( (c=fgetc(fp))!=EOF)
- {
- s=-1;
- fgets ( line, VERY_LONG_STRING,fp);
- if ( c=='!')
- {
- sscanf (line, "%s %d", name, &start);
- s=name_is_in_list (name,B->name,B->nseq,MAXNAMES);
- }
- if (s!=-1)
- offset[s]=start;
- }
-
- vfclose (fp);
-
- A=copy_aln (B, A);
- col=vcalloc ( A->len_aln, sizeof (int));
-
- fp=vfopen ( file, "r");
- while ( (c=fgetc(fp))!=EOF)
- {
- nline++;
- if ( c=='#' || c=='!')fgets ( line, VERY_LONG_STRING,fp);
- else
- {
- ungetc(c, fp);
- fgets ( line, VERY_LONG_STRING,fp);
-
- if (sscanf (line, "%s %d %d", name, &start, &end)==3);
- else if (sscanf (line, "%s %d", name, &start)==2)
- {
- end=start+1;
- }
- else
- {
- add_warning ( stderr, "Wrong format in coordinate file (line=%d) ** Line Ignored", nline);
- continue;
- }
- if ( end==0)end=A->len_aln+1;
-
- s=name_is_in_list (name,A->name,A->nseq,MAXNAMES);
-
-
- if ( s==-1 && !strm (name, "cons"))
- {
- add_warning ( stderr, "Seq %s does not belong to the alignment (line %d) ** Line ignored", name,nline);
- continue;
- }
- else if ( start>end)
- {
- add_warning ( stderr, "Illegal coordinates [%s %d %d] (line %d) ** Line ignored", name,start, end,nline);
- continue;
- }
- else
- {
- int done=0;
- if ( s!=-1)
- {
- start-=offset[s]-1;
- end-=offset[s]-1;
- }
- for (n=0, a=0; done!=1 && a< A->len_aln; a++)
- {
- i=(strm (name, "cons"))?1:!is_gap(A->seq_al[s][a]);
-
- n+=i;
- if (n>=start && n<end)
- {
- col[a]=1;
- }
- if (n>=end)done=1;
- //if (n>=start && n<end && !(i==0 && n==end-1))
- //{
- // col[a]=1;
- //}
- //else if ( n>=end)a=A->len_aln;
- }
- if ( done==0)
- {
- HERE ("Warning Missing positions in File %s",file );
- }
- }
- }
- }
- vfclose ( fp);
-
-
-
- /*Extract [start-end[*/
- for ( b=0,a=0; a< A->len_aln; a++)
- {
- if ( col[a])
- {
- for (c=0; c< A->nseq; c++)A->seq_al[c][b]=A->seq_al[c][a];
- b++;
- }
- }
- A->len_aln=b;
-
- for (c=0; c< A->nseq; c++)A->seq_al[c][A->len_aln]='\0';
- vfree (col);
-
- return A;
-
- }
-Alignment * trunkate_local_aln ( Alignment *A)
- {
- int a, b;
- int **pos;
- int **cache;
- int seq;
-
-
- cache=declare_int (return_max_int (A->order,read_size_int ( A->order,sizeof (int*)),0)+1,return_max_int (A->order,read_size_int ( A->order,sizeof (int*)),1)+A->len_aln+1);
- pos=aln2pos_simple(A,A->nseq);
-
- for ( b=0; b<A->len_aln; b++)
- for ( a=0; a< A->nseq; a++)
- {
- seq=A->order[a][0];
- if ( pos[a][b]<=0);
- else if ( pos[a][b]>0)
- {
-
- if (cache[seq][pos[a][b]]==0)cache[seq][pos[a][b]]++;
- else if ( cache[seq][pos[a][b]]>=1)
- {
- cache[seq][pos[a][b]]++;
- A->seq_al[a][b]='\0';
- }
- }
- }
-
- A->len_aln=get_shortest_string ( A->seq_al, A->nseq, NULL, NULL);
- pad_string_array ( A->seq_al, A->nseq, A->len_aln, '-');
-
- free_int (pos, -1);
- free_int ( cache,-1);
-
-
- return A;
- }
-
-int get_nol_aln_border ( Alignment *A, int start, int direction)
- {
- int a, b;
- int **pos;
- int **cache;
- int seq,end;
-
- /*This Function Returns the limit position for a non overlaping alignment*/
-
- cache=declare_int (return_max_int (A->order,read_size_int ( A->order,sizeof (int*)),0)+1,return_max_int (A->order,read_size_int ( A->order,sizeof (int)),1)+A->len_aln+1);
- pos=aln2pos_simple(A,A->nseq);
- end=(direction==GO_RIGHT)?A->len_aln:-1;
-
-
- for ( b=start; b!=end;b+=direction)
- for ( a=0; a< A->nseq; a++)
- {
- seq=A->order[a][0];
- if ( pos[a][b]<=0);
- else if ( pos[a][b]>0)
- {
-
- if (cache[seq][pos[a][b]]==0)cache[seq][pos[a][b]]++;
- else if ( cache[seq][pos[a][b]]>=1)
- {
- cache[seq][pos[a][b]]++;
- free_int(cache, -1);
- return b-direction;
- }
- }
- }
-
- free_int ( cache,-1);
- free_int (pos, -1);
- return end-direction;
- }
-
-
-
-
-
-char * extract_defined_seq ( char *in, int in_of, int in_start, int *aa_def, int dir, int *out_start, char *out)
- {
- int start=0, end,l;
- int b, c, d;
-
-
-
- if ( dir==GO_LEFT){start=in_start-1;}
- else if ( dir==GO_RIGHT){start=in_start+1;}
-
- end=start;
- while (aa_def[end]!=UNDEFINED)
- {
- end+=dir;
- }
- end-=dir;
-
- if (end<start)SWAP(end,start);
-
- l=strlen ( in);
- out_start[0]=-1;
- for (b=0,d=0,c=in_of;b<l; b++)
- {
- c+=1-is_gap(in[b]);
- if ( c>=start && c<=end)
- {
- if ( out_start[0]==-1)out_start[0]=c-!is_gap(in[b]);
- out[d++]=in[b];
- }
- }
- out[d]='\0';
-
-
- return out;
- }
-
-Alignment * aln2N_replicate (Alignment *A,char *nn, char *name)
-{
- int a, n;
- char *fname;
-
- fname=vcalloc (100, sizeof (char));
- if (nn)n=atoi(nn);
- else n=100;
- if (!name){name=vcalloc (100, sizeof (char)); sprintf (name, "replicate");}
-
-
- for (a=0; a< n;a++)
- {
- FILE *fp;
- sprintf (fname, "%s.%d.rep",name, a+1);
- fp=vfopen (fname, "w");
-
- vfclose(aln2replicate (A, fp));
- fprintf ( stdout, ">%s Alignment Replicate #%d\n",fname, a+1);
- }
- myexit (EXIT_SUCCESS);
-}
-FILE *aln2replicate (Alignment *A, FILE *fp)
-{
- int a, b;
- int *p;
- float tot=0;
- float corr;
- if (A->col_weight)for (a=0; a<A->len_aln; a++)tot+=A->col_weight[a];
- else tot=A->len_aln;
-
- p=vcalloc (A->len_aln, sizeof (int));
- corr=(float)A->len_aln/tot;
-
- for (a=0; a<A->len_aln; a++)
- {
- int x;
- x=rand()%(int)tot;
-
- p[a]=(int)(x*corr);
- }
-
- for (a=0; a<A->nseq; a++)
- {
- fprintf ( fp, ">%s\n", A->name[a]);
- //for (b=0;b<A->len_aln; b++)fprintf ( stdout, "%d ", (int)p[b]);
- for (b=0;b<A->len_aln; b++)fprintf ( fp, "%c", A->seq_al[a][p[b]]);
- fprintf ( fp, "\n");
- }
-
- vfree (p);
- return fp;
-}
-
-Alignment * orthologous_concatenate_aln (Alignment *A, Sequence *S, char *mode)
-{
- Alignment *C;
- char **name, *cname;
- int nname=0;
- int a, b,c, i;
-
- if (mode && strm (mode, "voronoi"))seq_weight2species_weight (A, S);
-
-
- cname=vcalloc ( 100, sizeof (char));
- name=declare_char (A->nseq, 100);
- for (a=0; a<A->nseq; a++)
- {
- char *p=strstr (A->name[a], "_");
- if (!p)
- {
- fprintf ( stderr, "\nWARNING: Seq %s could not be included.", A->name[a]);
- }
- p+=1;
- if ( name_is_in_list (p, name,nname, 100)==-1)
- {
- sprintf ( name[nname++], "%s", p);
- }
- }
-
- C=declare_aln2 (nname, (A->len_aln*S->nseq)+1);
- free_char (C->name,-1); C->name=name;
- C->nseq=nname;
- C->col_weight=vcalloc ( A->len_aln*S->nseq, sizeof(float));
-
- C->len_aln=0;
- for (a=0; a<S->nseq; a++)
- {
- for (b=0; b<C->nseq; b++)
- {
- sprintf (cname, "%s_%s", S->name[a],C->name[b]);
- if ((i=name_is_in_list (cname, A->name, A->nseq, 100))==-1)
- {
- char *s=generate_null (A->len_aln);
- strcat (C->seq_al[b], s);
- vfree (s);
- }
- else
- strcat (C->seq_al[b], A->seq_al[i]);
- }
- for (c=C->len_aln, b=0;b<A->len_aln;b++, c++)
- {
- C->col_weight[c]=(S->W)->SEQ_W[a];
- }
- C->len_aln+=A->len_aln;
- }
- return C;
-}
-
-
-Alignment * concatenate_aln ( Alignment *A1, Alignment *A2, char *spacer)
-{
- Alignment *A;
- int a, i;
-
- A=declare_aln2( A1->nseq+A2->nseq , A1->len_aln+A2->len_aln+1);
- for ( a=0; a< A1->nseq; a++)
- {
- if ((i=name_is_in_list ( A1->name[a], A2->name, A2->nseq, 100))!=-1)
- {
- sprintf ( A->name[A->nseq], "%s", A1->name[a]);
- sprintf (A->seq_al[A->nseq], "%s%s%s", A1->seq_al[a],(spacer)?spacer:"", A2->seq_al[i]);
- A->nseq++;
- }
- else
- {
- char *buf;
- buf=generate_string (A2->len_aln, '-');
- sprintf ( A->name[A->nseq], "%s", A1->name[a]);
- sprintf (A->seq_al[A->nseq], "%s%s", A1->seq_al[a], buf);
- A->nseq++;
- vfree (buf);
- }
- }
- for ( a=0; a< A2->nseq; a++)
- {
- if ((i=name_is_in_list ( A2->name[a], A1->name, A1->nseq, 100))==-1)
- {
- char *buf;
- buf=generate_string (A1->len_aln, '-');
- sprintf ( A->name[A->nseq], "%s", A2->name[a]);
- sprintf (A->seq_al[A->nseq], "%s%s", buf, A2->seq_al[a]);
- A->nseq++;
- vfree (buf);
- }
- }
- A->len_aln=A1->len_aln+A2->len_aln;
- return A;
-}
-Alignment * aln_cat ( Alignment *A, Alignment *B)
- {
- int a;
-
- if ( A->nseq!=B->nseq)
- {
- fprintf ( stderr, "\nERROR IN ALN CAT: DIFFERENT NSEQ\n");
- myexit(EXIT_FAILURE);
- }
-
- A=realloc_alignment2(A, A->nseq,A->len_aln+B->len_aln+1);
-
- for ( a=0;a< A->nseq; a++)
- {
- strcat ( A->seq_al[a], B->seq_al[a]);
- }
- A->len_aln+=B->len_aln;
- return A;
- }
-int verify_aln ( Alignment *A, Sequence *S, char *message)
- {
- int a, b, c,s,r;
-
-
- for ( a=0;a< A->nseq; a++)
- {
- s=A->order[a][0];
- r=A->order[a][1];
- for ( b=0, c=0; b< A->len_aln; b++)
- {
- if ( !is_gap(A->seq_al[a][b]))
- {
- if (tolower(A->seq_al[a][b])!=tolower(S->seq[s][c+r]))
- {
- fprintf ( stderr, "\n%s\nResidue [%c %d, %c %d] line %d seq %d",message,A->seq_al[a][b], b,S->seq[s][c+r], c+r,a,s);
- output_Alignment_with_res_number(A, stderr);
- myexit(EXIT_FAILURE);
- return 0;
- }
- c++;
- }
- }
- }
- return 1;
- }
-
-Alignment *adjust_est_aln ( Alignment *PW, Alignment *M, int s)
-{
- /*This function reajusts M, threading M onto PW
- two seqences in PW
- s+1 seq in M
-
- seq 0 PW ----> 0->s-1 in M
- seq 1 PW ----> 1->s in M;
-
- */
- int a, b;
- static char **array;
-
-
- int top_M=0;
- int bottom_M=0;
-
-
- if ( array==NULL)
- {
- array=declare_char (500, 100000);
- }
-
- for ( a=0; a< PW->len_aln; a++)
- {
- if ( is_gap(PW->seq_al[0][a]))
- {
- for ( b=0; b< s; b++)
- array[b][a]='-';
- }
- else
- {
- for ( b=0; b< s; b++)
- array[b][a]=M->seq_al[b][top_M];
- top_M++;
- }
-
- if ( is_gap(PW->seq_al[1][a]))
- {
- array[s][a]='-';
- }
- else
- {
-
- array[s][a]=M->seq_al[s][bottom_M];
- bottom_M++;
- }
- }
-
- M->len_aln=PW->len_aln;
- for (a=0; a<s; a++)
- {
- for (b=0; b<PW->len_aln; b++)
- M->seq_al[a][b]=array[a][b];
- M->seq_al[a][b]='\0';
- }
-
-
- M->nseq=s+1;
-
- return M;
-}
-
-
-Alignment * rename_seq_in_aln (Alignment *A, char ***list)
-{
- int n, i;
- if ( !A)return A;
-
-
-
- n=0;
- while ( list[n][0][0])
- {
- if ( (i=name_is_in_list (list[n][0], A->name, A->nseq, 100))!=-1)
- {
- sprintf ( A->name[i], "%s", list[n][1]);
- }
- n++;
- }
-
- A->S=rename_seq_in_seq (A->S, list);
- return A;
-}
-Sequence * rename_seq_in_seq (Sequence *A, char ***list)
-{
- int n, i;
- if ( !A || !list)return A;
-
- n=0;
- while ( list[n][0][0])
- {
- if ( (i=name_is_in_list (list[n][0], A->name, A->nseq, 100))!=-1)
- {
- sprintf ( A->name[i], "%s", list[n][1]);
- }
- n++;
- }
- return A;
-}
-/********************************************************************/
-/* */
-/* FLOAT SIMILARITIES */
-/* */
-/* */
-/* */
-/********************************************************************/
-float get_seq_fsim ( char *string1, char *string2, char *ignore, char *similarity_set,int **matrix, int MODE )
- {
- int len, a, r1, r2, nr1=0, nr2=0;
- float pos=0, sim=0;
-
-
- len=MIN((strlen (string1)),(strlen (string2)));
- if ( len==0)return 0;
-
- for ( a=0; a< len; a++)
- {
-
- r1=string1[a];
- r2=string2[a];
- nr1+=!is_gap(r1);
- nr2+=!is_gap(r2);
-
- if ( !is_in_set (r1, ignore) && !is_in_set (r2, ignore))
- {
- pos++;
- if ( matrix)sim+=matrix[r1-'A'][r2-'A'];
- else if (is_in_same_group_aa(r1,r2,0, NULL,similarity_set))
- {
- sim++;
- }
- }
- }
- if ( MODE==UNGAPED_POSITIONS)return ( sim*100)/pos;
- else if ( MODE==ALIGNED_POSITIONS)return (sim*100)/len;
- else if ( MODE==AVERAGE_POSITIONS)return (sim*200)/(nr1+nr2);
- else
- {
- return 0;
- }
-
- }
-float get_seq_fsim2 ( char *string1, char *string2, char *ignore, char *in_mode)
- {
- int len1;
- int a;
- int p1, p2;
- int r1=0,r2=0;
- char *p;
- char mode[1000];
- float r=0, pos1, pos2, pos0, gap, sim;
-
-
- sprintf ( mode, "%s", in_mode);
-
- /*mode: <mat>__<sim_mode>
- mat: idscore to get the alignment done
- any legal cw matrix
- sim_mode: sim1->identities/matches
- sim2->identities/min len
- */
-
-
- if ( (p=strstr (mode, "_"))!=NULL)
- {
- p[0]='\0';
- p++;
- }
-
-
- if (strstr (mode, "idscore"))
- {
- static int **mat;
- if (!mat) mat=read_matrice ("blosum62mt");
- return idscore_pairseq (string1, string2, -12, -1, mat,mode);
-
- }
-
- len1=strlen (string1);
- for ( sim=pos1=pos2=pos0=gap=0,a=0; a< len1; a++)
- {
- r1=string1[a];
- r2=string2[a];
- p1=1-is_in_set (r1, ignore);
- p2=1-is_in_set (r2, ignore);
- pos1+=p1; pos2+=p2;
- if (p1 && p2)
- {
- pos0++;
- if (is_in_same_group_aa(r1,r2,0, NULL, mode))
- {
- sim++;
- }
- }
- else if (p1+p2==1)
- {
- gap++;
- }
- }
-
- if ( p==NULL || strm (p, "sim1") || strm (p, "sim"))
- {
- r=(pos0==0)?0:(sim*MAXID)/pos0;
- }
- else if ( strm (p, "sim2"))
- {
- r=(pos1==0 || pos2==0)?0:(sim*MAXID)/MIN(pos1,pos2);
- }
- else if ( strm (p, "sim3"))
- {
- r=(pos1==0 || pos2==0)?0:(sim*MAXID)/MAX(pos1,pos2);
- }
- else if ( strm (p, "gap1"))
- {
- r=(len1==0)?MAXID:(gap*MAXID)/len1;
- r=MAXID-r;
- }
- else if ( strm (p, "logid"))
- {
- r=logid_score (pos0, sim);
- }
-
- return r;
-
- }
-
-/********************************************************************/
-/* */
-/* ALIGNMENT ANALYSES */
-/* */
-/* */
-/* */
-/********************************************************************/
-int **dist_array2sim_array ( int **p, int max)
-{
- int s1, s2, a, b;
- s1=read_array_size ((void *)p, sizeof (void *));
- s2=read_array_size ((void*)p[0],sizeof (int));
- /* s2=read_array_size ((void*)p[0],sizeof (void *)); OLD before 64 BITS*/
- for ( a=0; a< s1; a++)
- for ( b=0; b< s2; b++)
- {
- p[a][b]=max-p[a][b];
- }
- return p;
-}
-
-int **sim_array2dist_array ( int **p, int max)
-{
- int s1, s2, a, b;
- s1=read_array_size ((void *)p, sizeof (void *));
- s2=read_array_size ((void*)p[0],sizeof (int));
-
- /*s2=read_array_size ((void*)p[0],sizeof (void *)); OLD before 64 Bits stuff*/
- for ( a=0; a< s1; a++)
- for ( b=0; b< s2; b++)
- {
- p[a][b]=max-(int)p[a][b];
- }
- return p;
-}
-
-int **normalize_array (int **p, int max, int norm)
-{
-int s1, s2, a, b;
- s1=read_array_size ((void *)p, sizeof (void *));
- s2=read_array_size ((void*)p[0],sizeof (int));
-
- /*s2=read_array_size ((void*)p[0],sizeof (void *)); OLD before 64 Bits stuff*/
- for ( a=0; a< s1; a++)
- for ( b=0; b< s2; b++)
- {
- p[a][b]=(p[a][b]*norm)/max;
- }
- return p;
-}
-
-int aln2most_similar_sequence ( Alignment *A, char *mode)
-{
- int **w;
- int a, b;
- int avg, best_avg=0, best_seq=0;
- char *buf;
- int coverage;
-
-
- if ( !A) return -1;
- else if ( A->nseq==1)return 0;
- else
- {
- buf=vcalloc ( A->len_aln+1, sizeof (char));
- w=get_sim_aln_array ( A, mode);
-
- for ( a=0; a< A->nseq; a++)
- {
- sprintf ( buf, "%s", A->seq_al[a]);
- ungap(buf);
- coverage=(strlen(buf)*MAXID)/A->len_aln;
-
- for ( avg=0,b=0; b< A->nseq; b++)avg+=w[a][b]*coverage;
- if ( avg>best_avg){best_avg=avg; best_seq=a;}
- }
- free_int (w, -1);
- vfree (buf);
- return best_seq;
- }
-
-}
-
-int aln2coverage ( Alignment *A, int ref_seq)
-{
- int a,b;
- int cov_pos=0, npos=0;
-
-
- for ( a=0; a< A->len_aln; a++)
- {
- if ( !is_gap ( A->seq_al[ref_seq][a]))
- {
- npos++;
- for ( b=0; b< A->nseq; b++)
- {
- if ( b!=ref_seq && !is_gap ( A->seq_al[b][a])){cov_pos++;break;}
- }
- }
- }
-
- return (int) (npos==0)?0:(( MAXID*cov_pos)/npos);
-}
-
-
-int sub_aln2sim ( Alignment *A, int *ns, int **ls, char *mode)
-{
- int a, b, n;
- float avg;
-
- n=0; avg=0;
- if (!A || (ns==NULL && A->nseq<2))return -1;
- else if (ns==NULL)
- {
- for (a=0; a< A->nseq-1; a++)
- for ( b=a+1; b< A->nseq;b++, n++)
- avg+=generic_get_seq_sim (A->seq_al[a], A->seq_al[b], NULL, mode);
- }
- else
- {
- for (a=0; a<ns[0]; a++)
- for (b=0; b< ns[1]; b++, n++)
- {
- avg+=generic_get_seq_sim (A->seq_al[ls[0][a]], A->seq_al[ls[1][b]], NULL, mode);
- }
- }
- return (int)(n==0)?0:((float)avg/(float)n);
-}
-int sub_aln2max_sim ( Alignment *A, int *ns, int **ls, char *mode)
-{
- int a, b, n;
- float avg;
-
- n=0; avg=0;
- if (!A || (ns==NULL && A->nseq<2))return -1;
- else if (ns==NULL)
- {
- for (a=0; a< A->nseq-1; a++)
- for ( b=a+1; b< A->nseq;b++, n++)
- avg=MAX(avg,generic_get_seq_sim (A->seq_al[a], A->seq_al[b], NULL, mode));
- }
- else
- {
- for (a=0; a<ns[0]; a++)
- for (b=0; b< ns[1]; b++, n++)
- {
- avg=MAX(avg,generic_get_seq_sim (A->seq_al[ls[0][a]], A->seq_al[ls[1][b]], NULL, mode));
- }
- }
- return avg;
-}
-
-
-double aln2entropy (Alignment *A, int *in_ls, int in_ns, float gap_threshold)
-{
- int ns, a, s, col, r,ncol;
- int *ls;
- double *count;
- double entropy=0;
- float ng;
-
- ls=vcalloc ( A->nseq, sizeof (int));
- count=vcalloc ( 26, sizeof (double));
-
-
- if ( in_ls)
- {
- ns=in_ns;
- for ( a=0; a< ns; a++)ls[a]=in_ls[a];
- }
- else
- {
- ns=A->nseq;
- for ( a=0; a< ns; a++)ls[a]=a;
- }
-
- if ( ns==0)
- {
- vfree(ls);vfree(count);return 0;
- }
- for (ncol=0,col=0; col<A->len_aln; col++)
- {
- for (ng=0,a=0; a< ns; a++)
- {
- s=ls[a];
- ng+=is_gap(A->seq_al[s][col]);
- }
- ng/=ns;
- if ( ng>gap_threshold)continue;
-
- ncol++;
-
- for ( a=0; a<ns; a++)
- {
- s=ls[a];
- r=tolower(A->seq_al[s][col]);
- if (!is_gap(r))count[r-'a']++;
- }
- for (a=0; a<26; a++)
- {
- if ( count[a]==0);
- else
- {
- count[a]/=(double)ns;
-
- entropy+=count[a]*log(count[a]);
- count[a]=0;
- }
- }
- }
- entropy/=-ncol;
- vfree (ls); vfree(count);
-
- return entropy;
-}
-int aln2sim ( Alignment *A, char *mode)
-{
- return sub_aln2sim ( A, NULL, NULL, mode);
- /*
- if ( !A || A->nseq<2) return -1;
- w=get_sim_aln_array ( A, mode);
-
- for (c=0, a=0; a< A->nseq-1; a++)
- for ( b=a+1; b< A->nseq; b++, c++)
- {
- avg+=(float)w[a][b];
- }
- free_int (w, -1);
- return (int)((float)avg/(float)c);
- */
-}
-
-int aln_is_aligned ( Alignment *A)
-{
- int a, b;
-
- if ( !A)return 0;
- for (a=0; a< A->nseq; a++)
- for ( b=A->len_aln-1; b>0; b--)
- {
- if (!is_gap(A->seq_al[a][b]) && is_gap(A->seq_al[a][b-1]))return 1;
- }
- return 0;
-}
-
-
-int seq2aln2sim_old ( char *seq1, char *seq2, char *mode_aln, char *mode_id)
-{
- Alignment *A;
- int sim;
-
- A=align_two_sequences (seq1, seq2, "pam250mt", -10, -1, mode_aln);
- sim=aln2sim (A, mode_id);
- free_aln (A);
- return sim;
-}
-int seq2aln2sim ( char *seq1, char *seq2, char *mode_aln, char *mode_id)
-{
- Alignment *A;
- int sim;
- static int gop;
-
- if (!gop)
- {
- int **m;
- m=read_matrice ("blosum62mt");
- gop=get_avg_matrix_mm(m, AA_ALPHABET)*10;
- free_int (m, -1);
- }
-
- A=align_two_sequences (seq1, seq2, "blosum62mt",gop,-1, mode_aln);
- sim=aln2sim (A, mode_id);
- free_aln (A);
- return sim;
-}
-int* get_cdna_seq_winsim ( int *cache, char *string1, char *string2, char *ignore, char *mode,int *w )
- {
- int len1, len2;
- int a, x;
-
-
- len1=strlen (string1);
- len2=strlen (string2);
-
- if ( len1!=len2)
- {
- fatal_exit( stderr,EXIT_FAILURE, "\nTHE TWO cDNAs DO NOT HAVE THE SAME LENGTH [FATAL:get_cdna_seq_sim:%s", PROGRAM);
- }
-
- x=get_cdna_seq_sim(cache, string1, string2, ignore, "");
- for ( a=0; a< len1; a++)
- w[a]=x;
-
- add_warning (stderr, "\nWARNING: winsim not implemented for cDNA");
- return w;
- }
-
-int get_cdna_seq_sim ( int *cache, char *string1, char *string2, char *ignore, char *mode)
- {
- int len1;
- int len2;
- int a;
- int pos=0;
- int sim=0;
- char r1=0, r2=0;
-
- len1=strlen (string1);
- len2=strlen (string2);
-
-
-
- if ( len1!=len2)
- {
- fprintf ( stderr, "\nTHE TWO cDNAs DO NOT HAVE THE SAME LENGTH [FATAL:get_cdna_seq_sim:%s", PROGRAM);
- crash("");
- }
-
- for ( a=0; a< len1;)
- {
-
- if ( cache[a]==0){a++;continue;}
- else if ( cache[a]==1)
- {
-
- r1=translate_dna_codon (string1+a, 'x');
- r2=translate_dna_codon (string2+a, 'x');
- a+=3;
- }
-
- if ( !is_in_set (r1, ignore) && !is_in_set (r2, ignore))
- {
- pos++;
- if (is_in_same_group_aa(r1,r2,0, NULL,mode+4))
- {
- sim++;
- }
- }
- }
-
-
-
- if (pos==0)
- return 0;
- else
- return (int) (sim*MAXID)/pos;
-
- }
-
-int* get_seq_winsim ( char *string1, char *string2, char *ignore, char *mode, int*w)
- {
- int len1, len2, len;
- int left, right;
- int a,b;
- int sim=0;
- int window;
- int r1, r2;
-
- len1=strlen (string1);
- len2=strlen (string2);
- window=atoi(mode);
- len=2*window+1;
-
- if ( len1!=len2)return 0;
- if (window==0 || (window*2+1)>=len1)
- {
- sim=get_seq_sim (string1, string2, ignore, "");
- for (a=0; a<len1; a++)w[a]=sim;
- return w;
- }
-
-
- for ( a=0; a< len1; a++)
- {
-
- left =MAX(0, a-window);
- right=MIN(len1, left+len);
- for (sim=0,b=left; b<right; b++)
- {
- r1=string1[b];
- r2=string2[b];
- if ( !is_in_set (r1, ignore) && !is_in_set (r2, ignore))
- {
- if (r1==r2)sim++;
- }
- }
- w[a]=(sim*MAXID)/len;
- }
- return w;
- }
-
-
-int get_seq_sim ( char *string1, char *string2, char *ignore, char *in_mode)
- {
- int len1;
- int a;
- int pos1, pos2, pos0,gap=0, sim;
- int p1, p2;
- int r=0,r1=0,r2=0;
- char *p;
- static char *mode;
-
- if (!mode)mode=vcalloc (100, sizeof (char));
- else mode[0]='\0';
- if (in_mode)
- {
- while (in_mode[0]=='_')in_mode++;
- sprintf ( mode, "%s", in_mode);
- }
-
- /*mode: <mat>__<sim_mode>
- mat: idscore to get the alignment done
- any legal cw matrix
- sim_mode: sim1->identities/matches
- sim2->identities/min len
- */
-
-
- if ( (p=strstr (mode, "_"))!=NULL)
- {
- p[0]='\0';
- p++;
- }
-
-
- if (strstr (mode, "idscore"))
- {
- static int **mat;
- if (!mat) mat=read_matrice ("blosum62mt");
- return idscore_pairseq (string1, string2, -12, -1, mat,mode);
-
- }
- len1=strlen (string1);
- for ( sim=pos1=pos2=pos0=0,a=0; a< len1; a++)
- {
- r1=string1[a];
- r2=string2[a];
- p1=1-is_in_set (r1, ignore);
- p2=1-is_in_set (r2, ignore);
-
- pos1+=p1; pos2+=p2;
- if (p1 && p2)
- {
- pos0++;
- if (is_in_same_group_aa(r1,r2,0, NULL, mode))
- {
- sim++;
- }
- }
- else if (p1+p2==1)
- {
- gap++;
- }
- }
-
- if ( strstr (mode, "cov"))
- {
- r=(pos0+gap==0)?0:(pos0*MAXID)/(pos0+gap);
- }
- else if ( p==NULL || strm (p, "sim1") || strm (p, "sim"))
- {
- r=(pos0==0)?0:(sim*MAXID)/pos0;
- }
- else if ( strm (p, "sim2"))
- {
- r=(pos1==0 || pos2==0)?0:(sim*MAXID)/MIN(pos1,pos2);
- }
- else if ( strm (p, "sim3"))
- {
- r=(pos1==0 || pos2==0)?0:(sim*MAXID)/MAX(pos1,pos2);
- }
- else if ( strm (p, "gap1"))
- {
- r=(len1==0)?MAXID:(gap*MAXID)/len1;
- r=MAXID-r;
- }
- else if ( strm (p, "logid"))
- {
- r=logid_score (pos0, sim);
- }
- else if ( strstr (mode, "sim"))
- {
- r=(pos0==0)?0:(sim*MAXID)/pos0;
- }
-
-
- return r;
-
- }
-int get_seq_sim_2 ( char *string1, char *string2, char *ignore, char **gr, int ng)
- {
- int len1;
- int len2;
- int a;
- int pos=0;
- int sim=0;
- char r1, r2;
-
-
- len1=strlen (string1);
- len2=strlen (string2);
-
- if ( len1!=len2)return 0;
-
- for ( a=0; a< len1; a++)
- {
- r1=string1[a];
- r2=string2[a];
- if ( !is_in_set (r1, ignore) && !is_in_set (r2, ignore))
- {
- pos++;
- if (is_in_same_group_aa(r1,r2,ng, gr, NULL))
- {
- sim++;
- }
- }
- }
-
- if (pos==0)
- return 0;
- else
- return (int) (sim*MAXID)/pos;
-
- }
-
-int get_seq_sim_3 ( char *string1, char *string2, char *ignore, int **mat)
- {
- int len1;
- int len2;
- int a;
-
- int sim=0;
- char r1, r2;
-
-
- len1=strlen (string1);
- len2=strlen (string2);
-
- if ( len1!=len2)return 0;
-
- for ( a=0; a< len1; a++)
- {
- r1=string1[a];
- r2=string2[a];
- if ( !is_in_set (r1, ignore) && !is_in_set (r2, ignore))
- {
- sim+=mat[r1-'A'][r2-'A'];
- }
- }
- return sim;
-
- }
-int * get_aln_col_weight ( Alignment *A, char *mode)
- {
- int a, b;
- char *col;
- int *weight;
-
- col=vcalloc ( A->nseq, sizeof (int));
- weight=vcalloc (A->len_aln, sizeof (int));
-
- for (a=0; a< A->len_aln; a++)
- {
- for ( b=0; b< A->nseq; b++)
- col[b]=A->seq_al[b][a];
- weight[a]=(find_group_aa_distribution (col, A->nseq,0,NULL,NULL, mode )*MAXID)/A->nseq;
- }
- vfree (col);
- return weight;
-
- }
-
-int analyse_aln_column ( Alignment *B, int col)
- {
-
- char r=' ';
- int a, b, c=0;
- static char *mat;
- static int ng_cw_star;
- static char **cw_star;
- int *cw_star_count;
-
- static int ng_cw_col;
- static char **cw_col;
- int *cw_col_count;
-
- static int ng_cw_dot;
- static char **cw_dot;
- int *cw_dot_count;
-
-
-
-
-
-
- if ( !B->S || !(B->S)->type)B= get_aln_type (B);
-
- if ( !mat)mat=vcalloc ( STRING, sizeof (char));
-
- if ( !ng_cw_star)
- {
- cw_star=make_group_aa ( &ng_cw_star, strcpy ( mat,"idmat"));
- cw_col=make_group_aa ( &ng_cw_col, strcpy (mat,"clustalw_col"));
- cw_dot=make_group_aa ( &ng_cw_dot, strcpy (mat, "clustalw_dot"));
- }
-
- cw_star_count=vcalloc (ng_cw_star, sizeof (int));
- cw_col_count=vcalloc ( ng_cw_col, sizeof (int));
- cw_dot_count=vcalloc (ng_cw_dot, sizeof (int));
-
- for ( a=0; a< B->nseq; a++)
- {
- c=tolower (B->seq_al[a][col]);
- if (is_gap(c)){r=' ';break;}
-
- for ( b=0; b< ng_cw_star; b++)
- cw_star_count[b]+=is_in_set (c, cw_star[b]);
- for ( b=0; b< ng_cw_col; b++)
- cw_col_count[b]+=is_in_set (c, cw_col[b]);
- for ( b=0; b< ng_cw_dot; b++)
- cw_dot_count[b]+=is_in_set (c, cw_dot[b]);
- }
-
-
-
-
-
- if ( !is_gap(c) && r==' ')
- for ( b=0; b< ng_cw_star; b++)if ( cw_star_count[b]==B->nseq){r='*'; break;}
- if ( !is_gap(c) && r==' ' && !(strm((B->S)->type, "DNA")||strm ((B->S)->type,"RNA")))
- for ( b=0; b< ng_cw_col ; b++)if ( cw_col_count [b]==B->nseq){r=':'; break;}
- if ( !is_gap(c) && r==' ' && !(strm((B->S)->type, "DNA")||strm ((B->S)->type,"RNA")))
- for ( b=0; b< ng_cw_dot ; b++)if ( cw_dot_count [b]==B->nseq){r='.'; break;}
-
-
-
- vfree(cw_star_count);
- vfree(cw_col_count);
- vfree(cw_dot_count);
-
- return r;
- }
-
-
-int ** get_cov_aln_array ( Alignment *A, char *mode)
-{
- int **w;
- int a, b, c, t;
-
- w=declare_int ( A->nseq, A->nseq);
-
-
- for ( a=0; a< A->nseq-1; a++)
- {
- w[a][a]=100;
- for ( t=0,b=a+1; b< A->nseq; b++)
- {
- for ( c=0; c< A->len_aln; c++)
- {
- t+=(!is_gap(A->seq_al[a][c]) &&!is_gap(A->seq_al[b][c]));
- }
- w[a][b]=w[b][a]=(t*100)/A->len_aln;
- }
- }
- return w;
-}
-
-int ** get_cov_master_aln_array ( Alignment *A,int n, char *mode)
-{
- int **w;
- int b, c, t;
-
- w=declare_int ( A->nseq, A->nseq);
-
-
- for (b=0; b< A->nseq; b++)
- {
-
- for (t=0, c=0; c< A->len_aln; c++)
- {
- t+=(!is_gap(A->seq_al[n][c]) &&!is_gap(A->seq_al[n][c]));
- }
- w[n][b]=w[b][n]=(t*100)/A->len_aln;
- }
-
- return w;
-}
-int ** get_sim_master_aln_array ( Alignment *A,int n, char *mode)
- {
- int **w;
- int a;
-
- w=declare_int ( A->nseq, A->nseq);
-
-
- for ( a=0; a< A->nseq; a++)
- {
- if ( strm (mode, "cdna"))
- w[n][a]=w[a][n]=get_cdna_seq_sim ( A->cdna_cache[0], A->seq_al[a], A->seq_al[n],GAP_LIST, mode);
- else
- w[n][a]=w[a][n]=get_seq_sim ( A->seq_al[n], A->seq_al[a],GAP_LIST, mode);
- }
- return w;
- }
-int ** get_dist_aln_array ( Alignment *A, char *mode)
-{
-
- int **w;
-
- w=get_sim_aln_array ( A, mode);
- return sim_array2dist_array(w,MAXID);
-}
-Sequence * seq2filter (Sequence *Sin, int min, int max)
-{
- int *keep;
- char *tmpfile;
- Sequence *S, *Sout;
- int a, b, sim;
- int **M;
- FILE *fp;
- int n;
-
- S=duplicate_sequence (Sin);
- for (a=0; a<S->nseq; a++)ungap(S->seq[a]);
- keep=vcalloc (S->nseq, sizeof (int));
- M=read_matrice ("blossum62mt");
- for (a=0; a<S->nseq; a++)
- {
- output_completion ( stderr, a, S->nseq, 100, "Distance Matrix Computation: ");
- for ( b=a+1; b<S->nseq; b++)
- {
-
- sim=idscore_pairseq(S->seq[a], S->seq[b],-10, -2,M, "sim");
- if ( sim>min && sim<max)keep[a]=keep[b]=1;
- fprintf ( stderr, "\nSim %d Min %d Max %d", sim, min, max);
- }
- }
-
- tmpfile=vtmpnam (NULL);
- fp=vfopen (tmpfile, "w");
- for (n=0,a=0; a< S->nseq; a++)
- if ( keep[a])
- {
- fprintf ( fp, ">%s %s\n%s", S->name[a], S->seq_comment[a], S->seq[a]);
- n++;
- }
- vfclose (fp);
- if (n==0) return NULL;
- Sout=main_read_seq(tmpfile);
- free_int (M, -1); vfree (keep); free_sequence (S, -1);
- return Sout;
-}
-
-Alignment * grep_seq (Alignment *S,char *field, char *mode, char *string)
-{
- int a;
- FILE *fp;
- char *tmp;
- int n=0;
-
- tmp=vtmpnam (NULL);
- fp=vfopen (tmp, "w");
-
- if ( !strm(mode, "KEEP") && ! strm (mode, "REMOVE"))
- {
- add_warning ( stderr, "\nERROR: +grep <field> <KEEP|REMOVE> <string> [FATAL: %s]", PROGRAM);
- myexit (EXIT_FAILURE);
- }
- else if ( !strm(field, "SEQ") && ! strm (field, "COMMENT") && ! strm(field, "NAME"))
- {
- add_warning ( stderr, "\nERROR: +grep <NAME|COMMENT|SEQ> <mode> <string> [FATAL: %s]", PROGRAM);
- myexit (EXIT_FAILURE);
- }
-
-
- for (n=0, a=0; a< S->nseq; a++)
- {
- int found=0;
-
- if (strm(field, "NAME") && perl_strstr (S->name[a], string))found=1;
- else if (strm(field, "COMMENT") && S->seq_comment[a][0] && perl_strstr (S->seq_comment[a], string) )found=1;
- else if (strm(field, "SEQ") && perl_strstr (S->seq_al[a], string))found=1;
-
- if ( (strm (mode, "KEEP") && found) || (strm (mode, "REMOVE") && !found))
- {
- n++;
- fprintf (fp, ">%s", S->name[a]);
- if (S->seq_comment[a][0])fprintf (fp, " %s", S->seq_comment[a]);
- fprintf (fp, "\n%s\n", S->seq_al[a]);
- }
- }
-
- vfclose (fp);
-
- free_aln (S);
- if ( n==0) return NULL;
- else
- return main_read_aln (tmp, NULL);
-}
-
-Alignment * modify_seq (Alignment *S, char *field, char *string1, char *string2)
-{
- int a;
- FILE *fp;
- char *tmp;
-
- tmp=vtmpnam (NULL);
- fp=vfopen (tmp, "w");
- for ( a=0; a< S->nseq; a++)
- {
- if (strm(field, "NAME"))S->name[a]=substitute ( S->name[a], string1, string2);
- else if (strm(field, "COMMENT"))S->seq_comment[a]=substitute ( S->seq_comment[a], string1, string2);
- else if (strm(field, "SEQ"))S->seq_al[a]=substitute ( S->seq_al[a], string1, string2);
- fprintf (fp, ">%s", S->name[a]);
- if (S->aln_comment[a][0])fprintf (fp, " %s", S->aln_comment[a]);
- fprintf (fp, "\n%s\n", S->seq_al[a]);
- }
- vfclose (fp);
- free_aln (S);
- S=main_read_aln (tmp, NULL);
- return S;
-}
-
-int ** seq2sim_mat (Sequence *S, char *mode)
-{
- return seq2comp_mat ( S,mode, "sim");
-}
-int ** seq2cov_mat (Sequence *S, char *mode)
-{
- return seq2comp_mat ( S,mode, "cov");
-}
-
-int ** seq2comp_mat (Sequence *S, char *mode, char *comp_mode)
-{
- int a, b;
- int **sim;
- char file[1000];
- Alignment *A;
- char *name;
-
-
- /*Use pre_computed value if available in the current dir*/
-
- name=path2filename(S->file[0]);
- sprintf ( file, "%s%s.%s.%s_file", get_cache_dir(),name, mode, comp_mode);
- A=seq2aln(S,NULL, RM_GAP);
- if ( check_file_exists (file) && is_distance_matrix_file (file) && (sim=input_similarities(file, A, NULL))!=NULL)
- {
- display_input_filename (stderr, "SIMILARITY_MATRIX", "SIMILARITY_MATRIX_FORMAT_01", file, CHECK);
- fprintf ( stderr, "\n");
- }
- else
- {
- char mode2[1000];
- int **M;
-
- M=read_matrice (mode);
- sim=declare_int ( S->nseq, S->nseq);
- for ( a=0; a< S->nseq; a++)
- {
- ungap (S->seq[a]);
- sim[a][a]=100;
- }
-
- for ( a=0; a<S->nseq-1; a++)
- {
-
- output_completion4halfmat ( stderr, a, S->nseq, 100, "Similarity Matrix Computation: ");
- for ( b=a+1; b< S->nseq; b++)
- {
- sim[a][b]=sim[b][a]=idscore_pairseq(S->seq[a], S->seq[b],-12, -1,M, comp_mode);
- }
- }
- free_int (M,-1);
- sprintf ( mode2, "_memory_%ld", (long int)sim);
- output_similarities( file, A, mode2);
- display_output_filename (stderr, "SIMILARITY_MATRIX", "SIMILARITY_MATRIX_FORMAT_01", file, CHECK);
- fprintf ( stderr, "\n");
- }
- free_aln (A);
- return sim;
-}
-
-int ** fast_aln2sim_list (Alignment *A, char *mode, int *ns, int **ls)
-{
- int **simm;
- int p1, p2, p3, r1, r2;
- int gap,pos0,pos1,pos2,len,sim;
- int a, b, c, m, s=0,s1, s2, n;
- int free_ns=0;
-
- if (ns==NULL)
- {
- free_ns=1;
- ns=vcalloc (2, sizeof (int));
- ns[0]=ns[1]=A->nseq;
- ls=declare_int (2, A->nseq);
- for ( a=0; a< 2; a++)
- for (b=0; b<A->nseq; b++)
- ls[a][b]=b;
- }
-
-
- simm=declare_int (ns[0]*ns[1]+1, 3);
-
- if (strstr (mode, "sim1"))m=0;
- else if (strstr (mode, "sim2"))m=1;
- else if (strstr (mode, "sim3"))m=2;
- else if (strstr (mode, "gap1"))m=3;
- else if (strstr (mode, "cov1"))m=4;
- else if (strstr (mode, "logid"))m=5;
- else m=0;
-
-
-
- for (n=0,a=0; a<ns[0]; a++)
- {
- s1=ls[0][a];
- for ( b=0; b<ns[1]; b++, n++)
- {
- s2=ls[1][b];
- gap=pos0=pos1=pos2=len=sim=0;
-
- for ( c=0; c< A->len_aln; c++)
- {
- r1=tolower (A->seq_al[s1][c]);
- r2=tolower (A->seq_al[s2][c]);
- p1=(r1!='-')?1:0;
- p2=(r2!='-')?1:0;
- p3=p1+p2;
- if ( p3==0)continue;
- if ( p3==1)gap++;
- if ( r1==r2)sim++;
- pos1+=p1;
- pos2+=p2;
- pos0+=(p3==2)?1:0;
- len++;
- }
-
- if (m==0)s=(pos0==0)?0:(sim*MAXID)/pos0; //sim1
- else if (m==1) s=(MIN(pos1,pos2)==0)?0:(sim*MAXID)/MIN(pos1,pos2);//sim2
- else if (m==2) s=(MAX(pos1,pos2)==0)?0:(sim*MAXID)/MAX(pos1,pos2);//sim3
- else if (m==3) s=(len==0) ?0:((len-gap)*MAXID)/len;//gap1
- else if (m==4) s=(len==0) ?0:((pos0)*MAXID)/len; //cov
- else if (m==5)
- {
- s=logid_score ( sim, len);
- }
- simm[n][0]=s1;
- simm[n][1]=s2;
- simm[n][2]=s;
- }
- }
-
- if ( free_ns) {vfree(ns); free_int (ls, -1);}
- simm[n][0]=-1;
- return simm;
-}
-
-int ** fast_aln2sim_mat (Alignment *A, char *mode)
-{
- int **simm;
- int p1, p2, p3, r1, r2;
- int gap,pos0,pos1,pos2,len,sim;
- int a, b, c, m;
-
- simm=declare_int (A->nseq, A->nseq);
-
-
-
- if (strstr (mode, "sim1"))m=0;
- else if (strstr (mode, "sim2"))m=1;
- else if (strstr (mode, "sim3"))m=2;
- else if (strstr (mode, "gap1"))m=3;
- else if (strstr (mode, "cov1"))m=4;
- else if (strstr (mode, "logid"))m=5;
- else m=0;
-
-
-
- for ( a=0; a< A->nseq-1; a++)
- {
- simm[a][a]=MAXID;
- for ( b=a+1; b< A->nseq; b++)
- {
- gap=pos0=pos1=pos2=len=sim=0;
-
- for ( c=0; c< A->len_aln; c++)
- {
- r1=tolower (A->seq_al[a][c]);
- r2=tolower (A->seq_al[b][c]);
- p1=(r1!='-')?1:0;
- p2=(r2!='-')?1:0;
- p3=p1+p2;
- if ( p3==0)continue;
- if ( p3==1)gap++;
- if ( r1==r2)sim++;
- pos1+=p1;
- pos2+=p2;
- pos0+=(p3==2)?1:0;
- len++;
- }
-
- if (m==0)simm[a][b]=simm[b][a]=(pos0==0)?0:(sim*MAXID)/pos0; //sim1
- else if (m==1) simm[a][b]=simm[b][a]=(MIN(pos1,pos2)==0)?0:(sim*MAXID)/MIN(pos1,pos2);//sim2
- else if (m==2) simm[a][b]=simm[b][a]=(MAX(pos1,pos2)==0)?0:(sim*MAXID)/MAX(pos1,pos2);//sim3
- else if (m==3) simm[a][b]=simm[b][a]=(len==0) ?0:((len-gap)*MAXID)/len;//gap1
- else if (m==4) simm[a][b]=simm[b][a]=(len==0) ?0:((pos0)*MAXID)/len; //cov
- else if (m==5)
- {
-
- //Inspired from Muscle +mafft 5
- simm[a][b]=simm[b][a]=logid_score ( sim, len);
- }
- }
- }
- return simm;
-}
-int logid_score ( int sim, int len)
-{
- float score;
-
- if ( len==0)return (int)(0.33*(float)MAXID);
-
- score=(float)sim/(float)len;
- if (score>0.9) score=1.0;
- else score=-log10 (1.0-score);
-
- score=(score*MAXID);
- return score;
-}
-int ** aln2sim_mat (Alignment *A, char*mode)
-{
-
-
- if ( strstr (mode, "idmat"))return fast_aln2sim_mat(A, mode);
- return get_sim_aln_array(A, mode);
-}
-int ** aln2cov (Alignment *A)
-{
- int a, b, c;
- int r1, r2, gr1, gr2, pos0, gap;
- int **cov;
- cov=declare_int (A->nseq, A->nseq);
-
- for (a=0; a< A->nseq-1; a++)
- {
- cov[a][a]=100;
- for ( b=a+1; b<A->nseq; b++)
- {
- for (gap=0,pos0=0,c=0;c<A->len_aln; c++)
- {
- r1=A->seq_al[a][c];
- r2=A->seq_al[b][c];
- gr1=is_gap(r1); gr2=is_gap(r2);
- if ( gr1+gr2==0)pos0++;
- else if ( gr1+gr2<2)gap++;
- }
- cov[a][b]=cov[b][a]=((gap+pos0)==0)?0:((pos0*100)/(gap+pos0));
- }
- }
- return cov;
-}
-int ** get_raw_sim_aln_array (Alignment *A, char *mode)
-{
- int **w;
- int **M;
- int a, b, c, r1, r2, set, max, min;
-
- w=declare_int (A->nseq, A->nseq);
- if (strstr(mode, "sar"))M=NULL;
- else M=read_matrice (mode);
-
- HERE ("RAW STUFF");
-
- for ( set=0,a=0; a< A->nseq; a++)
- for (b=a; b<A->nseq; b++)
- {
- if (M)
- {
- for (c=0; c<A->len_aln; c++)
- {
- r1=A->seq_al[a][c];
- r2=A->seq_al[b][c];
-
- if ( !is_gap(r1) && !is_gap(r2))
- w[a][b]+=M[r1-'A'][r2-'A'];
- }
- }
- else if ( strm (mode, "sarmat2"))
- {
- w[a][b]=get_sar_sim2 (A->seq_al[a], A->seq_al[b]);
- }
- else
- {
- HERE ("ERROR: %s is an unknown mode of raw_sim\n", mode); myexit (EXIT_FAILURE);
- }
-
- w[b][a]=w[a][b];
- if (!set){min=max=w[a][b];set=1;}
- min=MIN(min,w[a][b]);
- max=MAX(max,w[a][b]);
- }
- for (a=0; a<A->nseq; a++)
- for (b=a; b<A->nseq; b++)
- {
- w[b][a]=((max-min)==0)?0:((w[b][a]-min)*100)/(max-min);
- w[a][b]=w[b][a];
- }
- free_int (M, -1);
- return w;
-}
-int ** get_sim_aln_array ( Alignment *A, char *mode)
- {
- int **w;
- int a, b;
-
-
- w=declare_int ( A->nseq, A->nseq);
-
- for ( a=0; a< A->nseq-1; a++)
- {
- for ( b=a+1; b< A->nseq; b++)
- {
-
- w[a][b]=w[b][a]=generic_get_seq_sim ( A->seq_al[a], A->seq_al[b], (A->cdna_cache)?A->cdna_cache[0]:NULL, mode);
- }
- }
- return w;
- }
-int generic_get_seq_sim ( char *seq1, char *seq2, int*cache, char *mode)
-{
-
-
- if ( strm (mode, "cdna"))
- return get_cdna_seq_sim ( cache, seq1, seq2,GAP_LIST, mode);
- else if ( strnm (mode, "ktup",4))
- return ktup_comparison (seq1, seq2,atoi(mode+4));
- else if ( strstr (mode, "sarmat2"))
- {
-
- return get_sar_sim2 (seq1, seq2);
- }
- else if ( strstr (mode, "sarmat"))
- return (int) get_sar_sim (seq1,seq2);
- else
- {
- return get_seq_sim ( seq1,seq2,GAP_LIST, mode);
- }
-}
-int *** get_winsim_aln_array ( Alignment *A,char *mode, int ***w)
- {
- int a, b;
- for ( a=0; a< A->nseq; a++)
- for ( b=0; b< A->nseq; b++)
- {
- if ( strm (mode, "cdna"))
- w[a][b]=get_cdna_seq_winsim ( A->cdna_cache[0], A->seq_al[a], A->seq_al[b],GAP_LIST, mode, w[a][b]);
- else
- w[a][b]=get_seq_winsim ( A->seq_al[a], A->seq_al[b],GAP_LIST, mode, w[a][b]);
- }
- return w;
- }
-
-Alignment * seq2profile (Sequence *S, int i)
-{
- Alignment *A;
-
- if ((A=seq2R_template_profile (S, i)))
- {
- return A;
- }
- else
- {
- char *tmp;
- FILE *fp;
- tmp=vtmpnam (NULL);
- fp=vfopen ( tmp, "w");
- fprintf (fp, ">%s\n%s\n", S->name[i], S->seq[i]);
- vfclose (fp);
-
- (S->T[i])->R=fill_R_template (S->name[i], tmp, S);
-
- return seq2R_template_profile (S, i);
- }
-}
-Alignment* remove_seq_from_aln (Alignment *A, char *seq)
-{
- int a, n;
- for (n=0,a=0; a<A->nseq; a++)
- {
- if ( strm (seq, A->name[a]))continue;
- else if ( n==a);
- else
- {
- sprintf (A->name[n], "%s",A->name[a]);
- sprintf (A->seq_al[n], "%s",A->seq_al[a]);
- if (A->seq_comment[a])sprintf (A->seq_comment[n], "%s", A->seq_comment[a]);
- if (A->aln_comment[a])sprintf (A->aln_comment[n], "%s", A->aln_comment[a]);
- A->order[n][0]=A->order[a][0];
- A->order[n][1]=A->order[a][1];
- }
- n++;
- }
- A->nseq=n;
- return A;
-}
-
-
-Alignment* aln2sub_aln_file (Alignment *A, int n, char **string)
-{
- char ***list;
- int a;
-
- list=vcalloc (A->nseq, sizeof (char***));
- if ( n==0)return A;
- else if (n>1)
- {
- int l;
- char *buf;
-
- for (l=0,a=0; a< n; a++)l+=strlen (string[a]);
- buf=vcalloc ( 2*n+l+1, sizeof (char));
- for (a=0; a< n; a++){buf=strcat (buf,string[a]), buf=strcat ( buf, " ");}
- list[0]=string2list (buf);
- vfree (buf);
- }
- else if ( file_exists (NULL,string[0]))
- {
- list=read_group (string[0]);
-
- }
- else
- {
- fprintf (stderr, "\nERROR: file <%s> does not exist [FATAL:%s]\n",string[0], PROGRAM);
- myexit (EXIT_FAILURE);
- }
-
-
- a=0;
- while (list[a])
- {
- int i, b;
- FILE *fp;
- n=atoi (list[a][0]);
- fp=vfopen (list[a][1], "w");
- for (b=2; b<n; b++)
- {
- i=name_is_in_list (list[a][b], A->name, A->nseq, MAXNAMES);
- if (n==3)ungap (A->seq_al[i]);
- fprintf (fp, ">%s\n%s\n", A->name[i], A->seq_al[i]);
- }
- vfclose (fp);
- free_char (list[a], -1);
- a++;
- }
- vfree(list);
- return A;
-}
-Sequence *remove_empty_sequence (Sequence *S)
-{
- int a, b;
- char *c;
- Sequence *NS;
-
- c=vcalloc ( S->max_len+1, sizeof (char));
-
- for (a=0, b=0; a< S->nseq; a++)
- {
- sprintf ( c, "%s",S->seq[a]);
- ungap (c);
- if ( strlen (c)==0)
- {
- //vfree (S->seq[a]);
- S->seq[a]=NULL;
- add_warning ( stderr, "WARNING: Sequence %s does not contain any residue: automatically removed from the set [WARNING:%s]",S->name[a], PROGRAM);
- }
- }
- NS=duplicate_sequence (S);
- free_sequence (S, S->nseq);
- vfree (c);
- return NS;
-}
-Alignment* aln2sub_seq (Alignment *A, int n, char **string)
-{
- char ***list;
- int a;
- Sequence *S=NULL;
-
- list=vcalloc (A->nseq, sizeof (char***));
- if ( n==0)return A;
- else if (n>1)
- {
- int l;
- char *buf;
-
- for (l=0,a=0; a< n; a++)l+=strlen (string[a]);
- buf=vcalloc ( 2*n+l+1, sizeof (char));
- for (a=0; a< n; a++){buf=strcat (buf,string[a]), buf=strcat ( buf, " ");}
- list[0]=string2list (buf);
- vfree (buf);
- }
- else if ( file_exists (NULL,string[0]))
- {
- list=read_group (string[0]);
-
- }
- else
- {
- fprintf (stderr, "\nERROR: file <%s> does not exist [FATAL:%s]\n",string[0], PROGRAM);
- myexit (EXIT_FAILURE);
- }
-
-
-
- a=0;
- while (list[a])
- {
- int t;
- Alignment *B;
- Sequence *subS;
-
-
- B=main_read_aln (list[a][1], NULL);
- t=aln2most_similar_sequence(B, "idmat");
- subS=extract_one_seq(B->name[t],0,0,B,KEEP_NAME);
- S=add_sequence (subS,S,0);
- free_aln (B);free_sequence (subS, -1);
- vremove (list[a][1]);
- a++;
- }
- vfree(list);
- return seq2aln (S, NULL, RM_GAP);
-}
-
-Alignment * aln2collapsed_aln (Alignment * A, int n, char **string)
-{
- Alignment *B;
- char ***list;
- char **list2;
- char *buf=NULL;
- FILE *fp;
- int a, b,c, ns, m, l;
- int *collapsed;
-
- list=vcalloc (A->nseq, sizeof (char***));
- ns=0;
- if ( n==0)return A;
- else if (n>1)
- {
- for (l=0,a=0; a< n; a++)l+=strlen (string[a]);
- buf=vcalloc ( 2*n+l+1, sizeof (char));
- for (a=0; a< n; a++){buf=strcat (buf,string[a]), buf=strcat ( buf, " ");}
-
- list[0]=string2list (buf);ns=1;
-
- }
- else if ( file_exists (NULL,string[0]))
- {
- /*Format: Fasta like, the name fo the group followed with the name of the sequences
- ><Group name> <First Seq> <second seq> ....
- Groups must NOT be overlaping
- */
- l=measure_longest_line_in_file (string[0])+1;
- buf=vcalloc (l, sizeof (char));
- ns=0;
- fp=vfopen (string[0], "r");
- while ((c=fgetc(fp))!=EOF)
- {
- buf=fgets (buf,l-1, fp);
- if ( c=='>')list[ns++]=string2list (buf);
- }
- vfclose (fp);
- }
- else
- {
- fprintf (stderr, "\nERROR: file <%s> does not exist [FATAL:%s]\n",string[0], PROGRAM);
- myexit (EXIT_FAILURE);
- }
-
- vfree (buf); buf=NULL;
-
- /*Identify lost sequences*/
- collapsed=vcalloc (A->nseq, sizeof (int));
- for ( a=0; a< ns; a++)
- {
- m=atoi (list[a][0]);
- for (b=2; b<m ; b++)
- {
- c=name_is_in_list (list[a][b], A->name, A->nseq, MAXNAMES);
- if ( c>=0)collapsed[c]=1;
- }
- }
- for ( a=0; a< A->nseq; a++)
- {
- if ( collapsed[a]==0)
- {
- list[ns]=declare_char (3, MAXNAMES);
- sprintf ( list[ns][0], "3");
- sprintf ( list[ns][1], "%s", A->name[a]);
- sprintf ( list[ns][2], "%s", A->name[a]);
- ns++;
- }
- }
- vfree (collapsed);
-
-
-
-
-
- list2=declare_char (A->nseq, 100);
- /*1 Collapse the alignment*/
- for ( a=0; a< ns; a++)
- {
- sprintf ( list2[a], "%s", list[a][2]);
- }
- B=extract_sub_aln2 ( A, ns, list2);
- /*2 Rename the sequences*/
- for ( a=0; a< ns; a++)
- {
- sprintf ( B->name[a], "%s", list[a][1]);
- }
- /*replace sequence with consensus*/
-
- for ( a=0; a< ns; a++)
- {
- m=atoi (list[a][0]);
- for (c=0, b=2; b<m;c++, b++)
- {
- sprintf ( list2[c], "%s", list[a][b]);
- }
- buf=sub_aln2cons_seq_mat2 ( A,m-2,list2, "blosum62mt");
- sprintf (B->seq_al[a], "%s", buf);
- }
- vfree (buf);
-
- free_aln (A);
- B->S=aln2seq(B);
- return B;
-}
-Alignment * aln2profile (Alignment * A)
- {
- Alignment *B=NULL;
- char *cons;
-
- if (!A->P)
- {
- A->P=declare_profile (AA_ALPHABET,A->len_aln+1);
- }
- B=copy_aln (A, B);
- free_int ((A->P)->count, -1);
- free_int ((A->P)->count2, -1);
- free_int ((A->P)->count3, -1);
- (A->P)->count=aln2count_mat (A);
- (A->P)->count2=aln2count_mat2 (A);
-
- cons=aln2cons_seq_mat (A, "blosum62mt");
-
- sprintf (B->seq_al[0], "%s", cons);
- B->nseq=1;
- (A->P)->count3=aln2count_mat2 (B);
- vfree (cons);
- free_aln (B);
-
-
-
- return A;
-
- }
-
-int** aln2count_mat2 ( Alignment *A)
-{
- return sub_aln2count_mat2 (A, 0, NULL);
-}
-
-int sub_aln2nseq_prf ( Alignment *A, int ns, int *ls)
-{
-
-
- int a, c, s;
- Alignment *R;
- int n;
- int free_ls=0;
-
-
- if ( ns==0)
- {
- n=ns=A->nseq;
- ls=vcalloc (n, sizeof (int));
- for ( a=0; a<A->nseq; a++)ls[a]=a;
- free_ls=1;
- }
- else
- {
- n=ns;
- }
-
- for (c=0,a=0; a<ns; a++)
- {
- s=ls[a];
- if ( A->S && (R=seq2R_template_profile (A->S, A->order[s][0]))!=NULL)
- {
- n+=R->nseq;
- }
- else
- {
- ;
- }
- }
-
- if ( free_ls) vfree (ls);
- return n;
-}
-
-int** sub_aln2count_mat2 ( Alignment *A, int ns, int *ls)
-{
- char **p;
- int **count;
- int a, b, c, s;
- Alignment *R;
- int n;
- int free_ls=0;
-
- if ( ns==0)
- {
- n=ns=A->nseq;
- p=vcalloc ( n, sizeof (char*));
- ls=vcalloc (n, sizeof (int));
- for ( a=0; a<A->nseq; a++)ls[a]=a;
- free_ls=1;
- }
- else
- {
- n=ns;
- p=vcalloc (n, sizeof (char*));
- }
-
- for (c=0,a=0; a<ns; a++)
- {
- s=ls[a];
- if ( A->S && (R=seq2R_template_profile (A->S, A->order[s][0]))!=NULL)
- {
- n+=R->nseq;
- p=vrealloc (p, n*sizeof (char*));
- for (b=0; b<R->nseq; b++)
- {
- p[c++]=R->seq_al[b];
- }
- }
- else
- {
- int w;
- w=A->order[s][4]+1;
-
- for (b=0; b<w; b++)
- p[c++]=A->seq_al[s];
- }
- }
- count=sub_aln2count_mat3 (p,c);
- vfree (p);
- if ( free_ls) vfree (ls);
- return count;
-}
-int** sub_aln2count_mat3 (char **al, int ns)
-{
- int **count;
- int used[1000];
- int a, b;
- int r;
-
- int len;
- int us;
-
-
- /*count[x][0]=n symbols in column
- count[x][1]=total_size of line
- count[x][2]=Gap frequency
-
- count[x][n]=symbol n
- count[x][n+1]=N occurence symbol n;
- count[x][n+2]=N frequence symbol n*100;
-
- special multi-channeling
- count[x][count[x][1]]=Nseq
- count[x][count[x][1]+s]=residue col x, sequence s
- */
-
-
- for (a=0; a< 1000; a++)used[a]=0;
- len=strlen (al[0]);
-
- count=declare_int (len+2,100+ns+2);
- count[len][0]=END_ARRAY;
- count[len][1]=ns;
- count[len][2]=len;
-
-
-
- for (a=0; a<len; a++)
- {
- for (us=ns, b=0; b<ns; b++)
- {
- r=tolower (al[b][a]);
-
- if (is_gap(r))us--;
- else if (used[r])
- {
- count[a][used[r]*3+1]++;
- }
- else
- {
- used[r]=++count[a][0];
- count[a][used[r]*3]=r;
- count[a][used[r]*3+1]++;
- }
- }
- count[a][1]=count[a][0]*3+2;
- /*count[a][2]=(A->nseq-us)*100/A->nseq;*/
- count[a][2]=ns-us;
-
- for (b=3; b<count[a][1]; b+=3)
- {
- count[a][b+2]=(count[a][b+1]*100)/us;
- used[count[a][b]]=0;
- }
-
-
- /*Option for multi channeling*/
-
- /*
- count[a][count[a][1]]=A->nseq;
- for (b=1; b<=A->nseq; b++)
- count [a][count[a][1]+b]=(is_gap(A->seq_al[b-1][a]))?0:A->seq_al[b-1][a];
- */
- }
-#ifdef XXXXXX
- HERE ("Display ");
- for (a=0; a< 5; a++)
- {
- fprintf ( stderr, "\n");
- for ( b=3; b< count[a][1]; b+=3)
- {
- fprintf ( stderr, "[%c %d]", count[a][b], count[a][b+1]);
- }
- fprintf ( stderr, "\n");
- for ( b=0; b<ns; b++)
- {
- fprintf ( stderr, "%c", al[b][a]);
- }
- }
- HERE ("End of Display");
-#endif
- return count;
-}
-
-int** aln2count_mat ( Alignment *A)
- { /*
- function documentation: start
-
- int output_freq_mat ( char *outfile, Aligmnent *A)
-
- This function counts the number of residues in each column of an alignment (Prot/NA)
- It outputs these values in the following format
-
- This format can be piped into:
- The routine used for computing the p-value gmat-inf-gc-v2c
-
- function documentation: end
- */
-
- int a, b,x;
- int **freq_mat;
- int alp_size;
-
- alp_size=sizeof (AA_ALPHABET);
- freq_mat=declare_int (alp_size+2, A->len_aln);
-
-
- for ( a=0; a<A->len_aln; a++)
- {
- for ( b=0; b< A->nseq; b++)
- {
- if ( is_gap ( A->seq_al[b][a]))freq_mat[alp_size][a]++;
- else
- {
- x=tolower(A->seq_al[b][a]);
- freq_mat[x-'a'][a]++;
- freq_mat[alp_size+1][a]++;
-
- }
- }
- }
-
- return freq_mat;
- }
-char *aln2random_seq (Alignment *A, int pn1, int pn2, int pn3, int gn)
- {
-
- /*
-
-
- Given the frequencies in A ( read as total counts of each Residue in
- freq[A->nseq][A->len_aln], and pn1, pn2 and pn3:
-
- 1-Generate a new amino-acid at each position
- 2-Insert Gaps, using a HMM.
-
-
- pn3=Weight of the noise induced with sub mat.
-
- pn1=% noise type 1 ( Varies with entropi)
- n1=Ratio noise type 1
-
- T =Nseq
- t1=Noise 1 expressed in Nseq
- al=alphabet size;
- ncat=number of non 0 cat for a given position
- ICi initial count for residue i
-
- Ci=freq[seq][AA]
- t1=T*n1*(1-1/ncat);
- t2=T*n2;
-
- Ci= ICi*(T-(t1+t2))/T +(t1)/al+(t2)/al
-
- */
-
- int **freq;
- int **count;
- float T, tot_t1, tot_t2,tot_t3, n1, n2, n3;
- float ncat;
-
- double gf;
- double *init_freq;
- double *blur_freq;
- double *t1, *t2,*t3;
- int a, b, c, x;
- char *seq;
- int tot;
- /*Viterbi Parameters */
-
- int p;
- int AL=0; /*Allowed Transition*/
- int F=-100000; /*Forbiden Transition*/
-
- int GAP_TRANSITION;
- int IGAP=0, IAA=1;
-
- int state,best_state=0, score, best_score=0;
- int p_state;
- int e=0;
- int **score_tab;
- int **state_tab;
- int nstate=2;
- int **transitions;
-
- int max;
-
- seq=vcalloc ( A->len_aln+1, sizeof (char));
- count=aln2count_mat(A);
- freq=aln2count_mat(A);
-
- T=100;
-
- n1=(float)pn1/100;
- n2=(float)pn2/100;
- n3=(float)pn3/100;
-
- for ( a=0; a< A->len_aln; a++)
- {
- for ( b=0; b<26; b++)
- freq[b][a]=freq[b][a]*((T)/(A->nseq-freq[26][a]));
- freq[26][a]= (freq[26][a]*T)/A->nseq;
- }
-
-
- init_freq=vcalloc ( 26, sizeof (double));
- blur_freq=vcalloc ( 26, sizeof (double));
-
- tot_t1=tot_t2=tot_t3=0;
-
- t1=vcalloc ( 27, sizeof (double));
- t2=vcalloc ( 27, sizeof (double));
- t3=vcalloc ( 27, sizeof (double));
- for (a=0; a< A->len_aln; a++)
- {
-
- /*Compute Frequencies*/
- for (tot=0, b=0; b<26; b++)
- {
- if ( is_aa(b+'A'))
- {
- init_freq[b]=freq[b][a];
- tot+=freq[b][a];
- }
- }
- /*Count the number of different amino acids*/
- for ( ncat=0, b=0; b<=26; b++)
- {
- ncat+=(freq[b][a]!=0)?1:0;
- }
- /*Blurr the distribution using */
- blur_freq=compute_matrix_p (init_freq,tot);
-
-
- /*compute noise 1: biased with blurred content * enthropy--> keeps prosite motifs*/
- tot_t1=T*n1*(1-1/ncat);
- for ( b=0; b< 26; b++)if ( is_aa(b+'A')){t1[b]=blur_freq[b]*(1-1/ncat)*n1;}
-
- /*Compute noise 2: completely random*/
- tot_t2=T*n2;
- for ( b=0; b< 26; b++)if ( is_aa(b+'A')){t2[b]=tot_t2/21;}
-
- /*compute noise 3: biased with the sole content(pam250mt)*/
- tot_t3=T*n3;
- for ( b=0; b<26; b++)if ( is_aa(b+'A')){t3[b]=blur_freq[b]*n3;}
-
- for ( b=0; b<26; b++)
- {
- if ( is_aa('A'+b))
- freq[b][a]=freq[b][a]*(T-(tot_t1+tot_t2+(tot_t3)))/T+t1[b]+t2[b]+t3[b];
- }
-
- /*end of the loop that mutates position a*/
- }
-
- vfree (blur_freq);
- vfree (init_freq);
- vfree ( t3);
-
- /*1-Generate the amino acids of the new sequence new*/
-
-
- vsrand (0);
-
- for ( a=0; a< A->len_aln; a++)
- {
-
- for (T=0,b=0; b<26; b++)T+=freq[b][a];
- x=rand ()%((int)T);
- for (c=0,b=0; b<26; b++)
- {
- c+=freq[b][a];
- if ( c>=x)
- {
- seq[a]='A'+b;
- c=-1;
- break;
- }
- }
- if ( c!=-1)seq[a]='-';
- }
- seq[a]='\0';
-
-
- /*2 Generate the gaps in the new sequence*/
-
-
-
- if ( gn<0);
- else
- {
-
- transitions=declare_int ( nstate, nstate);
- score_tab=declare_int ( A->len_aln+2, nstate );
- state_tab=declare_int ( A->len_aln+2, nstate );
-
-
-
- for (a=0; a<nstate;a++)
- for (b=0; b<nstate;b++)
- {transitions[a][b]=F;}
-
- GAP_TRANSITION=AL-gn;
-
- transitions[IGAP ][IGAP ]=AL;
- transitions[IAA][IAA]=AL;
- transitions[IAA ][IGAP]=GAP_TRANSITION;
- transitions[IGAP][IAA ]=GAP_TRANSITION;
-
-
- for ( p=1; p<=A->len_aln; p++){for (state=0; state< nstate; state++){score_tab[p][state]=F;state_tab[p][state]=-1;} }
-
- for (p=1; p<= A->len_aln; p++)
- {
- for (max=0,a=0; a<26; a++)max=MAX(max, freq[a][p-1]);
- max=(max*(A->nseq-count[26][p-1]))/A->nseq;
-
- for (state=0; state< nstate; state++)
- {
-
-
- gf=freq[26][p-1];
- if ( state==IGAP) e=gf-50;
- else if ( state==IAA ) e=max-50;
- for (p_state=0; p_state<nstate; p_state++)
- {
- score=(score_tab[p-1][p_state]==F)?F:(e+transitions[p_state][state]+score_tab[p-1][p_state]);
- if(p_state==0 || score>best_score){ best_score=score;best_state=p_state;}
- }
- score_tab[p][state]=best_score;
- state_tab[p][state]=best_state;
- }
- }
-
- for (state=0; state<nstate; state++)
- {
- if (state==0 || score_tab[p-1][state]>best_score){best_score=score_tab[p-1][state]; best_state=state;}
- }
-
- for (p=A->len_aln; p>0;)
- {
- if ( best_state==IGAP)
- {
- seq[p-1]='-';
- }
- else if ( best_state==IAA)
- {
- seq[p-1]=seq[p-1];
- }
- best_state=state_tab[p][best_state];
- p--;
- }
- }
-
- free_int (freq, -1);
- return seq;
- }
-
-/********************************************************************/
-/* */
-/* Weighting functions */
-/* */
-/* */
-/* */
-/********************************************************************/
-Alignment * master_trimseq( Alignment *A, Sequence *S,char *mode)
- {
- Alignment *NA;
- char *p;
- int a, b;
- int use_aln=0, upper_sim=0, min_nseq=0, lower_sim=0;
- float f_upper_sim, f_lower_sim;
- char weight_mode[1000];
- char method[1000];
- int statistics=0;
- int trim_direction=TOP;
- float **sim_weight;
- int *seq_list;
- int table=0;
-
-
-
-
- /*
- mode:
- (trim)_<seq or aln>_%<percentage of tot weight to keep>_n<number of seq to keep>_w<weight mode>
- */
-
-
-
- seq_list=vcalloc ( S->nseq, sizeof (int));
- for ( a=0; a< A->nseq; a++)
- {
- seq_list[a]=1;
- }
-
-
- use_aln=aln_is_aligned(A);
-
- if ( mode[0]=='\0')
- {
-
- upper_sim=50;
- lower_sim=0;
- min_nseq=0;
- sprintf (weight_mode, "pwsim");
- sprintf ( method, "clustering2");
- }
- else
- {
-
- upper_sim=lower_sim=min_nseq;
- sprintf (weight_mode, "pwsim");
- sprintf ( method, "clustering2");
- }
-
- /*
- U or % (deprecated) Upper bound for pairwise similarity
- L or m (depercated) Lower bound for pairwise similarity
- n max number of sequences
- N max number of sequences as a fraction of thet total
- S print Statistics
- T print Table of distances
- */
-
-
-
- while ( (p=strtok(mode, "_")))
- {
- mode=NULL;
- if (strm (p, "seq"))use_aln=0;
- else if ( strm(p,"aln"))use_aln=1;
- else if (p[0]=='s')statistics=1;
- else if (p[0]=='t')table=1;
- else if (p[0]=='U')upper_sim=atoi(p+1);
- else if (p[0]=='L')lower_sim=atoi(p+1);
- else if (p[0]=='n')min_nseq=atoi(p+1);
- else if (p[0]=='N')min_nseq=atoi(p+1)*-1;
- else if (p[0]=='B')trim_direction=BOTTOM;
- else if (p[0]=='T')trim_direction=TOP;
- else if (p[0]=='W')sprintf (weight_mode, "%s", p+1);
- else if (p[0]=='M')sprintf (method, "%s", p+1);
- else if (p[0]=='K')
- {
-
- while ((p=strtok(NULL, ":")))
- {
-
- if ( p[0]=='#')
- {
- seq_list[atoi(p+1)-1]=2;
- }
- else if ( (a=name_is_in_list (p, A->name, A->nseq, 100))!=-1)
-
- {
- seq_list[a]=2;
- }
- }
- }
- }
-
- if ( !upper_sim && !min_nseq && !lower_sim)upper_sim=50;
-
-
-
- if (!S)
- {
- fprintf ( stderr, "\ntrimseq requires a set of sequences[FATAL:%s]\n", PROGRAM);
- crash("");
- }
-
- else if ( min_nseq> S->nseq)
- {
- min_nseq=S->nseq;
- }
- else if ( min_nseq<0)
- {
- if ( min_nseq<-100)
- {
- add_warning ( stderr, "\nWARNING: trimseq: Nseq(N) max_val=100%% [Automatic reset]\n");
- min_nseq=-100;
- }
-
- min_nseq=(int)((float)S->nseq*((float)min_nseq/100)*-1);
- }
-
-
- NA=seq2subseq3 (A, S,use_aln,lower_sim,upper_sim,min_nseq,trim_direction, weight_mode,&sim_weight, seq_list );
-
- if ( table)
- {
- fprintf ( stderr, "\nSIMILARITY MATRIX\n");
- for ( a=0; a< A->nseq-1; a++)
- for ( b=a+1; b< A->nseq; b++)
- {
- fprintf ( stderr, "%15s Vs %15s : %3.2f %% id\n", A->name[a], A->name[b], 100-sim_weight[a][b]);
- }
- }
- if ( statistics)
- {
- f_upper_sim=(upper_sim>100)?((float)upper_sim/(float)100):upper_sim;
- f_lower_sim=(upper_sim>100)?((float)lower_sim/(float)100):lower_sim;
-
- fprintf ( stderr, "\nTRIM Informations:\n");
- fprintf ( stderr, "\tUse...........: %s\n",(use_aln)?"multiple_aln":"pairwise_aln");
- fprintf ( stderr, "\tcluster_mode..: %s\n" ,method);
- fprintf ( stderr, "\tsim_mode......: %s\n" ,weight_mode);
- fprintf ( stderr, "\tlower_id_bound: %.2f%%\n" ,(f_lower_sim==0)?-1:f_lower_sim);
- fprintf ( stderr, "\tupper_id_bound: %.2f%%\n",(f_upper_sim==0)?-1:f_upper_sim);
- fprintf ( stderr, "\tnseq_kept.....: %d (out of %d)\n" ,NA->nseq, S->nseq);
- fprintf ( stderr, "\treduction.....: %d%% of original set\n" ,(NA->nseq*100)/S->nseq);
- fprintf ( stderr, "\tTrim_direction: From %s \n" ,(trim_direction==BOTTOM)?"Bottom":"Top");
- }
-
- return NA;
- }
-
-Alignment *sim_filter (Alignment *A, char *in_mode, char *seq)
-{
- int **sim, **cov;
- int *list;
- int *keep;
- int maxnseq, nseq_ratio, nc;
- int new_nseq;
- int a, s, n, k;
- Alignment *R;
- char *mode;
- int outlayers;
- int direction=1;//remove the higher than
- int coverage=0; //remove based on coverage
- static char *field;
- int maxsim, minsim, maxcov, mincov;
-
- if ( !field) field=vcalloc (1000, sizeof (char));
-
- mode=vcalloc ( strlen (in_mode)+10, sizeof (char));
- sprintf ( mode, "_%s_", in_mode);
-
- strget_param ( mode, "_I", "100", "%d", &maxsim);
- strget_param ( mode, "_i", "0", "%d", &minsim);
- strget_param ( mode, "_C", "100", "%d", &maxcov);
- strget_param ( mode, "_c", "0", "%d", &mincov);
-
-
-
-
-
- keep=vcalloc ( A->nseq, sizeof (int));
- list=vcalloc ( A->nseq, sizeof (int));
-
-
-
-
-
-
- if (!seq)s=0;
- else s=name_is_in_list (seq, A->name, A->nseq, 100);
- if (s==-1)
- {
-
- if ( s==-1)printf_exit (EXIT_FAILURE, stderr, "ERROR: %s is not a valid sequence", seq);
- }
- else
- keep[s]=1;
-
- //get the distances
- if ( strstr (mode, "_seq_"))
- {
- char **seq;
- int **M;
-
- M=read_matrice ("blosum62mt");
- seq=declare_char (A->nseq, A->len_aln+1);
- for (a=0; a<A->nseq; a++)
- {
- sprintf ( seq[a], "%s", A->seq_al[a]);
- ungap (seq[a]);
- }
-
- sim=declare_int (A->nseq, A->nseq);
- cov=declare_int (A->nseq, A->nseq);
-
- for (a=0; a<A->nseq; a++)
- {
- if ( s!=a)
- {
- sim[s][a]=sim[a][s]=idscore_pairseq(seq[s], seq[a],-12, -1,M,"sim");
- cov[s][a]=cov[a][s]=idscore_pairseq(seq[s], seq[a],-12, -1,M,"cov");
-
- }
- }
- free_char (seq, -1);
- free_int (M,-1);
- }
- else
- {
- sim=aln2sim_mat (A, "idmat");
- cov=aln2cov (A);
- }
-
- for (a=0; a< A->nseq; a++)
- {
- if (a==s)continue;
- else
- {
- if ( sim[s][a]>maxsim || sim[s][a]<minsim|| cov[s][a]<mincov||cov[s][a]>maxcov)keep[a]=-1;
- else keep[a]=1;
- }
- }
-
- for ( n=0, a=0; a< A->nseq; a++)
- {
- if ( keep[a]!=-1)
- {
- list[n++]=a;
- }
- }
-
- R=extract_sub_aln (A, n, list);
- free_int (sim, -1); free_int (cov, -1);vfree (list);
-
- return R;
-}
-
-
-static int find_worst_seq ( int **sim, int n, int *keep, int max, int direction);
-Alignment *simple_trimseq (Alignment *A, Alignment *K, char *in_mode, char *seq_list, int **sim)
-{
- int *list;
- int *keep;
- int maxnseq, maxsim, nseq_ratio, nc;
- int new_nseq;
- int a,b, s, n, k;
- Alignment *R;
- char *mode;
- int outlayers;
- int direction=1;//remove the higher than
- int coverage=0; //remove based on coverage
- static char *field;
- int *tot_avg;
- int KeepN=0;
- int Print=0;
-
- if ( !field) field=vcalloc (1000, sizeof (char));
-
- mode=vcalloc ( strlen (in_mode)+10, sizeof (char));
- sprintf ( mode, "_%s_", in_mode);
-
- strget_param ( mode, "_%%", "0", "%d", &maxsim);
- strget_param ( mode, "_n", "0", "%d", &maxnseq);
- strget_param ( mode, "_N", "0", "%d", &nseq_ratio);
- strget_param ( mode, "_F", "0", "%d", &nc);
- strget_param ( mode, "_O", "0", "%d", &outlayers);
- strget_param ( mode, "_K", "0", "%d", &KeepN);
-
- strget_param ( mode, "_f", "NAME", "%s", field);
-
- if ( strstr (mode, "_P_"))Print=1;
-
- if ( strstr (mode, "_min"))direction=-1;
- else direction=1;
-
- if ( strstr (mode, "_cov"))coverage=1;
- else coverage=0;
-
-
- if ( nseq_ratio)
- {
- maxnseq=(A->nseq*nseq_ratio)/100;
- maxsim=0;
- }
- else if ( maxnseq)
- {
- maxsim=0;
- }
- else if ( !maxsim)
- {
- maxsim=100;
- }
-
-
- keep=vcalloc ( A->nseq, sizeof (int));
- list=vcalloc ( A->nseq, sizeof (int));
-
-
-
-
- /*Remove Sequences that do not have at least one residue in the first and last nc columns*/
- if ( nc)
- {
- int left, right, full_n,x, y;
- int *full_list;
-
- Alignment *F;
-
- full_list=vcalloc ( A->nseq, sizeof (int));
- full_n=0;
- for (x=0; x< A->nseq; x++)
- {
- for ( left=0,y=0; y<MIN(A->len_aln,nc); y++)
- if (!is_gap(A->seq_al[x][y]))left=1;
-
- for ( right=0,y=MAX(0,(A->len_aln-nc)); y<A->len_aln; y++)
- if (!is_gap(A->seq_al[x][y]))right=1;
-
- if ( left && right)full_list[full_n++]=x;
- }
- F=extract_sub_aln (A, full_n, full_list);
- free_aln (A);
- vfree (full_list);
- A=F;
- }
-
- /*Reorder the sequences according to the tree order: hopefully better phylogenetic coverage after trim*/
- if (strstr (mode, "_T"))
- {
- NT_node **T;
- Sequence *O;
-
- if (!sim)sim=sim_array2dist_array ( NULL, MAXID);
- T=int_dist2nj_tree (sim, A->name, A->nseq, NULL);
- O=tree2seq (T[3][0], NULL);
- A=reorder_aln (A, O->name, O->nseq);
-
- free_int (sim, -1);
- free_sequence (O, -1);
- }
-
- if ( coverage==0)
- {
- if ( strstr (mode, "seq_") && !sim)sim=seq2comp_mat (aln2seq(A), "blosum62mt", "sim");
- else sim=aln2sim_mat (A, "idmat");
- }
- else
- {
- int b;
- if ( strstr (mode, "seq_") && !sim)sim=seq2comp_mat (aln2seq(A), "blosum62mt", "cov");
- else sim=aln2cov (A);
-
- }
-
-
- if ( K && K->nseq>0)
- {
- for ( a=0; a< K->nseq; a++)
- if ( (k=name_is_in_list (K->name[a], A->name, A->nseq, MAXNAMES+1))!=-1)
- {
-
- keep[k]=1;
- }
- }
- if ( seq_list)
- {
- for ( a=0; a< A->nseq; a++)
- {
- if (strstr (field, "NAME") && perl_strstr (A->name[a], seq_list)){keep[a]=1;}
- else if (strstr (field, "COMMENT") && A->seq_comment && perl_strstr(A->seq_comment[a], seq_list)){keep[a]=1;}
- else if (strstr (field, "SEQ") && perl_strstr((A->S)->seq[a], seq_list)){keep[a]=1;}
- }
-
- }
- for (a=0; a<KeepN; a++)keep[a]=1;
-
- if (Print)
- {
- for ( a=0; a< A->nseq; a++)
- if ( keep[a]) fprintf ( stderr, "\nFORCED KEEP %s", A->name[a]);
- }
-
- new_nseq=A->nseq;
-
-
- while ( (s=find_worst_seq (sim, A->nseq, keep, maxsim, direction))!=-1 && new_nseq>maxnseq)
- {
- for ( a=0; a< A->nseq; a++)sim[a][s]=sim[s][a]=-1;
- keep[s]=-1;
- new_nseq--;
- }
-
- /*Trim Outlayers*/
- if (outlayers!=0)
- {
- int nn, b;
- tot_avg=vcalloc ( A->nseq, sizeof (int));
-
- for (a=0; a<A->nseq; a++)
- {
- if ( keep[a]==-1)tot_avg[a]=-1;
- else
- {
- for (nn=0, b=0; b< A->nseq; b++)
- {
- if (a==b || keep[b]==-1)continue;
- else
- {
- tot_avg[a]+=sim[a][b];
- nn++;
- }
- }
- tot_avg[a]=(nn==0)?-1:(tot_avg[a])/nn;
- }
- }
- for ( a=0; a<A->nseq; a++)
- {
- if (tot_avg[a]!=-1 && tot_avg[a]<outlayers)
- {
- fprintf ( stderr, "\nREMOVED OUTLAYER: %3d %% avg similarity with remaining sequences [Seq %s]", tot_avg[a],A->name[a]);
- keep[a]=-1;
- }
- }
- vfree ( tot_avg);
- }
-
- for ( n=0, a=0; a< A->nseq; a++)
- {
- if ( keep[a]!=-1)
- {
- list[n++]=a;
- }
- }
-
- R=extract_sub_aln (A, n, list);
- free_int (sim, -1); vfree (list);
-
- return R;
-}
-
-int find_worst_seq ( int **sim, int n, int *keep,int max,int direction)
-{
- int **sc;
- int a, b, r=0;
- int si;
-
- sc=declare_int (n, 2);
- if (direction==-1)max=100-max;
-
- for ( a=0; a< n; a++) sc[a][0]=a;
- for ( a=0; a< n-1; a++)
- {
- for ( b=a+1; b<n; b++)
- {
-
- if (sim[a][b]>=0)si=(direction==-1)?100-sim[a][b]:sim[a][b];
- else si=sim[a][b];
- if ( si>max)
- {
- if ( keep[a]!=1)sc[a][1]+=si;
- if ( keep[b]!=1)sc[b][1]+=si;
- }
- }
- }
-
- sort_int_inv ( sc, 2, 1, 0, n-1);
- if ( sc[0][1]>0)r=sc[0][0];
- else r=-1;
-
- free_int (sc, -1);
- if (r!=-1 && keep && keep[r])return -1;
- else return r;
-}
-
-int find_worst_seq_old ( int **sim, int n, int *keep,int max,int direction)
-{
- int **sc;
- int a, b, r=0;
-
- sc=declare_int (n, 2);
-
- for ( a=0; a< n; a++) sc[a][0]=a;
- for ( a=0; a< n-1; a++)
- {
- for ( b=a+1; b<n; b++)
- {
- if ( direction==1)
- {
- if ( sim[a][b]>max)
- {
- if ( keep[a]!=1)sc[a][1]+=sim[a][b];
- if ( keep[b]!=1)sc[b][1]+=sim[a][b];
- }
- }
- else if ( direction == -1)
- {
- if ( sim[a][b]<max && sim[a][b]>=0)
- {
- if ( keep[a]!=1)sc[a][1]+=sim[a][b];
- if ( keep[b]!=1)sc[b][1]+=sim[a][b];
- }
- }
- }
- }
-
- if ( direction ==1) //remove max
- {
- sort_int_inv ( sc, 2, 1, 0, n-1);
- if ( sc[0][1]>0)r=sc[0][0];
- else r=-1;
-
- }
- else if ( direction ==-1)//remove min
- {
- sort_int_inv ( sc, 2, 1, 0, n-1);
- if ( sc[0][1]>=0)r=sc[0][0];
- else r=-1;
- HERE ("** %d %d\n", r,sc[0][1]);
- }
- free_int (sc, -1);
- if (r!=-1 && keep && keep[r])return -1;
- else return r;
-}
-
-
-Alignment * trimseq( Alignment *A, Sequence *S,char *mode)
- {
- Alignment *NA;
- char *p;
- int a, b;
- int use_aln=0, upper_sim=0, min_nseq=0, lower_sim=0;
- char weight_mode[1000];
- char method[1000];
- int statistics=0;
- int trim_direction=TOP;
- float **sim_weight;
- int *seq_list;
- int table=0;
- int print_name=0;
- float f_lower_sim, f_upper_sim;
-
-
-
- /*
- mode:
- (trim)_<seq or aln>_%<percentage of tot weight to keep>_n<number of seq to keep>_w<weight mode>
- */
-
-
-
- seq_list=vcalloc ( S->nseq, sizeof (int));
- for ( a=0; a< A->nseq; a++)
- {
- seq_list[a]=1;
- }
-
-
- use_aln=aln_is_aligned(A);
-
-
- if ( mode[0]=='\0')
- {
-
- upper_sim=50;
- lower_sim=0;
- min_nseq=0;
- sprintf (weight_mode, "pwsim_fragment");
- sprintf ( method, "clustering2");
- }
- else
- {
-
- upper_sim=lower_sim=min_nseq;
- sprintf (weight_mode, "pwsim_fragment");
- sprintf ( method, "clustering2");
- }
-
- /*
- U or % (deprecated) Upper bound for pairwise similarity
- L or m (depercated) Lower bound for pairwise similarity
- n max number of sequences
- N max number of sequences as a fraction of thet total
- S print Statistics
- T print Table of distances
- */
-
-
-
- while ( (p=strtok(mode, "_")))
- {
- mode=NULL;
- if (strm (p, "seq"))use_aln=0;
- else if ( strm(p,"aln"))use_aln=1;
- else if (p[0]=='s')statistics=1;
- else if (p[0]=='t')table=1;
- else if (p[0]=='p')print_name=1;
- else if (p[0]=='U')upper_sim=atoi(p+1);
- else if (p[0]=='L')lower_sim=atoi(p+1);
- else if (p[0]=='n')min_nseq=atoi(p+1);
- else if (p[0]=='N')min_nseq=atoi(p+1)*-1;
- else if (p[0]=='B')trim_direction=BOTTOM;
- else if (p[0]=='T')trim_direction=TOP;
- else if (p[0]=='W')sprintf (weight_mode, "%s", p+1);
- else if (p[0]=='M')sprintf (method, "%s", p+1);
- else if (p[0]=='K')
- {
-
- while ((p=strtok(NULL, ":")))
- {
-
- if ( (a=name_is_in_list (p, A->name, A->nseq, 100))!=-1)
- {
- seq_list[a]=2;
- }
- }
- }
- }
-
- if ( !upper_sim && !min_nseq && !lower_sim)upper_sim=50;
-
-
-
- if (!S)
- {
- fprintf ( stderr, "\ntrimseq requires a set of sequences[FATAL:%s]\n", PROGRAM);
- crash("");
- }
-
- else if ( min_nseq> S->nseq)
- {
- min_nseq=S->nseq;
- }
- else if ( min_nseq<0)
- {
- if ( min_nseq<-100)
- {
- add_warning ( stderr, "\nWARNING: trimseq: Nseq(N) max_val=100%% [Automatic reset]\n");
- min_nseq=-100;
- }
-
- min_nseq=(int)((float)S->nseq*((float)min_nseq/100)*-1);
- }
-
-
- NA=seq2subseq2 (A, S,use_aln,lower_sim,upper_sim,min_nseq,trim_direction, weight_mode,&sim_weight, seq_list );
-
- if ( table)
- {
- fprintf ( stderr, "\nSIMILARITY MATRIX\n");
- for ( a=0; a< A->nseq-1; a++)
- for ( b=a+1; b< A->nseq; b++)
- {
- fprintf ( stderr, "%15s Vs %15s : %3.2f %% id\n", A->name[a], A->name[b], 100-sim_weight[a][b]);
- }
- }
-
- NA=seq_name2removed_seq_name(S, NA,sim_weight);
-
- if ( print_name)
- {
- fprintf ( stderr, "\nList of sequences with their closest removed neighbors\n");
- for ( a=0; a< NA->nseq; a++)fprintf ( stderr, "\n%s: %s\n", NA->name[a], NA->seq_comment[a]);
- }
-
- if ( statistics)
- {
- f_lower_sim=(lower_sim>100)?(float)lower_sim/100:lower_sim;
- f_upper_sim=(upper_sim>100)?(float)upper_sim/100:upper_sim;
-
- fprintf ( stderr, "\nTRIM seq Informations:\n");
- fprintf ( stderr, "\tUse...........: %s\n",(use_aln)?"multiple_aln":"pairwise_aln");
- fprintf ( stderr, "\tcluster_mode..: %s\n" ,method);
- fprintf ( stderr, "\tsim_mode......: %s\n" ,weight_mode);
- fprintf ( stderr, "\tlower_id_bound: %.2f%%\n" ,(f_lower_sim==0)?-1:f_lower_sim);
- fprintf ( stderr, "\tupper_id_bound: %.2f%%\n",(f_upper_sim==0)?-1:f_upper_sim);
- fprintf ( stderr, "\tnseq_kept.....: %d (out of %d)\n" ,NA->nseq, S->nseq);
- fprintf ( stderr, "\treduction.....: %d%% of original set\n" ,(NA->nseq*100)/S->nseq);
- fprintf ( stderr, "\tTrim_direction: From %s \n" ,(trim_direction==BOTTOM)?"Bottom":"Top");
- }
-
- return NA;
- }
-
-Alignment * tc_trimseq( Alignment *A, Sequence *S,char *mode)
- {
- Alignment *NA;
- Sequence *TS;
- char *trimfile, *alnfile;
- int *seq_list;
- int a, nseq=0, sim=0;
- char *p;
- char command[100000];
- char keep_list[10000];
-
- int top, bottom, middle, pmiddle;
-
- keep_list[0]='\0';
-
- seq_list=vcalloc ( S->nseq, sizeof (int));
- for ( a=0; a< A->nseq; a++)
- {
- seq_list[a]=1;
- }
-
- trimfile=vtmpnam (NULL);
- alnfile=vtmpnam (NULL);
- if ( !aln_is_aligned (A))
- {
- fprintf ( stderr, "\ntrimTC: computation of an Approximate MSA [");
- A=compute_tcoffee_aln_quick ( A, NULL);
- fprintf ( stderr, "DONE]\n");
- }
- output_clustal_aln (alnfile, A);
-
-
- while ( (p=strtok(mode, "#")))
- {
- mode=NULL;
-
-
- if (p[0]=='%' || p[0]=='S')sim=(p[1]=='%')?atoi(p+2):atoi(p+1);
- else if (p[0]=='n' || p[0]=='N')nseq=atoi(p+1);
- else if (p[0]=='K')
- {
- if ( (a=name_is_in_list (p+1, A->name, A->nseq, 100))!=-1)
- {
- seq_list[a]=2;
- }
-
- }
- }
- if ( nseq ==0 && sim ==0)
- {
- fprintf ( stderr, "\nERROR: trimTC\nIndicate the maximum number of sequences Nnseq\nOR the maximum average similarity of the chosen sequencesSx\nEX: +trimTC S20 OR +trimTC N5");
- fprintf ( stderr, "\n[FATAL:%s]", PROGRAM);
- myexit (EXIT_FAILURE);
- }
-
- for ( a=0; a<A->nseq; a++)if (seq_list[a]==2){strcat ( keep_list, A->name[a]);strcat ( keep_list," ");}
-
- if ( sim)
- {
- sprintf ( command , "%s -infile %s -trim -trimfile=%s -split_score_thres %d -convert -iterate 0 ",get_string_variable("t_coffee"), alnfile, trimfile,sim);
- if ( keep_list[0]){strcat ( command, " -seq_to_keep ");strcat ( command, keep_list);}
- my_system ( command);
- TS=read_sequences (trimfile);
- }
- else if ( nseq && A->nseq>nseq)
- {
-
- top=100;bottom=0;
- pmiddle=0;middle=50;
-
- sprintf ( command , "%s -infile %s -trim -trimfile=%s -split_score_thres %d -convert -iterate 0",get_string_variable("t_coffee"), alnfile, trimfile,middle);
- if ( keep_list[0]){strcat ( command, " -seq_to_keep ");strcat ( command, keep_list);}
- my_system ( command);
-
- TS=read_sequences (trimfile);
- fprintf ( stderr, "\n\tTrimTC: Sim %d Nseq %d\t",middle, TS->nseq);
-
- if ( TS->nseq>nseq)top=middle;
- else if ( TS->nseq<nseq)bottom=middle;
- pmiddle=middle;
- middle=(top-bottom)/2+bottom;
-
- while (TS->nseq!=nseq && pmiddle!=middle)
- {
-
- sprintf ( command , "%s -infile %s -trim -trimfile=%s -split_score_thres %d -convert -iterate 0 ",get_string_variable("t_coffee"), alnfile, trimfile,middle);
- if ( keep_list[0]){strcat ( command, " -seq_to_keep ");strcat ( command, keep_list);}
- my_system ( command);
- free_sequence (TS, -1);
- TS=read_sequences (trimfile);
- fprintf ( stderr, "\n\tTrimTC: Sim %d Nseq %d\t", middle, TS->nseq);
-
- if ( TS->nseq>nseq)top=middle;
- else if ( TS->nseq<nseq)bottom=middle;
- pmiddle=middle;
- middle=(top-bottom)/2+bottom;
- }
- }
- else
- {
- TS=aln2seq (A);
- }
- NA=seq2aln (TS, NULL, 1);
- vremove ( alnfile);
- fprintf ( stderr, "\n");
-
- return NA;
- }
-
-Alignment* seq2subseq3( Alignment *A, Sequence *S,int use_aln, int int_lower_sim,int int_upper_sim, int min_nseq, int trim_direction, char *weight_mode, float ***sim_weight, int *seq_list)
-{
- int a, b;
- int new_nseq;
-
- /*OUTPUT*/
- char **seq, **name;
- Sequence *NS;
- Alignment *NA;
- float sim, lower_sim, upper_sim;
-
- lower_sim=(int_lower_sim>100)?(float)int_lower_sim/100:int_lower_sim;
- upper_sim=(int_upper_sim>100)?(float)int_upper_sim/100:int_upper_sim;
-
- sim_weight[0]=get_weight ((use_aln)?A:NULL, S, weight_mode);
-
- name=declare_char (S->nseq, (MAXNAMES+1));
- seq= declare_char (S->nseq, S->max_len+1);
-
- /*
- Remove every sequence that is more than upper_sim and less than lower_sim similar to the master sequences
- the master sequence(s) are those for which seq_list[x]==2
- */
-
-
-
-
- new_nseq=A->nseq;
-
-
- for (a=0; a< A->nseq; a++)
- {
- if ( seq_list[a]==2)
- {
-
- for ( b=0; b< A->nseq;b++)
- {
- sim=100-sim_weight[0][a][b];
- if (seq_list[b]==1 && (sim>upper_sim || sim<lower_sim))
- {
- seq_list[b]=0;
- new_nseq--;
- }
- }
-
- }
- }
-
- /*Prepare the new sequence List*/
-
- for (b=0, a=0; a<S->nseq; a++)
- {
- if ( seq_list[a])
- {
- sprintf ( name[b], "%s", S->name[a]);
- sprintf ( seq[b] , "%s",(use_aln)?A->seq_al[a]: S->seq[a] );
- b++;
- }
- }
-
-
- NS=fill_sequence_struc (new_nseq,seq,name);
- NA=seq2aln(NS,NULL,1);
-
- if ( use_aln && A)
- {
- NA=realloc_aln2 ( NA,A->max_n_seq,A->len_aln+1);
-
- for (b=0, a=0; a<S->nseq; a++)
- {
- if ( seq_list[a])
- {
- sprintf ( NA->seq_al[b] , "%s",A->seq_al[a]);
- b++;
- }
- }
-
- NA->len_aln=A->len_aln;
- ungap_aln(NA);
- }
-
-
- return NA;
-}
-Alignment* seq2subseq2( Alignment *A, Sequence *S,int use_aln, int int_lower_sim,int int_upper_sim, int min_nseq, int trim_direction, char *weight_mode, float ***sim_weight, int *seq_list)
-{
- int a, b;
- int new_nseq;
- int seq_index=0;
- /*OUTPUT*/
- char **seq, **name;
- Sequence *NS;
- Alignment *NA;
- float lower_sim, upper_sim;
-
- lower_sim=(int_lower_sim>100)?(float)int_lower_sim/100:int_lower_sim;
- upper_sim=(int_upper_sim>100)?(float)int_upper_sim/100:int_upper_sim;
-
-
- sim_weight[0]=get_weight ((use_aln)?A:NULL, S, weight_mode);
-
- name=declare_char (S->nseq, (MAXNAMES+1));
- seq= declare_char (S->nseq, S->max_len+1);
-
- /*
- 1 REMOVE OUTLAYERS
- 2 REMOVE CLOSELY RELATED SEQUENCES
- 3 IF STILL TOO MANY SEQUENCES:
- REMOVE THE MOST CLOSELY RELATED ONES
- */
-
-
- /*1 Remove outlayers*/
-
- new_nseq=A->nseq;
-
-
- /*1 Remove outlayers*/
- while ( lower_sim && (extreme_seq(BOTTOM,A,sim_weight[0],seq_list, &seq_index) <lower_sim) && ((new_nseq)>min_nseq) && seq_index!=-1)
- {
-
- if ( seq_list[seq_index]==1)
- {
- seq_list[seq_index]=0;
- new_nseq--;
- }
- }
- /*2 Remove close relative*/
-
-
- while ( upper_sim && (extreme_seq(TOP, A,sim_weight[0],seq_list, &seq_index)>upper_sim) && ((new_nseq)>min_nseq)&& seq_index!=-1)
- {
-
- if ( seq_list[seq_index]==1)
- {
- seq_list[seq_index]=0;
- new_nseq--;
- }
- }
-
-
- /*Remove extra sequences*/
-
- while ( min_nseq>0 && new_nseq>min_nseq && seq_index!=-1)
- {
-
- extreme_seq(trim_direction, A,sim_weight[0],seq_list, &seq_index);
-
- if ( seq_index==-1)break;
- if ( seq_list[seq_index]==1)
- {
- seq_list[seq_index]=0;
- new_nseq--;
- }
- }
-
-
- /*Prepare the new sequence List*/
-
- for (b=0, a=0; a<S->nseq; a++)
- {
- if ( seq_list[a])
- {
- sprintf ( name[b], "%s", S->name[a]);
- sprintf ( seq[b] , "%s",(use_aln)?A->seq_al[a]: S->seq[a] );
- b++;
- }
- }
-
-
- NS=fill_sequence_struc (new_nseq,seq,name);
- NA=seq2aln(NS,NULL,1);
-
- if ( use_aln && A)
- {
- NA=realloc_aln2 ( NA,A->max_n_seq,A->len_aln+1);
-
- for (b=0, a=0; a<S->nseq; a++)
- {
- if ( seq_list[a])
- {
- sprintf ( NA->seq_al[b],"%s",A->seq_al[a]);
- b++;
- }
- }
-
- NA->len_aln=A->len_aln;
- ungap_aln(NA);
- }
-
-
- return NA;
-}
-
-float extreme_seq (int direction, Alignment *A,float **sim_weight,int *seq_list, int *seq_index)
-{
-
- /*find the closest relative of each sequence
- Return:
- Direction= BOTTOM: the sequence whose closest relative is the most distant
- Direction= TOP: the sequence whose closest relative is the closest
- weight: different sequences=100
- similar sequences =0
- */
- int a, b;
-
- float top_sim,bottom_sim, best_sim, sim;
- int top_seq, bottom_seq;
-
- bottom_seq=top_seq=seq_index[0]=-1;
- top_sim=-1;
- bottom_sim=101;
-
- for (a=0; a< A->nseq; a++)
- {
- if (seq_list[a]!=1)continue;
-
- for ( best_sim=0, b=0; b< A->nseq; b++)
- {
- if ( a==b || !seq_list[b])continue;
-
- sim=100-sim_weight[a][b];
- if (sim>best_sim)
- {
- best_sim=sim;
- }
- }
-
- if ( best_sim>top_sim)
- {
- top_seq=a;
- top_sim=best_sim;
- }
-
- if ( best_sim<bottom_sim)
- {
- bottom_seq=a;
- bottom_sim=best_sim;
- }
-
- }
- if ( direction==BOTTOM ){seq_index[0]= bottom_seq; return bottom_sim;}
- else if ( direction==TOP){seq_index[0]= top_seq; return top_sim;}
- else
- {
- seq_index[0]=-1;
- return -1;
- }
-}
-
-
-
-
-Alignment* seq2subseq1( Alignment *A, Sequence *S,int use_aln, int percent,int max_nseq, int ms,char *weight_mode)
- {
- float **pw_weight,**sim_weight, **seq_weight;
- int a,b,c,d;
- float sum, chosen,last_chosen, last_nchosen,nchosen;
- int condition1, condition2;
- Sequence *NS;
- Alignment *NA;
- char **name, **seq;
- float score, best_score;
- int best_seq=0;
- int *seq_list, *used_seq_list;
-
- /*
- mode:
- (trim)_<seq or aln>_%<percentage of tot weight to keep>_n<number of seq to keep>_w<weight mode>
- */
-
- sim_weight=get_weight ((use_aln)?A:NULL, S, weight_mode);
- pw_weight=declare_float (S->nseq, S->nseq);
- seq_weight=declare_float ( S->nseq, 2);
-
-
- for (best_score=0,a=0; a<S->nseq; a++)
- {
- for ( b=0; b<S->nseq; b++)
- {
- if ( a==b)continue;
- seq_weight[a][0]+=sim_weight[a][b];
- }
- seq_weight[a][0]=seq_weight[a][0]/(S->nseq-1);
- score=seq_weight[a][0]=100-seq_weight[a][0];
-
- if ( score>best_score)
- {
- best_seq=a;
- best_score=score;
- }
-
- }
- for (a=0; a<S->nseq; a++)
- {
- for ( b=0; b<S->nseq; b++)
- {
- if ( a==b)continue;
- pw_weight[a][b]=sim_weight[a][b]*seq_weight[a][0]*seq_weight[b][0]/(100*100);
-
- }
- }
-
-
- seq_list=vcalloc ( S->nseq, sizeof (int));
- used_seq_list=vcalloc ( S->nseq, sizeof (int));
-
-
-
- name=declare_char (S->nseq, (MAXNAMES+1));
- seq= declare_char (S->nseq, S->max_len+1);
-
- /*compute the normalization factor*/
- for (sum=0,d=0; d< S->nseq; d++)
- {
- for (score=0,c=0; c<S->nseq; c++)
- {
- if ( c!=d)
- score=MAX(score, 100-sim_weight[c][d]);
- }
- sum+=score;
- }
- sum=sum/S->nseq;
- /*chose the first sequence */
- for ( best_score=0,a=0; a< S->nseq; a++)
- {
- for (score=0, b=0; b< S->nseq; b++)
- {
- score+=100-sim_weight[a][b];
- }
- if ( score>best_score)
- {
- best_seq=a;
- best_score=score;
- }
-
- }
-
-
- last_chosen=chosen=((best_score/S->nseq)*100)/sum;
- nchosen=last_nchosen=1;
- seq_list[0]=best_seq;
- used_seq_list[best_seq]=1;
-
- sprintf ( name[0],"%s", S->name[seq_list[0]]);
- sprintf ( seq[0],"%s", S->seq[seq_list[0]]);
- nchosen=last_nchosen=1;
-
-
- fprintf ( stderr, "\nTRIM:\n");
- fprintf ( stderr, "\n1-Chosen Sequences\n");
- /*Assemble the list of sequences*/
- for (a=1; a< S->nseq; a++)
- {
- for (best_score=0,b=0; b< S->nseq; b++)
- {
- if (used_seq_list[b]);
- else
- {
- score=pw_weight[seq_list[0]][b]+1;
- for (c=0; c<a; c++)
- score=MIN(score,pw_weight[seq_list[c]][b]);
-
- if ( score>=best_score)
- {
- best_seq=b;
- best_score=score;
- }
-
- }
- }
- seq_list[a]=best_seq;
- used_seq_list[best_seq]=1;
-
-
-
- for ( chosen=0,d=0; d< S->nseq; d++)
- {
- for (score=0, c=0; c<=a; c++)
- {
- if ( seq_list[c]!=d)
- score=MAX(score, 100-sim_weight[seq_list[c]][d]);
- }
- chosen+=score;
-
- }
-
- chosen=((chosen/S->nseq)*100)/sum;
- nchosen=a+1;
-
- condition1= (int)chosen<=(int)percent || !percent;
- condition2=(nchosen)<=max_nseq || !max_nseq;
-
- if (condition1 && condition2)
- {
- fprintf ( stderr, "\tADD %s (set score: %.2f %%)\n", S->name[seq_list[a]], chosen);
- sprintf ( name[a],"%s", S->name[seq_list[a]]);
- sprintf ( seq[a],"%s", S->seq[seq_list[a]]);
-
- }
- else
- {
- break;
- }
- last_chosen=chosen;
- last_nchosen=nchosen;
- }
-
- NS=fill_sequence_struc (last_nchosen,seq,name);
- NA=seq2aln(NS,NULL,1);
- fprintf ( stderr, "\n2-Informations:\n");
- fprintf ( stderr, "\tUse...........: %s\n",(use_aln)?"multiple_aln":"pairwise_aln");
- fprintf ( stderr, "\tweight_mode...: %s\n" ,weight_mode);
- fprintf ( stderr, "\tpercent_weight: %.2f%% (max=%d%%)\n",last_chosen,percent);
- fprintf ( stderr, "\tn_seq.........: %d\n" ,NS->nseq);
- fprintf ( stderr, "\treduction.....: %d%% of original set\n" ,(NS->nseq*100)/S->nseq);
-
- return NA;
- }
-Sequence * seq_weight2species_weight (Alignment *A, Sequence *S)
-{
- float *wsp;
- float *wseq;
- int a,b;
-
- S->W=declare_weights(S->nseq);
- if (!A->S || !(A->S)->W)aln2voronoi_weights (A);
-
- wseq=((A->S)->W)->SEQ_W;
- wsp=(S->W)->SEQ_W;
- for ( a=0; a< S->nseq; a++)
- {
- for (b=0; b<A->nseq; b++)
- if ( strstr (A->name[b], S->name[a]))wsp[a]+=wseq[b];
- }
- for (a=0; a<S->nseq; a++)
- fprintf ( stderr, "\nVoronoi Weights: Species %s ---> %.2f\n", S->name[a], wsp[a]);
- return S;
-}
-Alignment * aln2voronoi_weights (Alignment *A)
-{
- int a, b, c;
- float t=0;
- int **tab;
- float *w;
-
- tab=declare_int (256, A->nseq+1);
- if (A->S)free_sequence (A->S, (A->S)->nseq);
- A->S=aln2seq(A);
- (A->S)->W=declare_weights (A->nseq);
- w=((A->S)->W)->SEQ_W;
-
- for (a=0; a<A->len_aln; a++)
- {
- for ( b=0; b<A->nseq; b++)
- {
- c= A->seq_al[b][a];
- if (!is_gap(c))
- {
- c=tolower(c);
- tab[c][++tab[c][0]]=b;
- }
- }
- for (c=0; c<256; c++)
- {
- if (tab[c][0])
- {
- for (b=1; b<=tab[c][0]; b++)
- {
- w[tab[c][b]]+=(float)1/(float)tab[c][0];
- t+=(float)1/(float)tab[c][0];
- }
- }
- tab[c][0]=0;
- }
- }
- for (a=0; a<A->nseq; a++)
- {
- w[a]=(w[a]/t)*A->nseq;
- }
-
- return A;
-}
-
-float ** get_weight ( Alignment *A, Sequence *S, char *mode)
-{
- char *aln_name;
- char *weight_name;
- char *seq_name;
- char command[LONG_STRING];
- char program[LONG_STRING];
- float **weight;
- FILE *fp;
- int c;
-
- if ( !mode || !mode[0] || strm (mode, "msa"))
- {
- if ( getenv ( "SEQ2MSA_WEIGHT")==NULL)sprintf (program, "%s",SEQ2MSA_WEIGHT);
- else sprintf ( program, "%s", (getenv ( "SEQ2MSA_WEIGHT")));
- }
- else if ( strm(mode, "pwsim") ||strm(mode, "pwsim_fragment") )
- {
- return seq2pwsim (A, S, mode);
- }
- else
- {
- if (getenv (mode))sprintf ( program, "%s", (getenv (mode)));
- else fprintf ( stderr, "\nERROR: %s is not a valid mode for weight computation [FATAL:%s]", mode, PROGRAM);
- }
-
- /*MSA weights*/
- seq_name=vtmpnam(NULL);
- aln_name=vtmpnam(NULL);
- weight_name=vtmpnam(NULL);
- weight=declare_float (S->nseq+1, 2);
-
-
-
- if (A)
- {
- output_clustal_aln (seq_name,A);
- output_fasta_seq (aln_name,A);
- sprintf ( command, "%s %s -i %s -w %s", program, seq_name, aln_name, weight_name);
- }
- else
- {
- A=seq2aln(S,A,1);
- output_fasta_seq (seq_name,A);
- sprintf ( command, "%s %s -w %s", program, seq_name, weight_name);
- }
-
-
- my_system ( command);
-
- fp=vfopen( weight_name, "r");
- while ( (c=fgetc(fp))!='$');
- c=fgetc(fp);
- c=0;
- while ( (fscanf (fp, "%*s %f\n",&(weight[c][1])))==1)
- {weight[c][0]=c;c++;}
- vfclose (fp);
-
-
- return weight;
-}
-
-float **seq2pwsim ( Alignment *A, Sequence *S, char *mode)
-{
- int a, b, c;
- float d,t;
- float **W;
- Alignment *B;
- W=declare_float (S->nseq, S->nseq);
-
-
-
- for (a=0; a< S->nseq; a++)
- for ( b=a; b<S->nseq; b++)
- {
- if ( a==b){d=1;}
- else if (!A)
- {
-
- B=align_two_sequences ((S)->seq[a], (S)->seq[b],"pam250mt", -10, -1, "fasta_pair_wise");
- for (t=0,d=0,c=0; c<B->len_aln; c++)
- {
- d+=(B->seq_al[0][c]==B->seq_al[1][c] && !is_gap(B->seq_al[0][c]));
- t+=(!is_gap(B->seq_al[0][c]) && !is_gap(B->seq_al[1][c]));
- }
- t=(strm ( mode, "pwsim_fragment"))?B->len_aln:t;
-
- d=d/((t==0)?1:t);
- free_aln(B);
- }
- else
- {
- for (t=0,d=0,c=0; c<A->len_aln; c++)
- {
- d+=(A->seq_al[a][c]==A->seq_al[b][c] && !is_gap(A->seq_al[a][c]));
- t+=(!is_gap(A->seq_al[a][c]) && !is_gap(A->seq_al[b][c]));
- }
- d=d/((t==0)?1:t);
- }
-
-
- W[a][b]=W[b][a]=(1-d)*100;
- }
-
-
- return W;
-
-}
-
-float **seq2pwsim_fragment ( Alignment *A, Sequence *S, char *mode)
-{
-
-
- int a, b, c;
- float d,t;
- float **W;
- Alignment *B;
- W=declare_float (S->nseq, S->nseq);
-
-
-
-
- for (a=0; a< S->nseq; a++)
- for ( b=a; b<S->nseq; b++)
- {
- if ( a==b){d=1;}
- else if (!A)
- {
-
- B=align_two_sequences ((S)->seq[a], (S)->seq[b],"pam250mt", -10, -1, "fasta_pair_wise");
- for (t=0,d=0,c=0; c<B->len_aln; c++)
- {
- d+=(B->seq_al[0][c]==B->seq_al[1][c] && !is_gap(B->seq_al[0][c]));
- t+=(!is_gap(B->seq_al[0][c]) && !is_gap(B->seq_al[1][c]));
- }
-
- d=d/((t==0)?1:t);
- free_aln(B);
- }
- else
- {
- for (t=0,d=0,c=0; c<A->len_aln; c++)
- {
- d+=(A->seq_al[a][c]==A->seq_al[b][c] && !is_gap(A->seq_al[a][c]));
- t+=(!is_gap(A->seq_al[a][c]) && !is_gap(A->seq_al[b][c]));
- }
- d=d/((t==0)?1:t);
- }
-
-
- W[a][b]=W[b][a]=(1-d)*100;
- }
-
-
- return W;
-
-}
-
-/********************************************************************/
-/* */
-/* AMINO ACID FUNCTIONS */
-/* */
-/* */
-/* */
-/********************************************************************/
-//Builds an extended alphabet from a string
-char** string2alphabet (char *string, int depth, int *falp_size)
-{
- int max_s;
- int a, b,c, l, n;
- char buf[1000];
- char **alp;
- int alp_size;
-
- char ***alp2;
- int *alp2_size;
-
- int *array;
- char **falp;
-
-
- l=strlen (string);
- array=vcalloc ( 256, sizeof (int));
-
-
- max_s=l+1;
- falp_size[0]=0;
- falp=declare_char (l+1, 2);
-
- alp=declare_char(l,2);
- alp_size=0;
-
- array=vcalloc ( 256, sizeof (int));
- for (a=0;a<l; a++)
- {
- if (!array[(int)string[a]])
- {
- array[(int)string[a]]=1;
- sprintf (alp[alp_size++], "%c", string[a]);
- sprintf (falp[falp_size[0]++], "%c", string[a]);
- }
- }
- sprintf ( falp[falp_size[0]++], "*");
- vfree (array);
-
- if ( depth==1)
- {
- free_char (alp, -1);
- return falp;
- }
- alp2=vcalloc ( depth, sizeof (char**));
- alp2_size=vcalloc (depth, sizeof (int));
-
- for (a=0; a<depth; a++)
- {
- alp2[a]=alp;
- alp2_size[a]=alp_size;
- }
-
-
- for (a=2; a<=depth; a++)
- {
- char ***result_array;
-
- result_array=generate_array_string_list (a, alp2, alp2_size, &n, NULL, NO_OVERLAP);
- max_s+=n+1;
- falp=vrealloc (falp, sizeof (char**)*max_s);
- for (b=0; b<n; b++)
- {
- buf[0]='\0';
- for (c=0; c<a; c++)
- {
- strcat (buf, result_array[b][c]);
- }
- falp[falp_size[0]]=vcalloc (strlen (buf)+1, sizeof (char));
- sprintf ( falp[falp_size[0]++], "%s", buf);
- vfree ( result_array[b]);
- }
- vfree (result_array);
-
- }
-
- falp[falp_size[0]]=vcalloc (2, sizeof (char));
- sprintf ( falp[falp_size[0]++], "*");
- free_char (alp, -1);
- return falp;
-}
-
-char** make_group_aa (int *ngroup, char *mode)
- {
-/*mode: indicates which matrix will be used for the grouping*/
-/*n_group: pointer to the number of groups */
-/*return value: an array of strings containing the AA of each group */
-
-
- int **matrix;
- int a, b,c,is_in;
- char buf[28];
- char **group_list;
- char *matrix_name;
- int extend=0;
- matrix_name=vcalloc ( 100, sizeof (char));
-
- if (ngroup[0]==-1)extend=1;
-
- ngroup[0]=0;
- group_list=declare_char ( 100, 27);
-
- if (extend)
- {
- sprintf ( group_list[ngroup[0]++], "gG");
- sprintf ( group_list[ngroup[0]++], "pP");
- sprintf ( group_list[ngroup[0]++], "aA");
- sprintf ( group_list[ngroup[0]++], "cC");
- sprintf ( group_list[ngroup[0]++], "dD");
- sprintf ( group_list[ngroup[0]++], "eE");
-
- sprintf ( group_list[ngroup[0]++], "fF");
- sprintf ( group_list[ngroup[0]++], "hH");
- sprintf ( group_list[ngroup[0]++], "iI");
- sprintf ( group_list[ngroup[0]++], "kK");
- sprintf ( group_list[ngroup[0]++], "lL");
- sprintf ( group_list[ngroup[0]++], "mM");
- sprintf ( group_list[ngroup[0]++], "nN");
- sprintf ( group_list[ngroup[0]++], "qQ");
- sprintf ( group_list[ngroup[0]++], "rR");
-
- sprintf ( group_list[ngroup[0]++], "sS");
- sprintf ( group_list[ngroup[0]++], "tT");
- sprintf ( group_list[ngroup[0]++], "vV");
- sprintf ( group_list[ngroup[0]++], "wW");
- sprintf ( group_list[ngroup[0]++], "*");
- }
-
- if ( mode && mode[0]=='_'){mode++;sprintf ( matrix_name, "%s", mode);}
-
- if (mode==NULL || mode[0]=='\0')sprintf ( matrix_name, "idmat");
- else if ( strstr (mode, "sim") || strm (mode, "idmat") || mode==NULL)
- {
- sprintf ( group_list[ngroup[0]++], "aA");
- sprintf ( group_list[ngroup[0]++], "bB");
- sprintf ( group_list[ngroup[0]++], "cC");
- sprintf ( group_list[ngroup[0]++], "dD");
- sprintf ( group_list[ngroup[0]++], "eE");
- sprintf ( group_list[ngroup[0]++], "fF");
- sprintf ( group_list[ngroup[0]++], "gG");
- sprintf ( group_list[ngroup[0]++], "hH");
- sprintf ( group_list[ngroup[0]++], "iI");
- sprintf ( group_list[ngroup[0]++], "jJ");
- sprintf ( group_list[ngroup[0]++], "kK");
- sprintf ( group_list[ngroup[0]++], "lL");
- sprintf ( group_list[ngroup[0]++], "mM");
- sprintf ( group_list[ngroup[0]++], "nN");
- sprintf ( group_list[ngroup[0]++], "oO");
- sprintf ( group_list[ngroup[0]++], "pP");
- sprintf ( group_list[ngroup[0]++], "qQ");
- sprintf ( group_list[ngroup[0]++], "rR");
- sprintf ( group_list[ngroup[0]++], "sS");
- sprintf ( group_list[ngroup[0]++], "tT");
- sprintf ( group_list[ngroup[0]++], "uU");
- sprintf ( group_list[ngroup[0]++], "vV");
- sprintf ( group_list[ngroup[0]++], "wW");
- sprintf ( group_list[ngroup[0]++], "xX");
- sprintf ( group_list[ngroup[0]++], "yY");
- sprintf ( group_list[ngroup[0]++], "zZ");
- vfree (matrix_name);
- return group_list;
- }
- else if ( strm (mode, "simple"))
- {
- sprintf ( group_list[ngroup[0]++], "avilmAVILM");
- sprintf ( group_list[ngroup[0]++], "dekrDEKR");
- sprintf ( group_list[ngroup[0]++], "stcnqhSTCNQH");
- sprintf ( group_list[ngroup[0]++], "wfyWFY");
- sprintf ( group_list[ngroup[0]++], "gG");
- sprintf ( group_list[ngroup[0]++], "pP");
- vfree (matrix_name);
- return group_list;
- }
-
- else if ( strm (mode, "mafft"))
- {
-
-
- sprintf ( group_list[ngroup[0]++],"agjopstAGJOPST");
- sprintf ( group_list[ngroup[0]++],"ilmvILMV");
- sprintf ( group_list[ngroup[0]++],"bdenqzBDENQZ");
- sprintf ( group_list[ngroup[0]++],"hkrHKR");
- sprintf ( group_list[ngroup[0]++],"fwyFWY");
- sprintf ( group_list[ngroup[0]++],"cC");
- vfree (matrix_name);
- return group_list;
- }
- else if ( strm (mode, "clustalw"))
- {
-
- sprintf ( group_list[ngroup[0]++],"astaASTA");
- sprintf ( group_list[ngroup[0]++],"bneqkBNEQK");
- sprintf ( group_list[ngroup[0]++],"cnhqkCNHQK");
- sprintf ( group_list[ngroup[0]++],"dndeqDNDEQ");
- sprintf ( group_list[ngroup[0]++],"eqhrkEQHRK");
- sprintf ( group_list[ngroup[0]++],"fmilvFMILV");
- sprintf ( group_list[ngroup[0]++],"gmilfGMILF");
- sprintf ( group_list[ngroup[0]++],"hhyHHY");
- sprintf ( group_list[ngroup[0]++],"ifywIFYW");
- sprintf ( group_list[ngroup[0]++],"jcJC");
- sprintf ( group_list[ngroup[0]++],"kpKP");
- vfree (matrix_name);
- return group_list;
- }
- else if ( strm (mode, "polarity"))
- {
-
- sprintf ( group_list[ngroup[0]++],"eqrsdnkhtEQRSDNKHT");
- sprintf ( group_list[ngroup[0]++],"pP");
- sprintf ( group_list[ngroup[0]++],"gG");
- sprintf ( group_list[ngroup[0]++],"cC");
- sprintf ( group_list[ngroup[0]++],"fywFYW");
- sprintf ( group_list[ngroup[0]++],"iavlmIAVLM");
- vfree (matrix_name);
- return group_list;
- }
- else if ( strm (mode, "vasiliky"))
- {
- ngroup[0]=0;
- sprintf ( group_list[ngroup[0]++], "rkRK");
- sprintf ( group_list[ngroup[0]++], "deDE");
- sprintf ( group_list[ngroup[0]++], "qhQH");
- sprintf ( group_list[ngroup[0]++], "vilmVILM");
- sprintf ( group_list[ngroup[0]++], "fyFY");
- sprintf ( group_list[ngroup[0]++], "sS");
- sprintf ( group_list[ngroup[0]++], "wW");
- sprintf ( group_list[ngroup[0]++], "aA");
- sprintf ( group_list[ngroup[0]++], "cC");
- sprintf ( group_list[ngroup[0]++], "gG");
- sprintf ( group_list[ngroup[0]++], "nN");
- sprintf ( group_list[ngroup[0]++], "pP");
- sprintf ( group_list[ngroup[0]++], "tT");
- vfree (matrix_name);
- return group_list;
- }
- else if ( strm (mode, "clustalw_col"))
- {
- sprintf ( group_list[ngroup[0]++], "staSTA");
- sprintf ( group_list[ngroup[0]++], "neqkNEQK");
- sprintf ( group_list[ngroup[0]++], "nhqkNHQK");
- sprintf ( group_list[ngroup[0]++], "ndeqNDEQ");
- sprintf ( group_list[ngroup[0]++], "qhrkQHRK");
- sprintf ( group_list[ngroup[0]++], "milvMILV");
- sprintf ( group_list[ngroup[0]++], "milfMILF");
- sprintf ( group_list[ngroup[0]++], "hyHY");
- sprintf ( group_list[ngroup[0]++], "fywFYW");
- sprintf ( group_list[ngroup[0]++], "gG");
- sprintf ( group_list[ngroup[0]++], "pP");
- sprintf ( group_list[ngroup[0]++], "cC");
- vfree (matrix_name);
-
- return group_list;
- }
- else if ( strm (mode, "clustalw_dot"))
- {
- sprintf ( group_list[ngroup[0]++], "csaCSA");
- sprintf ( group_list[ngroup[0]++], "atvATV");
- sprintf ( group_list[ngroup[0]++], "sagSAG");
- sprintf ( group_list[ngroup[0]++], "stnkSTNK");
- sprintf ( group_list[ngroup[0]++], "stpaSTPA");
- sprintf ( group_list[ngroup[0]++], "sgndSGND");
- sprintf ( group_list[ngroup[0]++], "sndeqkSNDEQK");
- sprintf ( group_list[ngroup[0]++], "ndeqhkNDEQHK");
- sprintf ( group_list[ngroup[0]++], "neqhrkNEQHRK");
- sprintf ( group_list[ngroup[0]++], "fvlimFVLIM");
- sprintf ( group_list[ngroup[0]++], "hfyHFY");
- vfree (matrix_name);
- return group_list;
- }
- else if ( strm (mode, "make_all"))
- {
- ngroup[0]=1;
- sprintf ( group_list[0], "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz");
- vfree (matrix_name);
- return group_list;
- }
- else sprintf ( matrix_name, "%s", mode);
-
- matrix=read_matrice ( matrix_name);
-
- for ( a=0;a< 26; a++)
- {
- if ( matrix[a][a]>0)
- {
- for ( c=0,b=0;b< 26; b++)
- {
-
- if ( matrix[a][b]>0 && matrix[b][b]>0)
- {
- buf[c++]=b+'A';
- buf[c++]=b+'a';
- }
- }
- buf[c]='\0';
- for ( is_in=0,b=0; b< ngroup[0]; b++)if ( strcmp (buf, group_list[b])==0)is_in=1;
- if (is_in==0)sprintf ( group_list[ngroup[0]++], "%s", buf);
-
- }
- }
- free_int (matrix, -1);
- vfree (matrix_name);
-
- return group_list;
- }
-char** make_group_aa_upgma (char*matrix, int max_n)
- {
- char **group_list;
- int **mat;
- int *used;
- int a, b, ba, bb, best, set, l, n;
- l=26;
-
- group_list=declare_char (l+1, l+1);
- for (a=0; a<l; a++)group_list[a][0]='a'+a;
- mat=read_matrice(matrix);
- used=vcalloc ( l, sizeof (int));
- n=l;
-
- while (n>max_n)
- {
- for (set=0,a=0; a<l-1; a++)
- for (b=a+1; b<l; b++)
- {
- if (used[a]||used[b])continue;
-
- if (set==0 || mat[a][b]>best)
- {
- best=mat[a][b];
- ba=a;
- bb=b;
- set=1;
- }
- }
-
- for (a=0; a<l; a++)
- {
- mat[ba][a]=mat[a][ba]=(mat [ba][a]+mat[bb][a])/2;
- used[bb]=1;
- }
- strcat (group_list[ba], group_list[bb]);
- vfree (group_list[bb]);
- group_list[bb]=NULL;
-
- n--;
- }
-
- for (n=0,a=0; a<l; a++)
- {
- if ( group_list[a])
- group_list[n++]=group_list[a];
- }
- vfree (used); free_int (mat, -1);
- return group_list;
- }
-
-int find_group_aa_distribution (char *col, int nseq,int n_group, char **gl, int *distrib, char *mode )
- {
- static int *distribution;
- static char **lgl;
- static int ln_group;
- int a, b, c;
- int *d;
- char **gl2;
- int n_group2;
-
-
-
- if ( lgl==NULL)
- lgl=make_group_aa ( &ln_group, mode);
-
- if ( gl==NULL)
- {
- gl2=lgl;
- n_group2=ln_group;
- }
- else
- {
- gl2=gl;
- n_group2=n_group;
- }
-
- if ( distribution==NULL || ln_group<n_group)distribution=vcalloc ( n_group2, sizeof (int));
- if ( distrib==NULL)d=distribution;
- else d=distrib;
-
-
- for ( a=0; a< n_group2; a++)d[a]=0;
-
- for ( a=0; a< nseq; a++)
- {
- for ( b=0; b< n_group2; b++)
- d[b]+=is_in_set (col[a], gl2[b]);
- }
- c=d[0];
- for ( a=0; a< n_group2; a++)
- c=(d[a]>c)?d[a]:c;
- return c;
- }
-
-
-
-int is_in_same_group_aa ( char r1, char r2, int n_group, char **gl, char *mode)
- {
- int a;
- static char **lgl;
- static int ln_group;
-
- char **gl2;
- int n_group2;
-
- /*use mode=idmat for similarity based on id*/
-
- r1=toupper(r1);
- r2=toupper(r2);
- if (mode==NULL)return (r1==r2)?1:0;
-
- if ( strm (mode, "clean"))
- {
- free_char (lgl, -1);
- lgl=NULL;
- ln_group=0;
- return 0;
- }
- else if ( strstr (mode, "cov"))
- {
- return 1;
- }
-
- if ( lgl==NULL)
- {
- lgl=make_group_aa ( &ln_group, mode);
- }
-
- if ( gl==NULL)
- {
- gl2=lgl;
- n_group2=ln_group;
- }
- else
- {
- gl2=gl;
- n_group2=n_group;
- }
-
- for ( a=0; a< n_group2; a++)
- if ( is_in_set ( r1, gl2[a]) && is_in_set ( r2, gl2[a]))return 1;
- return 0;
- }
-
-
-Alignment * gene2prot (Alignment *A){return A; }
-char * test_gene2prot (Constraint_list *CL, int s1)
- {
- int a, b,q, nal;
- int F=-10000000; /*FORBIDEN STATE*/
- int AL=0; /*ALLOWED STATE*/
- int SPLICE_PENALTY=1000;
- int FRAME_PENALTY=1000;
-
-
- int START, ORF1, ORF2, ORF3, s5NC;
- int s3NC,ORF3_G1, ORF3_T2, ORF3_NC, ORF3_A3, ORF3_T4;
- int U1_G1, U1_T2, U1_NC, U1_A3, U1_T4;
- int U2_G1, U2_T2, U2_NC, U2_A3, U2_T4;
- int U1, U2, U3, U4, U5, END;
-
- int nstate=0;
- int **transitions;
- int **v_tab;
- int **v_tab_p;
- int **last_coding;
- int **last_t4;
- int *potential;
- int v;
-
- int orf1, orf2, orf3, ncp, p, state, pstate, e, best_state_p=0, best_state_v=0, best_pstate_p=0, best_pstate_v;
- char *seq, *seq2, *seq3;
- int l;
- int *is_coding;
- int *is_t4;
- char *codon;
- int s, r, s2, r2, w2;
-
- static int *entry;
- int tot=0;
-
- seq=vcalloc ( strlen ((CL->S)->seq[s1])+1, sizeof (char));
- seq2=vcalloc ( strlen ((CL->S)->seq[s1])+1, sizeof (char));
- seq3=vcalloc ( strlen ((CL->S)->seq[s1])+1, sizeof (char));
- sprintf ( seq, "%s", (CL->S)->seq[s1]);
- ungap (seq);
-
- l=strlen (seq);
- for ( a=0; a< l; a++) seq[a]=tolower ( seq[a]);
- for ( a=0; a< l; a++) seq[a]=(seq[a]=='t')?'u': seq[a];
-
-
- potential=vcalloc (l+1, sizeof (int));
-
- for (nal=0, s=0; s<(CL->S)->nseq; s++)
- {
- for ( r=1; r<=(CL->S)->len[s]; r++)
- {
- for ( b=1; b<CL->residue_index[s1][r][0]; b++)
- {
-
- s2=CL->residue_index[s][r][b+SEQ2];
- r2=CL->residue_index[s][r][b+R2];
- w2=CL->residue_index[s][r][b+WE];
- if (s==s1)potential[r-1]+=w2;
- else if ( s2==s1)potential[r2-1]+=w2;
- tot+=w2;
- nal++;
- }
- }
- }
-
-
- SPLICE_PENALTY=10000;
- FRAME_PENALTY=1000;
-
-
- nstate=0;
- START=nstate++; ORF1=nstate++; ORF2=nstate++; ORF3=nstate++; s5NC=nstate++;
- s3NC=nstate++;
- ORF3_G1=nstate++;U1_G1=nstate++;U2_G1=nstate++;
- ORF3_T2=nstate++;U1_T2=nstate++;U2_T2=nstate++;
- ORF3_NC=nstate++;U1_NC=nstate++;U2_NC=nstate++;
- ORF3_A3=nstate++;U1_A3=nstate++;U2_A3=nstate++;
- ORF3_T4=nstate++;U1_T4=nstate++;U2_T4=nstate++;
-
-
- U1=nstate++; U2=nstate++; U3=nstate++; U4=nstate++; U5=nstate++;
- END=nstate++;
-
- is_coding=vcalloc ( nstate, sizeof (int));
- is_coding[ORF1]=is_coding[ORF2]=is_coding[ORF3]=is_coding[U1]=is_coding[U2]=1;
- is_coding[U3]=is_coding[U4]=is_coding[U5]=1;
-
- is_t4=vcalloc ( nstate, sizeof (int));
- is_t4[ORF3_T4]=is_t4[U1_T4]=is_t4[U2_T4]=1;
- transitions=declare_int ( nstate, nstate);
- for (a=0; a< nstate; a++)
- for ( b=0; b< nstate; b++)transitions[a][b]=F;
-
- transitions[START][ORF1]=AL;
- transitions[START][s5NC]=AL-FRAME_PENALTY;
- transitions[s5NC][s5NC]=AL;
-
- transitions[s5NC][ORF1]=AL-FRAME_PENALTY;
-
- transitions[ORF1][ORF2]=AL;
- transitions[ORF2][ORF3]=AL;
- transitions[ORF3][U1]=AL;
- transitions[ORF3][ORF1]=AL;
- transitions[ORF3][ORF3_G1]=AL-SPLICE_PENALTY;
-
-
- transitions[ORF3_G1][ORF3_T2]=AL;
- transitions[ORF3_T2][ORF3_NC]=AL;
- transitions[ORF3_NC][ORF3_NC]=AL;
- transitions[ORF3_NC][ORF3_A3]=AL;
- transitions[ORF3_A3][ORF3_T4]=AL;
- transitions[ORF3_T4][ORF1]=AL-SPLICE_PENALTY;
-
- transitions[U1][U2]=AL;
- transitions[U1][U1_G1]=AL-SPLICE_PENALTY;
- transitions[U1_G1][U1_T2]=AL;
- transitions[U1_T2][U1_NC]=AL;
- transitions[U1_NC][U1_NC]=AL;
- transitions[U1_NC][U1_A3]=AL;
- transitions[U1_A3][U1_T4]=AL;
- transitions[U1_T4][U3]=AL-SPLICE_PENALTY;
- transitions[U3][U4]=AL;
- transitions[U4][ORF1]=AL;
-
- transitions[U2][U2_G1]=AL-SPLICE_PENALTY;
- transitions[U2_G1][U2_T2]=AL;
- transitions[U2_T2][U2_NC]=AL;
- transitions[U2_NC][U2_NC]=AL;
- transitions[U2_NC][U2_A3]=AL;
- transitions[U2_A3][U2_T4]=AL;
- transitions[U2_T4][U5]=AL-SPLICE_PENALTY;
- transitions[U5][ORF1]=AL;
-
- transitions[ORF3][s3NC]=AL-FRAME_PENALTY;
- transitions[ORF3][END]=AL;
- transitions[s3NC][END]=AL;
-
-
- v_tab=declare_int ( l+1,nstate);
- v_tab_p=declare_int ( l+1,nstate);
- last_coding=declare_int ( l+1,nstate);
- last_t4=declare_int ( l+1,nstate);
-
- for (a=0; a< l; a++) potential[a]-=200;
-
- codon=vcalloc ( 4, sizeof (char));
- best_pstate_p=START;
- best_pstate_v=0;
- nal=0;
- for ( p=1; p<=l; p++)
- {
- if (translate_dna_codon (seq+(p-1), 'x')=='x' || p>(l-2))orf1=F;
- else orf1=potential[p-1];
-
- if (p<2 || translate_dna_codon (seq+(p-2), 'x')=='x' || p>(l-1))orf2=F;
- else orf2=potential[p-1];
-
-
- if (p<3 || translate_dna_codon (seq+(p-3), 'x')=='x' || p>l)orf3=F;
- else orf3=potential[p-1];
-
- if ( best_int (3, 1, &a, orf1, orf2, orf3)!=F)ncp=-best_int (3, 1, &a, orf1, orf2, orf3);
- else ncp=1000;
-
- for ( state=0; state< nstate; state++)
- {
-
- if ( state==ORF1)e=orf1;
- else if ( state==ORF2)e=orf2;
- else if ( state==ORF3)e=orf3;
- else if ( state>=U1 && state<=U3)
- {
- e=0;
- }
- else if ( state==U4)
- {
- codon[2]=seq[p-1];
- codon[1]=seq[last_coding[p-1][U3]-1];
- codon[0]=seq[last_coding[p-2][U1_T4]-1];
- if ( translate_dna_codon (codon, 'x')=='x')e=F;
- else e=0;
- }
- else if ( state==U5)
- {
- codon[2]=seq[p-1];
- codon[1]=seq[last_coding[p-1][U2_T4]-1];
- q=seq[last_coding[p-1][U2_T4]];
- codon[0]=seq[last_coding[q-1][U1]-1];
- if ( translate_dna_codon (codon, 'x')=='x')e=F;
- else e=0;
- }
-
- else if (state>=ORF3_G1 && state<=U2_G1)e=(p<l-1 && seq[p-1]=='g' && seq[p]=='u')?ncp:F;
- else if ( state>=ORF3_T2 && state<=U2_T2)
- {
- e=(p>1 && seq[p-2]=='g' && seq[p-1]=='u')?ncp:F;
- }
- else if ( state>=ORF3_A3 && state<=U2_A3)e=(seq[p-1]=='a')?ncp:F;
- else if ( state>=ORF3_T4 && state<=U2_T4)e=(seq[p-1]=='u')?ncp:F;
- else e=ncp;
-
- for ( pstate=0; pstate<nstate; pstate++)
- {
- if (e==F || transitions[pstate][state]==F || v_tab[p-1][pstate]==F)v=F;
- else v=e+transitions[pstate][state]+v_tab[p-1][pstate];
-
- if ( pstate==0 || v>best_pstate_v)
- {best_pstate_v=v;best_pstate_p=pstate;}
- }
- v_tab[p][state]=best_pstate_v;
- v_tab_p[p][state]=best_pstate_p;
-
- if (!is_coding[state])last_coding[p][state]=last_coding[p-1][best_pstate_p];
- else if (is_coding[state])last_coding[p][state]=p;
-
- if (!is_t4[state])
- {
- if (is_coding[state] && last_t4[p-1][best_pstate_p]==0)last_t4[p][state]=p;
- else last_t4[p][state]=last_t4[p-1][best_pstate_p];
- }
- else if (is_t4[state])last_t4[p][state]=p;
-
- if (state==0 ||best_pstate_v>best_state_v ){best_state_p=state; best_state_v=best_pstate_v;}
- }
- }
- tot=0;
- for ( p=l; p>0; p--)
- {
- if ( best_state_p>=ORF1 && best_state_p<=ORF3){seq2[tot++]=tolower (seq[p-1]);}
- else if ( best_state_p>=U1 && best_state_p<=U5){seq2[tot++]=tolower (seq[p-1]);}
- if (best_state_p==ORF1)seq[p-1]=toupper (seq[p-1]);
- else if (best_state_p==ORF2 || best_state_p==ORF3)seq[p-1]=tolower (seq[p-1]);
- else if ( best_state_p==ORF3_NC || best_state_p==U1_NC || best_state_p==U2_NC) seq[p-1]='.';
- else if ( best_state_p==U1 || best_state_p==U2 || best_state_p==U3 || best_state_p==U4 || best_state_p==U5) seq[p-1]=best_state_p-U1+'1';
- else seq[p-1]=toupper (seq[p-1]);
- best_state_p=v_tab_p[p][best_state_p];
- }
-
- for ( a=0, b=tot-1; b>=0; b--, a++)
- seq3[a]=seq2[b];
-
- fprintf ( stderr, "\n%s\n", seq);
- fprintf ( stderr, "\nN coding=%d\n", tot);
- for ( a=0; a< tot; a+=3)
- {
- b=translate_dna_codon (seq3+a, 'x');
- fprintf ( stderr, "%c",b);
- if ( b=='x'){fprintf ( stderr, "\n");myexit (EXIT_SUCCESS);}
- }
-
- fprintf ( stderr, "\n");
- myexit (EXIT_SUCCESS);
- return 0;
-
-
-
- }
-Alignment * dna_aln2_3frame_cdna_aln(Alignment *A,int *ns,int **l_s)
-{
- Alignment *B;
- int a;
- B=realloc_aln2 (NULL,6,strlen(A->seq_al[l_s[0][0]])+strlen(A->seq_al[l_s[1][0]]));
- for ( a=0; a< 3; a++)
- {
- B->seq_al[a]=translate_dna_seq (A->seq_al[l_s[0][0]]+a, 0, 'o',B->seq_al[a]);
- B->seq_al[a+3]=translate_dna_seq (A->seq_al[l_s[1][0]]+a, 0, 'o',B->seq_al[a+3]);
- }
- for ( a=1; a<3; a++)
- {
- if ( strlen(B->seq_al[a])<strlen(B->seq_al[0])) B->seq_al[a]=strcat ( B->seq_al[a], "x");
- if ( strlen(B->seq_al[a+3])<strlen(B->seq_al[3])) B->seq_al[a+3]=strcat ( B->seq_al[a+3], "x");
- }
-
- B->nseq=6;
- B->len_aln=strlen (B->seq_al[0]);
- return B;
-}
-
-//JM_ADD
-//For normal distribution scan
-#ifndef PI
-#define PI 3.141592653589793238462643
-#endif
-
-double normal(double x, double mean, double std)
-{
- return (1/(std*sqrt(2.0*PI)))*exp((-0.5*(x-mean)*(x-mean))/(std*std));
-}
-
-int ** get_sim_aln_array_normal_distribution ( Alignment *A, char *mode, int *STD, int *CENTER)
- {
- int **w;
- int a, b;
-
-
- w=declare_int ( A->nseq, A->nseq);
-
- for ( a=0; a< A->nseq-1; a++)
- {
- for ( b=a+1; b< A->nseq; b++)
- {
-
- w[a][b]=w[b][a]=generic_get_seq_sim_normal_distribution ( A->seq_al[a], A->seq_al[b], (A->cdna_cache)?A->cdna_cache[0]:NULL, mode, STD, CENTER);
- }
- }
- return w;
- }
-int generic_get_seq_sim_normal_distribution ( char *seq1, char *seq2, int*cache, char *mode, int *STD, int *CENTER)
-{
- return get_seq_sim_distribution ( seq1,seq2,GAP_LIST, mode, STD, CENTER);
-}
-
-int get_seq_sim_distribution ( char *string1, char *string2, char *ignore, char *in_mode, int *STD, int *CENTER)
- {
- int len1;
- int a;
- int pos0, gap=0;
- int p1, p2;
- int r=0,r1=0,r2=0;
- char *p;
- char mode[1000];
-
- double sim;
-
-
- sprintf ( mode, "%s", in_mode);
-
- /*mode: <mat>__<sim_mode>
- mat: idscore to get the alignment done
- any legal cw matrix
- sim_mode: sim1->identities/matches
- sim2->identities/min len
- */
-
-
- if ( (p=strstr (mode, "_"))!=NULL)
- {
- p[0]='\0';
- p++;
- }
-
-
- if (strstr (mode, "idscore"))
- {
- static int **mat;
- if (!mat) mat=read_matrice ("blosum62mt");
- return idscore_pairseq (string1, string2, -12, -1, mat,mode);
- }
-
- len1=strlen (string1);
- for ( sim=pos0=0,a=0; a< len1; a++)
- {
- r1=string1[a];
- r2=string2[a];
- p1=1-is_in_set (r1, ignore);
- p2=1-is_in_set (r2, ignore);
- if (p1 && p2)
- {
- pos0++;
- if (is_in_same_group_aa(r1,r2,0, NULL, mode))
- {
- sim += normal(a, *CENTER, *STD);
- }
- }
- else if (p1+p2==1)
- {
- gap++;
- }
- }
-
- if ( p==NULL || strm (p, "sim1") || strm (p, "sim"))
- {
- r=(pos0==0)?0:(sim*MAXID);
- }
-/* else if ( strm (p, "sim2"))
- {
- r=(pos1==0 || pos2==0)?0:(sim*MAXID)/MIN(pos1,pos2);
- }
- else if ( strm (p, "sim3"))
- {
- r=(pos1==0 || pos2==0)?0:(sim*MAXID)/MAX(pos1,pos2);
- }
- else if ( strm (p, "gap1"))
- {
- r=(len1==0)?MAXID:(gap*MAXID)/len1;
- r=MAXID-r;
- }
- else if ( strm (p, "logid"))
- {
- r=logid_score (pos0, sim);
- }*/
- return r;
-
- }
-
-
-
-Alignment *aln2clean_pw_aln (Alignment *A, OveralnP *F)// char *mode, int t, int f, int p1,int p2, int p3, char *fsa_mode)
-{
- int **C, **T;
- int a, b, c;
- Alignment *B;
-
-
- if (F->t==0)F->t=2;
-
- C=declare_int ( A->nseq, A->len_aln);
- T=declare_int ( A->nseq, A->len_aln);
- B=copy_aln (A, NULL);
-
- for (a=0; a< A->nseq;a++)
- {
- for (b=0; b<A->nseq; b++)
- {
- int *w;
- w=pw_aln2clean_aln_weight (A->seq_al[a], A->seq_al[b], 1,F);//f,p1, p2, p3, fsa_mode);
- for (c=0; c<A->len_aln; c++)
- {
- if (A->seq_al[a][c]=='-')continue;
- C[a][c]+=w[c];
- T[a][c]++;
- }
- vfree (w);
- }
- }
-
-
-
- for (a=0; a<A->nseq; a++)
- {
- for (b=0; b<A->len_aln; b++)
- {
- int c;
- c=A->seq_al[a][b];
- if ( c=='-');
- else if (T[a][b]==0);
- else
- {
- int r;
- r=(C[a][b]*10)/T[a][b];
- r=(r==10)?9:r;
- if (!F->mode || strm (F->mode, "number"))
- B->seq_al[a][b]='0'+r;
- else if ( F->mode && (strm (F->mode, "unalign") ||strm (F->mode, "unalign2")))
- B->seq_al[a][b]='0'+r;
- else if ( F->mode && strm (F->mode, "lower") )
- {
- if (r<=F->t)B->seq_al[a][b]=tolower (B->seq_al[a][b]);
- else B->seq_al[a][b]=toupper (B->seq_al[a][b]);
- }
- }
- }
- }
-
- if (F->mode && strm (F->mode, "unalign"))
- {
- A=unalign_aln (A, B, F->t);
- free_aln (B);
- B=copy_aln (A, NULL);
- }
- else if (F->mode && strm (F->mode, "unalign2"))
- {
- A=unalign_aln_2 (A, B, F->t);
- free_aln (B);
- B=copy_aln (A, NULL);
- }
-
-
-
- free_int (C, -1);
- free_int (T, -1);
-
- return B;
-}
-
-char **pw_aln2clean_pw_aln_fsa1 (char ** aln, OveralnP *F);
-char **pw_aln2clean_pw_aln_fsa2 (char ** aln, OveralnP *F);
-
-int * pw_aln2clean_aln_weight ( char *seq1, char *seq2, int w, OveralnP *F)
-{
- char **aln;
- int *weight;
- int l, a;
-
- if ( (l=strlen (seq1)) !=strlen (seq2))
- {
- HERE ("\n%s\n%s\n", seq1, seq2);
- printf_exit ( EXIT_FAILURE, stderr, "\nERROR: Comparing unaligned sequences [FATAL:%s]", PROGRAM);
-
- }
-
- aln=declare_char (2, l+1);
- sprintf ( aln[0], "%s", seq1);
- sprintf ( aln[1], "%s", seq2);
-
-
- aln=pw_aln2clean_pw_aln (aln, F);
-
- weight=vcalloc (l+1, sizeof (int));
- for (a=0; a<l; a++)
- {
- if ( aln[0][a] || seq1[a]=='x' || seq1[a]=='X' || seq2[a]=='x' || seq2[a]=='X')weight[a]=w;
- }
- free_char (aln, -1);
-
- return weight;
-}
-
-
-char **pw_aln2clean_pw_aln (char ** aln, OveralnP *F)
-{
-
- if ( strm (F->model, "fsa2"))return pw_aln2clean_pw_aln_fsa2 (aln,F);
- else if ( strm (F->model, "fsa1"))return pw_aln2clean_pw_aln_fsa1 (aln,F);
- else return pw_aln2clean_pw_aln_fsa1 (aln,F);
-}
-
-char **pw_aln2clean_pw_aln_fsa2 (char ** aln, OveralnP *FO)
-{
- int a, b, c, d, l, id;
- int c1, c2, e0, e1,tb, obs;
- int T0, T1,T2;
- int **mat, **tran, **p, **t, *s, *ids;
- int ns, ps, cs;
- int S, M1, M2, m1, m2,B1, B2,G1,G2, K;
- int F=-9999999;
- int MID_EXON_FACTOR=50;
- int best;
- static int **smat;
- int model_type=1;
- int *translate;
-
- if ( getenv ("MID_EXON_FACTOR"))MID_EXON_FACTOR=atoi (getenv ("MID_EXON_FACTOR"));
-
-
-
- if (!smat)smat=read_matrice ( "blosum62mt");
-
- l=strlen (aln[0]);
-
- if ( l!=strlen (aln[1]))
- {
- printf_exit ( EXIT_FAILURE, stderr, "\nERROR: unaligned strings");
- }
-
-
-
- s=vcalloc (l, sizeof (int));
- ids=vcalloc (l, sizeof (int));
-
- //record the id level of each posotion
- for (b=0; b<l; b++)
- {
- c1=tolower(aln[0][b]);c2=tolower(c2=aln[1][b]);
-
- if (c1=='-' || c2=='-' || c1=='X' || c2=='X' || c1!=c2)ids[b]=0;
- else ids[b]=1;
- }
-
- //record the state of each position: M, m, T, gap
- for (id=0,b=0,a=0;a<l; a++)
- {
- c1=aln[0][a];c2=aln[1][a];
- if (islower (c1))s[a]=3;
- else if (c1=='-' || c2=='-' || c1=='X' || c2=='X')s[a]=2;
- else
- {
- int sc;
- sc=smat[c1-'A'][c2-'A'];
- if (sc>=2){id++; s[a]=1;}
- else {s[a]=0;}
- b++;
- }
- }
-
- if (b==0)
- {
- vfree(s);vfree (ids);
- return aln;
- }
-
-
-
- FO->p1=(FO->p1==0)?5:FO->p1;
- FO->p2=(FO->p2==0)?15:FO->p2;
- FO->p3=(FO->p3==0)?0:FO->p3;
- FO->p4=(FO->p4==0)?100:FO->p4;
-
-
- T1=100*(float)id/(float)b;
- T2=(FO->f==0)?30:T1*(float)((float)FO->f/(float)100);
- T2=MAX(T2,20);
-
- //0: unaligned
- //1: aligned
- //2: gap
- //3: exon boundary
-
- ns=0;
- S=ns++;
- M1=ns++;//1 matched aligned
- m1=ns++;//2 mmatched aligned
- M2=ns++;//3 matched unaligned
- m2=ns++;//4 mmatched unaligned
- B1=ns++;//5 transition aligned
- B2=ns++;//6 transition unaligned
-
- mat=declare_int (ns, 4);
- tran=declare_int (ns, ns);
- p=declare_int (l+1, ns);
- t=declare_int (l+1, ns);
-
- //emission Values
- mat[M1][0]=F; //non id
- mat[M1][1]=T1;//id
- mat[M1][2]=0; //gap
- mat[M1][3]=F; //transition
-
- mat[M2][0]=F;
- mat[M2][1]=T2;
- mat[M2][2]=0;
- mat[M2][3]=F;
-
- mat[m1][0]=100-T1;
- mat[m1][1]=F;
- mat[m1][2]=0;
- mat[m1][3]=F;
-
- mat[m2][0]=100-T2;
- mat[m2][1]=F;
- mat[m2][2]=0;
- mat[m1][3]=F;
-
- mat[B1][0]=F;
- mat[B1][1]=F;
- mat[B1][2]=F;
- mat[B1][3]=0;
-
- mat[B2][0]=F;
- mat[B2][1]=F;
- mat[B2][2]=F;
- mat[B2][3]=0;
-
- //transition values
- tran[S][m1]=0;
- tran[S][m2]=0;
- tran[S][M1]=0;
- tran[S][M2]=0;
- tran[S][B1]=0;
- tran[S][B2]=0;
-
-
- tran[M1][m1]= 0;
- tran[M1][m2]=-FO->p4;
- tran[M1][M1]=+FO->p2;
- tran[M1][M2]= F;
- tran[M1][S ]= F;
- tran[M1][B1]= 0;
- tran[M1][B2]=-FO->p1;
-
- tran[M2][m1]= F;
- tran[M2][m2]=+FO->p3;
- tran[M2][M1]= F;
- tran[M2][M2]= 0;
- tran[M2][S] = F;
- tran[M2][B1]= F;
- tran[M2][B2]= 0;
-
-
- tran[m1][m1]= 0;
- tran[m1][m2]= F;
- tran[m1][M1]= 0;
- tran[m1][M2]= F;
- tran[m1][S] = F;
- tran[m1][B1]= 0;
- tran[m1][B2]=-FO->p1;
-
- tran[m2][m1]= F;
- tran[m2][m2]= 0;
- tran[m2][M1]= -FO->p4;
- tran[m2][M2]= +FO->p3;
- tran[m2][S] = F;
- tran[m2][B1]= F;
- tran[m2][B2]= 0;
-
- tran[B1][m1]= 0;
- tran[B1][m2]= F;
- tran[B1][M1]= 0;
- tran[B1][M2]= F;
- tran[B1][S]= F;
- tran[B1][B1]= F;
- tran[B1][B2]= F;
-
- tran[B2][m1]= -FO->p1;
- tran[B2][m2]= 0;
- tran[B2][M1]= -FO->p1;
- tran[B2][M2]= 0;
- tran[B2][S]= F;
- tran[B2][B1]= F;
- tran[B2][B2]= F;
-
- translate=vcalloc (ns, sizeof (int));
- translate[M1]=1;
- translate[m1]=1;
- translate[M2]=0;
- translate[m2]=0;
- translate[B1]=1;
- translate[B2]=0;
-
- for (a=1;a<=l; a++)
- {
- obs=s[a-1];
-
- for (cs=0; cs<ns; cs++)
- {
- for (ps=0; ps<ns; ps++)
- {
- c=p[a-1][ps]+mat[cs][obs]+tran[ps][cs];
- if (ps==0 || c>=best){t[a][cs]=ps;best=p[a][cs]=c;}
- }
-
- }
- }
-
-
- for (a=0; a<ns; a++)
- {
- if (a==0 || p[l][a]>=best){tb=a;best=p[l][a];}
- }
-
- for (a=l; a>0; a--)
- {
- int v;
- int p2;
-
- p2=a-1;
- aln[0][p2]=aln[1][p2]=translate[tb];
- tb=t[a][tb];
-
- }
-
- free_int (p, -1);
- vfree(s);
- free_int (t, -1);
- free_int (mat, -1);
- free_int (tran, -1);
- vfree (translate);
- return aln;
-}
-char **pw_aln2clean_pw_aln_fsa1 (char ** aln, OveralnP *FO)
-{
- int a, b, c, d, l, id;
- int c1, c2, e0, e1,tb, obs;
- int T0, T1,T2;
- int **mat, **tran, **p, **t, **s;
- int ns, ps, cs;
- int S, M1, M2, m1, m2, K;
- int F=-9999999;
- int best;
- static int **smat;
- int *translate;
-
-
- if (!smat)smat=read_matrice ( "blosum62mt");
-
- l=strlen (aln[0]);
-
- if ( l!=strlen (aln[1]))
- {
- printf_exit ( EXIT_FAILURE, stderr, "\nERROR: unaligned strings");
- }
-
-
- s=declare_int (l+1, 2);
- for (id=0,b=0,a=0;a<l; a++)
- {
- c1=aln[0][a];c2=aln[1][a];
-
- if ( c1=='-' || c2=='-' || c1=='x' || c1=='X' || c2=='x' || c2=='X')continue;
- else
- {
- int sc;
- sc=smat[c1-'A'][c2-'A'];
- if (sc>=2){id++; s[b][0]=1;}
- else {s[b][0]=0;}
- s[b][1]=a;
- b++;
-
- }
- }
- if (b==0)
- {
- free_int (s, -1);
- return aln;
- }
- FO->f=(FO->f==0)?30:FO->f;
- FO->p1=(FO->p1==0)?90:FO->p1;
- FO->p2=(FO->p2==0)?15:FO->p2;
- FO->p3=(FO->p3==0)?0:FO->p3;
-
- l=b;//length of the ungapped aln
- T1=100*(float)id/(float)b;
- T2=FO->f;//T1*f;
-
-
-
- //0: unaligned
- //1: aligned
-
-
- ns=0;
- S=ns++;
- M1=ns++;//1 matched aligned
- m1=ns++;//2 mmatched aligned
- M2=ns++;//3 matched unaligned
- m2=ns++;//4 mmatched unaligned
-
- mat=declare_int (ns, 2);
- tran=declare_int (ns, ns);
- p=declare_int (l+1, ns);
- t=declare_int (l+1, ns);
-
-
- mat[M1][0]=F;
- mat[M1][1]=T1;
-
- mat[M2][0]=F;
- mat[M2][1]=T2;
-
- mat[m1][0]=100-T1;
- mat[m1][1]=F;
-
- mat[m2][0]=100-T2;
- mat[m2][1]=F;
-
-
- tran[S][m1]=0;
- tran[S][m2]=0;
- tran[S][M1]=0;
- tran[S][M2]=0;
-
-
- tran[M1][m1]= 0;
- tran[M1][m2]=-FO->p1;// -P;
- tran[M1][M1]=+FO->p2;
- tran[M1][M2]= F;
- tran[M1][S] = F;
-
- tran[M2][m1]= F;
- tran[M2][m2]=+FO->p3;
- tran[M2][M1]= F;
- tran[M2][M2]= 0;
- tran[M2][S]= F;
-
- tran[m1][m1]= 0;
- tran[m1][m2]= F;
- tran[m1][M1]= 0;
- tran[m1][M2]= F;
- tran[m1][S]= F;
-
- tran[m2][m1]= F;
- tran[m2][m2]= 0;
- tran[m2][M1]=-FO->p1;
- tran[m2][M2]=+FO->p3;
- tran[m2][S]= F;
-
- translate=vcalloc (ns, sizeof (int));
- translate[M1]=1;
- translate[m1]=1;
- translate[M2]=0;
- translate[m2]=0;
- translate[S]=1;
-
-
- for (a=1;a<=l; a++)
- {
- obs=s[a-1][0];
-
- for (cs=0; cs<ns; cs++)
- {
- for (ps=0; ps<ns; ps++)
- {
- c=p[a-1][ps]+mat[cs][obs]+tran[ps][cs];
- if (ps==0 || c>=best){t[a][cs]=ps;best=p[a][cs]=c;}
- }
-
- }
- }
-
-
- for (a=0; a<ns; a++)
- {
- if (a==0 || p[l][a]>=best){tb=a;best=p[l][a];}
- }
- for (a=l; a>0; a--)
- {
- int p2=s[a-1][1];
- aln[0][p2]=aln[1][p2]=translate[tb];
-
- tb=t[a][tb];
- }
-
-
- free_int (p, -1);
- free_int (s, -1);
- free_int (t, -1);
- free_int (mat, -1);
- free_int (tran, -1);
- vfree (translate);
- return aln;
-}
-float* analyze_overaln ( Alignment *iA, Alignment *iB, char *mode, int filter, int f, int p1,int p2, int p3)
-{
- Alignment *C, *D;
- Alignment *A, *B;
- OveralnP *F;
-
- F=vcalloc (1, sizeof (OveralnP));
- F->p1=p1;
- F->p2=p2;
- F->p3=p3;
- F->f=f;
- F->t=filter;
- sprintf (F->mode, "%s", mode);
-
-
- float *r;
- A=copy_aln (iA, NULL);
- B=copy_aln (iB, NULL);
-
- C=aln2gap_cache (A,0);
- A=filter_aln_upper_lower (A, C, 0, 0);
- D=aln2clean_pw_aln (B, F);
- r=aln2pred (A,D,mode);
- free_aln (C);
- free_aln (D);
- free_aln (A);
- free_aln (B);
- return r;
-}
-float* aln2pred ( Alignment *A, Alignment*B, char *mode)
-{
- int a, b, c, d, i, l, salp, s, n;
- static char **list, *buf1, *buf2, *alp, *alp_lu;
- static int ***r;
- int T, N;
- int fp, fn, tn, tp;
- int tfp, tfn, ttn, ttp;
- float sp, sn, sen2, best, result;
- int print=1;
- float *fresult;
-
- fresult=vcalloc ( 3, sizeof (float));
-
- if ( mode && strstr (mode, "case"))
- {
- A=aln2case_aln (A,"u","l");
- B=aln2case_aln (B,"u","l");
- }
-
- if (mode && strstr (mode, "printaln"))
- {
- Sequence *S;
- Alignment *C;
- S=aln2seq (A);
- C=copy_aln (B, NULL);
- for (a=0; a<B->nseq; a++)
- {
- i=name_is_in_list (C->name[a], S->name, S->nseq, 100);
- if ( i==-1)
- for (b=0; b<C->len_aln; b++) C->seq_al[a][b]='-';
- else
- for (d=0,b=0; b<C->len_aln; b++)
- {
- if ( !is_gap (C->seq_al[a][b]))
- {
- if (C->seq_al[a][b]==S->seq[i][d])C->seq_al[a][b]=toupper(C->seq_al[a][b]);
- d++;
- }
- }
- }
- print_aln (C);
- }
-
- vfree (alp);vfree (alp_lu);
- alp=vcalloc ( 256, sizeof (char));
- alp_lu=vcalloc ( 256, sizeof (char));
-
- for (c=0; c<2; c++)
- {
- Alignment *AL;
- AL=(c==0)?A:B;
- for (salp=0,a=0; a<AL->nseq; a++)
- {
- for (b=0; b<AL->len_aln; b++)
- {
- c=AL->seq_al[a][b];
- if (!is_gap(c) && !alp[c])
- {
- salp++;
- alp_lu[salp]=c;
- alp[c]=salp;
- }
- }
- }
- }
-
- vfree (buf1); vfree(buf2);
- buf1=vcalloc ( A->len_aln+1, sizeof (char));
- buf2=vcalloc ( B->len_aln+1, sizeof (char));
-
- free_arrayN ((void **)r, 3);
- r=declare_arrayN(3, sizeof (int),A->nseq,salp+1,salp+1);
- free_char ( list, -1);
- list=declare_char ( A->nseq, 100);
- for (n=0,a=0; a< A->nseq; a++)
- {
- for ( b=0; b<B->nseq; b++)
- {
- if ( strm (A->name[a], B->name[b]))
- {
- sprintf ( buf1, "%s", A->seq_al[a]);
- sprintf ( buf2, "%s", B->seq_al[b]);
- ungap (buf1); ungap (buf2);
- if ((l=strlen (buf1))!=strlen (buf2))continue;
- else
- {
- sprintf ( list[n], "%s", A->name[a]);
- for (c=0; c<l; c++)
- {
- int c1, c2;
- c1=buf1[c];
- c2=buf2[c];
- r[n][alp[c1]][alp[c2]]++;
- }
- n++;
- }
- }
- }
- }
-
-
-
- for ( s=1; s<=salp; s++)
- {
- char type[4];
- sprintf (type, "_%c_", alp_lu[s]);
- ttp=ttn=tfp=tfn=0;
- for (a=0; a<n; a++)
- {
- tp=tn=fp=fn=0;
- for (b=1; b<=salp; b++)
- {
- for (c=1; c<=salp; c++)
- {
- if ( b==s && c==s) tp+=r[a][b][c];
- else if ( b==s && c!=s)fn+=r[a][b][c];
- else if ( b!=s && c==s)fp+=r[a][b][c];
- else if ( b!=s && b!=s)tn+=r[a][b][c];
- }
-
- }
-
- ttp+=tp;
- ttn+=tn;
- tfp+=fp;
- tfn+=fn;
- rates2sensitivity (tp, tn, fp, fn, &sp, &sn, &sen2, &best);
- if ( mode && strstr (mode, "printstat"))fprintf ( stdout, ">%s S=%c sp=%6.2f sn=%6.2f sen2=%6.2f best=%6.2f\n", list[a],alp_lu[s],sp, sn, sen2, best);
- }
-
- rates2sensitivity (ttp, ttn, tfp, tfn, &sp, &sn, &sen2, &best);
- if (mode && strstr (mode, "printstat"))fprintf ( stdout, ">TOT S=%c sp=%6.2f sn=%6.2f re=%6.2f best=%6.2f\n", alp_lu[s],sp, sn, sen2, best);
-
- if ( mode && strstr (mode, type))
- {
- fresult[0]=sn;
- fresult[1]=sp;
- fresult[2]=sen2;
- }
- }
- return fresult;
-}
-
-Alignment * mark_exon_boundaries (Alignment *A, Alignment *E)
-{
- char *buf, *buf2;
- int a, b, c, i, l;
-
- buf2=vcalloc ( E->len_aln+1, sizeof (char));
- buf =vcalloc ( E->len_aln+1, sizeof (char));
-
- for (a=0; a< A->nseq; a++)
- {
- i=name_is_in_list (A->name[a], E->name, E->nseq, 100);
- if ( i==-1) continue;
- sprintf (buf, "%s", E->seq_al[i]);
- ungap (buf);
- l=strlen (buf);
- //clean buf2
- for (c=0, b=0; b<l; b++)if (buf[b]!='o' && buf[b]!='b' && buf[b]!='j')buf2[c++]=toupper(buf[b]);
- buf2[c]='\0';
-
- //lowercase the boundaries of buf2;
- for ( c=0,b=0; b<l; b++)
- {
- //ENSEMBL: o: 0, b:1 j:2
- if (buf[b]=='b' || buf[b]=='o' && c>=1)buf2[c-1]=tolower(buf2[c-1]);
- else if (buf[b]=='j' &&c<l)buf2[c+1]=tolower(buf2[c+1]);
- else c++;
- }
-
- for (c=0,b=0; b<A->len_aln; b++)
- {
- if (!is_gap(A->seq_al[a][b]))
- {
- A->seq_al[a][b]=buf2[c++];
- }
- }
- }
- vfree (buf);
- vfree (buf2);
- return A;
-}
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-/******************************COPYRIGHT NOTICE*******************************/
-/*© Centro de Regulacio Genomica */
-/*and */
-/*Cedric Notredame */
-/*Fri Feb 18 08:27:45 CET 2011 - Revision 596. */
-/*All rights reserved.*/
-/*This file is part of T-COFFEE.*/
-/**/
-/* T-COFFEE is free software; you can redistribute it and/or modify*/
-/* it under the terms of the GNU General Public License as published by*/
-/* the Free Software Foundation; either version 2 of the License, or*/
-/* (at your option) any later version.*/
-/**/
-/* T-COFFEE is distributed in the hope that it will be useful,*/
-/* but WITHOUT ANY WARRANTY; without even the implied warranty of*/
-/* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the*/
-/* GNU General Public License for more details.*/
-/**/
-/* You should have received a copy of the GNU General Public License*/
-/* along with Foobar; if not, write to the Free Software*/
-/* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA*/
-/*............................................... |*/
-/* If you need some more information*/
-/* cedric.notredame@europe.com*/
-/*............................................... |*/
-/**/
-/**/
-/* */
-/******************************COPYRIGHT NOTICE*******************************/
git://source.jalview.org / jabaws.git / blobdiff