+++ /dev/null
-/********* Sequence input routines for CLUSTAL W *******************/
-/* DES was here. FEB. 1994 */
-/* Now reads PILEUP/MSF and CLUSTAL alignment files */
-
-#include <stdio.h>
-#include <string.h>
-#include <ctype.h>
-#include <stdlib.h>
-#include "io_lib_header.h"
-#include "util_lib_header.h"
-#include "define_header.h"
-
-/*
-* Prototypes
-*/
-
-extern Boolean linetype(char *,char *);
-extern Boolean blankline(char *);
-extern void warning(char *,...);
-extern void error(char *,...);
-extern char * rtrim(char *);
-extern char * blank_to_(char *);
-extern void getstr(char *,char *);
-
-void fill_chartab(void);
-
-
-static void get_seq(char *,char *,int *,char *);
-static void get_clustal_seq(char *,char *,int *,char *,int);
-static void get_msf_seq(char *,char *,int *,char *,int);
-static void check_infile(int *);
-
-
-
-
-static int count_clustal_seqs(void);
-static int count_msf_seqs(void);
-
-/*
- * Global variables
- */
-
-static FILE *fin;
-
-
-char *amino_acid_codes = "ABCDEFGHIKLMNPQRSTUVWXYZ-"; /* DES */
-char *nucleic_acid_order = "ACGTUN";
-static int seqFormat;
-static char chartab[128];
-
-void fill_chartab(void) /* Create translation and check table */
-{
- register int i;
- register int c;
-
-
- for(i=0;i<128;chartab[i++]=0);
- for(i=0,c=0;c<=amino_acid_codes[i];i++)
- chartab[c]=chartab[tolower(c)]=c;
-
-}
-
-static void get_msf_seq(char *sname,char *seq,int *len,char *tit,int seqno)
-/* read the seqno_th. sequence from a PILEUP multiple alignment file */
-{
- static char *line;
- int i,j,k;
- unsigned char c;
- if ( !line)line=vcalloc ( (MAXLINE+1), sizeof (char));
-
- fseek(fin,0,0); /* start at the beginning */
-
- *len=0; /* initialise length to zero */
- for(i=0;;i++) {
- if(fgets(line,MAXLINE+1,fin)==NULL) return; /* read the title*/
- if(linetype(line,"/") ) break; /* lines...ignore*/
- }
-
- while (fgets(line,MAXLINE+1,fin) != NULL) {
- if(!blankline(line)) {
-
- for(i=1;i<seqno;i++) fgets(line,MAXLINE+1,fin);
- for(j=0;j<=strlen(line);j++) if(line[j] != ' ') break;
- for(k=j;k<=strlen(line);k++) if(line[k] == ' ') break;
- strncpy(sname,line+j,MIN(MAXNAMES,k-j));
- sname[MIN(MAXNAMES,k-j)]=EOS;
- rtrim(sname);
- blank_to_(sname);
-
- for(i=k;*len < SEQ_MAX_LEN;i++) {
- c=line[i];
- if(c == '.') c = '-';
- if(c == '*') c = 'X';
- if(c == '\n' || c == EOS) break; /* EOL */
- if( (c=chartab[c])) seq[++(*len)]=c;
- }
- if(*len == SEQ_MAX_LEN) return;
-
- for(i=0;;i++) {
- if(fgets(line,MAXLINE+1,fin)==NULL) return;
- if(blankline(line)) break;
- }
- }
- }
-}
-
-
-static void get_clustal_seq(char *sname,char *seq,int *len,char *tit,int seqno)
-/* read the seqno_th. sequence from a clustal multiple alignment file */
-{
- static char *line;
- int i,j;
- unsigned char c;
- if ( !line)line=vcalloc ( (MAXLINE+1), sizeof (char));
- fseek(fin,0,0); /* start at the beginning */
-
- *len=0; /* initialise length to zero */
- fgets(line,MAXLINE+1,fin); /* read the title line...ignore it */
-
- while (fgets(line,MAXLINE+1,fin) != NULL) {
- if(!blankline(line)) {
-
- for(i=1;i<seqno;i++) fgets(line,MAXLINE+1,fin);
- for(j=0;j<=strlen(line);j++) if(line[j] != ' ') break;
- strncpy(sname,line+j,MAXNAMES-j); /* remember entryname */
- sname[MAXNAMES]=EOS;
- rtrim(sname);
- blank_to_(sname);
-
- for(i=14;*len < SEQ_MAX_LEN;i++) {
- c=line[i];
- if(c == '\n' || c == EOS) break; /* EOL */
- if( (c=chartab[c])) seq[++(*len)]=c;
- }
- if(*len == SEQ_MAX_LEN) return;
-
- for(i=0;;i++) {
- if(fgets(line,MAXLINE+1,fin)==NULL) return;
- if(blankline(line)) break;
- }
- }
- }
-}
-
-
-static void get_seq(char *sname,char *seq,int *len,char *tit)
-{
- static char *line;
- int i, offset, c=0;
-
- if ( !line)line=vcalloc ( (MAXLINE+1), sizeof (char));
- switch(seqFormat) {
-
-/************************************/
- case EMBLSWISS:
- while( !linetype(line,"ID") )
- fgets(line,MAXLINE+1,fin);
-
- for(i=5;i<=strlen(line);i++) /* DES */
- if(line[i] != ' ') break;
- strncpy(sname,line+i,MAXNAMES); /* remember entryname */
- sname[MAXNAMES]=EOS;
- rtrim(sname);
- blank_to_(sname);
- fprintf ( stderr, "\n%s", sname);
- while( !linetype(line,"SQ") )
- fgets(line,MAXLINE+1,fin);
-
- *len=0;
- while(fgets(line,MAXLINE+1,fin)) {
- for(i=0;*len < SEQ_MAX_LEN;i++) {
- c=line[i];
- if(c == '\n' || c == EOS || c == '/')
- break; /* EOL */
- if( (c=chartab[c]))
- seq[++(*len)]=c;
- }
- if(*len == SEQ_MAX_LEN || c == '/') break;
- }
- break;
-
-/************************************/
- case PIR:
- while(*line != '>')
- {
-
- fgets(line,MAXLINE+1,fin);
- }
- for(i=4;i<=strlen(line);i++) /* DES */
- if(line[i] != ' ') break;
- strncpy(sname,line+i,MAXNAMES); /* remember entryname */
- sname[MAXNAMES]=EOS;
- rtrim(sname);
- blank_to_(sname);
-
- fgets(line,MAXLINE+1,fin);
- strncpy(tit,line,MAXTITLES);
- tit[MAXTITLES]=EOS;
- i=strlen(tit);
- if(tit[i-1]=='\n') tit[i-1]=EOS;
-
- *len=0;
- while(fgets(line,MAXLINE+1,fin)) {
-
- for(i=0;*len < SEQ_MAX_LEN;i++)
- {
- c=line[i];
- if(c == '\n' || c == EOS || c == '*')
- break; /* EOL */
-
- if( (c=chartab[c]))
- seq[++(*len)]=c;
-
- }
- if(*len == SEQ_MAX_LEN || c == '*') break;
- }
- break;
-/***********************************************/
- case (PEARSON):
-
- while(*line != '>')
- {
- fgets(line,MAXLINE+1,fin);
- }
- for(i=1;i<=strlen(line);i++) /* DES */
- if(line[i] != ' ') break;
- strncpy(sname,line+i,MAXNAMES); /* remember entryname */
- sname[MAXNAMES]=EOS;
- rtrim(sname);
- blank_to_(sname);
-
- *tit=EOS;
-
- *len=0;
- while(fgets(line,MAXLINE+1,fin))
- {
- for(i=0;*len < SEQ_MAX_LEN;i++)
- {
- c=line[i];
- if(c == '\n' || c == EOS || c == '>')
- break; /* EOL */
-
- if( (c=chartab[c]))
- {seq[++(*len)]=c;
- }
- }
- if(*len == SEQ_MAX_LEN || c == '>') break;
- }
- break;
-/**********************************************/
- case GDE:
-
- while(*line != '#' ||*line != '%' )
- fgets(line,MAXLINE+1,fin);
-
-
-
-
- for (i=1;i<=MAXNAMES;i++) {
- if (line[i] == '(' || line[i] == '\n')
- {
- i--;
- break;
- }
- sname[i-1] = line[i];
- }
- sname[i]=EOS;
- offset=0;
- if (sname[i-1] == '(') sscanf(&line[i],"%d",&offset);
- else offset = 0;
- for(i=MAXNAMES-1;i > 0;i--)
- if(isspace(sname[i])) {
- sname[i]=EOS;
- break;
- }
- blank_to_(sname);
-
-
- *tit=EOS;
-
- *len=0;
- for (i=0;i<offset;i++) seq[++(*len)] = '-';
- while(fgets(line,MAXLINE+1,fin)) {
- if(*line == '%' || *line == '#' || *line == '"') break;
- for(i=0;*len < SEQ_MAX_LEN;i++) {
- c=line[i];
- if(c == '\n' || c == EOS)
- break; /* EOL */
-
- if( (c=chartab[c]))
- seq[++(*len)]=c;
- }
- if(*len == SEQ_MAX_LEN) break;
- }
- break;
-/***********************************************/
- }
-
- if(*len == SEQ_MAX_LEN)
- warning("Sequence %s truncated to %d residues",
- sname,(pint)SEQ_MAX_LEN);
-
- seq[*len+1]=EOS;
-}
-
-
-int readseqs(char *saga_file,char ***SAGA_SEQ, char*** SAGA_NAMES, int ***SAGA_LEN) /*first_seq is the #no. of the first seq. to read */
-{
-
- static char *line;
- static char *seq1;
- static char *sname1;
- static char *title;
- int i,j,no_seqs;
- static int l1;
- int a;
- int b, l;
- int first_seq=0;
-
- if ( !line) line=vcalloc ( (FILENAMELEN+1), sizeof (char));
- if ( !seq1) seq1=vcalloc ( (SEQ_MAX_LEN+2), sizeof (char));
- if ( !sname1)sname1=vcalloc ( (MAXNAMES+1), sizeof (char));
- if ( !title)title=vcalloc ( (MAXTITLES+1), sizeof (char));
-
- fill_chartab();
-
- fin=vfopen(saga_file,"r");
-
-
- no_seqs=0;
- check_infile(&no_seqs);
-
- if(no_seqs == 0)
- return 0; /* return the number of seqs. (zero here)*/
-
- SAGA_SEQ[0]= vcalloc ( no_seqs, sizeof ( char*));
- SAGA_NAMES[0]= vcalloc ( no_seqs, sizeof ( char*));
- SAGA_LEN[0]= declare_int ( no_seqs,3);
-
-
- for(i=first_seq;i<=first_seq+no_seqs-1;i++)
- { /* get the seqs now*/
- if(seqFormat == CLUSTAL)
- get_clustal_seq(sname1,seq1,&l1,title,i-first_seq+1);
- if(seqFormat == MSF)
- get_msf_seq(sname1,seq1,&l1,title,i-first_seq+1);
- else
- get_seq(sname1,seq1,&l1,title);
-
- if(l1 > SEQ_MAX_LEN)
- {
- error("Sequence too long. Maximum is %d",(pint)SEQ_MAX_LEN);
- return 0; /* also return zero if too many */
- }
-
-
-
- for ( a=0; a<l1; a++)
- seq1[a]=seq1[a+1];
- seq1[l1]='\0';
-
- (SAGA_SEQ[0])[i]=vcalloc ( strlen ( seq1)+1, sizeof ( char));
- (SAGA_NAMES[0])[i]=vcalloc ( strlen ( sname1)+1, sizeof ( char));
-
- l1=strlen (seq1);
- (SAGA_LEN[0])[i][0]=l1;
- (SAGA_SEQ[0])[i][l1]='\0';
-
- sprintf ( (SAGA_SEQ[0])[i], "%s", seq1);
- sprintf ( (SAGA_NAMES[0])[i], "%s", sname1);
-
- l=strlen (SAGA_NAMES[0][i]);
- for ( b=0; b< l; b++)
- {
- if ( isspace(SAGA_NAMES[0][i][b])){SAGA_NAMES[0][i][b]='\0';break;}
- }
-
-
- }
-
- fclose(fin);
-/*
- JULIE
- check sequence names are all different - otherwise phylip tree is
- confused.
-*/
- for(i=first_seq;i<=first_seq+no_seqs-1;i++) {
- for(j=i+1;j<=first_seq+no_seqs-1;j++) {
- if (strncmp((SAGA_NAMES[0])[i],(SAGA_NAMES[0])[j],MAXNAMES) == 0) {
- error("Multiple sequences found with same name (first %d chars are significant)", MAXNAMES);
- return -1;
- }
- }
- }
-
- return no_seqs; /* return the number of seqs. read in this call */
-}
-
-
-
-
-static void check_infile(int *nseqs)
-{
- static char *line;
- int i;
-
- if ( !line)line=vcalloc ( (MAXLINE+1), sizeof (char));
-
- for ( i=0; i<=MAXLINE; i++)line[i]='a';
- *nseqs=0;
- while (fgets(line,MAXLINE+1,fin) != NULL) {
- if ((*line != '\n') && (*line != ' ') && (*line != '\t'))
- break;
- }
-
- for(i=0;i<=6;i++) line[i] = toupper(line[i]);
-
- if( linetype(line,"ID") ) { /* EMBL/Swiss-Prot format ? */
- seqFormat=EMBLSWISS;
- (*nseqs)++;
- }
- else if( linetype(line,"CLUSTAL") ) {
- seqFormat=CLUSTAL;
- }
- else if( linetype(line,"PILEUP") ) {
- seqFormat = MSF;
- }
- else if(*line == '>') { /* no */
- seqFormat=(line[3] == ';')?PIR:PEARSON; /* distinguish PIR and Pearson */
- (*nseqs)++;
- }
- else if((*line == '"') || (*line == '%') || (*line == '#')) {
- seqFormat=GDE; /* GDE format */
- if (*line == '%') {
- (*nseqs)++;
-
- }
- else if (*line == '#') {
- (*nseqs)++;
-
- }
- }
- else {
- seqFormat=UNKNOWN;
- return;
- }
-
- while(fgets(line,MAXLINE+1,fin) != NULL) {
- switch(seqFormat) {
- case EMBLSWISS:
- if( linetype(line,"ID") )
- (*nseqs)++;
- break;
- case PIR:
- case PEARSON:
- if( *line == '>' )
- (*nseqs)++;
- break;
- case GDE:
- if(( *line == '%' ) )
- (*nseqs)++;
- else if (( *line == '#') )
- (*nseqs)++;
- break;
- case CLUSTAL:
- *nseqs = count_clustal_seqs();
-/* DES */ /* fprintf(stdout,"\nnseqs = %d\n",(pint)*nseqs); */
- fseek(fin,0,0);
- return;
- break;
- case MSF:
- *nseqs = count_msf_seqs();
- fseek(fin,0,0);
- return;
- break;
- case USER:
- default:
- break;
- }
- }
- fseek(fin,0,0);
-}
-
-
-static int count_clustal_seqs(void)
-/* count the number of sequences in a clustal alignment file */
-{
- static char *line;
- int nseqs;
-
- if ( !line)line=vcalloc ( (MAXLINE+1), sizeof (char));
-
- while (fgets(line,MAXLINE+1,fin) != NULL) {
- if(!blankline(line)) break; /* Look for next non- */
- } /* blank line */
- nseqs = 1;
-
- while (fgets(line,MAXLINE+1,fin) != NULL) {
- if(blankline(line)) return nseqs;
- nseqs++;
- }
-
- return 0; /* if you got to here-funny format/no seqs.*/
-}
-
-static int count_msf_seqs(void)
-{
-/* count the number of sequences in a PILEUP alignment file */
-
- static char *line;
- int nseqs;
-
- if ( !line)line=vcalloc ( (MAXLINE+1), sizeof (char));
-
- while (fgets(line,MAXLINE+1,fin) != NULL) {
- if(linetype(line,"/")) break;
- }
-
- while (fgets(line,MAXLINE+1,fin) != NULL) {
- if(!blankline(line)) break; /* Look for next non- */
- } /* blank line */
- nseqs = 1;
-
- while (fgets(line,MAXLINE+1,fin) != NULL) {
- if(blankline(line)) return nseqs;
- nseqs++;
- }
-
- return 0; /* if you got to here-funny format/no seqs.*/
-}
-
-
-
-/*********************************COPYRIGHT NOTICE**********************************/
-/*© Centro de Regulacio Genomica */
-/*and */
-/*Cedric Notredame */
-/*Tue Oct 27 10:12:26 WEST 2009. */
-/*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**********************************/
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