binaries/src/tcoffee/t_coffee_source/dev1.c

   1 #include <stdio.h>
   2 #include <stdlib.h>
   3 #include <math.h>
   4 #include <stdarg.h>
   5 #include <string.h>
   6
   7 #include "io_lib_header.h"
   8 #include "util_lib_header.h"
   9 #include "define_header.h"
  10 #include "dp_lib_header.h"
  11 #include "dev1_lib_header.h"
  12
  13 //Insert functions here
  14 void aln2hitMat_help()
  15 {
  16         fprintf ( stdout, "\n+aln2hitMat| _MODE_    : how to compare the two positions of the alignment (default:id)");
  17         fprintf ( stdout, "\n.................id    : the sequence identity of those two positions");
  18         fprintf ( stdout, "\n.............pairscore : the pairwise score of the residues of those two positions");
  19         fprintf ( stdout, "\n+aln2hitMat| _MATRIX_  : matrix used for the comparison (idmat, blosum62mt, pam250mt.. default:blosum62mt)\n");
  20         exit (EXIT_SUCCESS);
  21 }
  22
  23 void aln2hitMat (Alignment *A, char *phitmat)
  24 {
  25         float **ffpHitScoreMatrix;
  26         int i, j, k, l, s;
  27         int nl = A->len_aln;
  28         int inseq = A->nseq;
  29         int itmpScore;
  30         char matrix[100];
  31         char mode[100];
  32         int isim_count, itotal_count, r1, r2;
  33
  34 //Initialization for files
  35         char *pcFileName = A->file[0];
  36         char prefix[200] ={0};
  37         char *hit_matrix_file = vcalloc(200, sizeof (char));
  38         char *hit_html_file = vcalloc(200, sizeof (char));
  39         int len = (strrchr(pcFileName,'.')?strrchr(pcFileName,'.')-pcFileName:strlen(pcFileName));
  40
  41         strncpy(prefix, pcFileName, len);
  42         sprintf(hit_matrix_file, "%s%s", prefix, "_aln.hit_matrix");
  43         sprintf(hit_html_file, "%s%s", prefix, ".alnhit_html");
  44
  45         if ( phitmat && strstr ( phitmat, "help"))
  46                 aln2hitMat_help();
  47
  48         if(phitmat == NULL) phitmat = vcalloc(1, sizeof(char)); //such that program could get default value
  49
  50         strget_param (phitmat, "_MODE_", "id", "%s", mode);
  51         strget_param (phitmat, "_MATRIX_", "blosum62mt", "%s", matrix);
  52
  53         fprintf ( stdout, "[START] aln to hit matrix\n");
  54         fprintf ( stdout, "        Mode:%s\n", mode);
  55         fprintf ( stdout, "        Matrix:%s\n", matrix);
  56
  57         int **mat = read_matrice(matrix);
  58
  59         ffpHitScoreMatrix=vcalloc (nl, sizeof (float*));
  60         for(i = 0; i < nl; i++)
  61                 ffpHitScoreMatrix[i]=vcalloc (nl-i, sizeof (float));
  62
  63         fprintf (stdout, "Process positions\n", i);
  64         for(i = 0; i < nl; i++)
  65         {
  66                 fprintf (stdout, "%d, ", i);
  67                 for(j = i; j < nl; j++)
  68                 {
  69                         if(strm (mode, "id"))
  70                                 ffpHitScoreMatrix[i][j-i]=generic_get_seq_sim (aln_column2string(A, i), aln_column2string(A, j), (A->cdna_cache)?A->cdna_cache[0]:NULL, matrix);
  71                         else if(strm (mode, "pairscore"))
  72                         {
  73                                 isim_count = itotal_count = 0;
  74                                 for (k=0; k< inseq; k++)
  75                                 {
  76                                         r1=tolower(A->seq_al[k][i]);
  77                                         if (is_gap(r1))continue;
  78                                         for (l=0; l< inseq; l++)
  79                                         {
  80                                                 r2=tolower(A->seq_al[l][j]);
  81                                                 if (is_gap (r2))continue;
  82                                                 s=mat[r2-'A'][r1-'A'];
  83                                                 s=(s<=0)?0:1;
  84                                                 isim_count += s;
  85                                                 itotal_count++;
  86                                         }
  87                                 }
  88                                 r1=(isim_count*100)/itotal_count;
  89                                 ffpHitScoreMatrix[i][j-i] = r1;
  90                         }
  91                         else
  92                                 aln2hitMat_help();
  93                 }
  94         }
  95         fprintf (stdout, "\n");
  96         output_hit_matrix(hit_matrix_file, ffpHitScoreMatrix, nl);
  97
  98 //Output Hit Score into color html
  99         output_hit_color_html  (A, ffpHitScoreMatrix, nl, hit_html_file);
 100         vfree(ffpHitScoreMatrix);
 101         vfree(hit_matrix_file);
 102         vfree(hit_html_file);
 103         fprintf ( stdout, "[END] aln to hit matrix\n");
 104 }
 105 /*********************************COPYRIGHT NOTICE**********************************/
 106 /*© Centro de Regulacio Genomica */
 107 /*and */
 108 /*Cedric Notredame */
 109 /*Tue Oct 27 10:12:26 WEST 2009. */
 110 /*All rights reserved.*/
 111 /*This file is part of T-COFFEE.*/
 112 /**/
 113 /*    T-COFFEE is free software; you can redistribute it and/or modify*/
 114 /*    it under the terms of the GNU General Public License as published by*/
 115 /*    the Free Software Foundation; either version 2 of the License, or*/
 116 /*    (at your option) any later version.*/
 117 /**/
 118 /*    T-COFFEE is distributed in the hope that it will be useful,*/
 119 /*    but WITHOUT ANY WARRANTY; without even the implied warranty of*/
 120 /*    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the*/
 121 /*    GNU General Public License for more details.*/
 122 /**/
 123 /*    You should have received a copy of the GNU General Public License*/
 124 /*    along with Foobar; if not, write to the Free Software*/
 125 /*    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA*/
 126 /*...............................................                                                                                      |*/
 127 /*  If you need some more information*/
 128 /*  cedric.notredame@europe.com*/
 129 /*...............................................                                                                                                                                     |*/
 130 /**/
 131 /**/
 132 /*      */
 133 /*********************************COPYRIGHT NOTICE**********************************/