tools/data_tools/parser.c

   1 #include <stdio.h>
   2 #include <stdlib.h>
   3 #include <string.h>
   4
   5 #include "datastructures.h"
   6
   7 int parse_gff(char *filename, FILE* fid,struct gene*** allGenes) {
   8
   9    int buffer_size = 256;
  10    char* chr   = malloc(sizeof(char)*buffer_size);
  11    char* blah  = malloc(sizeof(char)*buffer_size);
  12    char* id    = malloc(sizeof(char)*buffer_size);
  13    char* desc    = malloc(sizeof(char)*buffer_size);
  14    int start  = 0;
  15    int stop   = 0;
  16    char* xy    = malloc(sizeof(char)*4);
  17    char* strand = malloc(sizeof(char)*4);
  18    char* xz    = malloc(sizeof(char)*4);
  19
  20    // do one pass through the gff line to determine the number of
  21    // genes
  22    int numGenes = 0;
  23
  24    int status = 0;
  25    while(1) {
  26       status = fscanf(fid,"%s\t%s\t%s\t%d\t%d\t%c\t%c\t%c\t%s\n",chr,blah,id,&start,&stop,xy,strand,xz,desc);
  27       if(status == EOF)
  28          break;
  29
  30       if ( status > 5 && strcmp(id,"gene")==0)
  31          numGenes++;
  32    }
  33    freopen(filename,"r",fid);
  34
  35    //printf("Found %d genes!\n",numGenes);
  36
  37    int idx = 0;
  38    (*allGenes) = malloc(sizeof(struct gene*)*numGenes);
  39    (*allGenes)[idx] = NULL;
  40
  41    int skippedLinesCounter = 0;
  42    while(1) {
  43       status = fscanf(fid,"%s\t%s\t%s\t%d\t%d\t%c\t%c\t%c\t%s\n",chr,blah,id,&start,&stop,xy,strand,xz,desc);
  44       if(status == EOF)
  45          break;
  46
  47       if (status < 7) {
  48          skippedLinesCounter++;
  49          continue;
  50       }
  51
  52       if (strcmp(id,"gene")==0) {
  53          if ( (*allGenes)[idx] !=NULL )
  54             idx++;
  55
  56          (*allGenes)[idx] = gene_alloc();
  57          (*allGenes)[idx]->start = start;
  58          (*allGenes)[idx]->stop = stop;
  59          (*allGenes)[idx]->strand = (*strand);
  60          //printf("gene start/stop: %d/%d\n",start,stop);
  61          continue;
  62       }
  63
  64       if (strcmp(id,"exon")==0) {
  65          add_exon((*allGenes)[idx],start,stop);
  66          //printf("exon start/stop: %d/%d\n",start,stop);
  67          continue;
  68       }
  69
  70       if (strcmp(id,"pseudogene")==0) {
  71          if ( (*allGenes)[idx] !=NULL )
  72             idx++;
  73       }
  74    }
  75
  76    if ( (*allGenes)[idx] !=NULL )
  77       idx++;
  78
  79    //printf("allGenes[0] is %d\n",(*allGenes)[0]);
  80    //printf("allGenes[1] is %d\n",(*allGenes)[1]);
  81    //printf("Skipped %d lines.\n",skippedLinesCounter);
  82
  83    free(chr);
  84    free(blah);
  85    free(id);
  86    free(desc);
  87    free(xy);
  88    free(strand);
  89    free(xz);
  90
  91    return numGenes;
  92 }
  93