tools/data_tools/parser.c

   1 #include <stdio.h>
   2 #include <stdlib.h>
   3 #include <string.h>
   4
   5 #include "datastructures.h"
   6
   7 void 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    allGenes = malloc(sizeof(struct gene)*numGenes);
  38    struct gene *currentGene = gene_alloc();
  39
  40    int skippedLinesCounter = 0;
  41    int idx = 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 ( currentGene->start != -1)
  54             allGenes[idx] = currentGene;
  55             idx++;
  56
  57          currentGene = gene_alloc();
  58          currentGene->start = start;
  59          currentGene->stop = stop;
  60          currentGene->strand = (*strand);
  61          //printf("gene start/stop: %d/%d\n",start,stop);
  62          continue;
  63       }
  64
  65       if (strcmp(id,"exon")==0) {
  66          add_exon(currentGene,start,stop);
  67          //printf("exon start/stop: %d/%d\n",start,stop);
  68          continue;
  69       }
  70
  71       if (strcmp(id,"pseudogene")==0) {
  72          if ( currentGene->start != -1)
  73             allGenes[idx] = currentGene;
  74             idx++;
  75       }
  76    }
  77
  78    if ( currentGene->start != -1)
  79       allGenes[idx] = currentGene;
  80       idx++;
  81
  82    free(chr);
  83    free(blah);
  84    free(id);
  85    free(desc);
  86    free(xy);
  87    free(strand);
  88    free(xz);
  89 }