00001 #include "log.h"
00002 #include "format.h"
00003 #include "gfr.h"
00004 #include <stdio.h>
00005
00006
00007
00008 int main (int argc, char *argv[])
00009 {
00010 GfrEntry *currGE;
00011 GfrInterRead *currGIR;
00012 int i;
00013 Stringa buffer;
00014 FILE *fp;
00015 int count;
00016
00017 count = 0;
00018 buffer = stringCreate (100);
00019 gfr_init ("-");
00020 puts (gfr_writeHeader ());
00021
00022 while (currGE = gfr_nextEntry ()){
00023 count++;
00024 if (strEqual (currGE->fusionType,"inter") || strEqual (currGE->fusionType,"trans") ) {
00025 puts (gfr_writeGfrEntry (currGE));
00026 continue;
00027 }
00028 stringPrintf (buffer,"%s.gff",currGE->id);
00029 fp = fopen (string (buffer),"w");
00030 if (fp == NULL) {
00031 die ("Unable to open GFF file");
00032 }
00033 fprintf (fp,"browser pack knownGene\n");
00034 fprintf (fp,"track name=\"%s\" visibility=2\n",currGE->id);
00035 for (i = 0; i < arrayMax (currGE->interReads); i++) {
00036 currGIR = arrp (currGE->interReads,i,GfrInterRead);
00037 fprintf (fp,"%s\tRNA_Seq\texon\t%d\t%d\t.\t.\t.\tTG%d\n",currGE->chromosomeTranscript1,currGIR->readStart1,currGIR->readEnd1,i);
00038 fprintf (fp,"%s\tRNA_Seq\texon\t%d\t%d\t.\t.\t.\tTG%d\n",currGE->chromosomeTranscript2,currGIR->readStart2,currGIR->readEnd2,i);
00039 }
00040 fclose (fp);
00041 puts (gfr_writeGfrEntry (currGE));
00042 }
00043 gfr_deInit ();
00044 stringDestroy (buffer);
00045 warn ("%s_numGfrEntries: %d",argv[0],count);
00046 return 0;
00047 }
00048
