00001 #include "log.h"
00002 #include "format.h"
00003 #include "util.h"
00004 #include "gfr.h"
00005 #include "geneFusionsConfig.h"
00006
00007
00008
00009 int main (int argc, char *argv[])
00010 {
00011 GfrEntry *currGE;
00012 Array kgXrefs;
00013 Stringa buffer;
00014 int count;
00015
00016 buffer = stringCreate (100);
00017 stringPrintf (buffer,"%s/%s",ANNOTATION_DIR,KNOWN_GENE_XREF_FILENAME);
00018 kgXrefs = util_readKnownGeneXrefs (string (buffer));
00019 arraySort (kgXrefs,(ARRAYORDERF)sortKgXrefsByTranscriptName);
00020 stringDestroy (buffer);
00021
00022 count = 0;
00023 gfr_init ("-");
00024 gfr_addNewColumnType (GFR_COLUMN_NAME_GENE_SYMBOL_TRANSCRIPT1);
00025 gfr_addNewColumnType (GFR_COLUMN_NAME_GENE_SYMBOL_TRANSCRIPT2);
00026 gfr_addNewColumnType (GFR_COLUMN_NAME_DESCRIPTION_TRANSCRIPT1);
00027 gfr_addNewColumnType (GFR_COLUMN_NAME_DESCRIPTION_TRANSCRIPT2);
00028 puts (gfr_writeHeader ());
00029 while (currGE = gfr_nextEntry ()){
00030 transcript2geneSymbolAndGeneDescription (kgXrefs,currGE->nameTranscript1,&currGE->geneSymbolTranscript1,&currGE->descriptionTranscript1);
00031 transcript2geneSymbolAndGeneDescription (kgXrefs,currGE->nameTranscript2,&currGE->geneSymbolTranscript2,&currGE->descriptionTranscript2);
00032 puts (gfr_writeGfrEntry (currGE));
00033 count++;
00034 }
00035 gfr_deInit ();
00036 warn ("%s_numGfrEntries: %d",argv[0],count);
00037 return 0;
00038 }
00039
