8b7a946061426398e6c6253e3478dd1ac84450ff
kent
  Fri Dec 18 16:42:59 2020 -0800
Adding geneName parameter

diff --git src/hg/txGraph/txgToGeneBed/txgToGeneBed.c src/hg/txGraph/txgToGeneBed/txgToGeneBed.c
index 0a0aea7..fac92df 100644
--- src/hg/txGraph/txgToGeneBed/txgToGeneBed.c
+++ src/hg/txGraph/txgToGeneBed/txgToGeneBed.c
@@ -1,30 +1,30 @@
 /* txgToGeneBed - Convert txg to a simple bed with one block and the most common gene name.. */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "txGraph.h"
 #include "obscure.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "txgToGeneBed - Convert txg to a simple bed with one block and the most common gene name.\n"
   "usage:\n"
-  "   txgToGeneBed in.txg txToGene.tsv	out.bed\n"
+  "   txgToGeneBed in.txg txToGene.tsv geneToName.tsv out.bed\n"
   "options:\n"
   "   -xxx=XXX\n"
   );
 }
 
 /* Command line validation table. */
 static struct optionSpec options[] = {
    {NULL, 0},
 };
 
 char *pickGene(struct txGraph *txg, struct hash *txToGeneHash)
 /* Pick out most commonly used name */
 {
 if (txg->sourceCount <= 2)  // If just one or two take first one
     return hashMustFindVal(txToGeneHash, txg->sources[0].accession);
@@ -37,39 +37,44 @@
     for (i=0; i<txg->sourceCount; ++i)
         {
 	char *gene = hashMustFindVal(txToGeneHash, txg->sources[i].accession);
 	int count = hashIncInt(geneHash, gene);
 	if (count > bestCount)
 	    {
 	    bestCount = count;
 	    bestGene = gene;
 	    }
 	}
     hashFree(&geneHash);
     return bestGene;
     }
 }
 
-void txgToGeneBed(char *inTxg, char *txToGeneFile, char *outBed)
+void txgToGeneBed(char *inTxg, char *txToGeneFile, char *geneToNameFile, char *outBed)
 /* txgToGeneBed - Convert txg to a simple bed with one block and the most common gene name.. */
 {
 struct hash *txToGeneHash = hashTwoColumnFile(txToGeneFile);
+struct hash *geneToNameHash = hashTwoColumnFile(geneToNameFile);
 struct txGraph *txgList = txGraphLoadAll(inTxg);
 FILE *f = mustOpen(outBed, "w");
 struct txGraph *txg;
 for (txg = txgList; txg != NULL; txg = txg->next)
     {
     char *gene = pickGene(txg, txToGeneHash);
-    fprintf(f, "%s\t%d\t%d\t%s\t0\t%s\n", txg->tName, txg->tStart, txg->tEnd,gene,txg->strand);
+    char *name = hashFindVal(geneToNameHash, gene);
+    if (name == NULL)
+        name = gene;
+    fprintf(f, "%s\t%d\t%d\t%s\t0\t%s\t%s\n", 
+	txg->tName, txg->tStart, txg->tEnd, gene, txg->strand, name);
     }
 carefulClose(&f);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
-if (argc != 4)
+if (argc != 5)
     usage();
-txgToGeneBed(argv[1], argv[2], argv[3]);
+txgToGeneBed(argv[1], argv[2], argv[3], argv[4]);
 return 0;
 }