0666a244c02cbb2638c35e82227a661594e8edcc
cline
  Tue Feb 15 14:40:01 2011 -0800
Updated the code that checks for selenocysteine exceptions, to match some apparent changes in the format of the selenocysteine exception entries
diff --git src/hg/lib/genbank.c src/hg/lib/genbank.c
index 8c42d68..a831c8e 100644
--- src/hg/lib/genbank.c
+++ src/hg/lib/genbank.c
@@ -192,31 +192,31 @@
 	struct hash **retSelenocysteineHash, struct hash **retAltStartHash)
 /* Will read a genbank exceptions file, and return two hashes parsed out of
  * it filled with the accessions having the two exceptions we can handle, 
  * selenocysteines, and alternative start codons. */
 {
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 struct hash *scHash = *retSelenocysteineHash  = hashNew(0);
 struct hash *altStartHash = *retAltStartHash = hashNew(0);
 char *row[3];
 while (lineFileRowTab(lf, row))
     {
     struct lineFile *lf = lineFileOpen(fileName, TRUE);
     char *row[3];
     while (lineFileRow(lf, row))
         {
-	if (sameString(row[1], "selenocysteine") && sameString(row[2], "yes"))
+	if (sameString(row[1], "translExcept") && (stringIn("aa:Sec", row[2]) != NULL))
 	    hashAdd(scHash, row[0], NULL);
 	if (sameString(row[1], "exception") 
 		&& sameString(row[2], "alternative_start_codon"))
 	    hashAdd(altStartHash, row[0], NULL);
 	}
     }
 lineFileClose(&lf);
 }
 
 struct genbankCds genbankCdsToGenome(struct genbankCds* cds, struct psl *psl)
 /* Convert set cdsStart/end from mrna to genomic coordinates using an
  * alignment.  Returns a genbankCds object with genomic (positive strand)
  * coordinates */
 {
 // FIXME: this is used only by genePred code, but since  frame was added,