4fe12bd2fbd2fabf3b5c9ca26f047b8a24af733d
hiram
Fri Mar 7 11:46:03 2014 -0800
were not correctly identifying on name2 in ensGene table refs #12796
diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c
index c9adb68..6bafc27 100644
--- src/hg/hgc/hgc.c
+++ src/hg/hgc/hgc.c
@@ -2491,31 +2491,31 @@
{
char *ensemblIdUrl = trackDbSetting(tdb, "ensemblIdUrl");
printf("Ensembl Transcript Id: ");
if (ensemblIdUrl != NULL)
printf("%s
", ensemblIdUrl,name,name);
else
printf("%s
",name);
}
if (gp->name2 != NULL && strlen(trimSpaces(gp->name2))> 0)
{
/* in Ensembl gene info downloaded from ftp site, sometimes the
name2 field is populated with "noXref" because there is
no alternate name. Replace this with "none" */
printf("Gene Symbol:");
- if (sameString(gp->name2, "noXref"))
+ if ((strlen(gp->name2) < 1) || (sameString(gp->name2, "noXref")))
printf(" none
\n");
else
printf(" %s
\n",gp->name2);
}
char *ensemblSource = NULL;
if (sameString("ensGene", table))
{
if (hTableExists(database, "ensemblSource"))
{
sqlSafef(query, sizeof(query),
"select source from ensemblSource where name='%s'", name);
ensemblSource = sqlQuickString(conn, query);
}
}
if ((gp->exonFrames != NULL) && (!genbankIsRefSeqNonCodingMRnaAcc(gp->name)))
@@ -8425,31 +8425,31 @@
char *ensemblSource = NULL;
if (hTableExists(database, "ensemblSource"))
{
sqlSafef(query, sizeof(query), "select source from ensemblSource where name='%s'", itemName);
ensemblSource = sqlQuickString(conn, query);
}
boolean nonCoding = FALSE;
sqlSafefFrag(query, sizeof(query), "name = \"%s\"", itemName);
struct genePred *gpList = genePredReaderLoadQuery(conn, "ensGene", query);
if (gpList && gpList->name2)
{
if (gpList->cdsStart == gpList->cdsEnd)
nonCoding = TRUE;
printf("Ensembl Gene Link: ");
- if (sameString(gpList->name2, "noXref"))
+ if ((strlen(gpList->name2) < 1) || sameString(gpList->name2, "noXref"))
printf("none
\n");
else
printf("%s
", ensUrl, gpList->name2, gpList->name2);
}
genePredFreeList(&gpList);
printf("Ensembl Transcript: ");
printf("", ensUrl, shortItemName);
printf("%s
", itemName);
if (hTableExists(database, "superfamily"))
{
sqlSafefFrag(cond_str, sizeof(cond_str), "transcript_name='%s'", shortItemName);