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("<b>Ensembl Transcript Id: </b>"); if (ensemblIdUrl != NULL) printf("<a href=\"%s%s\" target=\"_blank\">%s</a><br>", ensemblIdUrl,name,name); else printf("%s<br>",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("<b>Gene Symbol:"); - if (sameString(gp->name2, "noXref")) + if ((strlen(gp->name2) < 1) || (sameString(gp->name2, "noXref"))) printf("</b> none<br>\n"); else printf("</b> %s<br>\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("<B>Ensembl Gene Link: </B>"); - if (sameString(gpList->name2, "noXref")) + if ((strlen(gpList->name2) < 1) || sameString(gpList->name2, "noXref")) printf("none<BR>\n"); else printf("<A HREF=\"%s/geneview?gene=%s\" " "target=_blank>%s</A><BR>", ensUrl, gpList->name2, gpList->name2); } genePredFreeList(&gpList); printf("<B>Ensembl Transcript: </B>"); printf("<A HREF=\"%s/transview?transcript=%s\" " "target=_blank>", ensUrl, shortItemName); printf("%s</A><br>", itemName); if (hTableExists(database, "superfamily")) { sqlSafefFrag(cond_str, sizeof(cond_str), "transcript_name='%s'", shortItemName);