src/hg/hgc/hgc.c 1.1522

Index: src/hg/hgc/hgc.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgc/hgc.c,v
retrieving revision 1.1521
retrieving revision 1.1522
diff -b -B -U 4 -r1.1521 -r1.1522
--- src/hg/hgc/hgc.c	17 Mar 2009 19:54:55 -0000	1.1521
+++ src/hg/hgc/hgc.c	26 Mar 2009 17:33:59 -0000	1.1522
@@ -8562,12 +8562,25 @@
 printGadDetails(tdb, item, FALSE);
 printTrackHtml(tdb);
 }
 
+char *gbCdnaGetDescription(struct sqlConnection *conn, char *acc)
+/* return mrna description, or NULL if not available. freeMem result */
+{
+char query[128];
+safef(query, sizeof(query),
+      "select description.name from gbCdnaInfo,description where (acc = '%s') and (gbCdnaInfo.description = description.id)", acc);
+char *desc = sqlQuickString(conn, query);
+if ((desc == NULL) || sameString(desc, "n/a") || (strlen(desc) == 0))
+    freez(&desc);
+return desc;
+}
+
 void printOmimGeneDetails(struct trackDb *tdb, char *itemName, boolean encode)
 /* Print details of an OMIM Gene entry. */
 {
 struct sqlConnection *conn = hAllocConn(database);
+struct sqlConnection *conn2 = hAllocConn(database);
 char query[256];
 struct sqlResult *sr;
 char **row;
 char *url = tdb->url;
@@ -8575,8 +8588,10 @@
 char *title1 = NULL;
 char *title2 = NULL;
 char *geneSymbols = NULL;
 char *chrom, *chromStart, *chromEnd;
+char *kgDescription = NULL;
+char *refSeq;
 
 chrom      = cartOptionalString(cart, "c");
 chromStart = cartOptionalString(cart, "o");
 chromEnd   = cartOptionalString(cart, "t");
@@ -8595,9 +8610,9 @@
     sqlFreeResult(&sr);
 
     /* get corresponding KG ID */
     safef(query, sizeof(query),
-          "select k.name from kgXref x, knownGene k where k.chrom='%s' and k.txStart=%s and k.txEnd=%s and k.name=x.kgId ",
+	  "select k.transcript from knownCanonical k where k.chrom='%s' and k.chromStart=%s and k.chromEnd=%s",
 	  chrom, chromStart, chromEnd);
     sr = sqlMustGetResult(conn, query);
     row = sqlNextRow(sr);
     if (row != NULL)
@@ -8668,8 +8683,21 @@
     	printf("<A HREF=\"%s%s&hgg_chrom=none\" target=_blank>",
 	       "../cgi-bin/hgGene?hgg_gene=", kgId);
     	printf("%s</A></B>: ", kgId);
 
+	safef(query, sizeof(query), "select refseq from kgXref where kgId='%s';", kgId);
+    	sr = sqlMustGetResult(conn, query);
+    	row = sqlNextRow(sr);
+    	if (row != NULL)
+	    {
+	    refSeq = strdup(row[0]);
+	    kgDescription = gbCdnaGetDescription(conn2, refSeq);
+	    }
+	sqlFreeResult(&sr);
+        hFreeConn(&conn2);
+
+	if (kgDescription == NULL)
+	{
     	safef(query, sizeof(query), "select description from kgXref where kgId='%s';", kgId);
     	sr = sqlMustGetResult(conn, query);
     	row = sqlNextRow(sr);
     	if (row != NULL)
@@ -8677,8 +8705,14 @@
 	    printf("%s", row[0]);
 	    }
 
 	sqlFreeResult(&sr);
+	}
+	else
+    	    {
+	    printf("%s", kgDescription);
+	    }
+
         printf("<BR>\n");
 	}
     }
 
@@ -9047,20 +9081,8 @@
     }
 return ver;
 }
 
-char *gbCdnaGetDescription(struct sqlConnection *conn, char *acc)
-/* return mrna description, or NULL if not available. freeMem result */
-{
-char query[128];
-safef(query, sizeof(query),
-      "select description.name from gbCdnaInfo,description where (acc = '%s') and (gbCdnaInfo.description = description.id)", acc);
-char *desc = sqlQuickString(conn, query);
-if ((desc == NULL) || sameString(desc, "n/a") || (strlen(desc) == 0))
-    freez(&desc);
-return desc;
-}
-
 void prRefGeneInfo(struct sqlConnection *conn, char *rnaName,
                    char *sqlRnaName, struct refLink *rl, boolean isXeno)
 /* print basic details information and links for a RefGene */
 {