src/hg/utils/refSeqGet/refSeqGet.c 1.2

Index: src/hg/utils/refSeqGet/refSeqGet.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/utils/refSeqGet/refSeqGet.c,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 4 -r1.1 -r1.2
--- src/hg/utils/refSeqGet/refSeqGet.c	23 Nov 2009 02:56:20 -0000	1.1
+++ src/hg/utils/refSeqGet/refSeqGet.c	23 Nov 2009 17:45:19 -0000	1.2
@@ -190,28 +190,40 @@
     return buf;
     }
 }
 
+static char *getCds(struct sqlConnection *conn, char *acc)
+/* get CDS for an NM, results should be freed */
+{
+char query[128];
+safef(query, sizeof(query), "SELECT cds.name FROM gbCdnaInfo,cds WHERE (gbCdnaInfo.acc = \"%s\") AND (gbCdnaInfo.cds = cds.id)", acc);
+return sqlNeedQuickString(conn, query);
+}
+
 static void processMetaData(FILE *fh, struct sqlConnection *conn, struct sqlConnection *conn2, struct refSeqVerInfo *rsvi)
 /* get meta data for an accession */
 {
+boolean isCoding = genbankIsRefSeqCodingMRnaAcc(rsvi->acc);
 char query[128];
 safef(query, sizeof(query), "SELECT name,product,protAcc,locusLinkId FROM refLink WHERE mrnaAcc = \"%s\"", rsvi->acc);
 struct sqlResult *sr = sqlGetResult(conn, query);
 char **row = sqlNextRow(sr);
 if (row == NULL)
     errAbort("no RefLink entry for %s", rsvi->acc);
 char buf[32];
 char *protAccVer = getProtAccVerIf(conn2, rsvi->acc, row[2], buf, sizeof(buf));
-fprintf(fh, "%s.%d\t%s\t%s\t%s\t%s\n", rsvi->acc, rsvi->ver, protAccVer, row[0], row[3], row[1]);
+char *cds = isCoding ? getCds(conn2, rsvi->acc) : "";
+fprintf(fh, "%s.%d\t%s\t%s\t%s\t%s\t%s\n", rsvi->acc, rsvi->ver, protAccVer, row[0], row[3], cds, row[1]);
 sqlFreeResult(&sr);
+if (isCoding)
+    freeMem(cds);
 }
 
 static void getMetaData(struct sqlConnection *conn, struct hash *refSeqVerInfoTbl, char *outFile)
 /* get request prot sequences from database */
 {
 struct sqlConnection *conn2 = sqlConnect(sqlGetDatabase(conn));
-static char *hdr = "#mrnaAcc\t" "protAcc\t" "geneName\t" "ncbiGeneId\t" "product\n";
+static char *hdr = "#mrnaAcc\t" "protAcc\t" "geneName\t" "ncbiGeneId\t" "cds\t" "product\n";
 FILE *fh = mustOpen(outFile, "w");
 fputs(hdr, fh);
 struct hashCookie cookie = hashFirst(refSeqVerInfoTbl);
 struct hashEl *hel;