84052670e60a22211510df04f8ac91045e2f9a00 fanhsu Mon May 23 09:30:35 2011 -0700 Revamped omimGene2 processing logic and minor edits of links to OMIM page at omim.org. diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c index 6b1b65c..5bec707 100644 --- src/hg/hgc/hgc.c +++ src/hg/hgc/hgc.c @@ -9361,53 +9361,49 @@ printf("", "../cgi-bin/hgGene?hgg_gene=", row[0]); printf("%s", row[0]); printedCnt++; } if (printedCnt >= 1) printf("
\n"); } sqlFreeResult(&sr); } } printf("
"); printPosOnChrom(chrom, atoi(chromStart), atoi(chromEnd), NULL, FALSE, itemName); } void printOmimGene2Details(struct trackDb *tdb, char *itemName, boolean encode) -/* Print details of an OMIM Class 3 Gene entry. */ +/* Print details of an omimGene2 entry. */ { struct sqlConnection *conn = hAllocConn(database); -struct sqlConnection *conn2 = hAllocConn(database); char query[256]; struct sqlResult *sr; char **row; char *url = tdb->url; -char *kgId= NULL; char *title1 = NULL; char *title2 = NULL; char *geneSymbol = NULL; char *chrom, *chromStart, *chromEnd; -char *kgDescription = NULL; -char *refSeq; chrom = cartOptionalString(cart, "c"); chromStart = cartOptionalString(cart, "o"); chromEnd = cartOptionalString(cart, "t"); if (url != NULL && url[0] != 0) { - printf("OMIM Gene: ");fflush(stdout); + printf("OMIM page at omim.org: ");fflush(stdout); printf("", url, itemName); printf("%s", itemName); safef(query, sizeof(query), "select title1, title2 from omimGeneMap where omimId=%s;", itemName); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { if (row[0] != NULL) { title1 = cloneString(row[0]); printf(" %s", title1); } if (row[1] != NULL) { @@ -9420,168 +9416,115 @@ printf("
\n"); printf("OMIM page at NCBI: "); printf("", ncbiOmimUrl, itemName); printf("%s
", itemName); safef(query, sizeof(query), "select geneSymbol from omimGeneMap where omimId=%s;", itemName); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { geneSymbol = cloneString(row[0]); } sqlFreeResult(&sr); - /* get corresponding KG ID */ - safef(query, sizeof(query), - "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) - { - kgId = cloneString(row[0]); - } - sqlFreeResult(&sr); - - /* use geneSymbol from omimMorbidMap if available */ if (geneSymbol!= NULL) { boolean disorderShown; char *phenotypeClass, *phenotypeId, *disorder; printf("Gene symbol(s): %s", geneSymbol); printf("
\n"); - /* display disorder for genes in morbidmap */ + /* display disorder(s) */ safef(query, sizeof(query), "select description, phenotypeClass, phenotypeId from omimPhenotype where omimId=%s order by description", itemName); sr = sqlMustGetResult(conn, query); disorderShown = FALSE; while ((row = sqlNextRow(sr)) != NULL) { if (!disorderShown) { printf("Disorder(s):\n"); sqlFreeResult(&sr); } - else - { - /* display gene symbol(s) from omimGenemap */ - safef(query, sizeof(query), "select geneSymbol from omimGeneMap where omimId=%s;", itemName); - sr = sqlMustGetResult(conn, query); - row = sqlNextRow(sr); - if (row != NULL) - { - printf("OMIM Gene Symbol: %s", row[0]); - printf("
\n"); - sqlFreeResult(&sr); - } - else - { - /* get gene symbol from kgXref if the entry is not in morbidmap and omim genemap */ - safef(query, sizeof(query), "select geneSymbol from kgXref where kgId='%s';", kgId); + // show RefSeq Gene link(s) + safef(query, sizeof(query), + "select distinct r.name from refLink l, mim2gene g, refGene r where l.omimId=%s and g.geneId=l.locusLinkId and g.entryType='gene' and chrom='%s' and txStart = %s and txEnd= %s", + itemName, chrom, chromStart, chromEnd); sr = sqlMustGetResult(conn, query); - row = sqlNextRow(sr); - if (row != NULL) - { - printf("UCSC Gene Symbol: %s", row[0]); - printf("
\n"); - } - sqlFreeResult(&sr); - } - } - - if (kgId != NULL) + if (sr != NULL) { - printf("UCSC Canonical Gene: "); - printf("", - "../cgi-bin/hgGene?hgg_gene=", kgId); - printf("%s ", kgId); - - safef(query, sizeof(query), "select refseq from kgXref where kgId='%s';", kgId); - sr = sqlMustGetResult(conn, query); - row = sqlNextRow(sr); - if (row != NULL) + int printedCnt; + printedCnt = 0; + while ((row = sqlNextRow(sr)) != NULL) { - refSeq = strdup(row[0]); - kgDescription = gbCdnaGetDescription(conn2, refSeq); + if (printedCnt < 1) + printf("RefSeq Gene(s): "); + else + printf(", "); + printf("", "../cgi-bin/hgc?g=refGene&i=", row[0], chromStart, chromEnd); + printf("%s", row[0]); + printedCnt++; } - 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) - { - printf("%s", row[0]); + if (printedCnt >= 1) printf("
\n"); } - sqlFreeResult(&sr); - } - else - { - printf("%s", kgDescription); - } - printf("
\n"); + // show Related UCSC Gene links safef(query, sizeof(query), - "select i.transcript from knownIsoforms i, knownCanonical c where c.transcript='%s' and i.clusterId=c.clusterId and i.transcript <>'%s'", - kgId, kgId); + "select distinct kgId from kgXref x, refLink l, mim2gene g where x.refseq = mrnaAcc and l.omimId=%s and g.omimId=l.omimId and g.entryType='gene'", + itemName); sr = sqlMustGetResult(conn, query); if (sr != NULL) { int printedCnt; printedCnt = 0; while ((row = sqlNextRow(sr)) != NULL) { if (printedCnt < 1) - printf("Other UCSC Gene(s) in the same cluster: "); + printf("Related UCSC Gene(s): "); else printf(", "); printf("", "../cgi-bin/hgGene?hgg_gene=", row[0]); printf("%s", row[0]); printedCnt++; } if (printedCnt >= 1) printf("
\n"); } sqlFreeResult(&sr); } - } printf("
"); printPosOnChrom(chrom, atoi(chromStart), atoi(chromEnd), NULL, FALSE, itemName); } void printOmimLocationDetails(struct trackDb *tdb, char *itemName, boolean encode) /* Print details of an OMIM Class 3 Gene entry. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlConnection *conn2 = hAllocConn(database); char query[256]; struct sqlResult *sr; char **row; char *url = tdb->url; char *kgId= NULL; @@ -9589,31 +9532,31 @@ char *title2 = NULL; char *geneSymbol = NULL; char *chrom, *chromStart, *chromEnd; char *kgDescription = NULL; char *refSeq; char *omimId; chrom = cartOptionalString(cart, "c"); chromStart = cartOptionalString(cart, "o"); chromEnd = cartOptionalString(cart, "t"); omimId = itemName; if (url != NULL && url[0] != 0) { - printf("OMIM Entry ");fflush(stdout); + printf("OMIM page at omim.org: ");fflush(stdout); printf("", url, itemName); printf("%s", itemName); safef(query, sizeof(query), "select title1, title2 from omimGeneMap where omimId=%s;", itemName); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { if (row[0] != NULL) { title1 = cloneString(row[0]); printf(": %s", title1); } if (row[1] != NULL) { @@ -9837,31 +9780,31 @@ title1 = cloneString(row[0]); } if (row[1] != NULL) { title2 = cloneString(row[1]); } avDesc = cloneString(row[3]); } sqlFreeResult(&sr); printf("OMIM Allelic Variant: "); printf("", url, avString); printf("%s", avId); printf(" %s", avDesc); - printf("
OMIM Entry "); + printf("
OMIM page at omim.org: "); printf("", url, itemName); printf("%s", itemName); if (title1 != NULL) printf(": %s", title1); if (title2 != NULL) printf(" %s ", title2); printf("
\n"); printf("OMIM page at NCBI: "); printf("", ncbiOmimUrl, itemName); printf("%s
", itemName); safef(query, sizeof(query), "select replStr from omimAvRepl where avId=%s;", avId); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL)