4b3fe214cfd89ea4ff51f009bcd7b914bbf54f74 chmalee Mon Jul 22 13:44:16 2019 -0700 Change CGIs to use new omimGeneMap2 table diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c index 8234dec..c1f6236 100644 --- src/hg/hgc/hgc.c +++ src/hg/hgc/hgc.c @@ -10417,31 +10417,30 @@ 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; char *kgId= NULL; 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"); if (url != NULL && url[0] != 0) { /* check if the entry is in morbidmap, if so remember the assoicated gene symbols */ sqlSafef(query, sizeof(query), "select geneSymbols from omimMorbidMap where omimId=%s;", itemName); sr = sqlMustGetResult(conn, query); @@ -10471,75 +10470,70 @@ printf("
\n"); /* display disorder for genes in morbidmap */ sqlSafef(query, sizeof(query), "select description from omimMorbidMap where omimId=%s;", itemName); sr = sqlMustGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { printf("Disorder: %s", row[0]); printf("
\n"); } sqlFreeResult(&sr); } else { - /* display gene symbol(s) from omimGenemap */ - sqlSafef(query, sizeof(query), "select geneSymbol from omimGeneMap where omimId=%s;", itemName); + /* display gene symbol(s) from omimGeneMap2 */ + sqlSafef(query, sizeof(query), "select geneSymbol from omimGeneMap2 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 */ sqlSafef(query, sizeof(query), "select geneSymbol from kgXref where kgId='%s';", kgId); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { printf("UCSC Gene Symbol: %s", row[0]); printf("
\n"); } sqlFreeResult(&sr); } } printf("OMIM Database "); printf("", url, itemName); printf("%s", itemName); sqlSafef(query, sizeof(query), - "select title1, title2 from omimGeneMap where omimId=%s;", itemName); + "select geneName from omimGeneMap2 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) - { - title2 = cloneString(row[1]); - printf(" %s ", title2); - } } sqlFreeResult(&sr); printf("
\n"); if (kgId != NULL) { printf("UCSC Canonical Gene "); printf("", "../cgi-bin/hgGene?hgg_gene=", kgId); printf("%s: ", kgId); sqlSafef(query, sizeof(query), "select refseq from kgXref where kgId='%s';", kgId); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); @@ -10597,76 +10591,70 @@ printf("
"); printPosOnChrom(chrom, atoi(chromStart), atoi(chromEnd), NULL, FALSE, itemName); } #include "omim.h" void printOmimGene2Details(struct trackDb *tdb, char *itemName, boolean encode) /* Print details of an omimGene2 entry. */ { struct sqlConnection *conn = hAllocConn(database); char query[256]; struct sqlResult *sr; char **row; char *url = tdb->url; char *title1 = NULL; -char *title2 = NULL; char *geneSymbol = NULL; char *chrom, *chromStart, *chromEnd; chrom = cartOptionalString(cart, "c"); chromStart = cartOptionalString(cart, "o"); chromEnd = cartOptionalString(cart, "t"); if (url != NULL && url[0] != 0) { printf("OMIM: "); printf("", url, itemName); printf("%s", itemName); sqlSafef(query, sizeof(query), - "select title1, title2 from omimGeneMap where omimId=%s;", itemName); + "select geneName from omimGeneMap2 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) - { - title2 = cloneString(row[1]); - printf(" %s ", title2); - } } else { printf("
"); } sqlFreeResult(&sr); // disable NCBI link until they work it out with OMIM /* printf("
\n"); printf("OMIM page at NCBI: "); printf("", ncbiOmimUrl, itemName); printf("%s", itemName); */ sqlSafef(query, sizeof(query), - "select geneSymbol from omimGeneMap where omimId=%s;", itemName); + "select geneSymbol from omimGeneMap2 where omimId=%s;", itemName); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { geneSymbol = cloneString(row[0]); } sqlFreeResult(&sr); if (geneSymbol!= NULL) { boolean disorderShown; char *phenotypeClass, *phenotypeId, *disorder; printf("
Gene symbol(s): %s", geneSymbol); printf("
\n"); @@ -10791,94 +10779,88 @@ 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; char *title1 = NULL; -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: "); printf("", url, itemName); printf("%s", itemName); sqlSafef(query, sizeof(query), - "select title1, title2 from omimGeneMap where omimId=%s;", itemName); + "select geneName from omimGeneMap2 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) - { - title2 = cloneString(row[1]); - printf(" %s ", title2); - } } sqlFreeResult(&sr); printf("
"); // disable NCBI link until they work it out with OMIM /* printf("OMIM page at NCBI: "); printf("", ncbiOmimUrl, itemName); printf("%s
", itemName); */ printf("Location: "); sqlSafef(query, sizeof(query), - "select location from omimGeneMap where omimId=%s;", itemName); + "select location from omimGeneMap2 where omimId=%s;", itemName); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { if (row[0] != NULL) { char *locStr; locStr= cloneString(row[0]); printf("%s\n", locStr); } } sqlFreeResult(&sr); printf("
\n"); sqlSafef(query, sizeof(query), - "select geneSymbol from omimGeneMap where omimId=%s;", itemName); + "select geneSymbol from omimGeneMap2 where omimId=%s;", itemName); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { geneSymbol = cloneString(row[0]); } sqlFreeResult(&sr); sqlSafef(query, sizeof(query),"select omimId from omimPhenotype where omimId=%s\n", omimId); if (sqlQuickNum(conn, query) > 0) { char *phenotypeClass, *phenotypeId, *disorder; printf("Gene symbol(s): %s", geneSymbol); printf("
\n"); @@ -10903,31 +10885,31 @@ printf("%s)", phenotypeId); } if (!sameWord(phenotypeClass, "-1")) { printf(" (%s)", phenotypeClass); } } printf("
\n"); } printf("\n"); sqlFreeResult(&sr); } else { /* display gene symbol(s) from omimGenemap */ - sqlSafef(query, sizeof(query), "select geneSymbol from omimGeneMap where omimId=%s;", itemName); + sqlSafef(query, sizeof(query), "select geneSymbol from omimGeneMap2 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 */ sqlSafef(query, sizeof(query), "select geneSymbol from kgXref where kgId='%s';", kgId); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); @@ -11010,89 +10992,83 @@ { genericHeader(tdb, item); printOmimLocationDetails(tdb, item, FALSE); printTrackHtml(tdb); } void printOmimAvSnpDetails(struct trackDb *tdb, char *itemName, boolean encode) /* Print details of an OMIM AvSnp entry. */ { struct sqlConnection *conn = hAllocConn(database); char query[256]; struct sqlResult *sr; char **row; char *url = tdb->url; char *title1 = NULL; -char *title2 = NULL; char *chrom, *chromStart, *chromEnd; char *avId; char *dbSnpId; char *chp; char avString[255]; char *avDesc = NULL; chrom = cartOptionalString(cart, "c"); chromStart = cartOptionalString(cart, "o"); chromEnd = cartOptionalString(cart, "t"); avId = strdup(itemName); chp = strstr(avId, "-"); if (chp != NULL) *chp = '\0'; safef(avString, sizeof(avString), "%s", itemName); chp = strstr(itemName, "."); *chp = '\0'; chp = avString; chp = strstr(avString, "."); *chp = '#'; if (url != NULL && url[0] != 0) { sqlSafef(query, sizeof(query), - "select title1, title2, format(seqNo/10000,4), v.description" - " from omimGeneMap m, omimAv v" + "select m.geneName, format(seqNo/10000,4), v.description" + " from omimGeneMap2 m, omimAv v" " where m.omimId=%s and m.omimId=v.omimId and v.avId='%s';", itemName, avId); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { if (row[0] != NULL) { title1 = cloneString(row[0]); } - if (row[1] != NULL) - { - title2 = cloneString(row[1]); - } - avDesc = cloneString(row[3]); + avDesc = cloneString(row[2]); } sqlFreeResult(&sr); printf("OMIM Allelic Variant: "); printf("", url, avString); printf("%s", avId); printf(" %s", avDesc); printf("
OMIM: "); printf("", url, itemName); printf("%s", itemName); if (title1 != NULL) printf(": %s", title1); - if (title2 != NULL) printf(" %s ", title2); // disable NCBI link until they work it out with OMIM /* printf("
\n"); printf("OMIM page at NCBI: "); printf("", ncbiOmimUrl, itemName); printf("%s
", itemName); */ sqlSafef(query, sizeof(query), "select repl2 from omimAv where avId=%s;", avId); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) {