void doGetMrnaSeq(struct sqlConnection *conn, char *geneId, char *geneName)
/* Get mRNA sequence in a simple page. */
{
if (genomeOptionalSetting("knownGeneMrna") != NULL)
showSeq(conn, geneId, geneName, "knownGeneMrna");
else
showMrnaFromGenePred(conn, geneId, geneName);
}
void printMrnaSeqLink(struct sqlConnection *conn, char *geneId)
/* Print out link to fetch mRNA. */
{
char *title = "mRNA";
char *tableId = "knownGene";
if (genomeOptionalSetting("knownGeneMrna") != NULL)
{
title = "mRNA (may differ from genome)";
tableId = "knownGeneMrna";
}
printSeqLink(conn, geneId, tableId, hggDoGetMrnaSeq, title, 2);
}
static char *findGeneId(struct sqlConnection *conn, char *name)
/* Given some sort of gene name, see if it is in our primary gene table, and if not
* look it up in alias table if we have one. */
{
/* Just check if it's in the main gene table, and if so return input name. */
char *mainTable = genomeSetting("knownGene");
char query[256];
sqlSafef(query, sizeof(query), "select count(*) from %s where name = '%s'", mainTable, name);
if (sqlQuickNum(conn, query) > 0)
return name;
else
{
/* check OMIM gene symbol table first */
if (sqlTableExists(conn, "omimGeneSymbol"))
{
sqlSafef(query, sizeof(query), "select geneSymbol from omimGeneSymbol where geneSymbol= '%s'", name);
char *symbol = sqlQuickString(conn, query);
if (symbol != NULL)
{
sqlSafef(query, sizeof(query), "select kgId from kgXref where geneSymbol = '%s'", symbol);
char *kgId = sqlQuickString(conn, query);
if (kgId != NULL)
{
/* The canonical gene is preferred */
sqlSafef(query, sizeof(query),
"select c.transcript from knownCanonical c,knownIsoforms i where i.transcript = '%s' and i.clusterId=c.clusterId", kgId);
char *canonicalKgId = sqlQuickString(conn, query);
if (canonicalKgId != NULL)
{
return canonicalKgId;
}
else
return(kgId);
}
}
}
}
char *alias = genomeOptionalSetting("kgAlias");
if (alias != NULL && sqlTableExists(conn, alias))
{
sqlSafef(query, sizeof(query), "select kgID from %s where alias = '%s'", alias, name);
char *id = sqlQuickString(conn, query);
if (id == NULL)
hUserAbort("Couldn't find %s in %s.%s or %s.%s", name, database, mainTable, database, alias);
return id;
}
else
hUserAbort("Couldn't find %s in %s.%s", name, database, mainTable);
return NULL;
}
char *descriptionString(char *id, struct sqlConnection *conn)
/* return description as it would be printed in html, can free after use */
{
char *descrBySql = NULL;
char *summaryTables = genomeOptionalSetting("summaryTables");
struct dyString *description = dyStringNew(0);
descrBySql = genoQuery(id, "descriptionSql", conn);
dyStringPrintf(description, "<B>Description:</B> ");
if (descrBySql != NULL)
dyStringPrintf(description, "%s<BR>\n", descrBySql);
else
dyStringPrintf(description, "%s<BR>\n", "No description available");
freez(&descrBySql);
if (summaryTables != NULL)
{
if (sqlTablesExist(conn, summaryTables))
{
char *summary = genoQuery(id, "summarySql", conn);
if (summary != NULL && summary[0] != 0)
{
summary = abbreviateSummary(summary);
dyStringPrintf(description, "<B>%s",
genomeSetting("summarySource"));
if (genomeOptionalSetting("summaryIdSql"))
{
char *summaryId = genoQuery(id, "summaryIdSql", conn);
if (summaryId != NULL)
dyStringPrintf(description, " (%s)", summaryId);
}
dyStringPrintf(description, ":</B> %s", summary);
freez(&summary);
dyStringPrintf(description, "<BR>\n");
}
}
}
return dyStringCannibalize(&description);
}
static void synonymPrint(struct section *section,
struct sqlConnection *conn, char *id)
/* Print out SwissProt comments - looking up typeId/commentVal. */
{
char *protAcc = getSwissProtAcc(conn, spConn, id);
char *spDisplayId;
char *refSeqAcc = "";
char *mrnaAcc = "";
char *oldDisplayId;
char condStr[255];
char *kgProteinID;
char *parAcc; /* parent accession of a variant splice protein */
char *chp;
if (isRgdGene(conn))
{
rgdGene2SynonymPrint(section,conn, id);
return;
}
if (sqlTablesExist(conn, "kgAlias"))
printAlias(id, conn);
if (sameWord(genome, "Zebrafish"))
{
char *xrefTable = "ensXRefZfish";
char *geneIdCol = "ensGeneId";
/* get Gene Symbol and RefSeq accession from Zebrafish-specific */
/* cross-reference table */
printGeneSymbol(id, xrefTable, geneIdCol, conn);
refSeqAcc = getRefSeqAcc(id, xrefTable, geneIdCol, conn);
hPrintf("<B>ENSEMBL ID:</B> %s", id);
}
else
{
char query[256];
char *toRefTable = genomeOptionalSetting("knownToRef");
if (toRefTable != NULL && sqlTableExists(conn, toRefTable))
{
safef(query, sizeof(query), "select value from %s where name='%s'", toRefTable,
id);
refSeqAcc = emptyForNull(sqlQuickString(conn, query));
}
if (sqlTableExists(conn, "kgXref"))
{
safef(query, sizeof(query), "select mRNA from kgXref where kgID='%s'", id);
mrnaAcc = emptyForNull(sqlQuickString(conn, query));
}
if (sameWord(genome, "C. elegans"))
hPrintf("<B>WormBase ID:</B> %s<BR>", id);
else
hPrintf("<B>UCSC ID:</B> %s<BR>", id);
}
if (refSeqAcc[0] != 0)
{
hPrintf("<B>RefSeq Accession: </B> <A HREF=\"");
printOurRefseqUrl(stdout, refSeqAcc);
hPrintf("\">%s</A><BR>\n", refSeqAcc);
}
else if (mrnaAcc[0] != 0)
{
safef(condStr, sizeof(condStr), "acc = '%s'", mrnaAcc);
if (sqlGetField(database, "gbCdnaInfo", "acc", condStr) != NULL)
{
hPrintf("<B>Representative RNA: </B> <A HREF=\"");
printOurMrnaUrl(stdout, mrnaAcc);
hPrintf("\">%s</A><BR>\n", mrnaAcc);
}
else
/* do not show URL link if it is not found in gbCdnaInfo */
{
hPrintf("<B>Representative RNA: %s </B>", mrnaAcc);
}
}
if (protAcc != NULL)
{
kgProteinID = cloneString("");
if (hTableExists(sqlGetDatabase(conn), "knownGene")
&& (isNotEmpty(cartOptionalString(cart, hggChrom)) &&
differentWord(cartOptionalString(cart, hggChrom),"none")))
{
safef(condStr, sizeof(condStr), "name = '%s' and chrom = '%s' and txStart=%s and txEnd=%s",
id, cartOptionalString(cart, hggChrom),
cartOptionalString(cart, hggStart),
cartOptionalString(cart, hggEnd));
kgProteinID = sqlGetField(database, "knownGene", "proteinID", condStr);
}
hPrintf("<B>Protein: ");
if (strstr(kgProteinID, "-") != NULL)
{
parAcc = cloneString(kgProteinID);
chp = strstr(parAcc, "-");
*chp = '\0';
/* show variant splice protein and the UniProt link here */
hPrintf("<A HREF=\"http://www.uniprot.org/uniprot%s\" "
"TARGET=_blank>%s</A></B>, splice isoform of ",
kgProteinID, kgProteinID);
hPrintf("<A HREF=\"http://www.uniprot.org/uniprot/%s\" "
"TARGET=_blank>%s</A></B>\n",
parAcc, parAcc);
}
else
{
hPrintf("<A HREF=\"http://www.uniprot.org/uniprot/%s\" "
"TARGET=_blank>%s</A></B>\n",
protAcc, protAcc);
}
/* show SWISS-PROT display ID if it is different than the accession ID */
/* but, if display name is like: Q03399 | Q03399_HUMAN, then don't show display name */
spDisplayId = spAnyAccToId(spConn, protAcc);
if (spDisplayId == NULL)
{
errAbort("<br>%s seems to no longer be a valid protein ID in our latest UniProtKB DB.", protAcc);
}
if (strstr(spDisplayId, protAcc) == NULL)
{
hPrintf(" (aka %s", spDisplayId);
/* show once if the new and old displayId are the same */
oldDisplayId = oldSpDisplayId(spDisplayId);
if (oldDisplayId != NULL)
{
if (!sameWord(spDisplayId, oldDisplayId)
&& !sameWord(protAcc, oldDisplayId))
{
hPrintf(" or %s", oldDisplayId);
}
}
hPrintf(")<BR>\n");
}
}
printCcds(id, conn);
}
