static boolean localizationExists(struct section *section,
struct sqlConnection *conn, char *geneId)
/* Return TRUE if localization and existance tables exist and have something
* on this one. */
{
char query[256];
/* mitopred - prediction of nuclear-encoded mitochondrial proteins */
if (swissProtAcc != NULL && sqlTableExists(conn, "mitopred"))
{
sqlSafef(query, sizeof(query),
"select count(*) from mitopred where name = '%s' or name = '%s'",
swissProtAcc, spAnyAccToId(spConn, swissProtAcc));
if (sqlQuickNum(conn, query) > 0)
return TRUE;
}
/* SGD (Sacchromyces Genome Database) localization & abundance data */
if (sqlTablesExist(conn, "sgdLocalization sgdAbundance"))
{
sqlSafef(query, sizeof(query),
"select count(*) from sgdLocalization where name = '%s'", geneId);
if (sqlQuickNum(conn, query) > 0)
return TRUE;
sqlSafef(query, sizeof(query),
"select count(*) from sgdAbundance where name = '%s'", geneId);
if (sqlQuickNum(conn, query) > 0)
return TRUE;
}
return FALSE;
}
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);
}
static void rgdGene2SynonymPrint(struct section *section,
struct sqlConnection *conn, char *rgdGeneId)
{
char *geneSym = NULL, *geneName = NULL;
char query[256], **row;
struct sqlResult *sr;
if (rgdGeneId != NULL)
{
safef(query, sizeof(query),
"select old_symbol, old_name from genes_rat where gene_rgd_id = '%s'",
rgdGeneId+4L);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
{
if (row[0][0] != 0 && !sameString(row[0], "n/a"))
{
geneSym = cloneString(row[0]);
hPrintf("<B>Symbol:</B> %s ", addComma(row[0]));
//hPrintf("<BR>\n");
}
if (row[1][0] != 0 && !sameString(row[0], "n/a"))
{
geneName = cloneString(row[1]);
hPrintf("<BR><B>Name:</B> %s ", addComma(geneName));
hPrintf("<BR>\n");
}
}
sqlFreeResult(&sr);
safef(query, sizeof(query),
"select value from rgdGene2ToRefSeq where name= '%s'", rgdGeneId);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
{
hPrintf("<B>RefSeq Accession: </B> <A HREF=\"");
printOurRefseqUrl(stdout, row[0]);
hPrintf("\">%s</A><BR>\n", row[0]);
}
sqlFreeResult(&sr);
safef(query, sizeof(query),
"select value from rgdGene2ToUniProt where name= '%s'", rgdGeneId);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
{
char *spId, *spDisplayId, *oldDisplayId;
spId = row[0];
hPrintf("<B>Protein: </B>");
hPrintf("<A HREF=\"http://www.uniprot.org/uniprot/%s\" "
"TARGET=_blank>%s</A>\n",
spId, spId);
/* 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, spId);
if (spDisplayId == NULL)
{
errAbort("<br>The corresponding protein %s of this gene is not found in our current UniProtKB DB.", spId);
}
if (strstr(spDisplayId, spId) == 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(spId, oldDisplayId))
{
hPrintf(" or %s", oldDisplayId);
}
}
hPrintf(")<BR>\n");
}
}
sqlFreeResult(&sr);
}
}
void txGeneXref(char *genomeDb, char *uniProtDb, char *genePredFile, char *infoFile, char *pickFile,
char *evFile, char *outFile)
/* txGeneXref - Make kgXref type table for genes.. */
{
/* Load picks into hash. We don't use cdsPicksLoadAll because empty fields
* cause that autoSql-generated routine problems. */
struct hash *pickHash = newHash(18);
struct hash *geneToProtHash = makeGeneToProtHash(genePredFile);
struct cdsPick *pick;
struct lineFile *lf = lineFileOpen(pickFile, TRUE);
char *row[CDSPICK_NUM_COLS];
while (lineFileRowTab(lf, row))
{
pick = cdsPickLoad(row);
removePickVersions(pick);
hashAdd(pickHash, pick->name, pick);
}
/* Load evidence into hash */
struct hash *evHash = newHash(18);
struct txRnaAccs *ev, *evList = txRnaAccsLoadAll(evFile);
for (ev = evList; ev != NULL; ev = ev->next)
hashAdd(evHash, ev->name, ev);
/* Open connections to our databases */
struct sqlConnection *gConn = sqlConnect(genomeDb);
struct sqlConnection *uConn = sqlConnect(uniProtDb);
/* Read in info file, and loop through it to make out file. */
struct txInfo *info, *infoList = txInfoLoadAll(infoFile);
FILE *f = mustOpen(outFile, "w");
for (info = infoList; info != NULL; info = info->next)
{
char *kgID = info->name;
char *mRNA = "";
char *spID = "";
char *spDisplayID = "";
char *geneSymbol = NULL;
char *refseq = "";
char *protAcc = "";
char *description = NULL;
char query[256];
char *proteinId = hashMustFindVal(geneToProtHash, info->name);
boolean isAb = sameString(info->category, "antibodyParts");
pick = hashFindVal(pickHash, info->name);
ev = hashFindVal(evHash, info->name);
if (pick != NULL)
{
/* Fill in the relatively straightforward fields. */
refseq = pick->refSeq;
if (info->orfSize > 0)
{
protAcc = pick->refProt;
spID = proteinId;
if (sameString(protAcc, spID))
spID = pick->uniProt;
if (spID[0] != 0)
spDisplayID = spAnyAccToId(uConn, spID);
}
/* Fill in gene symbol and description from refseq if possible. */
if (refseq[0] != 0)
{
struct sqlResult *sr;
safef(query, sizeof(query), "select name,product from refLink where mrnaAcc='%s'",
refseq);
sr = sqlGetResult(gConn, query);
char **row = sqlNextRow(sr);
if (row != NULL)
{
geneSymbol = cloneString(row[0]);
if (!sameWord("unknown protein", row[1]))
description = cloneString(row[1]);
}
sqlFreeResult(&sr);
}
/* If need be try uniProt for gene symbol and description. */
if (spID[0] != 0 && (geneSymbol == NULL || description == NULL))
{
char *acc = spLookupPrimaryAcc(uConn, spID);
if (description == NULL)
description = spDescription(uConn, acc);
if (geneSymbol == NULL)
{
struct slName *nameList = spGenes(uConn, acc);
if (nameList != NULL)
geneSymbol = cloneString(nameList->name);
slFreeList(&nameList);
}
}
}
/* If it's an antibody fragment use that as name. */
if (isAb)
{
geneSymbol = cloneString("abParts");
description = cloneString("Parts of antibodies, mostly variable regions.");
isAb = TRUE;
}
if (ev == NULL)
{
mRNA = cloneString("");
if (!isAb)
{
errAbort("%s is %s but not %s\n", info->name, infoFile, evFile);
}
}
else
{
mRNA = cloneString(ev->primary);
chopSuffix(mRNA);
}
/* Still no joy? Try genbank RNA records. */
if (geneSymbol == NULL || description == NULL)
{
if (ev != NULL)
{
int i;
for (i=0; i<ev->accCount; ++i)
{
char *acc = ev->accs[i];
chopSuffix(acc);
if (geneSymbol == NULL)
{
safef(query, sizeof(query),
"select geneName.name from gbCdnaInfo,geneName "
"where geneName.id=gbCdnaInfo.geneName and gbCdnaInfo.acc = '%s'", acc);
geneSymbol = sqlQuickString(gConn, query);
if (geneSymbol != NULL)
{
if (sameString(geneSymbol, "n/a"))
geneSymbol = NULL;
}
}
if (description == NULL)
{
safef(query, sizeof(query),
"select description.name from gbCdnaInfo,description "
"where description.id=gbCdnaInfo.description "
"and gbCdnaInfo.acc = '%s'", acc);
description = sqlQuickString(gConn, query);
if (description != NULL)
{
if (sameString(description, "n/a"))
description = NULL;
}
}
}
}
}
if (geneSymbol == NULL)
geneSymbol = mRNA;
if (description == NULL)
description = mRNA;
/* Get rid of some characters that will cause havoc downstream. */
stripChar(geneSymbol, '\'');
subChar(geneSymbol, '<', '[');
subChar(geneSymbol, '>', ']');
/* Abbreviate geneSymbol if too long */
if (strlen(geneSymbol) > 40)
strcpy(geneSymbol+37, "...");
fprintf(f, "%s\t", kgID);
fprintf(f, "%s\t", mRNA);
fprintf(f, "%s\t", spID);
fprintf(f, "%s\t", spDisplayID);
fprintf(f, "%s\t", geneSymbol);
fprintf(f, "%s\t", refseq);
fprintf(f, "%s\t", protAcc);
fprintf(f, "%s\n", description);
}
carefulClose(&f);
}
static void localizationPrint(struct section *section,
struct sqlConnection *conn, char *geneId)
/* Print out localization and abundance links. */
{
char query[256], **row, *s = NULL;
struct sqlResult *sr;
boolean firstTime = TRUE;
/* mitopred - prediction of nuclear-encoded mitochondrial proteins */
if (swissProtAcc != NULL && sqlTableExists(conn, "mitopred"))
{
sqlSafef(query, sizeof(query),
"select confidence from mitopred where name = '%s' or name = '%s'",
swissProtAcc, spAnyAccToId(spConn, swissProtAcc));
sr = sqlGetResult(conn, query);
firstTime = TRUE;
while ((row = sqlNextRow(sr)) != NULL)
{
if (firstTime)
{
hPrintf("<B>Mitopred:</B> mitochondrion, confidence level: ");
firstTime = FALSE;
}
else
{
hPrintf(", ");
}
hPrintf("%s", row[0]);
}
sqlFreeResult(&sr);
if (!firstTime)
{
hPrintf("<BR>");
hPrintf("Prediction of nuclear-encoded mitochondrial proteins from "
"Guda et al., Bioinformatics. 2004 Jul 22;20(11):1785-94.<BR>"
"For more information see "
"<A HREF=\"http://mitopred.sdsc.edu/\" TARGET=_blank>"
"http://mitopred.sdsc.edu/</A>.<P>");
}
}
/* SGD (Sacchromyces Genome Database) localization & abundance data */
if (sqlTablesExist(conn, "sgdLocalization sgdAbundance"))
{
sqlSafef(query, sizeof(query),
"select value from sgdLocalization where name = '%s'", geneId);
sr = sqlGetResult(conn, query);
firstTime = TRUE;
while ((row = sqlNextRow(sr)) != NULL)
{
if (firstTime)
{
hPrintf("<B>SGD Localization:</B> ");
firstTime = FALSE;
}
else
{
hPrintf(", ");
}
hPrintf("%s", row[0]);
}
sqlFreeResult(&sr);
if (!firstTime)
{
hPrintf("<BR>");
}
sqlSafef(query, sizeof(query),
"select abundance from sgdAbundance where name = '%s'", geneId);
s = sqlQuickString(conn, query);
if (s != NULL)
{
hPrintf("<B>SGD Abundance:</B> %s (range from 41 to 1590000)<BR>\n",
s);
freez(&s);
}
hPrintf("Protein localization data from "
"Huh et al. (2003), Nature 425:686-691<BR>"
"Protein abundance data from "
"Ghaemmaghami et al. (2003) Nature 425:737-741<BR>"
"For more information see "
"<A HREF=\"http://yeastgfp.yeastgenome.org\" TARGET=_blank>"
"http://yeastgfp.yeastgenome.org</A>.");
}
}
