| \n",
+ collapseGroupVar, collapseGroupVar, isOpen ? "0" : "1");
+printf("\n",
+ cgiScriptName(), cartSidUrlString(cart), collapseGroupVar, (isOpen ? "1" : "0"), section);
+char *buttonImage = (isOpen ? "../images/remove_sm.gif" : "../images/add_sm.gif");
+printf(" | \n",
+ section, track,
+ section, buttonImage, (isOpen ? "-" : "+"), (isOpen ? "Collapse": "Expand"));
+printf("%s | ||||
| ", isOpen ? "" : "style='display: none' ", section, 1); +} + +void endCollapsibleSection() +/* End the collapsible | |||||
| %s allele: | " "%s | \n", orthoName, orthoAllele); if (!sameString(orthoAllele, "?")) { printf("%s strand: | " "%s | \n", orthoName, orthoStrand); printf("%s position: | " "\n", orthoName); if (isNotEmpty(orthoDb)) linkToOtherBrowser(orthoDb, orthoChrom, orthoStart-TINYPADDING, orthoEnd+TINYPADDING); printf("%s:%d-%d\n", orthoChrom, orthoStart+1, orthoEnd); - printf("%s | \n", + printf("%s\n", isNotEmpty(orthoDb) ? "" : ""); } else printf(FOURBLANKCELLS"\n"); printf("
| %s | %s | " +#define firstTwoColumnsPctS " | |||
| %s | %s | "
void getSnp125RefCodonAndSnpPos(struct snp125 *snp, struct genePred *gene, int exonIx,
int *pSnpCodonPos, char refCodon[4], char *pRefAA)
/* Given a single-base snp and a coding gene/exon containing it, determine the snp's position
* in the codon and the reference codon & amino acid. */
{
boolean geneIsRc = sameString(gene->strand, "-");
int snpStart = snp->chromStart, snpEnd = snp->chromEnd;
int exonStart = gene->exonStarts[exonIx], exonEnd = gene->exonEnds[exonIx];
int cdsStart = gene->cdsStart, cdsEnd = gene->cdsEnd;
int exonFrame = gene->exonFrames[exonIx];
if (exonFrame == -1)
exonFrame = 0;
if (cdsEnd < exonEnd) exonEnd = cdsEnd;
if (cdsStart > exonStart) exonStart = cdsStart;
@@ -15611,66 +15643,66 @@
}
slAddHead(&gpList, gp);
}
sqlFreeResult(&sr);
hFreeConn(&conn2);
return gpList;
}
void printSnp125Function(struct trackDb *tdb, struct snp125 *snp)
/* If the user has selected a gene track for functional annotation,
* report how this SNP relates to any nearby genes. */
{
char varName[512];
safef(varName, sizeof(varName), "%s_geneTrack", tdb->track);
struct slName *geneTracks = cartOptionalSlNameList(cart, varName);
-if (geneTracks == NULL)
+if (geneTracks == NULL && !cartListVarExists(cart, varName))
{
char *defaultGeneTracks = trackDbSetting(tdb, "defaultGeneTracks");
if (isNotEmpty(defaultGeneTracks))
geneTracks = slNameListFromComma(defaultGeneTracks);
else
return;
}
struct sqlConnection *conn = hAllocConn(database);
struct slName *gt;
boolean first = TRUE;
for (gt = geneTracks; gt != NULL; gt = gt->next)
- if (!sameString(gt->name, "persistentShadow") && sqlTableExists(conn, gt->name))
+ if (sqlTableExists(conn, gt->name))
{
if (first)
{
printf(" UCSC's predicted function relative to selected gene tracks:\n"); - printf(" \n"); hFreeConn(&conn); } char *dbSnpFuncFromInt(unsigned char funcCode) /* Translate an integer function code from NCBI into an abbreviated description. * Do not free return value! */ // Might be a good idea to flesh this out with all codes, libify, and share with // snpNcbiToUcsc instead of partially duplicating. { switch (funcCode) { case 3: return "coding-synon"; case 8: return "cds-reference"; @@ -15739,97 +15771,246 @@ puts(" "); continue; } if (gotRef) printf("%s (%s) --> ", anno->peptides[0], highlightCodonBase(anno->codons[0], anno->frame)); printf("%s (%s) \n", anno->peptides[i], highlightCodonBase(anno->codons[i], anno->frame)); } } sqlFreeResult(&sr); } hFreeConn(&conn); } -void printSnp125Info(struct trackDb *tdb, struct snp125 snp, int version) +void printSnp132ExtraColumns(struct trackDb *tdb, struct snp132Ext *snp) +/* Print columns new in snp132 */ +{ +// Skip exceptions column; handled below in writeSnpExceptionWithVersion +printf(" | |||
| Submitter Handles | "); +int i; +for (i=0; i < snp->submitterCount; i++) + printf("%s" + "%s", (i > 0 ? ", " : ""), snp->submitters[i], snp->submitters[i]); +printf(" | ||||
| Allele Frequencies | "); + for (i = 0; i < snp->alleleFreqCount; i++) + { + printf("%s%s: %.3f%% ", (i > 0 ? "; " : ""), snp->alleles[i], (snp->alleleFreqs[i]*100.0)); + // alleleNs should be integers (counts of chromosomes in which allele was observed) + // but dbSNP extrapolates them from reported frequency and reported sample count, + // so sometimes they are not integers. Present them as integers when we can, warn + // when we can't. + double f = snp->alleleFreqs[i], n = snp->alleleNs[i]; + if (f > 0) + { + total2N = round(n / f); + int roundedN = round(n); + if (fabs(n - roundedN) < 0.01) + printf("(%d / %d)", roundedN, total2N); + else + { + gotNonIntN = TRUE; + printf("(%.3f / %d)", n, total2N); + } + } + } + printf(" | ||||
Miscellaneous properties annotated by dbSNP:" + "\n\n"); + struct slName *bitfields = slNameListFromComma(snp->bitfields); + if (slNameInList(bitfields, "clinically-assoc")) + printf("
***clinically associated*** " + "(SNP is in OMIM/OMIA and/or " + "at least one submitter is a Locus-Specific Database)\n"); + if (slNameInList(bitfields, "has-omim-omia")) + printf("
SNP is in OMIM/OMIA\n"); + if (slNameInList(bitfields, "microattr-tpa")) + printf("
SNP has a microattribution or third-party annotation\n"); + if (slNameInList(bitfields, "submitted-by-lsdb")) + printf("
SNP was submitted by LSDB\n"); + if (slNameInList(bitfields, "maf-5-all-pops")) + printf("
Minor Allele Frequency is at least 5%% in all " + "populations assayed\n"); + else if (slNameInList(bitfields, "maf-5-some-pop")) + printf("
Minor Allele Frequency is at least 5%% in at least one " + "population assayed\n"); + if (slNameInList(bitfields, "genotype-conflict")) + printf("
Quality check: Different genotypes have been submitted " + "for the same individual\n"); + if (slNameInList(bitfields, "rs-cluster-nonoverlapping-alleles")) + printf("
Quality check: The reference SNP cluster contains " + "submitted SNPs with non-overlapping alleles\n"); + if (slNameInList(bitfields, "observed-mismatch")) + printf("
Quality check: The reference sequence allele at the " + "mapped position is not present in the SNP allele list\n"); + puts("
"); + } +} + +// Defined below -- call has since moved up from doSnpWithVersion to printSnp125Info +// so exceptions appear before our coding annotations. +void writeSnpExceptionWithVersion(struct trackDb *tdb, struct snp132Ext *snp, int version); +/* Print out descriptions of exceptions, if any, for this snp. */ + +void printSnp125Info(struct trackDb *tdb, struct snp132Ext *snp, int version) /* print info on a snp125 */ { -printSnpOrthoSummary(tdb, snp.name, snp.observed); -if (differentString(snp.strand,"?")) - printf("Strand: %s
\n", snp.strand); -printf("Observed: %s
\n", snp.observed); -printSnpAlleleAndOrthos(tdb, &snp, version); +struct snp125 *snp125 = (struct snp125 *)snp; +printSnpOrthoSummary(tdb, snp->name, snp->observed); +if (differentString(snp->strand,"?")) + printf("Strand: %s
\n", snp->strand); +printf("Observed: %s
\n", snp->observed); +printSnpAlleleAndOrthos(tdb, snp125, version); +puts("
| Location Type | %s |
| Class | %s |
| Validation | %s |
| Function | %s |
| Molecule Type | %s |
| Average Heterozygosity | " + "%.3f +/- %.3f |
| Weight | %d |
UCSC Annotations:
\n"); + printf("%s
\n", desc); + return TRUE; + } +return FALSE; +} + +void writeSnpExceptionFromTable(struct trackDb *tdb, char *itemName) /* Print out exceptions, if any, for this snp. */ { char *exceptionsTableSetting = trackDbSetting(tdb, "snpExceptions"); char exceptionsTable[128]; if (exceptionsTableSetting) safecpy(exceptionsTable, sizeof(exceptionsTable), exceptionsTableSetting); else safef(exceptionsTable, sizeof(exceptionsTable), "%sExceptions", tdb->table); -char *excDescTableSetting = trackDbSetting(tdb, "snpExceptionDesc"); -char excDescTable[128]; -if (excDescTableSetting) - safecpy(excDescTable, sizeof(excDescTable), excDescTableSetting); -else - safef(excDescTable, sizeof(excDescTable), "%sExceptionDesc", tdb->table); +char *excDescTable = getExcDescTable(tdb); if (hTableExists(database, exceptionsTable) && hTableExists(database, excDescTable)) { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[1024]; int start = cartInt(cart, "o"); - int count = 0; safef(query, sizeof(query), "select description, %s.exception from %s, %s " "where chrom = \"%s\" and chromStart = %d and name = \"%s\" " "and %s.exception = %s.exception", excDescTable, excDescTable, exceptionsTable, seqName, start, itemName, excDescTable, exceptionsTable); sr = sqlGetResult(conn, query); + boolean gotExc = FALSE; while ((row = sqlNextRow(sr))!=NULL) - { - /* Don't bother reporting MultipleAlignments here -- right after - * this, we have a whole section about the other mappings. */ - if (sameString(row[1], "MultipleAlignments")) - continue; - if (count == 0) - printf("
Annotations:
\n"); - printf("%s
\n", row[0]); - count++; + gotExc |= writeOneSnpException(row[1], row[0], gotExc); + sqlFreeResult(&sr); + hFreeConn(&conn); } +} + +static void writeSnpExceptionFromColumn(struct trackDb *tdb, struct snp132Ext *snp) +/* Hash the contents of exception description table, and for each exception listed + * in snp->exceptions, print out its description. */ +{ +char *excDescTable = getExcDescTable(tdb); +if (hTableExists(database, excDescTable)) + { + static struct hash *excDesc = NULL; + if (excDesc == NULL) + { + excDesc = hashNew(0); + struct sqlConnection *conn = hAllocConn(database); + char query[512]; + safef(query, sizeof(query), "select exception,description from %s", excDescTable); + struct sqlResult *sr = sqlGetResult(conn, query); + char **row; + while ((row = sqlNextRow(sr))!=NULL) + hashAdd(excDesc, row[0], cloneString(row[1])); sqlFreeResult(&sr); hFreeConn(&conn); } + struct slName *excList = slNameListFromComma(snp->exceptions), *exc; + boolean gotExc = FALSE; + for (exc = excList; exc != NULL; exc = exc->next) + { + char *desc = hashFindVal(excDesc, exc->name); + gotExc |= writeOneSnpException(exc->name, desc, gotExc); + } + } +} + +void writeSnpExceptionWithVersion(struct trackDb *tdb, struct snp132Ext *snp, int version) +/* Print out descriptions of exceptions, if any, for this snp. */ +{ +if (version >= 132) + writeSnpExceptionFromColumn(tdb, snp); +else + writeSnpExceptionFromTable(tdb, snp->name); } struct snp *snp125ToSnp(struct snp125 *snp125) /* Copy over the bed6 plus observed fields. */ { struct snp *snp; AllocVar(snp); snp->chrom = cloneString(snp125->chrom); snp->chromStart = snp125->chromStart; snp->chromEnd = snp125->chromEnd; snp->name = cloneString(snp125->name); snp->score = snp125->score; if (sameString(snp125->strand, "+")) snp->strand[0] = '+'; else if (sameString(snp125->strand, "-")) @@ -15845,41 +16026,42 @@ { char *hgdpGeoTable = "hgdpGeo"; // make this a trackDb setting if (!hTableExists(database, hgdpGeoTable)) return; struct sqlResult *sr; char **row; char query[512]; safef(query, sizeof(query), "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", hgdpGeoTable, itemName, seqName, start); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { struct hgdpGeo geo; hgdpGeoStaticLoad(row+1, &geo); - printf("
Human Genome Diversity Project SNP
\n"); + beginCollapsibleSection(tdb->track, "hgdpGeo", "Human Genome Diversity Project SNP", FALSE); printf("Note: These annotations are taken directly from the " "HGDP Selection Browser, " "and may indicate the allele on the opposite strand from that given above.
\n"); printf("Ancestral Allele: %c
\n", geo.ancestralAllele); printf("Derived Allele: %c
\n", geo.derivedAllele); printf("
| \n"); hgdpGeoFreqTable(&geo); printf(" | \n"); hgdpGeoImg(&geo); printf(" |
\n"); + printf("\"> HapMap SNP