Select Variants
\n");
/* Check for variant custom tracks. If there are none, tell the user that they should add one. */
struct slRef *varTrackList = NULL, *varGroupList = NULL;
tdbFilterGroupTrack(fullTrackList, fullGroupList, isVariantCustomTrack, NULL,
&varGroupList, &varTrackList);
if (varTrackList == NULL)
{
printf("Your session doesn't have any custom tracks or hub tracks in " PGSNP_OR_VCF
" format.\n");
hOnClickButton("selVar_AddPgpVcfCt", "return hgva.goToAddCustomTrack();",
"add pgSnp or VCF custom track");
if (hubConnectTableExists())
{
nbSpaces(2);
hOnClickButton("selVar_AddTrkHub", "document.trackHubForm.submit(); return false;", "add track hub");
}
puts(""); } else if (slCount(varTrackList) > 1) { printf("If you have more than one custom track or hub track in " PGSNP_OR_VCF " format, please select the one you wish to annotate:
\n"); } printf("variants: "); printf("
\n"); printf("
\n",
differentString(selected, hgvaUseHgvs) ? " style='display: none;'" : "");
printf("Enter HGVS terms: one term per line; blank lines and comment lines beginning with '#' "
"are ignored.
\n"); char *oldPasted = cartUsualString(cart, hgvaHgvs, ""); cgiMakeTextArea(hgvaHgvs, oldPasted, 10, 70); puts("
");
if (hasSnps)
{
printf("\n"); char *oldPasted = cartUsualString(cart, hgvaHgvs, ""); cgiMakeTextArea(hgvaHgvs, oldPasted, 10, 70); puts("
\n",
differentString(selected, hgvaUseVariantIds) ? " style='display: none;'" : "");
printf("Enter dbSNP rs# identifiers separated by whitespace or commas:
\n"); char *oldPasted = cartUsualString(cart, hgvaVariantIds, ""); cgiMakeTextArea(hgvaVariantIds, oldPasted, 10, 70); puts("
");
}
printf("maximum number of variants to be processed:\n");
char *curLimit = cartUsualString(cart, "hgva_variantLimit", "10000");
char *limitLabels[] = { "10", "100", "1,000", "10,000", "100,000" };
char *limitValues[] = { "10", "100", "1000", "10000", "100000" };
cgiMakeDropListWithVals("hgva_variantLimit", limitLabels, limitValues, ArraySize(limitLabels),
curLimit);
printCtAndHubButtons();
puts("\n"); char *oldPasted = cartUsualString(cart, hgvaVariantIds, ""); cgiMakeTextArea(hgvaVariantIds, oldPasted, 10, 70); puts("
"); } boolean isGeneTrack(struct trackDb *tdb, void *filterData) /* This is a TdbFilterFunction to get genePred tracks. */ { return (startsWith("genePred", tdb->type) || sameString("bigGenePred", tdb->type)); } char *selectGenes() /* Let user select a gene predictions track; return NULL if there are no genePred tracks. */ { struct slRef *trackRefList = NULL; tdbFilterGroupTrack(fullTrackList, fullGroupList, isGeneTrack, NULL, NULL, &trackRefList); boolean gotGP = (trackRefList != NULL); if (!gotGP) warn("This assembly (%s) has no gene prediction tracks, " "so the VAI will not be able to annotate it.", database); printf("
Select Genes
\n");
if (gotGP)
printf("The gene predictions selected here will be used ");
else
printf("Gene predictions are required in order ");
printf("to determine the effect of "
"each variant on genes, for example intronic, missense, splice site, intergenic etc.");
if (!gotGP)
printf(" Since this assembly has no gene prediction tracks, "
"the VAI can't provide functional annotations. "
"Please select a different genome."); printf("
\n"); if (! gotGP) return NULL; char *firstTrack = ((struct trackDb *)(trackRefList->val))->track; char *cartGeneTrack = cartOptionalString(cart, "hgva_geneTrack"); if (isNotEmpty(cartGeneTrack)) { // Make sure it's actually in trackRefList (might have been carried over from other db) boolean exists = FALSE; struct slRef *ref; for (ref = trackRefList; ref != NULL; ref = ref->next) { struct trackDb *tdb = ref->val; if (sameString(cartGeneTrack, tdb->track)) { exists = TRUE; break; } } if (!exists) cartGeneTrack = NULL; } char *selected = isNotEmpty(cartGeneTrack) ? cartGeneTrack : firstTrack; //#*** should show more info about each track... button to pop up track desc? if (gotGP) { printf("
"); } return selected; } //#*** We really need a dbNsfp.[ch]: enum PolyPhen2Subset { noSubset, HDIV, HVAR }; char *formatDesc(char *url, char *name, char *details, boolean doHtml) /* Return a description with URL for name plus extra details. If doHtml, * wrap URL in .... */ { char desc[1024]; if (doHtml) safef(desc, sizeof(desc), "%s %s", url, name, details); else safef(desc, sizeof(desc), "(%s) %s %s", url, name, details); return cloneString(desc); } char *dbNsfpDescFromTableName(char *tableName, enum PolyPhen2Subset subset, boolean doHtml) /* Return a description for table name... if these become tracks, use tdb of course. */ { if (sameString(tableName, "dbNsfpSift")) return formatDesc("http://sift.bii.a-star.edu.sg/", "SIFT", "(D = damaging, T = tolerated)", doHtml); else if (sameString(tableName, "dbNsfpPolyPhen2")) { if (subset == HDIV) return formatDesc("http://genetics.bwh.harvard.edu/pph2/", "PolyPhen-2", "with HumDiv training set " "(D = probably damaging, P = possibly damaging, B = benign)", doHtml); else if (subset == HVAR) return formatDesc("http://genetics.bwh.harvard.edu/pph2/", "PolyPhen-2", "with HumVar training set " "(D = probably damaging, P = possibly damaging, B = benign)", doHtml); else errAbort("dbNsfpDescFromTableName: invalid PolyPhen2 subset type (%d)", subset); } else if (sameString(tableName, "dbNsfpMutationTaster")) return formatDesc("http://www.mutationtaster.org/", "MutationTaster", "(A = disease causing automatic, D = disease causing, " "N = polymorphism, P = polymorphism automatic)", doHtml); else if (sameString(tableName, "dbNsfpMutationAssessor")) return formatDesc("http://mutationassessor.org/", "MutationAssessor", "(high or medium: predicted functional; " "low or neutral: predicted non-functional)", doHtml); else if (sameString(tableName, "dbNsfpLrt")) return formatDesc("http://www.genetics.wustl.edu/jflab/lrt_query.html", "Likelihood ratio test (LRT)", "(D = deleterious, N = Neutral, U = unknown)", doHtml); else if (sameString(tableName, "dbNsfpVest")) return formatDesc("http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3665549/", "Variant Effect Scoring Tool (VEST)", "(scores [0-1] predict confidence that a change is deleterious", doHtml); else if (sameString(tableName, "dbNsfpGerpNr")) return formatDesc("http://mendel.stanford.edu/SidowLab/downloads/gerp/index.html", "GERP++", "Neutral Rate (NR)", doHtml); else if (sameString(tableName, "dbNsfpGerpRs")) return formatDesc("http://mendel.stanford.edu/SidowLab/downloads/gerp/index.html", "GERP++", "Rejected Substitutions (RS)", doHtml); else if (sameString(tableName, "dbNsfpInterPro")) return formatDesc("http://www.ebi.ac.uk/interpro/", "InterPro", "protein domains", doHtml); return NULL; } struct slName *findDbNsfpTables() /* See if this database contains dbNSFP tables. */ { if (startsWith(hubTrackPrefix, database)) return NULL; struct sqlConnection *conn = hAllocConn(database); struct slName *dbNsfpTables = sqlListTablesLike(conn, "LIKE 'dbNsfp%'"); hFreeConn(&conn); return dbNsfpTables; } void printDbNsfpSource(char *table, enum PolyPhen2Subset subset) /* If we know what to do with table, make a checkbox with descriptive label. */ { char *description = dbNsfpDescFromTableName(table, subset, TRUE); if (description != NULL) { char cartVar[512]; if (subset == HDIV) safef(cartVar, sizeof(cartVar), "hgva_track_%s_%s:HDIV", database, table); else if (subset == HVAR) safef(cartVar, sizeof(cartVar), "hgva_track_%s_%s:HVAR", database, table); else safef(cartVar, sizeof(cartVar), "hgva_track_%s_%s", database, table); boolean defaultChecked = (sameString("dbNsfpSift", table) || sameString("dbNsfpPolyPhen2", table)); cartMakeCheckBox(cart, cartVar, defaultChecked); printf("%s
\n", description); } } void selectDbNsfp(struct slName *dbNsfpTables) /* Let user select scores/predicitions from various tools collected by dbNSFP. */ { if (dbNsfpTables == NULL) return; startCollapsibleSection("dbNsfp", "Database of Non-synonymous Functional Predictions (dbNSFP)", TRUE); //#*** hardcoded version info... we need metadata (#11462) char *dbNsfpVersion = "3.1a"; char *txVersion = "Gencode release 22 (Ensembl 79, Mar. 2015)"; char *refYear = "2015"; char *refUrl = "http://onlinelibrary.wiley.com/doi/10.1002/humu.22932/abstract"; // For the time being hg19 is still on version 2.0: if (sameString(database, "hg19")) { dbNsfpVersion = "2.0"; txVersion = "Gencode release 9 (Ensembl 64, Dec. 2011)"; refYear = "2013"; refUrl = "http://onlinelibrary.wiley.com/doi/10.1002/humu.22376/abstract"; } printf("dbNSFP " "(Liu et al. %s) " "release %s " "provides pre-computed scores and predictions of functional significance " "from a variety of tools. Every possible coding change to transcripts in " "%s gene predictions " "has been evaluated. " "Note: This may not encompass all transcripts in your " "selected gene set.
\n", refUrl, refYear, dbNsfpVersion, txVersion); //#*** Another cheap hack: reverse alph order happens to be what we want (until VEST??), //#*** but priorities would be cleaner: slReverse(&dbNsfpTables); jsMakeSetClearContainer(); struct slName *table; for (table = dbNsfpTables; table != NULL; table = table->next) { if (sameString(table->name, "dbNsfpPolyPhen2")) { printDbNsfpSource(table->name, HDIV); printDbNsfpSource(table->name, HVAR); } else printDbNsfpSource(table->name, 0); } jsEndContainer(); puts("
"); endCollapsibleSection(); } boolean findSnpBed4(char *suffix, char **retFileName, struct trackDb **retTdb) /* If we can find the latest snpNNNsuffix table, or better yet a bigBed file for it (faster), * set the appropriate ret* and return TRUE, otherwise return FALSE. */ { struct trackDb *tdb = hFindLatestSnpTrack(database, suffix, &fullTrackList); if (tdb == NULL) return FALSE; boolean foundIt = FALSE; // Do we happen to have a bigBed version? Better yet, bed4 only for current uses: char origFileName[HDB_MAX_PATH_STRING]; safef(origFileName, sizeof(origFileName), "/gbdb/%s/vai/%s.bed4.bb", database, tdb->table); char* fileName = hReplaceGbdb(origFileName); if (fileExists(fileName)) { if (retFileName != NULL) *retFileName = fileName; foundIt = TRUE; } else { // Not bed4; try just .bb: freez(&fileName); safef(origFileName, sizeof(origFileName), "/gbdb/%s/vai/%s.bb", database, tdb->table); fileName = hReplaceGbdb(origFileName); if (fileExists(fileName)) { if (retFileName != NULL) *retFileName = fileName; foundIt = TRUE; } } if (retTdb == NULL) return foundIt; else *retTdb = tdb; return TRUE; } void selectDbSnp(boolean gotSnp) /* Offer to include rsID (and other fields, or leave that for advanced output??) if available */ { if (!gotSnp) return; startCollapsibleSection("dbSnp", "Known variation", TRUE); cartMakeCheckBox(cart, "hgva_rsId", TRUE); printf("Include dbSNP " "rs# ID if one exists
\n"); puts("
"); endCollapsibleSection(); } #define GENCODE_PREFIX "wgEncodeGencode" struct slName *getGencodeTagVersions() /* Return a list of version strings from the ends of wgEncodeGencodeTag% tables. */ { static struct slName *tagVersions = NULL; if (tagVersions == NULL) { struct sqlConnection *conn = hAllocConn(database); struct slName *tagTables = sqlQuickList(conn, NOSQLINJ "show tables like '"GENCODE_PREFIX"Tag%'"); int offset = strlen(GENCODE_PREFIX"Tag"); struct slName *tt; for (tt = tagTables; tt != NULL; tt = tt->next) slAddHead(&tagVersions, slNameNew(tt->name + offset)); hFreeConn(&conn); } return slNameCloneList(tagVersions); } boolean knownGeneHasGencodeTags() /* Return TRUE if this database has knownToTag for knownGene. */ { return hTableExists(database, "knownGene") && hTableExists(database, "knownToTag"); } boolean hasGencodeTags() /* Return TRUE if GENCODE tags can be associated with some gene track in database. */ { return knownGeneHasGencodeTags() || (getGencodeTagVersions() != NULL); } void genbankGetDbTable(char *db, char *gbTable, char **retGenbankDb, char **retTableName) /* Genbank tables (e.g. gbCdnaInfoTable) may now include a 'db.' prefix, e.g. * hgFixed.gbCdnaInfo. If so, separate out the database and table name. If gbTable * does not have a 'db.' prefix then use the configured genbankDb if given, else db. */ { char *genbankDb = cfgOptionEnv("GENBANKDB", "genbankDb"); char *tableName = gbTable; char tableCopy[strlen(gbTable)+1]; safecpy(tableCopy, sizeof(tableCopy), gbTable); char *words[2]; int wordCount = chopByChar(tableCopy, '.', words, ArraySize(words)); if (wordCount == 2) { genbankDb = words[0]; tableName = words[1]; } else if (isEmpty(genbankDb)) genbankDb = db; if (retGenbankDb) *retGenbankDb = cloneString(genbankDb); if (retTableName) *retTableName = cloneString(tableName); } boolean genbankTableExists(char *db, char *gbTable) /* Return TRUE if table (which may or may not be prefixed by genbankDb) exists in * genbankDb or db. */ { char *genbankDb=NULL, *tableName=NULL; genbankGetDbTable(db, gbTable, &genbankDb, &tableName); return hTableExists(genbankDb, tableName); } boolean hasTxStatus() /* Return TRUE if any gene track in database has some kind of transcript status info * like knownCanonical, GENCODE tags and/or RefSeq status. */ { if (hasGencodeTags()) return TRUE; if (hTableExists(database, "knownGene") && hTableExists(database, "knownCanonical")) return TRUE; if (hTableExists(database, "refGene") && genbankTableExists(database, refSeqStatusTable)) return TRUE; return FALSE; } char *getLatestGencodeVersion(struct slName *versionList) /* Return the numerically largest version found in versionList. */ { int maxVersionNum = -1; char *maxVersion = NULL; struct slName *version; for (version = versionList; version != NULL; version = version->next) { int versionNum = atoi(skipToNumeric(version->name)); if (versionNum > maxVersionNum) { maxVersionNum = versionNum; maxVersion = version->name; } } return cloneString(maxVersion); } INLINE char *gencodeTableName(char *suffix, char *version, char *buf, size_t bufSize) /* Write wgEncodeGencode
",
maybeKnownGene, maybeRefGene, maybeEnsGene, versions,
isVisible ? "block" : "none");
cartMakeCheckBox(cart, "hgva_txStatus_gencode", FALSE);
puts("Include the GENCODE tags (if any) "
"associated with each transcript.
"); puts("
");
}
if (hTableExists(database, "knownGene") && hTableExists(database, "knownCanonical"))
{
boolean isVisible = sameString(geneTrack, "knownGene");
somethingIsVisible |= isVisible;
printf(""); puts("
",
isVisible ? "block" : "none");
cartMakeCheckBox(cart, "hgva_txStatus_knownCanonical", FALSE);
char *desc = hTableExists(database, "knownToTag") ?
"based on "
"APPRIS status or inclusion in "
"GENCODE Basic subset: "
"principal > alternative > basic > longest isoform" :
"generally the longest isoform of a gene";
printf("Indicate whether each transcript is 'canonical' (%s).
\n", desc); puts("
");
}
if (hTableExists(database, "refGene") && genbankTableExists(database, refSeqStatusTable))
{
boolean isVisible = sameString(geneTrack, "refGene");
somethingIsVisible |= isVisible;
printf("\n", desc); puts("
",
isVisible ? "block" : "none");
cartMakeCheckBox(cart, "hgva_txStatus_refSeqStatus", FALSE);
puts("Include the "
"RefSeq status of each transcript.
"); puts("
");
}
printf(""); puts("
",
somethingIsVisible ? "none" : "block");
puts("No transcript status data are available for the selected gene track.");
puts("
");
puts(""); endCollapsibleSection(); } +static boolean canDoHgvsOut(char *geneTrack) +/* Return TRUE if we're able to make HGVS output terms for transcripts in geneTrack. */ +{ +return sameString(geneTrack, "refGene") || startsWith("ncbiRefSeq", geneTrack); +} + static void selectHgvsOut(char *geneTrack) /* Offer HGVS output choices if RefSeq Genes are selected */ { startCollapsibleSection("hgvsOut", "HGVS variant nomenclature", TRUE); printf("The Human Genome Variation Society (HGVS) " "has established a " "sequence variant nomenclature, " "an international standard used to report variation in " "genomic, transcript and protein sequences.
\n"); -boolean refSeqSelected = sameString(geneTrack, "refGene") || startsWith("ncbiRefSeq", geneTrack); -printf("
", refSeqSelected ? "block" : "none");
+boolean hgvsOk = canDoHgvsOut(geneTrack);
+printf("
"); endCollapsibleSection(); } boolean isHg19RegulatoryTrack(struct trackDb *tdb, void *filterData) /* For now, just look for a couple specific tracks by tableName. */ { //#*** NEED METADATA return (sameString("wgEncodeRegDnaseClusteredV3", tdb->table) || sameString("wgEncodeRegTfbsClusteredV3", tdb->table)); } boolean isHg38RegulatoryTrack(struct trackDb *tdb, void *filterData) /* For now, just look for a couple specific tracks by tableName. */ { //#*** NEED METADATA return (sameString("wgEncodeRegDnaseClustered", tdb->table) || sameString("wgEncodeRegTfbsClusteredV3", tdb->table)); } struct slRef *findRegulatoryTracks() /* Look for the very limited set of Regulation tracks that hgVai offers. */ { struct slRef *regTrackRefList = NULL; if (sameString(database, "hg19")) tdbFilterGroupTrack(fullTrackList, fullGroupList, isHg19RegulatoryTrack, NULL, NULL, ®TrackRefList); else if (sameString(database, "hg38")) tdbFilterGroupTrack(fullTrackList, fullGroupList, isHg38RegulatoryTrack, NULL, NULL, ®TrackRefList); return regTrackRefList; } void selectRegulatory() /* If trackRefList is non-NULL, make a section with a checkbox for each track, * labelled with longLabel, and optionally some filtering options. */ { struct slRef *trackRefList = findRegulatoryTracks(); if (trackRefList != NULL) { puts("
"); printf("");
struct slRef *ref;
for (ref = trackRefList; ref != NULL; ref = ref->next)
{
struct trackDb *tdb = ref->val;
char cartVar[512];
safef(cartVar, sizeof(cartVar), "hgva_track_%s_%s", database, tdb->track);
puts("
");
}
}
boolean isConsElTrack(struct trackDb *tdb, void *filterData)
/* This is a TdbFilterFunction to get "phastConsNwayElements" tracks. */
{
return (startsWith("phastCons", tdb->table) && stringIn("Elements", tdb->table));
}
boolean isConsScoreTrack(struct trackDb *tdb, void *filterData)
/* This is a TdbFilterFunction to get tracks that start with "phastCons" (no Elements)
* or "phyloP". */
{
return ((startsWith("phastCons", tdb->table) && !stringIn("Elements", tdb->table))
|| startsWith("phyloP", tdb->table));
}
void findCons(struct slRef **retElTrackRefList, struct slRef **retScoreTrackRefList)
/* See if this database has Conserved Elements and/or Conservation Scores */
{
tdbFilterGroupTrack(fullTrackList, fullGroupList, isConsElTrack,
NULL, NULL, retElTrackRefList);
tdbFilterGroupTrack(fullTrackList, fullGroupList, isConsScoreTrack,
NULL, NULL, retScoreTrackRefList);
}
boolean trackNameMatches(struct trackDb *tdb, void *filterData)
/* This is a TdbFilterFunction to get track(s) whose tdb->track matches name (filterData). */
{
char *name = filterData;
return sameString(tdb->track, name);
}
struct slRef *findTrackRefByName(char *name)
/* Return a reference to the named track, if found. */
{
struct slRef *trackRefList = NULL;
tdbFilterGroupTrack(fullTrackList, fullGroupList, trackNameMatches, name, NULL, &trackRefList);
return trackRefList;
}
void trackCheckBoxSection(char *sectionSuffix, char *title, struct slRef *trackRefList)
/* If trackRefList is non-NULL, make a collapsible section with a checkbox for each track,
* labelled with longLabel. */
{
if (trackRefList != NULL)
{
startCollapsibleSection(sectionSuffix, title, FALSE);
struct slRef *ref;
for (ref = trackRefList; ref != NULL; ref = ref->next)
{
struct trackDb *tdb = ref->val;
char cartVar[512];
safef(cartVar, sizeof(cartVar), "hgva_track_%s_%s", database, tdb->track);
cartMakeCheckBox(cart, cartVar, FALSE);
struct trackDb *topTdb = trackDbTopLevelSelfOrParent(tdb);
printf("%s
\n", hgTrackUiName(), cartSidUrlString(cart), topTdb->track, tdb->longLabel); } puts("
"); endCollapsibleSection(); } } void selectAnnotations(char *geneTrack) /* Beyond predictions of protein-coding effect, what other basic data can we integrate? */ { struct slName *dbNsfpTables = findDbNsfpTables(); boolean gotSnp = findSnpBed4("", NULL, NULL); struct slRef *elTrackRefList = NULL, *scoreTrackRefList = NULL; findCons(&elTrackRefList, &scoreTrackRefList); struct slRef *cosmicTrackRefList = findTrackRefByName("cosmic"); boolean hasTxStat = hasTxStatus(); if (dbNsfpTables == NULL && !gotSnp && elTrackRefList == NULL && scoreTrackRefList == NULL && cosmicTrackRefList == NULL && !hasTxStat) return; puts("
"); printf("");
selectDbNsfp(dbNsfpTables);
selectTxStatus(hasTxStat, geneTrack);
selectHgvsOut(geneTrack);
selectDbSnp(gotSnp);
trackCheckBoxSection("Cosmic", "COSMIC", cosmicTrackRefList);
trackCheckBoxSection("ConsEl", "Conserved elements", elTrackRefList);
trackCheckBoxSection("ConsScore", "Conservation scores", scoreTrackRefList);
puts("
");
}
void selectFiltersFunc()
/* Options to restrict variants based on gene region/soTerm from gpFx */
{
startCollapsibleSection("filtersFunc", "Functional role", FALSE);
printf("Include variants annotated as
\n"); jsMakeSetClearContainer(); cartMakeCheckBox(cart, "hgva_include_intergenic", TRUE); printf("intergenic
\n"); cartMakeCheckBox(cart, "hgva_include_upDownstream", TRUE); printf("upstream/downstream of gene
\n"); cartMakeCheckBox(cart, "hgva_include_nmdTranscript", TRUE); printf("in transcript already subject to nonsense-mediated decay (NMD)
\n"); cartMakeCheckBox(cart, "hgva_include_exonLoss", TRUE); printf("exon loss caused by deletion
\n"); cartMakeCheckBox(cart, "hgva_include_utr", TRUE); printf("5' or 3' UTR
\n"); cartMakeCheckBox(cart, "hgva_include_cdsSyn", TRUE); printf("CDS - synonymous coding change
\n"); cartMakeCheckBox(cart, "hgva_include_cdsNonSyn", TRUE); printf("CDS - non-synonymous (missense, stop gain/loss, frameshift etc)
\n"); cartMakeCheckBox(cart, "hgva_include_intron", TRUE); printf("intron
\n"); cartMakeCheckBox(cart, "hgva_include_splice", TRUE); printf("splice site or splice region
\n"); cartMakeCheckBox(cart, "hgva_include_nonCodingExon", TRUE); printf("exon of non-coding gene
\n"); cartMakeCheckBox(cart, "hgva_include_noVariation", TRUE); printf("\"variants\" for which no alternate allele has been observed
\n"); struct slRef *regTrackRefList = findRegulatoryTracks(); if (regTrackRefList != NULL) { cartMakeCheckBox(cart, "hgva_include_regulatory", TRUE); printf("regulatory element (note: these are detected only if one or more tracks " "are selected in Regulatory regions above)
\n"); } jsEndContainer(); puts("
"); endCollapsibleSection(); } void selectFiltersKnownVar() /* Options to restrict output based on overlap with known variants. */ { boolean gotCommon = findSnpBed4("Common", NULL, NULL); boolean gotMult = findSnpBed4("Mult", NULL, NULL); if (!gotCommon && !gotMult) return; startCollapsibleSection("filtersVar", "Known variation", FALSE); if (gotMult) { cartMakeCheckBox(cart, "hgva_include_snpMult", TRUE); printf("Include variants even if they are co-located with variants that have been mapped to " "multiple genomic locations by dbSNP
\n"); } if (gotCommon) { cartMakeCheckBox(cart, "hgva_include_snpCommon", TRUE); printf("Include variants even if they are co-located with \"common\" variants " "(uniquely mapped variants with global minor allele frequency (MAF) " "of at least 1%% according to dbSNP)
\n"); } puts("
"); endCollapsibleSection(); } void selectFiltersCons() /* Options to restrict output based on overlap with conserved elements. */ { struct slRef *elTrackRefList = NULL; tdbFilterGroupTrack(fullTrackList, fullGroupList, isConsElTrack, NULL, NULL, &elTrackRefList); if (elTrackRefList == NULL) return; startCollapsibleSection("filtersCons", "Conservation", FALSE); // Use a little table to indent radio buttons (if we do those) past checkbox: puts("
");
}
else
{
puts("");
char *selected = cartUsualString(cart, "hgva_require_consEl_track", "");
struct slRef *ref;
for (ref = elTrackRefList; ref != NULL; ref = ref->next)
{
printf("");
struct trackDb *tdb = ref->val;
cgiMakeOnEventRadioButtonWithClass("hgva_require_consEl_track", tdb->track,
sameString(tdb->track, selected),
NULL, "click", "setCheckboxList('hgva_require_consEl', true);");
printf("%s
"); printf("");
selectFiltersFunc();
selectFiltersKnownVar();
selectFiltersCons();
puts("
");
}
void selectOutput()
/* Just VEP text for now... should also have VEP HTML with limited # lines too.
* Next: custom track with same subset of info as we would stuff in VEP */
{
puts("
"); printf("
\n"); char *compressType = cartUsualString(cart, "hgva_compressType", textOutCompressNone); char *fileName = cartUsualString(cart, "hgva_outFile", ""); printf("output file: "); cgiMakeTextVar("hgva_outFile", fileName, 29); printf(" (leave blank to keep output in browser)
\n"); printf("file type returned: "); cgiMakeRadioButton("hgva_compressType", textOutCompressNone, sameWord(textOutCompressNone, compressType)); printf(" plain text "); cgiMakeRadioButton("hgva_compressType", textOutCompressGzip, sameWord(textOutCompressGzip, compressType)); printf(" gzip compressed (ignored if output file is blank)"); puts("
"); } void submitAndDisclaimer() { puts("
"); printf("
\n");
printf("\n");
cgiMakeOnClickButton("subDisclmAgrd","hgva.submitQueryIfDisclaimerAgreed();", "Get results");
puts("
"); } /* * When user clicks submit, we need to roll a JSON querySpec from form selections, * and show data from a submission to hgAnnoGrator. redirect from this CGI? * or have javascript submit directly? * * primary: variants, from custom track * * if there are genes, those w/annoGratorGpVar * * if there are {dbSNP, dbNsfp, regulatory, cons} selections, grator for each of those * * vep output config * * If we get bold & offer 1000Genomes VCF, will def. need handling of split chroms. * Are we really going to offer genome-wide in hgVai? * Up-front limit on #rows of input ? * * Eventually, we might want a FormatVep that produces structs that are passed * forward to multiple output writers... I would want to send it lots of gratorData * like a formatter, but it would produce rows like an annoGrator. * Maybe annoGrators should accept a bunch of input rows like formatters? * or would this grator wrap all the input grators inside? */ void doMainPage() /* Print out initial HTML of control page. */ { jsInit(); webIncludeResourceFile("jquery-ui.css"); webIncludeResourceFile("ui.dropdownchecklist.css"); boolean alreadyAgreed = cartUsualBoolean(cart, "hgva_agreedToDisclaimer", FALSE); jsInlineF( "$(document).ready(function() { hgva.disclaimer.init(%s, hgva.userClickedAgree); });\n" , alreadyAgreed ? "true" : "false"); addSomeCss(); printAssemblySection(); puts("
"); // Make wrapper table for collapsible sections: selectVariants(); char *geneTrack = selectGenes(); if (geneTrack != NULL) { selectRegulatory(); selectAnnotations(geneTrack); selectFilters(); selectOutput(); submitAndDisclaimer(); } printf(""); jsReloadOnBackButton(cart); webNewSection("Using the Variant Annotation Integrator"); webIncludeHelpFileSubst("hgVaiHelpText", cart, FALSE); jsIncludeFile("jquery-ui.js", NULL); jsIncludeFile("hgVarAnnogrator.js", NULL); jsIncludeFile("ui.dropdownchecklist.js", NULL); jsIncludeFile("ddcl.js", NULL); } void doUi() /* Set up globals and make web page */ { cartWebStart(cart, database, "Variant Annotation Integrator"); doMainPage(); cartWebEnd(); /* Save variables. */ cartCheckout(&cart); } void checkVariantTrack(struct trackDb *tdb) /* variantTrack should be either pgSnp or VCF. */ { if (! sameString(tdb->type, "pgSnp") && ! startsWith("vcf", tdb->type)) { errAbort("Expected variant track '%s' to be type pgSnp, vcf or vcfTabix, but it's '%s'", tdb->track, tdb->type); } } char *fileNameFromTable(char *table) /* Get fileName from a bigData table (for when we don't have a trackDb, just table). */ { struct sqlConnection *conn = hAllocConn(database); char query[512]; sqlSafef(query, sizeof(query), "select fileName from %s", table); char *fileName = sqlQuickString(conn, query); hFreeConn(&conn); char *fileNameRewrite = hReplaceGbdb(fileName); freez(&fileName); return fileNameRewrite; } void textOpen() /* Start serving up plain text, possibly via a pipeline to gzip. */ { char *fileName = textOutSanitizeHttpFileName(cartUsualString(cart, "hgva_outFile", "")); char *compressType = cartUsualString(cart, "hgva_compressType", textOutCompressGzip); compressPipeline = textOutInit(fileName, compressType, NULL); } void setGpVarFuncFilter(struct annoGrator *gpVarGrator) /* Use cart variables to configure gpVarGrator's filtering by functional category. */ { struct annoGratorGpVarFuncFilter aggvFuncFilter; ZeroVar(&aggvFuncFilter); aggvFuncFilter.intergenic = cartUsualBoolean(cart, "hgva_include_intergenic", TRUE); aggvFuncFilter.upDownstream = cartUsualBoolean(cart, "hgva_include_upDownstream", TRUE); aggvFuncFilter.nmdTranscript = cartUsualBoolean(cart, "hgva_include_nmdTranscript", TRUE); aggvFuncFilter.exonLoss = cartUsualBoolean(cart, "hgva_include_exonLoss", TRUE); aggvFuncFilter.utr = cartUsualBoolean(cart, "hgva_include_utr", TRUE); aggvFuncFilter.cdsSyn = cartUsualBoolean(cart, "hgva_include_cdsSyn", TRUE); aggvFuncFilter.cdsNonSyn = cartUsualBoolean(cart, "hgva_include_cdsNonSyn", TRUE); aggvFuncFilter.intron = cartUsualBoolean(cart, "hgva_include_intron", TRUE); aggvFuncFilter.splice = cartUsualBoolean(cart, "hgva_include_splice", TRUE); aggvFuncFilter.nonCodingExon = cartUsualBoolean(cart, "hgva_include_nonCodingExon", TRUE); aggvFuncFilter.noVariation = cartUsualBoolean(cart, "hgva_include_noVariation", TRUE); annoGratorGpVarSetFuncFilter(gpVarGrator, &aggvFuncFilter); } static void setHgvsOutOptions(struct annoGrator *gpVarGrator, char *geneTrack) /* Use cart variables to configure gpVarGrator's HGVS output. */ { uint hgvsOutOptions = 0; -if (sameString(geneTrack, "refGene") || startsWith("ncbiRefSeq", geneTrack)) +if (canDoHgvsOut(geneTrack)) { if (cartUsualBoolean(cart, "hgva_hgvsG", FALSE)) hgvsOutOptions |= HGVS_OUT_G; if (cartUsualBoolean(cart, "hgva_hgvsCN", FALSE)) hgvsOutOptions |= HGVS_OUT_CN; if (cartUsualBoolean(cart, "hgva_hgvsP", FALSE)) hgvsOutOptions |= HGVS_OUT_P; if (cartUsualBoolean(cart, "hgva_hgvsPAddParens", FALSE)) hgvsOutOptions |= HGVS_OUT_P_ADD_PARENS; if (cartUsualBoolean(cart, "hgva_hgvsBreakDelIns", FALSE)) hgvsOutOptions |= HGVS_OUT_BREAK_DELINS; - annoGratorGpVarSetHgvsOutOptions(gpVarGrator, hgvsOutOptions); } +annoGratorGpVarSetHgvsOutOptions(gpVarGrator, hgvsOutOptions); } struct annoGrator *gratorForSnpBed4(struct hash *gratorsByName, char *suffix, struct annoAssembly *assembly, char *chrom, enum annoGratorOverlap overlapRule, char **retDescription) /* Look up snpNNNsuffix; if we find it, return a grator (possibly for a bigBed 4 file), * otherwise return NULL. */ { char *fileName = NULL; struct trackDb *tdb = NULL; if (! findSnpBed4(suffix, &fileName, &tdb)) return NULL; struct annoGrator *grator = NULL; // First look in gratorsByName to see if this grator has already been constructed: if (tdb != NULL) { grator = hashFindVal(gratorsByName, tdb->table); if (retDescription) *retDescription = cloneString(tdb->longLabel); } if (grator != NULL) { // Set its overlap behavior and we're done. grator->setOverlapRule(grator, overlapRule); return grator; } // If not in gratorsByName, then attempt to construct it here: if (fileName != NULL) grator = hAnnoGratorFromBigFileUrl(fileName, NULL, assembly, ANNO_NO_LIMIT, overlapRule); else grator = hAnnoGratorFromTrackDb(assembly, tdb->table, tdb, chrom, ANNO_NO_LIMIT, NULL, overlapRule, NULL); if (grator != NULL) hashAdd(gratorsByName, tdb->table, grator); return grator; } char *tableNameFromSourceName(char *sourceName) /* Strip sourceName (file path or db.table) to just the basename or table name. */ { char *tableName = cloneString(sourceName); char *p = strrchr(tableName, '/'); if (p != NULL) { // file path; strip to basename char dir[PATH_LEN], name[FILENAME_LEN], extension[FILEEXT_LEN]; splitPath(tableName, dir, name, extension); safecpy(tableName, strlen(tableName)+1, name); } else { // database.table -- skip database. p = strchr(tableName, '.'); if (p != NULL) tableName = p+1; } return tableName; } char *tagFromTableName(char *tableName, char *suffix) /* Generate a tag for VEP's extras column or VCF's info column. */ { char *p = strstr(tableName, "dbNsfp"); if (p != NULL) tableName = p + strlen("dbNsfp"); int suffixLen = (suffix == NULL) ? 0 : strlen(suffix); int tagSize = strlen(tableName) + suffixLen + 1; char *tag = cloneStringZ(tableName, tagSize); if (isNotEmpty(suffix)) safecat(tag, tagSize, suffix); touppers(tag); // Some custom shortenings, to avoid very long tag names: (void)strSwapStrs(tag, tagSize, "POLYPHEN", "PP"); (void)strSwapStrs(tag, tagSize, "MUTATION", "MUT"); (void)strSwapStrs(tag, tagSize, "PHYLOP", "PHP"); (void)strSwapStrs(tag, tagSize, "PHASTCONS", "PHC"); (void)strSwapStrs(tag, tagSize, "ELEMENTS", "EL"); (void)strSwapStrs(tag, tagSize, "PRIMATES", "PRIM"); (void)strSwapStrs(tag, tagSize, "PLACENTAL", "PLAC"); if (regexMatch(tag, "^PH.*[0-9]WAY")) (void)strSwapStrs(tag, tagSize, "WAY", "W"); (void)strSwapStrs(tag, tagSize, "WGENCODEREGDNASECLUSTERED", "DNASE"); (void)strSwapStrs(tag, tagSize, "WGENCODEREGTFBSCLUSTERED", "TFBS"); return tag; } enum PolyPhen2Subset stripSubsetFromTrackName(char *trackName) /* trackName may have a _suffix for a subset of PolyPhen2; convert that to enum * and zero out the suffix so we have the real trackName. */ { enum PolyPhen2Subset subset = noSubset; char *p = strchr(trackName, ':'); if (p != NULL) { if (sameString(p+1, "HDIV")) subset = HDIV; else if (sameString(p+1, "HVAR")) subset = HVAR; else errAbort("unrecognized suffix in track_suffix '%s'", trackName); *p = '\0'; } return subset; } void updateGratorListAndVepExtra(struct annoGrator *grator, struct annoGrator **pGratorList, struct annoFormatter *vepOut, enum PolyPhen2Subset subset, char *column, char *description, boolean isReg) /* If grator is non-NULL, add it to gratorList and vepOut's list of items for EXTRAs column. */ { if (grator == NULL) return; slAddHead(pGratorList, grator); if (vepOut != NULL) { char *tableName = tableNameFromSourceName(grator->streamer.name); char *suffix = NULL; if (subset == HDIV) suffix = "HDIV"; else if (subset == HVAR) suffix = "HVAR"; char *tag = tagFromTableName(tableName, suffix); if (isEmpty(description)) description = grator->streamer.name; if (isReg) annoFormatVepAddRegulatory(vepOut, (struct annoStreamer *)grator, tag, description, column); else annoFormatVepAddExtraItem(vepOut, (struct annoStreamer *)grator, tag, description, column, FALSE); } } INLINE void updateGratorList(struct annoGrator *grator, struct annoGrator **pGratorList) /* If grator is non-NULL, add it to gratorList. */ { updateGratorListAndVepExtra(grator, pGratorList, NULL, 0, NULL, NULL, FALSE); } void addDbNsfpSeqChange(char *trackName, struct annoAssembly *assembly, struct hash *gratorsByName, struct annoGrator **pGratorList) // If the user has selected dbNsfp* data, we also need the underlying dbNsfpSeqChange // data, so annoFormatVep can tell whether the variant and gpFx are consistent with the // variant and transcript that dbNsfp used to calculate scores. { //#*** Yet another place where we need metadata: char *seqChangeTable = "dbNsfpSeqChange"; if (hashFindVal(gratorsByName, seqChangeTable) == NULL) { char *fileName = fileNameFromTable(seqChangeTable); if (fileName == NULL) errAbort("'%s' requested, but I can't find fileName for %s", trackName, seqChangeTable); struct annoGrator *grator = hAnnoGratorFromBigFileUrl(fileName, NULL, assembly, ANNO_NO_LIMIT, agoNoConstraint); updateGratorList(grator, pGratorList); hashAdd(gratorsByName, seqChangeTable, grator); } } static struct dyString *dyInfo = NULL; struct hash *getTrackFilterVars(char *track) /* Return a hash of filter variable names (cart variable suffixes) to slName lists of values. */ { char filterPrefix[512]; safef(filterPrefix, sizeof(filterPrefix), "hgva_filter_%s_", track); struct slPair *filterVars = cartVarsWithPrefix(cart, filterPrefix), *var; int prefixLen = strlen(filterPrefix); struct hash *varHash = hashNew(0); for (var = filterVars; var != NULL; var = var->next) { char *varName = var->name+prefixLen; char *val = var->val; struct hashEl *hel = hashLookup(varHash, varName); if (hel != NULL) slNameAddHead((struct slName **)(&hel->val), val); else hashAdd(varHash, varName, slNameNew(val)); } return varHash; } INLINE boolean isNotAll(struct slName *valList) /* Return TRUE unless valList has one element with name "All" (for multiselects). */ { if (slCount(valList) == 1 && sameString(valList->name, "All")) return FALSE; return TRUE; } void factorSourceGratorAddFilter(struct annoGrator *grator, char *name, struct slName *valList) /* Add filter to factorSource grator. */ //#*** Do these smarts belong here in hgVai? Probably not -- should be an hg/lib module with //#*** UI/metadata smarts. { struct annoStreamer *gStreamer = (struct annoStreamer *)grator; struct annoFilter *filter = NULL; if (sameString(name, "name") || sameString(name, "cellType") || sameString(name, "treatment")) { if (valList && isNotAll(valList)) filter = annoFilterFromAsColumn(gStreamer->asObj, name, afMatch, valList); } else if (sameString(name, "score")) filter = annoFilterFromAsColumn(gStreamer->asObj, name, afGTE, valList); else errAbort("Unrecognized filter name '%s' for %s, type=factorSource", name, gStreamer->name); if (filter) gStreamer->addFilters(gStreamer, filter); } void bed5AddFilter(struct annoGrator *grator, char *name, struct slName *valList) /* Add filter to bed 5 grator. */ { struct annoStreamer *gStreamer = (struct annoStreamer *)grator; struct annoFilter *filter = NULL; if (sameString(name, "name")) { if (valList && isNotAll(valList)) filter = annoFilterFromAsColumn(gStreamer->asObj, name, afMatch, valList); } else if (sameString(name, "score")) filter = annoFilterFromAsColumn(gStreamer->asObj, name, afGTE, valList); else errAbort("Unrecognized filter name '%s' for %s, type=bed 5", name, gStreamer->name); if (filter) gStreamer->addFilters(gStreamer, filter); } void addFiltersToGrator(struct annoGrator *grator, struct trackDb *tdb) /* Look for filter variables in the cart and add filters to grator accordingly. */ { struct hash *varHash = getTrackFilterVars(tdb->track); struct hashEl *hel, *helList = hashElListHash(varHash); for (hel = helList; hel != NULL; hel = hel->next) { char *filterName = hel->name; struct slName *valList = hel->val; //#*** Need a much better way to dispatch... if (sameString("factorSource", tdb->type)) factorSourceGratorAddFilter(grator, filterName, valList); else if (startsWith("bed 5", tdb->type)) bed5AddFilter(grator, filterName, valList); else dyStringPrintf(dyInfo, "Ignoring %s filter %s\n", tdb->track, filterName); } hashFree(&varHash); } void addOutputTracks(struct annoGrator **pGratorList, struct hash *gratorsByName, struct annoFormatter *vepOut, struct annoAssembly *assembly, char *chrom, boolean doHtml, boolean *retHasRegulatory) // Construct grators for tracks selected to appear in EXTRAS column { boolean includeReg = cartUsualBoolean(cart, "hgva_include_regulatory", TRUE); boolean haveReg = FALSE; char trackPrefix[128]; safef(trackPrefix, sizeof(trackPrefix), "hgva_track_%s_", database); int trackPrefixLen = strlen(trackPrefix); struct slPair *trackVar, *trackVars = cartVarsWithPrefix(cart, trackPrefix); for (trackVar = trackVars; trackVar != NULL; trackVar = trackVar->next) { char *val = trackVar->val; if (! (sameWord(val, "on") || atoi(val) > 0)) continue; char *trackName = trackVar->name + trackPrefixLen; if (sameString(trackName, "dbNsfpPolyPhen2")) // PolyPhen2 must have a suffix now -- skip obsolete cartVar from existing carts continue; struct annoGrator *grator = hashFindVal(gratorsByName, trackName); if (grator != NULL) // We already have this as a grator: continue; enum PolyPhen2Subset subset = noSubset; char *description = NULL; char *column = NULL; boolean isReg = FALSE; if (startsWith("dbNsfp", trackName)) { // trackName for PolyPhen2 has a suffix for subset -- strip it if we find it: subset = stripSubsetFromTrackName(trackName); description = dbNsfpDescFromTableName(trackName, subset, doHtml); addDbNsfpSeqChange(trackName, assembly, gratorsByName, pGratorList); char *fileName = fileNameFromTable(trackName); if (fileName != NULL) grator = hAnnoGratorFromBigFileUrl(fileName, NULL, assembly, ANNO_NO_LIMIT, agoNoConstraint); } else { struct trackDb *tdb = tdbForTrack(database, trackName, &fullTrackList); if (tdb != NULL) { grator = hAnnoGratorFromTrackDb(assembly, tdb->table, tdb, chrom, ANNO_NO_LIMIT, NULL, agoNoConstraint, NULL); if (grator != NULL) { //#*** Need something more sophisticated but this works for our //#*** limited selection of extra tracks: if (asColumnFind(grator->streamer.asObj, "name") != NULL) column = "name"; addFiltersToGrator(grator, tdb); } description = tdb->longLabel; isReg = (includeReg && ((sameString(database, "hg19") && isHg19RegulatoryTrack(tdb, NULL)) || (sameString(database, "hg38") && isHg38RegulatoryTrack(tdb, NULL)))); } } haveReg |= isReg; updateGratorListAndVepExtra(grator, pGratorList, vepOut, subset, column, description, isReg); if (grator != NULL) hashAdd(gratorsByName, trackName, grator); } if (retHasRegulatory) *retHasRegulatory = haveReg; } void addFilterTracks(struct annoGrator **pGratorList, struct hash *gratorsByName, struct annoAssembly *assembly, char *chrom) // Add grators for filters (not added to vepOut): { if (!cartUsualBoolean(cart, "hgva_include_snpCommon", TRUE)) { struct annoGrator *grator = gratorForSnpBed4(gratorsByName, "Common", assembly, chrom, agoMustNotOverlap, NULL); updateGratorList(grator, pGratorList); } if (!cartUsualBoolean(cart, "hgva_include_snpMult", TRUE)) { struct annoGrator *grator = gratorForSnpBed4(gratorsByName, "Mult", assembly, chrom, agoMustNotOverlap, NULL); updateGratorList(grator, pGratorList); } if (cartUsualBoolean(cart, "hgva_require_consEl", FALSE)) { char *consElTrack = cartString(cart, "hgva_require_consEl_track"); struct annoGrator *grator = hashFindVal(gratorsByName, consElTrack); if (grator == NULL) { struct trackDb *tdb = tdbForTrack(database, consElTrack, &fullTrackList); if (tdb != NULL) grator = hAnnoGratorFromTrackDb(assembly, tdb->table, tdb, chrom, ANNO_NO_LIMIT, NULL, agoMustOverlap, NULL); updateGratorList(grator, pGratorList); } else grator->setOverlapRule(grator, agoMustOverlap); } } static void getCartPosOrDie(char **retChrom, uint *retStart, uint *retEnd) /* Get chrom:start-end from cart, errAbort if any problems. */ { char *position = cartString(cart, hgvaRange); if (! parsePosition(position, retChrom, retStart, retEnd)) errAbort("Expected position to be chrom:start-end but got '%s'", position); } static char *sampleVariantsPath(struct annoAssembly *assembly, char *geneTrack) /* Construct a path for a trash file of contrived example variants for this assembly * and gene track. */ { char *chrom = NULL; uint start = 0, end = 0; getCartPosOrDie(&chrom, &start, &end); mkdirTrashDirectory(hgvsTrashSubDir); struct dyString *dy = dyStringCreate("%s/%s/%s_%s_%s_%u-%u.vcf", trashDir(), hgvsTrashSubDir, assembly->name, geneTrack, chrom, start, end); return dyStringCannibalize(&dy); } static char *makeMinimalVcfHeader(char *db, char *headerDefs) /* Return a string containing a simple no-genotypes VCF header. db must be non-NULL. * headerDefs can be NULL or empty or line(s) starting with '##' and ending w/'\n' */ { struct dyString *dy = dyStringCreate("##fileformat=VCFv4.2\n" "##reference=%s\n" "%s" "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n", db, (headerDefs ? headerDefs : "")); return dyStringCannibalize(&dy); } static void writeMinimalVcfHeader(FILE *f, char *db, char *headerDefs) /* Write header for VCF with no genotype data. db must be non-NULL. * headerDefs can be NULL or empty or line(s) starting with '##' and ending w/'\n' */ { char *headerString = makeMinimalVcfHeader(db, headerDefs); fputs(headerString, f); freeMem(headerString); } static void mutateBase(char *pBase) /* Change *pBase into a different base. */ { static char *bases = "ACGT"; char c; // In real life the probabilities aren't even, but this is easier. while ((c = bases[(uint)(floor(drand48() * 4.0))]) == *pBase) ; *pBase = c; } static void writeMinimalVcfRow(FILE *f, struct vcfRecord *rec) /* Write a minimalist VCF row (coords, name, alleles and placeholders). */ { // VCF columns: #CHROM POS ID REF ALT QUAL FILTER INFO fprintf(f, "%s\t%u\t%s\t%s\t", rec->chrom, rec->chromStart+1, rec->name, rec->alleles[0]); // Comma-separated alt alleles: int i; for (i = 1; i < rec->alleleCount; i++) fprintf(f, "%s%s", (i > 1 ? "," : ""), rec->alleles[i]); // Placeholder qual, filter, info. fprintf(f, "\t.\t.\t.\n"); } static void writeMinimalVcfRowFromBed(FILE *f, struct bed4 *bed, struct dnaSeq *seq, uint seqOffset) /* Write a minimalist VCF row with a mutation of the reference sequence at the given * position. */ { uint indelBase = 0, start = bed->chromStart, end = bed->chromEnd; if (end != start+1) { // VCF treats indels in a special way: pos is the base to the left of the indel, // and both ref and alt alleles include the base to the left of the indel. indelBase = 1; } // Get reference allele sequence: uint refAlLen = end - start + indelBase; char ref[refAlLen+1]; uint seqStart = start - indelBase - seqOffset; safencpy(ref, sizeof(ref), seq->dna+seqStart, refAlLen); touppers(ref); // Alternate allele seq needs extra room in case of single-base insertion: char alt[refAlLen+2]; alt[0] = ref[0]; alt[1] = '\0'; if (start == end) // insertion: alt gets extra base safecpy(alt+1, sizeof(alt)-1, "A"); else if (end == start+1) // single nucleotide variant mutateBase(alt); // else deletion: leave alt truncated after the shared base to left of indel // VCF columns: #CHROM POS ID REF ALT QUAL FILTER INFO fprintf(f, "%s\t%u\t%s\t%s\t%s\t.\t.\t.\n", bed->chrom, start+1-indelBase, bed->name, ref, alt); } static void writeArbitraryVariants(FILE *f, struct annoAssembly *assembly) /* Concoct some variants at an arbitrary position on some assembly sequence. * We shouldn't ever get here unless the selected geneTrack is empty. */ { char *chrom = "NULL"; uint start = 0, end = 0; getCartPosOrDie(&chrom, &start, &end); struct bed4 *bed = bed4New(chrom, start, start, "ex_ins"); struct dnaSeq *seq = twoBitReadSeqFragLower(assembly->tbf, chrom, start-1, start+100); writeMinimalVcfRowFromBed(f, bed, seq, start-1); dnaSeqFree(&seq); } static void addGpFromRow(struct genePred **pGpList, struct annoRow *row, boolean *pNeedCoding, boolean *pNeedNonCoding, boolean isBig) /* If row is coding and we need a coding gp, add it to pGpList and update pNeedCoding; * likewise for noncoding. */ { struct genePred *gp = isBig ? (struct genePred *)genePredFromBigGenePredRow(row->data) : genePredLoad(row->data); if (gp->cdsStart != gp->cdsEnd && *pNeedCoding) { slAddHead(pGpList, gp); *pNeedCoding = FALSE; } else if (gp->cdsStart == gp->cdsEnd && *pNeedNonCoding) { slAddHead(pGpList, gp); *pNeedNonCoding = FALSE; } } static void addGpFromPos(struct annoStreamer *geneStream, char *chrom, uint start, uint end, struct genePred **pGpList, boolean *pNeedCoding, boolean *pNeedNonCoding, struct lm *lm, boolean isBig) /* Get up to 10 rows from position; if we find one coding and one non-coding gene, * add them to pGpList and update pNeed* accordingly. */ { geneStream->setRegion(geneStream, chrom, start, end); int rowCount = 0; struct annoRow *row = NULL; while (rowCount < 10 && (*pNeedCoding || *pNeedNonCoding) && (row = geneStream->nextRow(geneStream, NULL, 0, lm)) != NULL) addGpFromRow(pGpList, row, pNeedCoding, pNeedNonCoding, isBig); } static struct genePred *genesFromPosition(struct annoStreamer *geneStream, boolean isBig, boolean *retGotCoding, boolean *retGotNonCoding) /* Try to get a coding and non-coding gene from geneStream at cart position. * If there are none, try whole chrom; if none there, first in assembly. */ { struct genePred *gpList = NULL; struct lm *lm = lmInit(0); char *chrom = NULL; uint start = 0, end = 0; getCartPosOrDie(&chrom, &start, &end); boolean needCoding = TRUE, needNonCoding = TRUE; // First, look for both coding and noncoding genes at cart position: addGpFromPos(geneStream, chrom, start, end, &gpList, &needCoding, &needNonCoding, lm, isBig); // If that didn't do it, try querying whole chrom if (needCoding || needNonCoding) addGpFromPos(geneStream, chrom, 0, 0, &gpList, &needCoding, &needNonCoding, lm, isBig); // If we still haven't found either coding or non-coding on the cart's current chrom, // try whole genome: if (needCoding && needNonCoding) addGpFromPos(geneStream, NULL, 0, 0, &gpList, &needCoding, &needNonCoding, lm, isBig); slSort(&gpList, genePredCmp); lmCleanup(&lm); if (retGotCoding) *retGotCoding = !needCoding; if (retGotNonCoding) *retGotNonCoding = !needNonCoding; return gpList; } static void addSnv(struct bed4 **pBedList, char *chrom, uint start, char *name) /* Add a single-nucleotide bed4 item. */ { slAddHead(pBedList, bed4New(chrom, start, start+1, name)); } // Stuff within this range (see gpFx.h) is considered upstream/downstream of a transcript: #define UPSTREAMFUDGE GPRANGE static struct bed4 *sampleVarBedFromGenePred(struct genePred *gp, struct annoAssembly *assembly, uint txSeqStart, uint txSeqEnd, boolean exonOnly) /* Construct imaginary variants that hit various parts of the transcript * described in gp, using reference base values from assembly. */ { uint basesLeft = gp->txStart - txSeqStart, basesRight = txSeqEnd - gp->txEnd; struct bed4 *bedList = NULL; if (!exonOnly && basesLeft > UPSTREAMFUDGE) // SNV, intergenic to the left addSnv(&bedList, gp->chrom, txSeqStart, "ex_igLeft"); if (!exonOnly && basesLeft > 0) // SNV, up/downstream to the left addSnv(&bedList, gp->chrom, gp->txStart - 1, "ex_updownLeft"); if (!exonOnly && gp->exonCount > 1) { // SNV, intron uint start = (gp->exonEnds[0] + gp->exonStarts[1]) / 2; addSnv(&bedList, gp->chrom, start, "ex_intron"); // SNV, splice addSnv(&bedList, gp->chrom, gp->exonStarts[1] - 2, "ex_splice"); } boolean isCoding = (gp->cdsStart != gp->cdsEnd); if (isCoding) { if (gp->txStart < gp->cdsStart) // SNV, UTR to the left addSnv(&bedList, gp->chrom, gp->txStart + 1, "ex_utrLeft"); int cdsExon = 0; while (gp->cdsStart > gp->exonEnds[cdsExon] && cdsExon < gp->exonCount) cdsExon++; uint start = gp->cdsStart + 2; // single-base insertion, leftmost codon slAddHead(&bedList, bed4New(gp->chrom, start, start, "ex_codonLeftIns")); // 3-base deletion leftmost codon slAddHead(&bedList, bed4New(gp->chrom, start, start+3, "ex_codonLeftDel")); // SNV, leftmost codon addSnv(&bedList, gp->chrom, start+1, "ex_codonLeft"); if (gp->txEnd > gp->cdsEnd) // SNV, UTR to the right addSnv(&bedList, gp->chrom, gp->txEnd - 1, "ex_utrRight"); } else { // noncoding exon variant uint start = (gp->exonStarts[0] + gp->exonEnds[0]) / 2; addSnv(&bedList, gp->chrom, start, "ex_nce"); } if (!exonOnly && basesRight > 0) // SNV, up/downstream to the left addSnv(&bedList, gp->chrom, gp->txEnd + 1, "ex_updownRight"); return bedList; } // margin for intergenic variants around transcript: #define IGFUDGE 5 static struct annoStreamer *makeSampleVariantsStreamer(struct annoAssembly *assembly, struct trackDb *geneTdb, int maxOutRows) /* Construct a VCF file of example variants for db (unless it already exists) * and return an annoStreamer for that file. If possible, make the variants hit a gene. */ { char *sampleFile = sampleVariantsPath(assembly, geneTdb->track); boolean forceRebuild = cartUsualBoolean(cart, "hgva_rebuildSampleVariants", FALSE); if (! fileExists(sampleFile) || forceRebuild) { struct annoStreamer *geneStream = hAnnoStreamerFromTrackDb(assembly, geneTdb->table, geneTdb, NULL, ANNO_NO_LIMIT, NULL); boolean isBig = sameString(geneTdb->type, "bigGenePred"); boolean gotCoding = FALSE, gotNonCoding = FALSE; struct genePred *gpList = genesFromPosition(geneStream, isBig, &gotCoding, &gotNonCoding); FILE *f = mustOpen(sampleFile, "w"); writeMinimalVcfHeader(f, assembly->name, NULL); if (gpList == NULL) { warn("Unable to find any gene transcripts in '%s' (%s)", geneTdb->shortLabel, geneTdb->track); writeArbitraryVariants(f, assembly); } else { struct bed4 *bedList = NULL; uint chromSize = annoAssemblySeqSize(assembly, gpList->chrom); uint minSeqStart = chromSize, maxSeqEnd = 0; struct genePred *gp; for (gp = gpList; gp != NULL; gp = gp->next) { int txSeqStart = gp->txStart - (UPSTREAMFUDGE + IGFUDGE); uint txSeqEnd = gp->txEnd + UPSTREAMFUDGE + IGFUDGE; if (txSeqStart < 0) txSeqStart = 0; if (txSeqEnd > chromSize) txSeqEnd = chromSize; if (txSeqStart < minSeqStart) minSeqStart = txSeqStart; if (txSeqEnd > maxSeqEnd) maxSeqEnd = txSeqEnd; // If we got a coding gp, but this gp is non-coding, just do its exon variant: boolean exonOnly = gotCoding && (gp->cdsStart == gp->cdsEnd); slCat(&bedList, sampleVarBedFromGenePred(gp, assembly, txSeqStart, txSeqEnd, exonOnly)); } slSort(&bedList, bedCmp); struct dnaSeq *txSeq = twoBitReadSeqFragLower(assembly->tbf, gpList->chrom, minSeqStart, maxSeqEnd); struct bed4 *bed; for (bed = bedList; bed != NULL; bed = bed->next) { writeMinimalVcfRowFromBed(f, bed, txSeq, minSeqStart); } dnaSeqFree(&txSeq); bed4FreeList(&bedList); } geneStream->close(&geneStream); carefulClose(&f); } return annoStreamVcfNew(sampleFile, NULL, FALSE, assembly, maxOutRows); } static char *md5TrashPath(struct annoAssembly *assembly, char *string) /* Use the md5sum of a string to make a hopefully unique trash filename. */ { char *md5sum = md5HexForString(string); mkdirTrashDirectory(hgvsTrashSubDir); struct dyString *dy = dyStringCreate("%s/%s/%s_%s.vcf", trashDir(), hgvsTrashSubDir, assembly->name, md5sum); return dyStringCannibalize(&dy); } static struct slName *hashListNames(struct hash *hash) /* Return a list of all element names in the hash (if any). */ { struct slName *list = NULL; struct hashCookie cookie = hashFirst(hash); struct hashEl *hel; while ((hel = hashNext(&cookie)) != NULL) slAddHead(&list, slNameNew(hel->name)); return list; } static char *encloseInAngleBracketsDbSnp(char *stringIn) /* Return a string that has, with spaces replaced by '_'s. */
{
int stringInLen = strlen(stringIn);
int stringOutLen = stringInLen + strlen("") + 1;
char *stringOut = needMem(stringOutLen);
safef(stringOut, stringOutLen, "", stringIn);
subChar(stringOut, ' ', '_');
return stringOut;
}
// dbSNP named alleles have many ways to describe a deletion from the reference,
// for example "LARGEDELETION", "LARGE DELETION", "... DELETED", "... DEL":
static const char *dbSnpDelRegex = "^\\(.*(DELET.*| DEL)\\)$";
static char **parseDbSnpAltAlleles(char *refAl, char *obsAls, boolean minusStrand,
int *retAltAlCount, boolean *retNeedLeftBase)
/* Given a non-symbolic reference allele and slash-sep observed alleles from dbSNP,
* return an array of +-strand alleles that are not the same as the reference.
* If any allele is "-" (deleted, zero-length), then set retNeedLeftBase to TRUE
* because in this case VCF requires that the reference base to the left of the indel
* must be added to all alleles, and the start coord also moves one base to the left.
* Also, if any alt allele is symbolic, padding is required.
* Note: this trashes obsAls. Resulting array can be freed but not its contents. */
{
int obsCount = countChars(obsAls, '/') + 1;
char *obsWords[obsCount];
chopByChar(obsAls, '/', obsWords, obsCount);
boolean obsHasDeletion = FALSE;
int i;
for (i = 0; i < obsCount; i++)
if (sameString(obsWords[i], "-"))
{
obsHasDeletion = TRUE;
break;
}
char **altAls;
AllocArray(altAls, obsCount);
int altCount = 0;
boolean needLeftBase = isEmpty(refAl) || sameString(refAl, "-");
for (i = 0; i < obsCount; i++)
{
char *altAl = obsWords[i];
int altAlLen = strlen(altAl);
if (minusStrand && isAllNt(altAl, altAlLen))
reverseComplement(altAl, altAlLen);
if (differentString(altAl, refAl))
{
if (sameString(altAl, "-"))
{
altAls[altCount] = "";
needLeftBase = TRUE;
}
else
{
// It would be nice to expand the "(CA)11/12/14/15/16/17/18/19/20" syntax of
// some dbSNP observed's. What are these?: "(D1S243)", "(D1S2870)"
// Unfortunately for observed="lengthTooLong" we just can't get the correct allele
// sequence. (76,130 of those in snp138)
// Hmmm, I guess we could at least stick in the right number of N's if we can
// parse "(245 BP INSERTION)". (2403 rows rlike "[0-9]+ BP ?INSERTION" in snp138)
if (!isAllNt(altAl, altAlLen))
{
// Symbolic allele: left base required, and enclose it in 's.
// But if it's one of dbSNP's LARGEDELETION kind of alleles, that is redundant
// with the reference allele, so if we know there is already a "-" allele,
// skip it.
if (obsHasDeletion && regexMatch(altAl, dbSnpDelRegex))
continue;
needLeftBase = TRUE;
altAl = encloseInAngleBracketsDbSnp(altAl);
}
altAls[altCount] = altAl;
}
altCount++;
}
}
*retAltAlCount = altCount;
*retNeedLeftBase = needLeftBase;
return altAls;
}
char *firstNCommaSep(struct slName *nameList, int n)
/* Return a comma-separated string with the first n names in nameList. */
{
struct dyString *dy = dyStringNew(0);
int i;
struct slName *el;
for (i=0, el=nameList; i < 5 && el != NULL; i++, el = el->next)
{
if (i > 0)
dyStringAppend(dy, ", ");
dyStringPrintf(dy, "'%s'", el->name);
}
return dyStringCannibalize(&dy);
}
//#*** Variant ID-matching should be metadata-driven too. termRegex -> data source.
static const char *rsIdRegex = "^rs[0-9]+$";
static void rsIdsToVcfRecords(struct annoAssembly *assembly, struct slName *rsIds,
struct vcfFile *vcff, struct vcfRecord **pRecList,
struct slName **pCommentList)
/* If possible, look up coordinates and alleles of dbSNP rs IDs. */
{
if (rsIds == NULL)
return;
struct trackDb *tdb = hFindLatestSnpTrack(database, NULL, &fullTrackList);
if (tdb == NULL)
return;
struct sqlConnection *conn = hAllocConn(assembly->name);
// Build a 'name in (...)' query, and build a hash of IDs so we can test whether all were found
struct dyString *dq = sqlDyStringCreate("select chrom, chromStart, chromEnd, name, strand, "
"refUCSC, observed from %s where name in (",
tdb->table);
struct hash *idHash = hashNew(0);
struct slName *id;
for (id = rsIds; id != NULL; id = id->next)
{
tolowers(id->name);
dyStringPrintf(dq, "%s'%s'", (id != rsIds ? "," : ""), id->name);
hashStoreName(idHash, id->name);
}
dyStringAppend(dq, ");");
struct sqlResult *sr = sqlGetResult(conn, dq->string);
// Construct a minimal VCF row to make a vcfRecord for each variant.
char *vcfRow[9];
vcfRow[5] = vcfRow[6] = vcfRow[7] = "."; // placeholder for qual, filter, info
// It would be cool to someday add snpNNN's exceptions column to the filter or info.
struct dyString *dyAltAlStr = dyStringNew(0);
int i;
char **row;
while ((row = sqlNextRow(sr)) != NULL)
{
char *chrom = row[0];
uint chromStart = atoll(row[1]);
uint chromEnd = atoll(row[2]);
char *name = row[3];
char *strand = row[4];
char refAl[max(strlen(row[5]), chromEnd-chromStart) + 2];
safecpy(refAl, sizeof(refAl), row[5]);
if (sameString(refAl, "-"))
refAl[0] = '\0';
else if (! isAllNt(refAl, strlen(refAl)))
{
// refUCSC is symbolic like "( 2548bp insertion )" -- just use the actual reference
// sequence for now, to keep things simple downstream.
//#*** Need something more efficient, like a sequence cache inside assembly!
struct dnaSeq *seq = twoBitReadSeqFragLower(assembly->tbf, chrom, chromStart, chromEnd);
safecpy(refAl, sizeof(refAl), seq->dna);
toUpperN(refAl, seq->size);
dnaSeqFree(&seq);
}
char *obsAls = row[6];
int altAlCount = 0;
boolean needLeftBase = FALSE;
char **altAls = parseDbSnpAltAlleles(refAl, obsAls, sameString(strand, "-"),
&altAlCount, &needLeftBase);
needLeftBase |= (chromStart == chromEnd); // should be redundant, but just in case.
hashRemove(idHash, name);
uint vcfStart = chromStart + 1;
dyStringClear(dyAltAlStr);
// If this is a non-symbolic indel, we'll have to move start one base to the left
// and add the reference base to the left of the actual alleles
if (needLeftBase)
{
vcfStart--;
//#*** Need something more efficient, like a sequence cache inside assembly!
struct dnaSeq *seq = twoBitReadSeqFragLower(assembly->tbf, chrom,
chromStart-1, chromStart);
toUpperN(seq->dna, 1);
char leftBase = seq->dna[0];
dnaSeqFree(&seq);
char refAlPlus[strlen(refAl)+2];
safef(refAlPlus, sizeof(refAlPlus), "%c%s", leftBase, refAl);
safecpy(refAl, sizeof(refAl), refAlPlus);
for (i = 0; i < altAlCount; i++)
{
if (i > 0)
dyStringAppendC(dyAltAlStr, ',');
if (isAllNt(altAls[i], strlen(altAls[i])))
dyStringPrintf(dyAltAlStr, "%c%s", leftBase, altAls[i]);
else
dyStringAppend(dyAltAlStr, altAls[i]);
}
}
else
{
// Not an indel, just make comma-sep string of alt alleles.
for (i = 0; i < altAlCount; i++)
{
if (i > 0)
dyStringAppendC(dyAltAlStr, ',');
dyStringAppend(dyAltAlStr, altAls[i]);
}
}
char vcfStartStr[64];
safef(vcfStartStr, sizeof(vcfStartStr), "%d", vcfStart);
vcfRow[0] = chrom;
vcfRow[1] = vcfStartStr;
vcfRow[2] = name;
vcfRow[3] = refAl;
vcfRow[4] = dyAltAlStr->string;
struct vcfRecord *rec = vcfRecordFromRow(vcff, vcfRow);
slAddHead(pRecList, rec);
}
dyStringFree(&dyAltAlStr);
// Check for IDs not found
struct slName *notFoundIds = hashListNames(idHash);
if (notFoundIds != NULL)
{
char *namesNotFound = firstNCommaSep(notFoundIds, 5);
struct dyString *dy = dyStringCreate("%d rs# IDs not found, e.g. %s",
slCount(notFoundIds), namesNotFound);
slAddTail(pCommentList, slNameNew(dy->string));
freeMem(namesNotFound);
dyStringFree(&dy);
}
slNameFreeList(¬FoundIds);
}
static struct vcfRecord *parseVariantIds(struct annoAssembly *assembly, char *variantIdText,
struct slName **pCommentList)
/* Return a sorted list of minimal vcfRecords (coords, name, ref and alt alleles)
* corresponding to each pasted variant. */
{
struct vcfRecord *recList = NULL;
char *p = cloneString(variantIdText), *id;
struct slName *rsIds = NULL, *unknownIds = NULL;
subChar(p, ',', ' ');
while ((id = nextWord(&p)) != NULL)
{
if (regexMatchNoCase(id, rsIdRegex))
slNameAddHead(&rsIds, id);
else
slNameAddHead(&unknownIds, id);
}
if (unknownIds != NULL)
{
slReverse(&unknownIds);
char *firstUnknownIds = firstNCommaSep(unknownIds, 5);
struct dyString *dy = dyStringCreate("%d variant identifiers are unrecognized, e.g. %s",
slCount(unknownIds), firstUnknownIds);
slAddTail(pCommentList, slNameNew(dy->string));
freeMem(firstUnknownIds);
dyStringFree(&dy);
}
struct vcfFile *vcff = vcfFileNew();
rsIdsToVcfRecords(assembly, rsIds, vcff, &recList, pCommentList);
slSort(&recList, vcfRecordCmp);
slNameFreeList(&rsIds);
slNameFreeList(&unknownIds);
return recList;
}
static void adjustRangeForVariants(struct vcfRecord *recList, char **pChrom,
uint *pStart, uint *pEnd)
/* Given a *sorted* list of VCF records, look at the first and last records and if
* they fall outside of the range, expand the range to include them. */
{
if (pChrom != NULL && *pChrom != NULL && recList != NULL)
{
// We have a non-empty sorted list of records, and search is not genome-wide;
// look at first and last variants to see if they're not already included in search range.
struct vcfRecord *first = recList, *last = recList;
while (last->next)
last = last->next;
if (differentString(*pChrom, first->chrom) || differentString(*pChrom, last->chrom))
{
// Variants span multiple chroms; force genome-wide search.
*pChrom = NULL;
*pStart = *pEnd = 0;
}
else
{
// Variant(s) are on the same chrom as search range; check starts and ends.
if (*pStart > first->chromEnd)
*pStart = first->chromEnd;
if (*pEnd < last->chromStart)
*pEnd = last->chromStart;
}
}
}
static struct annoStreamer *makeVariantIdStreamer(struct annoAssembly *assembly, int maxOutRows,
char **pChrom, uint *pStart, uint *pEnd,
struct slName **pCommentList)
/* Translate user's pasted/uploaded variant IDs into minimal VCF if possible.
* Return a VCF streamer for those, and if the current search position is too narrow
* to include all of the variants, widen it as necessary. */
{
// Hash variant text to get trash filename. Use if exists, otherwise build it.
char *variantIds = cartString(cart, hgvaVariantIds);
char *varFile = md5TrashPath(assembly, variantIds);
boolean forceRebuild = cartUsualBoolean(cart, "hgva_rebuildVariantIds", FALSE);
if (! fileExists(varFile) || forceRebuild)
{
struct vcfRecord *varList = parseVariantIds(assembly, variantIds, pCommentList);
//#*** If no variants were recognized, we should probably show main page with a warning.
adjustRangeForVariants(varList, pChrom, pStart, pEnd);
FILE *f = mustOpen(varFile, "w");
writeMinimalVcfHeader(f, assembly->name, NULL);
struct vcfRecord *var;
for (var = varList; var != NULL; var = var->next)
writeMinimalVcfRow(f, var);
carefulClose(&f);
}
return annoStreamVcfNew(varFile, NULL, FALSE, assembly, maxOutRows);
}
static struct vcfRecord *parseHgvs(struct vcfFile *vcff, struct annoAssembly *assembly,
char *hgvsTerms, struct slName **pCommentList)
/* Return a sorted list of vcfRecords . */
{
struct vcfRecord *recList = NULL;
struct slName *failedTerms = NULL;
struct dyString *dyError = dyStringNew(0);
struct lineFile *lf = lineFileOnString("user-provided HGVS terms", TRUE, cloneString(hgvsTerms));
char *term = NULL;
while (lineFileNextReal(lf, &term))
{
eraseTrailingSpaces(term);
dyStringClear(dyError);
struct vcfRow *vcfRow = hgvsToVcfRow(assembly->name, term, FALSE, dyError);
if (vcfRow)
{
char *row[8];
row[0] = vcfRow->chrom;
char posStr[64];
safef(posStr, sizeof(posStr), "%d", vcfRow->pos);
row[1] = posStr;
row[2] = vcfRow->id;
row[3] = vcfRow->ref;
row[4] = vcfRow->alt;
row[5] = ".";
row[6] = vcfRow->filter;
row[7] = vcfRow->info;
slAddHead(&recList, vcfRecordFromRow(vcff, row));
}
else
slNameAddHead(&failedTerms, dyStringContents(dyError));
}
if (failedTerms != NULL)
{
slReverse(&failedTerms);
char *firstUnknownIds = firstNCommaSep(failedTerms, 5);
struct dyString *dy = dyStringCreate("%d HGVS terms could not be parsed and/or mapped to %s, "
"e.g. %s",
slCount(failedTerms), assembly->name, firstUnknownIds);
slAddTail(pCommentList, slNameNew(dy->string));
freeMem(firstUnknownIds);
dyStringFree(&dy);
}
slSort(&recList, vcfRecordCmp);
slNameFreeList(&failedTerms);
dyStringFree(&dyError);
lineFileClose(&lf);
return recList;
}
static struct annoStreamer *makeHgvsStreamer(struct annoAssembly *assembly, int maxOutRows,
char **pChrom, uint *pStart, uint *pEnd,
struct slName **pCommentList)
/* Translate user's pasted/uploaded variant IDs into minimal VCF if possible.
* Return a VCF streamer for those., and if the current search position is too narrow
* to include all of the variants, widen it as necessary. */
{
// Hash HGVS input to get trash filename. Use if exists, otherwise build it.
char *hgvsTerms = cartString(cart, hgvaHgvs);
char *varFile = md5TrashPath(assembly, hgvsTerms);
boolean forceRebuild = cartUsualBoolean(cart, "hgva_rebuildHgvs", FALSE);
if (! fileExists(varFile) || forceRebuild)
{
char *headerString = makeMinimalVcfHeader(assembly->name, HGVS_VCF_HEADER_DEFS);
struct vcfFile *vcff = vcfFileFromHeader("hgVaiHgvs", headerString, VCF_IGNORE_ERRS);
struct vcfRecord *varList = parseHgvs(vcff, assembly, hgvsTerms, pCommentList);
//#*** If no HGVS terms could be mapped, we should probably show main page with a warning.
adjustRangeForVariants(varList, pChrom, pStart, pEnd);
FILE *f = mustOpen(varFile, "w");
writeMinimalVcfHeader(f, assembly->name, HGVS_VCF_HEADER_DEFS);
struct vcfRecord *var;
for (var = varList; var != NULL; var = var->next)
writeMinimalVcfRow(f, var);
carefulClose(&f);
vcfFileFree(&vcff);
}
return annoStreamVcfNew(varFile, NULL, FALSE, assembly, maxOutRows);
}
static struct trackDb *getVariantTrackDb(char *variantTrack)
/* Get a tdb for the user's selected variant track, or warn and return NULL
* (main page will be displayed) */
{
struct trackDb *varTdb = tdbForTrack(database, variantTrack, &fullTrackList);
if (varTdb == NULL)
{
if (isHubTrack(variantTrack))
warn("Can't find hub track '%s'", variantTrack);
else
warn("Can't find tdb for variant track '%s'", variantTrack);
}
else
checkVariantTrack(varTdb);
return varTdb;
}
static char *gencodeVersionFromTrack(char *track)
/* If track is a GENCODE table, find and return a pointer to the version at the end;
* otherwise return NULL. */
{
if (startsWithGencodeGene(track))
{
char *v = strrchr(track, 'V');
return v;
}
return NULL;
}
static char *gencodeTagTableForTrack(char *db, char *track)
/* If there is a wgEncodeGencodeTag table that can be associated with track,
* return it; otherwise return NULL. */
{
struct slName *versionList = getGencodeTagVersions();
if (startsWithGencodeGene(track))
{
char *version = gencodeVersionFromTrack(track);
if (version != NULL)
{
char table[PATH_LEN];
return cloneString(gencodeTableName("Tag", version, table, sizeof(table)));
}
}
else if (sameString(track, "refGene") && refGeneHasGencodeTags(versionList))
{
char *version = getLatestGencodeVersion(versionList);
char table[PATH_LEN];
if (hTableExists(db, gencodeTableName("RefSeq", version, table, sizeof(table))))
return cloneString(gencodeTableName("Tag", version, table, sizeof(table)));
}
else if (sameString(track, "knownGene") && knownGeneHasGencodeTags())
{
if (hTableExists(db, "knownToTag"))
return cloneString("knownToTag");
}
return NULL;
}
static struct joinerDtf *getTxStatusExtras(char *db, char *track)
// Several kinds of transcript status may be enabled in the cart; if any are enabled,
// and if they apply to track, return the tables & fields to be joined with the track.
{
struct joinerDtf *txStatusExtras = NULL;
if (cartUsualBoolean(cart, "hgva_txStatus_gencode", FALSE))
{
char *gencodeTagTable = gencodeTagTableForTrack(db, track);
if (gencodeTagTable != NULL)
{
char *field = "tag";
if (sameString("knownToTag", gencodeTagTable))
field = "value";
slAddHead(&txStatusExtras, joinerDtfNew(db, gencodeTagTable, field));
}
}
if (cartUsualBoolean(cart, "hgva_txStatus_knownCanonical", FALSE) &&
sameString(track, "knownGene") &&
hTableExists(db, "knownCanonical"))
{
slAddHead(&txStatusExtras, joinerDtfNew(db, "knownCanonical", "transcript"));
}
if (cartUsualBoolean(cart, "hgva_txStatus_refSeqStatus", FALSE) &&
sameString(track, "refGene") &&
genbankTableExists(db, refSeqStatusTable))
{
char *genbankDb=NULL, *tableName=NULL;
genbankGetDbTable(db, refSeqStatusTable, &genbankDb, &tableName);
slAddHead(&txStatusExtras, joinerDtfNew(genbankDb, tableName, "status"));
}
return txStatusExtras;
}
static void configAddDtf(struct dyString *dy, struct joinerDtf *dtf, boolean *pIsFirst)
/* Add a JSON object with [db].table and (list of one) field. */
{
if (! *pIsFirst)
dyStringAppend(dy, ", ");
// The convention for related tables in same db as track is to prepend "." instead of ".":
char *db = (sameString(dtf->database, database) ? "" : dtf->database);
dyStringPrintf(dy, "{ \"table\": \"%s.%s\", \"fields\": [\"%s\"] }", db, dtf->table, dtf->field);
*pIsFirst = FALSE;
}
static void configAddTableField(struct dyString *dy, char *table, char *field, boolean *pIsFirst)
/* Add a JSON object with current database, table and (list of one) field. */
{
struct joinerDtf dtf;
dtf.database = database;
dtf.table = table;
dtf.field = field;
configAddDtf(dy, &dtf, pIsFirst);
}
static struct jsonElement *configForStreamer(char *db, struct trackDb *tdb,
struct joinerDtf *txStatusExtras)
/* Add VAI-specific config options, if applicable. */
{
struct jsonElement *config = NULL;
char *track = tdb->track;
struct dyString *dyConfig = dyStringCreate("{ \"naForMissing\": false,"
" \"relatedTables\": [ ");
boolean isFirst = TRUE;
// If track is sql-based knownGene and we have kgXref, then add kgXref.geneSymbol after
// the columns of knownGene.
if (sameString(track, "knownGene") &&
!isCustomTrack(track) && !isHubTrack(track) &&
!trackDbSetting(tdb, "bigDataUrl") &&
hTableExists(db, "kgXref"))
{
configAddTableField(dyConfig, "kgXref", "geneSymbol", &isFirst);
}
struct joinerDtf *txStatDtf;
for (txStatDtf = txStatusExtras; txStatDtf != NULL; txStatDtf = txStatDtf->next)
configAddDtf(dyConfig, txStatDtf, &isFirst);
// If any of the above apply, close the relatedTables list and config object
// and parse into jsonElements.
if (! isFirst)
{
dyStringAppend(dyConfig, " ] }");
config = jsonParse(dyConfig->string);
dyStringFree(&dyConfig);
}
return config;
}
static void adjustGpVarOverlapRule(struct annoGrator *gpVarGrator, boolean haveRegulatory)
/* If we're able to detect regulatory elements, and want to keep those annotations, loosen up
* gpVarGrator's overlap rule from the default (must overlap). */
{
if (haveRegulatory && cartUsualBoolean(cart, "hgva_include_regulatory", TRUE))
gpVarGrator->setOverlapRule(gpVarGrator, agoNoConstraint);
}
static void addTxStatusExtras(struct annoFormatter *vepOut, char *geneTrack,
struct annoGrator *gpVarGrator,
struct joinerDtf *txStatusExtras)
/* Given a list of tables and fields that will be joined with geneTrack to provide transcript
* status info, configure vepOut to put them in the EXTRAs column. */
{
struct joinerDtf *txStatDtf;
for (txStatDtf = txStatusExtras; txStatDtf != NULL; txStatDtf = txStatDtf->next)
{
char *tag = NULL, *description = NULL;
boolean isBoolean = FALSE;
// Double-check that we're not joining in some table from a different assembly database:
if (differentString(txStatDtf->database, database) &&
differentString(txStatDtf->database, "hgFixed"))
errAbort("addTxStatusExtras: Expected db=%s or hgFixed in txStatDtf but got %s",
database, txStatDtf->database);
if ((startsWith(GENCODE_PREFIX"Tag", txStatDtf->table) &&
sameString(txStatDtf->field, "tag")) ||
(sameString(txStatDtf->table, "knownToTag") &&
sameString(txStatDtf->field, "value")))
{
tag = "GENCODE_TAG";
description = "GENCODE tags for the transcript";
}
else if (sameString(txStatDtf->table, "knownCanonical") &&
sameString(txStatDtf->field, "transcript"))
{
tag = "CANONICAL";
description = "If present, the transcript is the 'canonical' transcript of the gene "
"(generally the longest isoform of the gene)";
isBoolean = TRUE;
}
else if (sameString(txStatDtf->table, "refSeqStatus") &&
sameString(txStatDtf->field, "status"))
{
tag = "REFSEQ_STATUS";
description = "RefSeq status of the transcript";
}
else
{
errAbort("addTxStatusExtras: Unrecognized {table,field}: {%s,%s}",
txStatDtf->table, txStatDtf->field);
}
char *column = annoStreamDbColumnNameFromDtf(database, geneTrack, txStatDtf);
annoFormatVepAddExtraItem(vepOut, (struct annoStreamer *)gpVarGrator,
tag, description, column, isBoolean);
}
}
void doQuery()
/* Translate simple form inputs into anno* components and execute query. */
{
dyInfo = dyStringNew(0);
char *chrom = NULL;
uint start = 0, end = 0;
if (sameString(regionType, hgvaRegionTypeRange))
getCartPosOrDie(&chrom, &start, &end);
struct annoAssembly *assembly = hAnnoGetAssembly(database);
boolean isCommandLine = (cgiOptionalString("cgiSpoof") != NULL);
char *geneTrack = cartString(cart, "hgva_geneTrack");
struct trackDb *geneTdb = tdbForTrack(database, geneTrack, &fullTrackList);
if (geneTdb == NULL)
{
warn("Can't find tdb for gene track %s", geneTrack);
if (! isCommandLine)
doUi();
return;
}
int maxVarRows = cartUsualInt(cart, "hgva_variantLimit", 10);
struct annoStreamer *primary = NULL;
char *primaryLongLabel = NULL;
char *variantTrack = cartString(cart, "hgva_variantTrack");
struct slName *commentList = NULL;
if (sameString(variantTrack, hgvaSampleVariants))
{
primary = makeSampleVariantsStreamer(assembly, geneTdb, maxVarRows);
primaryLongLabel = hgvaSampleVariantsLabel;
// Sample variants can't always be made within the currently selected position range,
// so just for these, force search to be genome-wide.
chrom = NULL;
start = 0;
end = 0;
}
else if (sameString(variantTrack, hgvaUseVariantIds))
{
// Override search position if cart position doesn't include all variants:
primary = makeVariantIdStreamer(assembly, maxVarRows, &chrom, &start, &end, &commentList);
primaryLongLabel = hgvaVariantIdsLabel;
}
else if (sameString(variantTrack, hgvaUseHgvs))
{
primary = makeHgvsStreamer(assembly, maxVarRows, &chrom, &start, &end, &commentList);
primaryLongLabel = hgvaHgvsLabel;
}
else if (sameString(variantTrack, hgvaUseVariantFileOrUrl))
{
char *fileOrUrl = cartString(cart, hgvaVariantFileOrUrl);
char *type = cartOptionalString(cart, hgvaVariantFileOrUrlType);
primary = hAnnoStreamerFromBigFileUrl(fileOrUrl, NULL, assembly, maxVarRows, type);
primaryLongLabel = hgvaVariantFileOrUrlLabel;
}
else
{
struct trackDb *varTdb = getVariantTrackDb(variantTrack);
if (varTdb == NULL)
{
if (! isCommandLine)
doUi();
return;
}
primary = hAnnoStreamerFromTrackDb(assembly, varTdb->table, varTdb, chrom, maxVarRows, NULL);
primaryLongLabel = varTdb->longLabel;
}
enum annoGratorOverlap geneOverlapRule = agoMustOverlap;
struct joinerDtf *txStatusExtras = getTxStatusExtras(database, geneTrack);
struct jsonElement *gpConfig = configForStreamer(database, geneTdb, txStatusExtras);
struct annoGrator *gpVarGrator = hAnnoGratorFromTrackDb(assembly, geneTdb->table, geneTdb, chrom,
ANNO_NO_LIMIT, primary->asObj,
geneOverlapRule, gpConfig);
setGpVarFuncFilter(gpVarGrator);
setHgvsOutOptions(gpVarGrator, geneTdb->track);
// Some grators may be used as both filters and output values. To avoid making
// multiple grators for the same source, hash them by trackName:
struct hash *gratorsByName = hashNew(8);
struct annoGrator *snpGrator = NULL;
char *snpDesc = NULL;
if (cartUsualBoolean(cart, "hgva_rsId", TRUE))
snpGrator = gratorForSnpBed4(gratorsByName, "", assembly, chrom, agoNoConstraint, &snpDesc);
// Now construct gratorList in the order in which annoFormatVep wants to see them,
// i.e. first the gpVar, then the snpNNN, then whatever else:
struct annoGrator *gratorList = NULL;
slAddHead(&gratorList, gpVarGrator);
if (snpGrator != NULL)
slAddHead(&gratorList, snpGrator);
// Text or HTML output?
char *outFormat = cartUsualString(cart, "hgva_outFormat", "vepTab");
boolean doHtml = sameString(outFormat, "vepHtml");
// Initialize VEP formatter:
struct annoFormatter *vepOut = annoFormatVepNew("stdout", doHtml,
primary, primaryLongLabel,
(struct annoStreamer *)gpVarGrator,
geneTdb->longLabel,
(struct annoStreamer *)snpGrator,
snpDesc, assembly);
addTxStatusExtras(vepOut, geneTrack, gpVarGrator, txStatusExtras);
boolean haveRegulatory = FALSE;
addOutputTracks(&gratorList, gratorsByName, vepOut, assembly, chrom, doHtml, &haveRegulatory);
adjustGpVarOverlapRule(gpVarGrator, haveRegulatory);
addFilterTracks(&gratorList, gratorsByName, assembly, chrom);
slReverse(&gratorList);
if (doHtml)
{
webStart(cart, database, "Annotated Variants in VEP/HTML format");
}
else if (! isCommandLine)
{
// Undo the htmlPushEarlyHandlers() because after this point they make ugly text:
popWarnHandler();
popAbortHandler();
textOpen();
webStartText();
}
if (isNotEmpty(dyInfo->string))
puts(dyInfo->string);
struct annoGratorQuery *query = annoGratorQueryNew(assembly, primary, gratorList, vepOut);
struct slName *comment;
for (comment = commentList; comment != NULL; comment = comment->next)
vepOut->comment(vepOut, comment->name);
if (chrom != NULL)
annoGratorQuerySetRegion(query, chrom, start, end);
annoGratorQueryExecute(query);
annoGratorQueryFree(&query);
if (doHtml)
webEnd();
else if (! isCommandLine)
textOutClose(&compressPipeline, NULL);
}
int main(int argc, char *argv[])
/* Process command line. */
{
long enteredMainTime = clock1000();
if (hIsPrivateHost())
pushCarefulMemHandler(LIMIT_2or6GB);
cgiSpoof(&argc, argv);
boolean isCommandLine = (cgiOptionalString("cgiSpoof") != NULL);
if (!isCommandLine)
htmlPushEarlyHandlers(); /* Make errors legible during initialization. */
oldVars = hashNew(10);
boolean startQuery = (cgiUsualString("hgva_startQuery", NULL) != NULL);
if (startQuery)
{
if (isCommandLine)
// No HTTP header for command-line use.
cart = cartForSession(hUserCookie(), excludeVars, oldVars);
else
cart = cartAndCookieNoContent(hUserCookie(), excludeVars, oldVars);
}
else
cart = cartAndCookie(hUserCookie(), excludeVars, oldVars);
// Try to deal with virt chrom position used by hgTracks.
if (startsWith("virt:", cartUsualString(cart, "position", "")))
cartSetString(cart, "position", cartUsualString(cart, "nonVirtPosition", ""));
/* Set up global variables. */
getDbAndGenome(cart, &database, &genome, oldVars);
initGenbankTableNames(database);
regionType = cartUsualString(cart, hgvaRegionType, hgvaRegionTypeGenome);
if (isEmpty(cartOptionalString(cart, hgvaRange)))
cartSetString(cart, hgvaRange, hDefaultPos(database));
int timeout = cartUsualInt(cart, "udcTimeout", 300);
if (udcCacheTimeout() < timeout)
udcSetCacheTimeout(timeout);
knetUdcInstall();
cartTrackDbInit(cart, &fullTrackList, &fullGroupList, TRUE);
if (lookupPosition(cart, hgvaRange))
{
if (startQuery)
doQuery();
else if (! isCommandLine)
doUi();
}
else
{
// Revert to lastPosition if we have multiple matches or warnings,
// especially in case user manually edits browser location as in #13009:
char *position = cartUsualString(cart, "lastPosition", hDefaultPos(database));
cartSetString(cart, hgvaRange, position);
if (webGotWarnings())
{
// We land here when lookupPosition pops up a warning box.
// Reset the problematic position and show the main page.
doMainPage();
}
// If lookupPosition returned FALSE and didn't report warnings,
// then it wrote HTML showing multiple position matches & links.
}
cartCheckout(&cart);
if (! isCommandLine)
cgiExitTime("hgVai", enteredMainTime);
return 0;
}
", hgvsOk ? "block" : "none");
cartMakeCheckBox(cart, "hgva_hgvsG", FALSE);
printf("Include HGVS genomic (g.) terms in output
\n"); cartMakeCheckBox(cart, "hgva_hgvsCN", FALSE); printf("Include HGVS coding (c.) terms if applicable, otherwise noncoding (n.) terms, in output" "
\n"); cartMakeCheckBox(cart, "hgva_hgvsP", FALSE); printf("Include HGVS protein (p.) terms (if applicable) in output
\n"); cartMakeCheckBox(cart, "hgva_hgvsPAddParens", FALSE); printf("When including HGVS protein (p.) terms, add parentheses around changes to emphasize " "that they are predictions
\n"); cartMakeCheckBox(cart, "hgva_hgvsBreakDelIns", FALSE); printf("For variants that involve both a deletion and insertion, " "including multi-nucleotide variants, " "include the deleted sequence (e.g. show \"delAGinsTT\" instead of only \"delinsTT\")" "
\n"); puts("
");
printf("\n"); cartMakeCheckBox(cart, "hgva_hgvsCN", FALSE); printf("Include HGVS coding (c.) terms if applicable, otherwise noncoding (n.) terms, in output" "
\n"); cartMakeCheckBox(cart, "hgva_hgvsP", FALSE); printf("Include HGVS protein (p.) terms (if applicable) in output
\n"); cartMakeCheckBox(cart, "hgva_hgvsPAddParens", FALSE); printf("When including HGVS protein (p.) terms, add parentheses around changes to emphasize " "that they are predictions
\n"); cartMakeCheckBox(cart, "hgva_hgvsBreakDelIns", FALSE); printf("For variants that involve both a deletion and insertion, " "including multi-nucleotide variants, " "include the deleted sequence (e.g. show \"delAGinsTT\" instead of only \"delinsTT\")" "
\n"); puts("
",
- refSeqSelected ? "none" : "block");
+ hgvsOk ? "none" : "block");
printf("Select RefSeq Genes in the \"Select Genes\" section above "
"in order to make options appear.\n");
puts("
");
puts(""); endCollapsibleSection(); } boolean isHg19RegulatoryTrack(struct trackDb *tdb, void *filterData) /* For now, just look for a couple specific tracks by tableName. */ { //#*** NEED METADATA return (sameString("wgEncodeRegDnaseClusteredV3", tdb->table) || sameString("wgEncodeRegTfbsClusteredV3", tdb->table)); } boolean isHg38RegulatoryTrack(struct trackDb *tdb, void *filterData) /* For now, just look for a couple specific tracks by tableName. */ { //#*** NEED METADATA return (sameString("wgEncodeRegDnaseClustered", tdb->table) || sameString("wgEncodeRegTfbsClusteredV3", tdb->table)); } struct slRef *findRegulatoryTracks() /* Look for the very limited set of Regulation tracks that hgVai offers. */ { struct slRef *regTrackRefList = NULL; if (sameString(database, "hg19")) tdbFilterGroupTrack(fullTrackList, fullGroupList, isHg19RegulatoryTrack, NULL, NULL, ®TrackRefList); else if (sameString(database, "hg38")) tdbFilterGroupTrack(fullTrackList, fullGroupList, isHg38RegulatoryTrack, NULL, NULL, ®TrackRefList); return regTrackRefList; } void selectRegulatory() /* If trackRefList is non-NULL, make a section with a checkbox for each track, * labelled with longLabel, and optionally some filtering options. */ { struct slRef *trackRefList = findRegulatoryTracks(); if (trackRefList != NULL) { puts("
"); printf("
Select Regulatory Annotations
\n");
printf("The annotations in this section provide predicted regulatory regions "
"based on various experimental data. "
"When a variant overlaps an annotation selected here, the consequence term "
"regulatory_region_variant will be assigned. "
"Follow the links to description pages that explain how each dataset was "
"constructed. "
"Some datasets cover a significant portion of the genome and it may be "
"desirable to filter these annotations by cell type and/or score in order "
"to avoid an overabundance of hits. ");
// Use a table with checkboxes in one column and label/other stuff that depends on
// checkbox in other column.
puts("| "); cartMakeCheckBox(cart, cartVar, FALSE); puts(" | ");
struct trackDb *topTdb = trackDbTopLevelSelfOrParent(tdb);
printf("%s \n", hgTrackUiName(), cartSidUrlString(cart), topTdb->track, tdb->longLabel); printFilterOptions(tdb); puts(" |
\n", hgTrackUiName(), cartSidUrlString(cart), topTdb->track, tdb->longLabel); } puts("
"); endCollapsibleSection(); } } void selectAnnotations(char *geneTrack) /* Beyond predictions of protein-coding effect, what other basic data can we integrate? */ { struct slName *dbNsfpTables = findDbNsfpTables(); boolean gotSnp = findSnpBed4("", NULL, NULL); struct slRef *elTrackRefList = NULL, *scoreTrackRefList = NULL; findCons(&elTrackRefList, &scoreTrackRefList); struct slRef *cosmicTrackRefList = findTrackRefByName("cosmic"); boolean hasTxStat = hasTxStatus(); if (dbNsfpTables == NULL && !gotSnp && elTrackRefList == NULL && scoreTrackRefList == NULL && cosmicTrackRefList == NULL && !hasTxStat) return; puts("
"); printf("
Select More Annotations (optional)
\n");
// Make wrapper table for collapsible sections:
puts("\n"); jsMakeSetClearContainer(); cartMakeCheckBox(cart, "hgva_include_intergenic", TRUE); printf("intergenic
\n"); cartMakeCheckBox(cart, "hgva_include_upDownstream", TRUE); printf("upstream/downstream of gene
\n"); cartMakeCheckBox(cart, "hgva_include_nmdTranscript", TRUE); printf("in transcript already subject to nonsense-mediated decay (NMD)
\n"); cartMakeCheckBox(cart, "hgva_include_exonLoss", TRUE); printf("exon loss caused by deletion
\n"); cartMakeCheckBox(cart, "hgva_include_utr", TRUE); printf("5' or 3' UTR
\n"); cartMakeCheckBox(cart, "hgva_include_cdsSyn", TRUE); printf("CDS - synonymous coding change
\n"); cartMakeCheckBox(cart, "hgva_include_cdsNonSyn", TRUE); printf("CDS - non-synonymous (missense, stop gain/loss, frameshift etc)
\n"); cartMakeCheckBox(cart, "hgva_include_intron", TRUE); printf("intron
\n"); cartMakeCheckBox(cart, "hgva_include_splice", TRUE); printf("splice site or splice region
\n"); cartMakeCheckBox(cart, "hgva_include_nonCodingExon", TRUE); printf("exon of non-coding gene
\n"); cartMakeCheckBox(cart, "hgva_include_noVariation", TRUE); printf("\"variants\" for which no alternate allele has been observed
\n"); struct slRef *regTrackRefList = findRegulatoryTracks(); if (regTrackRefList != NULL) { cartMakeCheckBox(cart, "hgva_include_regulatory", TRUE); printf("regulatory element (note: these are detected only if one or more tracks " "are selected in Regulatory regions above)
\n"); } jsEndContainer(); puts("
"); endCollapsibleSection(); } void selectFiltersKnownVar() /* Options to restrict output based on overlap with known variants. */ { boolean gotCommon = findSnpBed4("Common", NULL, NULL); boolean gotMult = findSnpBed4("Mult", NULL, NULL); if (!gotCommon && !gotMult) return; startCollapsibleSection("filtersVar", "Known variation", FALSE); if (gotMult) { cartMakeCheckBox(cart, "hgva_include_snpMult", TRUE); printf("Include variants even if they are co-located with variants that have been mapped to " "multiple genomic locations by dbSNP
\n"); } if (gotCommon) { cartMakeCheckBox(cart, "hgva_include_snpCommon", TRUE); printf("Include variants even if they are co-located with \"common\" variants " "(uniquely mapped variants with global minor allele frequency (MAF) " "of at least 1%% according to dbSNP)
\n"); } puts("
"); endCollapsibleSection(); } void selectFiltersCons() /* Options to restrict output based on overlap with conserved elements. */ { struct slRef *elTrackRefList = NULL; tdbFilterGroupTrack(fullTrackList, fullGroupList, isConsElTrack, NULL, NULL, &elTrackRefList); if (elTrackRefList == NULL) return; startCollapsibleSection("filtersCons", "Conservation", FALSE); // Use a little table to indent radio buttons (if we do those) past checkbox: puts("
| "); cartMakeCheckBox(cart, "hgva_require_consEl", FALSE); printf(" | Include only the variants that overlap:");
if (slCount(elTrackRefList) == 1)
{
struct trackDb *tdb = elTrackRefList->val;
printf(" %s \n", tdb->longLabel); cgiMakeHiddenVar("hgva_require_consEl_track", tdb->track); puts(" |
"); printf("
Define Filters
\n");
puts(""); printf("
Configure Output
\n");
printf("output format: ");
char *selected = cartUsualString(cart, "hgva_outFormat", "vepTab");
printf("\n"); char *compressType = cartUsualString(cart, "hgva_compressType", textOutCompressNone); char *fileName = cartUsualString(cart, "hgva_outFile", ""); printf("output file: "); cgiMakeTextVar("hgva_outFile", fileName, 29); printf(" (leave blank to keep output in browser)
\n"); printf("file type returned: "); cgiMakeRadioButton("hgva_compressType", textOutCompressNone, sameWord(textOutCompressNone, compressType)); printf(" plain text "); cgiMakeRadioButton("hgva_compressType", textOutCompressGzip, sameWord(textOutCompressGzip, compressType)); printf(" gzip compressed (ignored if output file is blank)"); puts("
"); } void submitAndDisclaimer() { puts("
");
puts("This tool is for research use only. While this tool is open to the "
"public, users seeking information about a personal medical or genetic "
"condition are urged to consult with a qualified physician for "
"diagnosis and for answers to personal questions.");
puts("
"); printf("
\n");
printf(""); } /* * When user clicks submit, we need to roll a JSON querySpec from form selections, * and show data from a submission to hgAnnoGrator. redirect from this CGI? * or have javascript submit directly? * * primary: variants, from custom track * * if there are genes, those w/annoGratorGpVar * * if there are {dbSNP, dbNsfp, regulatory, cons} selections, grator for each of those * * vep output config * * If we get bold & offer 1000Genomes VCF, will def. need handling of split chroms. * Are we really going to offer genome-wide in hgVai? * Up-front limit on #rows of input ? * * Eventually, we might want a FormatVep that produces structs that are passed * forward to multiple output writers... I would want to send it lots of gratorData * like a formatter, but it would produce rows like an annoGrator. * Maybe annoGrators should accept a bunch of input rows like formatters? * or would this grator wrap all the input grators inside? */ void doMainPage() /* Print out initial HTML of control page. */ { jsInit(); webIncludeResourceFile("jquery-ui.css"); webIncludeResourceFile("ui.dropdownchecklist.css"); boolean alreadyAgreed = cartUsualBoolean(cart, "hgva_agreedToDisclaimer", FALSE); jsInlineF( "$(document).ready(function() { hgva.disclaimer.init(%s, hgva.userClickedAgree); });\n" , alreadyAgreed ? "true" : "false"); addSomeCss(); printAssemblySection(); puts("
"); // Make wrapper table for collapsible sections: selectVariants(); char *geneTrack = selectGenes(); if (geneTrack != NULL) { selectRegulatory(); selectAnnotations(geneTrack); selectFilters(); selectOutput(); submitAndDisclaimer(); } printf(""); jsReloadOnBackButton(cart); webNewSection("Using the Variant Annotation Integrator"); webIncludeHelpFileSubst("hgVaiHelpText", cart, FALSE); jsIncludeFile("jquery-ui.js", NULL); jsIncludeFile("hgVarAnnogrator.js", NULL); jsIncludeFile("ui.dropdownchecklist.js", NULL); jsIncludeFile("ddcl.js", NULL); } void doUi() /* Set up globals and make web page */ { cartWebStart(cart, database, "Variant Annotation Integrator"); doMainPage(); cartWebEnd(); /* Save variables. */ cartCheckout(&cart); } void checkVariantTrack(struct trackDb *tdb) /* variantTrack should be either pgSnp or VCF. */ { if (! sameString(tdb->type, "pgSnp") && ! startsWith("vcf", tdb->type)) { errAbort("Expected variant track '%s' to be type pgSnp, vcf or vcfTabix, but it's '%s'", tdb->track, tdb->type); } } char *fileNameFromTable(char *table) /* Get fileName from a bigData table (for when we don't have a trackDb, just table). */ { struct sqlConnection *conn = hAllocConn(database); char query[512]; sqlSafef(query, sizeof(query), "select fileName from %s", table); char *fileName = sqlQuickString(conn, query); hFreeConn(&conn); char *fileNameRewrite = hReplaceGbdb(fileName); freez(&fileName); return fileNameRewrite; } void textOpen() /* Start serving up plain text, possibly via a pipeline to gzip. */ { char *fileName = textOutSanitizeHttpFileName(cartUsualString(cart, "hgva_outFile", "")); char *compressType = cartUsualString(cart, "hgva_compressType", textOutCompressGzip); compressPipeline = textOutInit(fileName, compressType, NULL); } void setGpVarFuncFilter(struct annoGrator *gpVarGrator) /* Use cart variables to configure gpVarGrator's filtering by functional category. */ { struct annoGratorGpVarFuncFilter aggvFuncFilter; ZeroVar(&aggvFuncFilter); aggvFuncFilter.intergenic = cartUsualBoolean(cart, "hgva_include_intergenic", TRUE); aggvFuncFilter.upDownstream = cartUsualBoolean(cart, "hgva_include_upDownstream", TRUE); aggvFuncFilter.nmdTranscript = cartUsualBoolean(cart, "hgva_include_nmdTranscript", TRUE); aggvFuncFilter.exonLoss = cartUsualBoolean(cart, "hgva_include_exonLoss", TRUE); aggvFuncFilter.utr = cartUsualBoolean(cart, "hgva_include_utr", TRUE); aggvFuncFilter.cdsSyn = cartUsualBoolean(cart, "hgva_include_cdsSyn", TRUE); aggvFuncFilter.cdsNonSyn = cartUsualBoolean(cart, "hgva_include_cdsNonSyn", TRUE); aggvFuncFilter.intron = cartUsualBoolean(cart, "hgva_include_intron", TRUE); aggvFuncFilter.splice = cartUsualBoolean(cart, "hgva_include_splice", TRUE); aggvFuncFilter.nonCodingExon = cartUsualBoolean(cart, "hgva_include_nonCodingExon", TRUE); aggvFuncFilter.noVariation = cartUsualBoolean(cart, "hgva_include_noVariation", TRUE); annoGratorGpVarSetFuncFilter(gpVarGrator, &aggvFuncFilter); } static void setHgvsOutOptions(struct annoGrator *gpVarGrator, char *geneTrack) /* Use cart variables to configure gpVarGrator's HGVS output. */ { uint hgvsOutOptions = 0; -if (sameString(geneTrack, "refGene") || startsWith("ncbiRefSeq", geneTrack)) +if (canDoHgvsOut(geneTrack)) { if (cartUsualBoolean(cart, "hgva_hgvsG", FALSE)) hgvsOutOptions |= HGVS_OUT_G; if (cartUsualBoolean(cart, "hgva_hgvsCN", FALSE)) hgvsOutOptions |= HGVS_OUT_CN; if (cartUsualBoolean(cart, "hgva_hgvsP", FALSE)) hgvsOutOptions |= HGVS_OUT_P; if (cartUsualBoolean(cart, "hgva_hgvsPAddParens", FALSE)) hgvsOutOptions |= HGVS_OUT_P_ADD_PARENS; if (cartUsualBoolean(cart, "hgva_hgvsBreakDelIns", FALSE)) hgvsOutOptions |= HGVS_OUT_BREAK_DELINS; - annoGratorGpVarSetHgvsOutOptions(gpVarGrator, hgvsOutOptions); } +annoGratorGpVarSetHgvsOutOptions(gpVarGrator, hgvsOutOptions); } struct annoGrator *gratorForSnpBed4(struct hash *gratorsByName, char *suffix, struct annoAssembly *assembly, char *chrom, enum annoGratorOverlap overlapRule, char **retDescription) /* Look up snpNNNsuffix; if we find it, return a grator (possibly for a bigBed 4 file), * otherwise return NULL. */ { char *fileName = NULL; struct trackDb *tdb = NULL; if (! findSnpBed4(suffix, &fileName, &tdb)) return NULL; struct annoGrator *grator = NULL; // First look in gratorsByName to see if this grator has already been constructed: if (tdb != NULL) { grator = hashFindVal(gratorsByName, tdb->table); if (retDescription) *retDescription = cloneString(tdb->longLabel); } if (grator != NULL) { // Set its overlap behavior and we're done. grator->setOverlapRule(grator, overlapRule); return grator; } // If not in gratorsByName, then attempt to construct it here: if (fileName != NULL) grator = hAnnoGratorFromBigFileUrl(fileName, NULL, assembly, ANNO_NO_LIMIT, overlapRule); else grator = hAnnoGratorFromTrackDb(assembly, tdb->table, tdb, chrom, ANNO_NO_LIMIT, NULL, overlapRule, NULL); if (grator != NULL) hashAdd(gratorsByName, tdb->table, grator); return grator; } char *tableNameFromSourceName(char *sourceName) /* Strip sourceName (file path or db.table) to just the basename or table name. */ { char *tableName = cloneString(sourceName); char *p = strrchr(tableName, '/'); if (p != NULL) { // file path; strip to basename char dir[PATH_LEN], name[FILENAME_LEN], extension[FILEEXT_LEN]; splitPath(tableName, dir, name, extension); safecpy(tableName, strlen(tableName)+1, name); } else { // database.table -- skip database. p = strchr(tableName, '.'); if (p != NULL) tableName = p+1; } return tableName; } char *tagFromTableName(char *tableName, char *suffix) /* Generate a tag for VEP's extras column or VCF's info column. */ { char *p = strstr(tableName, "dbNsfp"); if (p != NULL) tableName = p + strlen("dbNsfp"); int suffixLen = (suffix == NULL) ? 0 : strlen(suffix); int tagSize = strlen(tableName) + suffixLen + 1; char *tag = cloneStringZ(tableName, tagSize); if (isNotEmpty(suffix)) safecat(tag, tagSize, suffix); touppers(tag); // Some custom shortenings, to avoid very long tag names: (void)strSwapStrs(tag, tagSize, "POLYPHEN", "PP"); (void)strSwapStrs(tag, tagSize, "MUTATION", "MUT"); (void)strSwapStrs(tag, tagSize, "PHYLOP", "PHP"); (void)strSwapStrs(tag, tagSize, "PHASTCONS", "PHC"); (void)strSwapStrs(tag, tagSize, "ELEMENTS", "EL"); (void)strSwapStrs(tag, tagSize, "PRIMATES", "PRIM"); (void)strSwapStrs(tag, tagSize, "PLACENTAL", "PLAC"); if (regexMatch(tag, "^PH.*[0-9]WAY")) (void)strSwapStrs(tag, tagSize, "WAY", "W"); (void)strSwapStrs(tag, tagSize, "WGENCODEREGDNASECLUSTERED", "DNASE"); (void)strSwapStrs(tag, tagSize, "WGENCODEREGTFBSCLUSTERED", "TFBS"); return tag; } enum PolyPhen2Subset stripSubsetFromTrackName(char *trackName) /* trackName may have a _suffix for a subset of PolyPhen2; convert that to enum * and zero out the suffix so we have the real trackName. */ { enum PolyPhen2Subset subset = noSubset; char *p = strchr(trackName, ':'); if (p != NULL) { if (sameString(p+1, "HDIV")) subset = HDIV; else if (sameString(p+1, "HVAR")) subset = HVAR; else errAbort("unrecognized suffix in track_suffix '%s'", trackName); *p = '\0'; } return subset; } void updateGratorListAndVepExtra(struct annoGrator *grator, struct annoGrator **pGratorList, struct annoFormatter *vepOut, enum PolyPhen2Subset subset, char *column, char *description, boolean isReg) /* If grator is non-NULL, add it to gratorList and vepOut's list of items for EXTRAs column. */ { if (grator == NULL) return; slAddHead(pGratorList, grator); if (vepOut != NULL) { char *tableName = tableNameFromSourceName(grator->streamer.name); char *suffix = NULL; if (subset == HDIV) suffix = "HDIV"; else if (subset == HVAR) suffix = "HVAR"; char *tag = tagFromTableName(tableName, suffix); if (isEmpty(description)) description = grator->streamer.name; if (isReg) annoFormatVepAddRegulatory(vepOut, (struct annoStreamer *)grator, tag, description, column); else annoFormatVepAddExtraItem(vepOut, (struct annoStreamer *)grator, tag, description, column, FALSE); } } INLINE void updateGratorList(struct annoGrator *grator, struct annoGrator **pGratorList) /* If grator is non-NULL, add it to gratorList. */ { updateGratorListAndVepExtra(grator, pGratorList, NULL, 0, NULL, NULL, FALSE); } void addDbNsfpSeqChange(char *trackName, struct annoAssembly *assembly, struct hash *gratorsByName, struct annoGrator **pGratorList) // If the user has selected dbNsfp* data, we also need the underlying dbNsfpSeqChange // data, so annoFormatVep can tell whether the variant and gpFx are consistent with the // variant and transcript that dbNsfp used to calculate scores. { //#*** Yet another place where we need metadata: char *seqChangeTable = "dbNsfpSeqChange"; if (hashFindVal(gratorsByName, seqChangeTable) == NULL) { char *fileName = fileNameFromTable(seqChangeTable); if (fileName == NULL) errAbort("'%s' requested, but I can't find fileName for %s", trackName, seqChangeTable); struct annoGrator *grator = hAnnoGratorFromBigFileUrl(fileName, NULL, assembly, ANNO_NO_LIMIT, agoNoConstraint); updateGratorList(grator, pGratorList); hashAdd(gratorsByName, seqChangeTable, grator); } } static struct dyString *dyInfo = NULL; struct hash *getTrackFilterVars(char *track) /* Return a hash of filter variable names (cart variable suffixes) to slName lists of values. */ { char filterPrefix[512]; safef(filterPrefix, sizeof(filterPrefix), "hgva_filter_%s_", track); struct slPair *filterVars = cartVarsWithPrefix(cart, filterPrefix), *var; int prefixLen = strlen(filterPrefix); struct hash *varHash = hashNew(0); for (var = filterVars; var != NULL; var = var->next) { char *varName = var->name+prefixLen; char *val = var->val; struct hashEl *hel = hashLookup(varHash, varName); if (hel != NULL) slNameAddHead((struct slName **)(&hel->val), val); else hashAdd(varHash, varName, slNameNew(val)); } return varHash; } INLINE boolean isNotAll(struct slName *valList) /* Return TRUE unless valList has one element with name "All" (for multiselects). */ { if (slCount(valList) == 1 && sameString(valList->name, "All")) return FALSE; return TRUE; } void factorSourceGratorAddFilter(struct annoGrator *grator, char *name, struct slName *valList) /* Add filter to factorSource grator. */ //#*** Do these smarts belong here in hgVai? Probably not -- should be an hg/lib module with //#*** UI/metadata smarts. { struct annoStreamer *gStreamer = (struct annoStreamer *)grator; struct annoFilter *filter = NULL; if (sameString(name, "name") || sameString(name, "cellType") || sameString(name, "treatment")) { if (valList && isNotAll(valList)) filter = annoFilterFromAsColumn(gStreamer->asObj, name, afMatch, valList); } else if (sameString(name, "score")) filter = annoFilterFromAsColumn(gStreamer->asObj, name, afGTE, valList); else errAbort("Unrecognized filter name '%s' for %s, type=factorSource", name, gStreamer->name); if (filter) gStreamer->addFilters(gStreamer, filter); } void bed5AddFilter(struct annoGrator *grator, char *name, struct slName *valList) /* Add filter to bed 5 grator. */ { struct annoStreamer *gStreamer = (struct annoStreamer *)grator; struct annoFilter *filter = NULL; if (sameString(name, "name")) { if (valList && isNotAll(valList)) filter = annoFilterFromAsColumn(gStreamer->asObj, name, afMatch, valList); } else if (sameString(name, "score")) filter = annoFilterFromAsColumn(gStreamer->asObj, name, afGTE, valList); else errAbort("Unrecognized filter name '%s' for %s, type=bed 5", name, gStreamer->name); if (filter) gStreamer->addFilters(gStreamer, filter); } void addFiltersToGrator(struct annoGrator *grator, struct trackDb *tdb) /* Look for filter variables in the cart and add filters to grator accordingly. */ { struct hash *varHash = getTrackFilterVars(tdb->track); struct hashEl *hel, *helList = hashElListHash(varHash); for (hel = helList; hel != NULL; hel = hel->next) { char *filterName = hel->name; struct slName *valList = hel->val; //#*** Need a much better way to dispatch... if (sameString("factorSource", tdb->type)) factorSourceGratorAddFilter(grator, filterName, valList); else if (startsWith("bed 5", tdb->type)) bed5AddFilter(grator, filterName, valList); else dyStringPrintf(dyInfo, "Ignoring %s filter %s\n", tdb->track, filterName); } hashFree(&varHash); } void addOutputTracks(struct annoGrator **pGratorList, struct hash *gratorsByName, struct annoFormatter *vepOut, struct annoAssembly *assembly, char *chrom, boolean doHtml, boolean *retHasRegulatory) // Construct grators for tracks selected to appear in EXTRAS column { boolean includeReg = cartUsualBoolean(cart, "hgva_include_regulatory", TRUE); boolean haveReg = FALSE; char trackPrefix[128]; safef(trackPrefix, sizeof(trackPrefix), "hgva_track_%s_", database); int trackPrefixLen = strlen(trackPrefix); struct slPair *trackVar, *trackVars = cartVarsWithPrefix(cart, trackPrefix); for (trackVar = trackVars; trackVar != NULL; trackVar = trackVar->next) { char *val = trackVar->val; if (! (sameWord(val, "on") || atoi(val) > 0)) continue; char *trackName = trackVar->name + trackPrefixLen; if (sameString(trackName, "dbNsfpPolyPhen2")) // PolyPhen2 must have a suffix now -- skip obsolete cartVar from existing carts continue; struct annoGrator *grator = hashFindVal(gratorsByName, trackName); if (grator != NULL) // We already have this as a grator: continue; enum PolyPhen2Subset subset = noSubset; char *description = NULL; char *column = NULL; boolean isReg = FALSE; if (startsWith("dbNsfp", trackName)) { // trackName for PolyPhen2 has a suffix for subset -- strip it if we find it: subset = stripSubsetFromTrackName(trackName); description = dbNsfpDescFromTableName(trackName, subset, doHtml); addDbNsfpSeqChange(trackName, assembly, gratorsByName, pGratorList); char *fileName = fileNameFromTable(trackName); if (fileName != NULL) grator = hAnnoGratorFromBigFileUrl(fileName, NULL, assembly, ANNO_NO_LIMIT, agoNoConstraint); } else { struct trackDb *tdb = tdbForTrack(database, trackName, &fullTrackList); if (tdb != NULL) { grator = hAnnoGratorFromTrackDb(assembly, tdb->table, tdb, chrom, ANNO_NO_LIMIT, NULL, agoNoConstraint, NULL); if (grator != NULL) { //#*** Need something more sophisticated but this works for our //#*** limited selection of extra tracks: if (asColumnFind(grator->streamer.asObj, "name") != NULL) column = "name"; addFiltersToGrator(grator, tdb); } description = tdb->longLabel; isReg = (includeReg && ((sameString(database, "hg19") && isHg19RegulatoryTrack(tdb, NULL)) || (sameString(database, "hg38") && isHg38RegulatoryTrack(tdb, NULL)))); } } haveReg |= isReg; updateGratorListAndVepExtra(grator, pGratorList, vepOut, subset, column, description, isReg); if (grator != NULL) hashAdd(gratorsByName, trackName, grator); } if (retHasRegulatory) *retHasRegulatory = haveReg; } void addFilterTracks(struct annoGrator **pGratorList, struct hash *gratorsByName, struct annoAssembly *assembly, char *chrom) // Add grators for filters (not added to vepOut): { if (!cartUsualBoolean(cart, "hgva_include_snpCommon", TRUE)) { struct annoGrator *grator = gratorForSnpBed4(gratorsByName, "Common", assembly, chrom, agoMustNotOverlap, NULL); updateGratorList(grator, pGratorList); } if (!cartUsualBoolean(cart, "hgva_include_snpMult", TRUE)) { struct annoGrator *grator = gratorForSnpBed4(gratorsByName, "Mult", assembly, chrom, agoMustNotOverlap, NULL); updateGratorList(grator, pGratorList); } if (cartUsualBoolean(cart, "hgva_require_consEl", FALSE)) { char *consElTrack = cartString(cart, "hgva_require_consEl_track"); struct annoGrator *grator = hashFindVal(gratorsByName, consElTrack); if (grator == NULL) { struct trackDb *tdb = tdbForTrack(database, consElTrack, &fullTrackList); if (tdb != NULL) grator = hAnnoGratorFromTrackDb(assembly, tdb->table, tdb, chrom, ANNO_NO_LIMIT, NULL, agoMustOverlap, NULL); updateGratorList(grator, pGratorList); } else grator->setOverlapRule(grator, agoMustOverlap); } } static void getCartPosOrDie(char **retChrom, uint *retStart, uint *retEnd) /* Get chrom:start-end from cart, errAbort if any problems. */ { char *position = cartString(cart, hgvaRange); if (! parsePosition(position, retChrom, retStart, retEnd)) errAbort("Expected position to be chrom:start-end but got '%s'", position); } static char *sampleVariantsPath(struct annoAssembly *assembly, char *geneTrack) /* Construct a path for a trash file of contrived example variants for this assembly * and gene track. */ { char *chrom = NULL; uint start = 0, end = 0; getCartPosOrDie(&chrom, &start, &end); mkdirTrashDirectory(hgvsTrashSubDir); struct dyString *dy = dyStringCreate("%s/%s/%s_%s_%s_%u-%u.vcf", trashDir(), hgvsTrashSubDir, assembly->name, geneTrack, chrom, start, end); return dyStringCannibalize(&dy); } static char *makeMinimalVcfHeader(char *db, char *headerDefs) /* Return a string containing a simple no-genotypes VCF header. db must be non-NULL. * headerDefs can be NULL or empty or line(s) starting with '##' and ending w/'\n' */ { struct dyString *dy = dyStringCreate("##fileformat=VCFv4.2\n" "##reference=%s\n" "%s" "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n", db, (headerDefs ? headerDefs : "")); return dyStringCannibalize(&dy); } static void writeMinimalVcfHeader(FILE *f, char *db, char *headerDefs) /* Write header for VCF with no genotype data. db must be non-NULL. * headerDefs can be NULL or empty or line(s) starting with '##' and ending w/'\n' */ { char *headerString = makeMinimalVcfHeader(db, headerDefs); fputs(headerString, f); freeMem(headerString); } static void mutateBase(char *pBase) /* Change *pBase into a different base. */ { static char *bases = "ACGT"; char c; // In real life the probabilities aren't even, but this is easier. while ((c = bases[(uint)(floor(drand48() * 4.0))]) == *pBase) ; *pBase = c; } static void writeMinimalVcfRow(FILE *f, struct vcfRecord *rec) /* Write a minimalist VCF row (coords, name, alleles and placeholders). */ { // VCF columns: #CHROM POS ID REF ALT QUAL FILTER INFO fprintf(f, "%s\t%u\t%s\t%s\t", rec->chrom, rec->chromStart+1, rec->name, rec->alleles[0]); // Comma-separated alt alleles: int i; for (i = 1; i < rec->alleleCount; i++) fprintf(f, "%s%s", (i > 1 ? "," : ""), rec->alleles[i]); // Placeholder qual, filter, info. fprintf(f, "\t.\t.\t.\n"); } static void writeMinimalVcfRowFromBed(FILE *f, struct bed4 *bed, struct dnaSeq *seq, uint seqOffset) /* Write a minimalist VCF row with a mutation of the reference sequence at the given * position. */ { uint indelBase = 0, start = bed->chromStart, end = bed->chromEnd; if (end != start+1) { // VCF treats indels in a special way: pos is the base to the left of the indel, // and both ref and alt alleles include the base to the left of the indel. indelBase = 1; } // Get reference allele sequence: uint refAlLen = end - start + indelBase; char ref[refAlLen+1]; uint seqStart = start - indelBase - seqOffset; safencpy(ref, sizeof(ref), seq->dna+seqStart, refAlLen); touppers(ref); // Alternate allele seq needs extra room in case of single-base insertion: char alt[refAlLen+2]; alt[0] = ref[0]; alt[1] = '\0'; if (start == end) // insertion: alt gets extra base safecpy(alt+1, sizeof(alt)-1, "A"); else if (end == start+1) // single nucleotide variant mutateBase(alt); // else deletion: leave alt truncated after the shared base to left of indel // VCF columns: #CHROM POS ID REF ALT QUAL FILTER INFO fprintf(f, "%s\t%u\t%s\t%s\t%s\t.\t.\t.\n", bed->chrom, start+1-indelBase, bed->name, ref, alt); } static void writeArbitraryVariants(FILE *f, struct annoAssembly *assembly) /* Concoct some variants at an arbitrary position on some assembly sequence. * We shouldn't ever get here unless the selected geneTrack is empty. */ { char *chrom = "NULL"; uint start = 0, end = 0; getCartPosOrDie(&chrom, &start, &end); struct bed4 *bed = bed4New(chrom, start, start, "ex_ins"); struct dnaSeq *seq = twoBitReadSeqFragLower(assembly->tbf, chrom, start-1, start+100); writeMinimalVcfRowFromBed(f, bed, seq, start-1); dnaSeqFree(&seq); } static void addGpFromRow(struct genePred **pGpList, struct annoRow *row, boolean *pNeedCoding, boolean *pNeedNonCoding, boolean isBig) /* If row is coding and we need a coding gp, add it to pGpList and update pNeedCoding; * likewise for noncoding. */ { struct genePred *gp = isBig ? (struct genePred *)genePredFromBigGenePredRow(row->data) : genePredLoad(row->data); if (gp->cdsStart != gp->cdsEnd && *pNeedCoding) { slAddHead(pGpList, gp); *pNeedCoding = FALSE; } else if (gp->cdsStart == gp->cdsEnd && *pNeedNonCoding) { slAddHead(pGpList, gp); *pNeedNonCoding = FALSE; } } static void addGpFromPos(struct annoStreamer *geneStream, char *chrom, uint start, uint end, struct genePred **pGpList, boolean *pNeedCoding, boolean *pNeedNonCoding, struct lm *lm, boolean isBig) /* Get up to 10 rows from position; if we find one coding and one non-coding gene, * add them to pGpList and update pNeed* accordingly. */ { geneStream->setRegion(geneStream, chrom, start, end); int rowCount = 0; struct annoRow *row = NULL; while (rowCount < 10 && (*pNeedCoding || *pNeedNonCoding) && (row = geneStream->nextRow(geneStream, NULL, 0, lm)) != NULL) addGpFromRow(pGpList, row, pNeedCoding, pNeedNonCoding, isBig); } static struct genePred *genesFromPosition(struct annoStreamer *geneStream, boolean isBig, boolean *retGotCoding, boolean *retGotNonCoding) /* Try to get a coding and non-coding gene from geneStream at cart position. * If there are none, try whole chrom; if none there, first in assembly. */ { struct genePred *gpList = NULL; struct lm *lm = lmInit(0); char *chrom = NULL; uint start = 0, end = 0; getCartPosOrDie(&chrom, &start, &end); boolean needCoding = TRUE, needNonCoding = TRUE; // First, look for both coding and noncoding genes at cart position: addGpFromPos(geneStream, chrom, start, end, &gpList, &needCoding, &needNonCoding, lm, isBig); // If that didn't do it, try querying whole chrom if (needCoding || needNonCoding) addGpFromPos(geneStream, chrom, 0, 0, &gpList, &needCoding, &needNonCoding, lm, isBig); // If we still haven't found either coding or non-coding on the cart's current chrom, // try whole genome: if (needCoding && needNonCoding) addGpFromPos(geneStream, NULL, 0, 0, &gpList, &needCoding, &needNonCoding, lm, isBig); slSort(&gpList, genePredCmp); lmCleanup(&lm); if (retGotCoding) *retGotCoding = !needCoding; if (retGotNonCoding) *retGotNonCoding = !needNonCoding; return gpList; } static void addSnv(struct bed4 **pBedList, char *chrom, uint start, char *name) /* Add a single-nucleotide bed4 item. */ { slAddHead(pBedList, bed4New(chrom, start, start+1, name)); } // Stuff within this range (see gpFx.h) is considered upstream/downstream of a transcript: #define UPSTREAMFUDGE GPRANGE static struct bed4 *sampleVarBedFromGenePred(struct genePred *gp, struct annoAssembly *assembly, uint txSeqStart, uint txSeqEnd, boolean exonOnly) /* Construct imaginary variants that hit various parts of the transcript * described in gp, using reference base values from assembly. */ { uint basesLeft = gp->txStart - txSeqStart, basesRight = txSeqEnd - gp->txEnd; struct bed4 *bedList = NULL; if (!exonOnly && basesLeft > UPSTREAMFUDGE) // SNV, intergenic to the left addSnv(&bedList, gp->chrom, txSeqStart, "ex_igLeft"); if (!exonOnly && basesLeft > 0) // SNV, up/downstream to the left addSnv(&bedList, gp->chrom, gp->txStart - 1, "ex_updownLeft"); if (!exonOnly && gp->exonCount > 1) { // SNV, intron uint start = (gp->exonEnds[0] + gp->exonStarts[1]) / 2; addSnv(&bedList, gp->chrom, start, "ex_intron"); // SNV, splice addSnv(&bedList, gp->chrom, gp->exonStarts[1] - 2, "ex_splice"); } boolean isCoding = (gp->cdsStart != gp->cdsEnd); if (isCoding) { if (gp->txStart < gp->cdsStart) // SNV, UTR to the left addSnv(&bedList, gp->chrom, gp->txStart + 1, "ex_utrLeft"); int cdsExon = 0; while (gp->cdsStart > gp->exonEnds[cdsExon] && cdsExon < gp->exonCount) cdsExon++; uint start = gp->cdsStart + 2; // single-base insertion, leftmost codon slAddHead(&bedList, bed4New(gp->chrom, start, start, "ex_codonLeftIns")); // 3-base deletion leftmost codon slAddHead(&bedList, bed4New(gp->chrom, start, start+3, "ex_codonLeftDel")); // SNV, leftmost codon addSnv(&bedList, gp->chrom, start+1, "ex_codonLeft"); if (gp->txEnd > gp->cdsEnd) // SNV, UTR to the right addSnv(&bedList, gp->chrom, gp->txEnd - 1, "ex_utrRight"); } else { // noncoding exon variant uint start = (gp->exonStarts[0] + gp->exonEnds[0]) / 2; addSnv(&bedList, gp->chrom, start, "ex_nce"); } if (!exonOnly && basesRight > 0) // SNV, up/downstream to the left addSnv(&bedList, gp->chrom, gp->txEnd + 1, "ex_updownRight"); return bedList; } // margin for intergenic variants around transcript: #define IGFUDGE 5 static struct annoStreamer *makeSampleVariantsStreamer(struct annoAssembly *assembly, struct trackDb *geneTdb, int maxOutRows) /* Construct a VCF file of example variants for db (unless it already exists) * and return an annoStreamer for that file. If possible, make the variants hit a gene. */ { char *sampleFile = sampleVariantsPath(assembly, geneTdb->track); boolean forceRebuild = cartUsualBoolean(cart, "hgva_rebuildSampleVariants", FALSE); if (! fileExists(sampleFile) || forceRebuild) { struct annoStreamer *geneStream = hAnnoStreamerFromTrackDb(assembly, geneTdb->table, geneTdb, NULL, ANNO_NO_LIMIT, NULL); boolean isBig = sameString(geneTdb->type, "bigGenePred"); boolean gotCoding = FALSE, gotNonCoding = FALSE; struct genePred *gpList = genesFromPosition(geneStream, isBig, &gotCoding, &gotNonCoding); FILE *f = mustOpen(sampleFile, "w"); writeMinimalVcfHeader(f, assembly->name, NULL); if (gpList == NULL) { warn("Unable to find any gene transcripts in '%s' (%s)", geneTdb->shortLabel, geneTdb->track); writeArbitraryVariants(f, assembly); } else { struct bed4 *bedList = NULL; uint chromSize = annoAssemblySeqSize(assembly, gpList->chrom); uint minSeqStart = chromSize, maxSeqEnd = 0; struct genePred *gp; for (gp = gpList; gp != NULL; gp = gp->next) { int txSeqStart = gp->txStart - (UPSTREAMFUDGE + IGFUDGE); uint txSeqEnd = gp->txEnd + UPSTREAMFUDGE + IGFUDGE; if (txSeqStart < 0) txSeqStart = 0; if (txSeqEnd > chromSize) txSeqEnd = chromSize; if (txSeqStart < minSeqStart) minSeqStart = txSeqStart; if (txSeqEnd > maxSeqEnd) maxSeqEnd = txSeqEnd; // If we got a coding gp, but this gp is non-coding, just do its exon variant: boolean exonOnly = gotCoding && (gp->cdsStart == gp->cdsEnd); slCat(&bedList, sampleVarBedFromGenePred(gp, assembly, txSeqStart, txSeqEnd, exonOnly)); } slSort(&bedList, bedCmp); struct dnaSeq *txSeq = twoBitReadSeqFragLower(assembly->tbf, gpList->chrom, minSeqStart, maxSeqEnd); struct bed4 *bed; for (bed = bedList; bed != NULL; bed = bed->next) { writeMinimalVcfRowFromBed(f, bed, txSeq, minSeqStart); } dnaSeqFree(&txSeq); bed4FreeList(&bedList); } geneStream->close(&geneStream); carefulClose(&f); } return annoStreamVcfNew(sampleFile, NULL, FALSE, assembly, maxOutRows); } static char *md5TrashPath(struct annoAssembly *assembly, char *string) /* Use the md5sum of a string to make a hopefully unique trash filename. */ { char *md5sum = md5HexForString(string); mkdirTrashDirectory(hgvsTrashSubDir); struct dyString *dy = dyStringCreate("%s/%s/%s_%s.vcf", trashDir(), hgvsTrashSubDir, assembly->name, md5sum); return dyStringCannibalize(&dy); } static struct slName *hashListNames(struct hash *hash) /* Return a list of all element names in the hash (if any). */ { struct slName *list = NULL; struct hashCookie cookie = hashFirst(hash); struct hashEl *hel; while ((hel = hashNext(&cookie)) != NULL) slAddHead(&list, slNameNew(hel->name)); return list; } static char *encloseInAngleBracketsDbSnp(char *stringIn) /* Return a string that has