93f69886bca04e521aa482b21f075cca9dcde37b angie Mon Jun 3 15:25:58 2013 -0700 Added a couple of Galt's new sqlSafef's. diff --git src/hg/hgVai/hgVai.c src/hg/hgVai/hgVai.c index d7d9dc7..4eeb61c 100644 --- src/hg/hgVai/hgVai.c +++ src/hg/hgVai/hgVai.c @@ -1,1105 +1,1105 @@ /* hgVai - Variant Annotation Integrator. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "options.h" #include "jksql.h" #include "htmshell.h" #include "web.h" #include "cheapcgi.h" #include "cart.h" #include "hui.h" #include "grp.h" #include "hCommon.h" #include "hgFind.h" #include "hPrint.h" #include "jsHelper.h" #include "memalloc.h" #include "textOut.h" #include "trackHub.h" #include "hubConnect.h" #include "udc.h" #include "knetUdc.h" #include "annoGratorQuery.h" #include "annoGratorGpVar.h" #include "annoFormatVep.h" #include "annoStreamBigBed.h" #include "libifyMe.h" /* Global Variables */ struct cart *cart; /* CGI and other variables */ struct hash *oldVars = NULL; /* The cart before new cgi stuff added. */ char *genome = NULL; /* Name of genome - mouse, human, etc. */ char *database = NULL; /* Current genome database - hg17, mm5, etc. */ char *regionType = NULL; /* genome, ENCODE pilot regions, or specific position range. */ struct grp *fullGroupList = NULL; /* List of all groups. */ struct trackDb *fullTrackList = NULL; /* List of all tracks in database. */ static struct pipeline *compressPipeline = (struct pipeline *)NULL; // Null terminated list of CGI Variables we don't want to save permanently: char *excludeVars[] = {"Submit", "submit", NULL,}; #define hgvaRange "position" #define hgvaRegionType "hgva_regionType" #define hgvaRegionTypeEncode "encode" #define hgvaRegionTypeGenome "genome" #define hgvaRegionTypeRange "range" #define hgvaPositionContainer "positionContainer" void addSomeCss() /*#*** This should go in a .css file of course. */ { printf("<style>\n" "div.sectionLite { border-width: 1px; border-color: #"HG_COL_BORDER"; border-style: solid;" " background-color: #"HG_COL_INSIDE"; padding-left: 10px; padding-right: 10px; " " padding-top: 8px; padding-bottom: 5px; margin-top: 5px; margin-bottom: 5px }\n" ".sectionLiteHeader { font-weight: bold; font-size:larger; color:#000000;" " text-align:left; vertical-align:bottom; white-space:nowrap; }\n" "div.sectionLiteHeader.noReorderRemove { padding-bottom:5px; }\n" "div.sourceFilter { padding-top: 5px; padding-bottom: 5px }\n" "</style>\n"); } INLINE void startCollapsibleSection(char *sectionSuffix, char *title, boolean onByDefault) // Wrap shared args to jsBeginCollapsibleSectionFontSize { jsBeginCollapsibleSectionFontSize(cart, "hgva", sectionSuffix, title, FALSE, "1.1em"); } #define endCollapsibleSection jsEndCollapsibleSection static struct dyString *onChangeStart() /* Start up a javascript onChange command */ { struct dyString *dy = jsOnChangeStart(); jsTextCarryOver(dy, hgvaRegionType); jsTextCarryOver(dy, hgvaRange); return dy; } static char *onChangeClade() /* Return javascript executed when they change clade. */ { struct dyString *dy = onChangeStart(); jsDropDownCarryOver(dy, "clade"); dyStringAppend(dy, " document.hiddenForm.org.value=0;"); dyStringAppend(dy, " document.hiddenForm.db.value=0;"); dyStringAppend(dy, " document.hiddenForm." hgvaRange ".value='';"); return jsOnChangeEnd(&dy); } static char *onChangeOrg() /* Return javascript executed when they change organism. */ { struct dyString *dy = onChangeStart(); jsDropDownCarryOver(dy, "clade"); jsDropDownCarryOver(dy, "org"); dyStringAppend(dy, " document.hiddenForm.db.value=0;"); dyStringAppend(dy, " document.hiddenForm." hgvaRange ".value='';"); return jsOnChangeEnd(&dy); } static char *onChangeDb() /* Return javascript executed when they change database. */ { struct dyString *dy = onChangeStart(); jsDropDownCarryOver(dy, "clade"); jsDropDownCarryOver(dy, "db"); dyStringAppend(dy, " document.hiddenForm." hgvaRange ".value='';"); return jsOnChangeEnd(&dy); } INLINE void printOption(char *val, char *selectedVal, char *label) /* For rolling our own select without having to build conditional arrays/lists. */ { printf("<OPTION VALUE='%s'%s>%s\n", val, (sameString(selectedVal, val) ? " SELECTED" : ""), label); } void printRegionListHtml(char *db) /* Make a dropdown choice of region type, with position input box that appears if needed. * Unlike hgTables, don't bother with ENCODE pilot regions -- unless someone misses it. * Return the selected region type. */ { printf("<SELECT ID='"hgvaRegionType"' NAME='"hgvaRegionType"' " "onchange=\"hgva.changeRegion();\">\n"); struct sqlConnection *conn = hAllocConn(db); hFreeConn(&conn); printOption(hgvaRegionTypeGenome, regionType, "genome"); printOption(hgvaRegionTypeRange, regionType, "position or search term"); printf("</SELECT>"); } void topLabelSpansStart(char *label) { printf("<span style='display: inline-block; padding-right: 5px;'>" "<span style='display: block;'>%s</span>\n" "<span style='display: block; padding-bottom: 5px;'>\n", label); } void topLabelSpansEnd() { printf("</span></span>"); } char *makePositionInput() /* Return HTML for the position input. */ { struct dyString *dy = dyStringCreate("<INPUT TYPE=TEXT NAME=\"%s\" SIZE=%d VALUE=\"%s\">", hgvaRange, 26, addCommasToPos(NULL, cartString(cart, hgvaRange))); return dyStringCannibalize(&dy); } void printCtAndHubButtons() /* Print a div with buttons for hgCustom and hgHubConnect */ { puts("<div style='padding-top: 5px; padding-bottom: 5px'>"); hOnClickButton("document.customTrackForm.submit(); return false;", hasCustomTracks(cart) ? CT_MANAGE_BUTTON_LABEL : CT_ADD_BUTTON_LABEL); printf(" "); if (hubConnectTableExists()) hOnClickButton("document.trackHubForm.submit(); return false;", "track hubs"); nbSpaces(3); printf("To reset <B>all</B> user cart settings (including custom tracks), \n" "<A HREF=\"/cgi-bin/cartReset?destination=%s\">click here</A>.\n", cgiScriptName()); puts("</div>"); } void hgGatewayCladeGenomeDb() /* Make a row of labels and row of buttons like hgGateway, but not using tables. */ { boolean gotClade = hGotClade(); if (gotClade) { topLabelSpansStart("clade"); printCladeListHtml(genome, onChangeClade()); topLabelSpansEnd(); } topLabelSpansStart("genome"); if (gotClade) printGenomeListForCladeHtml(database, onChangeOrg()); else printGenomeListHtml(database, onChangeOrg()); topLabelSpansEnd(); topLabelSpansStart("assembly"); printAssemblyListHtml(database, onChangeDb()); topLabelSpansEnd(); puts("<BR>"); topLabelSpansStart("region to annotate"); printRegionListHtml(database); topLabelSpansEnd(); topLabelSpansStart(""); // Yet another span, for hiding/showing position input and lookup button: printf("<span id='"hgvaPositionContainer"'%s>\n", differentString(regionType, hgvaRegionTypeRange) ? " style='display: none;'" : ""); puts(makePositionInput()); printf("</span>\n"); topLabelSpansEnd(); puts("<BR>"); } void printAssemblySection() /* Print assembly-selection stuff. * Redrawing the whole page when the assembly changes seems fine to me. */ { //#*** ---------- More copied verbatim, from hgTables/mainPage.c: ----------- /* Hidden form - for benefit of javascript. */ { static char *saveVars[] = { "clade", "org", "db", hgvaRange, hgvaRegionType }; jsCreateHiddenForm(cart, cgiScriptName(), saveVars, ArraySize(saveVars)); } /* Hidden form for jumping to custom tracks CGI. */ printf("<FORM ACTION='%s' NAME='customTrackForm'>", hgCustomName()); cartSaveSession(cart); printf("</FORM>\n"); /* Hidden form for jumping to track hub manager CGI. */ printf("<FORM ACTION='%s' NAME='trackHubForm'>", hgHubConnectName()); //#*** well, almost verbatim... lib version should use cgiScriptName. cgiMakeHiddenVar(hgHubConnectCgiDestUrl, cgiScriptName()); cartSaveSession(cart); printf("</FORM>\n"); printf("<FORM ACTION=\"%s\" NAME=\"mainForm\" ID=\"mainForm\" METHOD=%s>\n", cgiScriptName(), cartUsualString(cart, "formMethod", "GET")); cartSaveSession(cart); //#*** ------------------ end verbatim --------------- printf("<div class='sectionLiteHeader noReorderRemove'>" "Select Genome Assembly and Region</div>\n"); /* Print clade, genome and assembly line. */ hgGatewayCladeGenomeDb(); //#*** No longer ending form here... } void askUserForVariantCustomTrack() /* Tell the user that we need a custom track of variants to work on. */ { puts("<BR>"); printf("<div class='sectionLiteHeader'>Upload Variants as Custom Track</div>\n"); printf("Please create a custom track containing your variants of interest, using either " "<A HREF='../FAQ/FAQformat.html#format10' TARGET=_BLANK>pgSnp</A> or " "<A HREF='../goldenPath/help/vcf.html' TARGET=_BLANK>VCF</A> format:<BR>\n"); printCtAndHubButtons(); puts("<BR>"); } typedef boolean TdbFilterFunction(struct trackDb *tdb, void *filterData); /* Return TRUE if tdb passes filter criteria. */ void rFilterTrackList(struct trackDb *trackList, struct slRef **pPassingRefs, TdbFilterFunction *filterFunc, void *filterData) /* Recursively apply filterFunc and filterData to all tracks in fullTrackList and * their subtracks. Add an slRef to pPassingRefs for each track/subtrack that passes. * Caller should slReverse(pPassingRefs) when recursion is all done. */ { struct trackDb *tdb; for (tdb = trackList; tdb != NULL; tdb = tdb->next) { if (tdb->subtracks != NULL) rFilterTrackList(tdb->subtracks, pPassingRefs, filterFunc, filterData); if (filterFunc(tdb, filterData)) slAddHead(pPassingRefs, slRefNew(tdb)); } } void tdbFilterGroupTrack(struct trackDb *fullTrackList, struct grp *fullGroupList, TdbFilterFunction *filterFunc, void *filterData, struct slRef **retGroupRefList, struct slRef **retTrackRefList) /* Apply filterFunc and filterData to each track in fullTrackList and all subtracks; * make an slRef list of tracks that pass the filter (retTrackRefList) and an slRef * list of groups to which the passing tracks belong (retGroupRefList). */ { struct slRef *trackRefList = NULL; rFilterTrackList(fullTrackList, &trackRefList, filterFunc, filterData); slReverse(&trackRefList); if (retTrackRefList != NULL) *retTrackRefList = trackRefList; if (retGroupRefList != NULL) { // Which groups have tracks that passed the filter? struct hash *hash = hashNew(0); struct slRef *trackRef; for (trackRef = trackRefList; trackRef != NULL; trackRef = trackRef->next) { struct trackDb *tdb = trackRef->val; hashAddInt(hash, tdb->grp, TRUE); } struct slRef *groupRefList = NULL; struct grp *grp; for (grp = fullGroupList; grp != NULL; grp = grp->next) { if (hashIntValDefault(hash, grp->name, FALSE)) slAddHead(&groupRefList, slRefNew(grp)); } hashFree(&hash); slReverse(&groupRefList); *retGroupRefList = groupRefList; } } boolean isVariantCustomTrack(struct trackDb *tdb, void *filterData) /* This is a TdbFilterFunction to get custom or hub tracks with type pgSnp or vcfTabix. */ { return ((sameString(tdb->grp, "user") || isHubTrack(tdb->track)) && (sameString(tdb->type, "pgSnp") || sameString(tdb->type, "vcfTabix"))); } void selectVariants(struct slRef *varGroupList, struct slRef *varTrackList) /* Offer selection of user's variant custom tracks. */ { printf("<div class='sectionLiteHeader'>Select Variants</div>\n"); printf("If you have more than one custom track in " "<A HREF='../FAQ/FAQformat.html#format10' TARGET=_BLANK>pgSnp</A> or " "<A HREF='../goldenPath/help/vcf.html' TARGET=_BLANK>VCF</A> format, " "please select the one you wish to annotate.<BR>\n"); printf("<B>variants: </B>"); printf("<SELECT ID='hgva_variantTrack' NAME='hgva_variantTrack'>\n"); char *selected = cartUsualString(cart, "hgva_variantTrack", ""); struct slRef *ref; for (ref = varTrackList; ref != NULL; ref = ref->next) { struct trackDb *tdb = ref->val; printOption(tdb->track, selected, tdb->longLabel); } printf("</SELECT><BR>\n"); printf("<B>maximum number of variants to be processed:</B>\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("<BR>"); } boolean isGeneTrack(struct trackDb *tdb, void *filterData) /* This is a TdbFilterFunction to get genePred tracks. */ { return (startsWith("genePred", tdb->type)); } void selectGenes() /* Let user select a gene predictions track */ { struct slRef *trackRefList = NULL; tdbFilterGroupTrack(fullTrackList, fullGroupList, isGeneTrack, NULL, NULL, &trackRefList); if (trackRefList == NULL) return; printf("<div class='sectionLiteHeader'>Select Genes</div>\n"); printf("The gene predictions selected here will be used to determine the effect of " "each variant on genes, for example intronic, missense, splice site, intergenic etc." "<BR>\n"); char *selected = cartUsualString(cart, "hgva_geneTrack", ""); //#*** per-db cart vars?? //#*** should show more info about each track... button to pop up track desc? printf("<SELECT ID='hgva_geneTrack' NAME='hgva_geneTrack'>\n"); struct slRef *ref; for (ref = trackRefList; ref != NULL; ref = ref->next) { struct trackDb *tdb = ref->val; if (tdb->subtracks == NULL) printOption(tdb->track, selected, tdb->longLabel); } puts("</SELECT><BR>"); } char *dbNsfpDescFromTableName(char *tableName) /* Return a description for table name... if these become tracks, use tdb of course. */ { if (sameString(tableName, "dbNsfpSift")) return "<A HREF='http://sift.bii.a-star.edu.sg/' TARGET=_BLANK>" "SIFT</A> scores"; else if (sameString(tableName, "dbNsfpPolyPhen2")) return "<A HREF='http://genetics.bwh.harvard.edu/pph2/' TARGET=_BLANK>" "PolyPhen-2</A> scores and predictions (HDIV, HVAR, UniProt...)"; else if (sameString(tableName, "dbNsfpMutationTaster")) return "<A HREF='http://www.mutationtaster.org/' TARGET=_BLANK>" "MutationTaster</A> scores and predictions"; else if (sameString(tableName, "dbNsfpMutationAssessor")) return "<A HREF='http://mutationassessor.org/' TARGET=_BLANK>" "MutationAssessor</A> scores and predictions"; //else if (sameString(tableName, "dbNsfpGerpNr")) // return "<A HREF='http://mendel.stanford.edu/SidowLab/downloads/gerp/index.html' " // "TARGET=_BLANK>GERP++</A> neutral rate (NR) score"; //else if (sameString(tableName, "dbNsfpGerpRs")) // return "<A HREF='http://mendel.stanford.edu/SidowLab/downloads/gerp/index.html' " // "TARGET=_BLANK>GERP++</A> Rejected Substitutions (RS) score"; else if (sameString(tableName, "dbNsfpLrt")) return "<A HREF='http://www.mutationtaster.org' TARGET=_BLANK>" "Likelihood ratio test (LRT)</A> scores"; else if (sameString(tableName, "dbNsfpInterpro")) return "Protein domains from <A HREF='http://www.ebi.ac.uk/interpro/' TARGET=_BLANK" "Interpro</A>"; return NULL; } struct slName *findDbNsfpTables() /* See if this database contains dbNSFP tables. */ { struct sqlConnection *conn = hAllocConn(database); struct slName *dbNsfpTables = sqlQuickList(conn, "show tables like 'dbNsfp%'"); hFreeConn(&conn); return dbNsfpTables; } void selectDbNsfp(struct slName *dbNsfpTables) /* Let user select scores/predicitions from various tools collected by dbNSFP. */ { if (dbNsfpTables == NULL) return; startCollapsibleSection("dbNsfp", "Non-synonymous functional predictions", FALSE); printf("The " "<A HREF='https://sites.google.com/site/jpopgen/dbNSFP' TARGET=_BLANK>" "Database of Non-Synonymous Functional Predictions (dbNSFP)</A> release 2.0 " "provides pre-computed scores and predictions of functional significance " "from a variety of tools. Every possible coding change to transcripts in " //#*** hardcoded version info... sigh, we need trackDb... or metaDb?? "Gencode release 9 (Ensembl 64, Dec. 2011) gene predictions " "has been evaluated. " "<em>Note: This may not encompass all transcripts in your " "selected gene set.</em><BR>\n"); //#*** Another cheap hack: reverse alph order happens to be what we want, //#*** but priorities would be cleaner: slReverse(&dbNsfpTables); struct slName *table; for (table = dbNsfpTables; table != NULL; table = table->next) { char *description = dbNsfpDescFromTableName(table->name); if (description != NULL) { char cartVar[512]; safef(cartVar, sizeof(cartVar), "hgva_track_%s_%s", database, table->name); boolean defaultChecked = (sameString("dbNsfpSift", table->name) || sameString("dbNsfpPolyPhen2", table->name)); cartMakeCheckBox(cart, cartVar, defaultChecked); printf("%s<BR>\n", description); } } puts("<BR>"); endCollapsibleSection(); } boolean findSnpBed4(char *suffix, char **retFileName, struct trackDb **retTdb) /* If we can find the latest snpNNNsuffix track using 'show tables rlike "regex"', * or better yet a bigBed file for it (faster), * set the appropriate ret* and return TRUE, otherwise return FALSE. */ { if (suffix == NULL) suffix = ""; char query[64]; -safef(query, sizeof(query), "show tables like 'snp1__%s'", suffix); +sqlSafef(query, sizeof(query), "show tables like 'snp1__%s'", suffix); struct sqlConnection *conn = hAllocConn(database); struct slName *snpNNNTables = sqlQuickList(conn, query); hFreeConn(&conn); if (snpNNNTables == NULL) return FALSE; // Skip to last in list -- highest number (show tables can't use rlike or 'order by'): struct slName *table = snpNNNTables; while (table->next != NULL && isdigit(table->next->name[4]) && isdigit(table->next->name[5])) table = table->next; // Do we happen to have a bigBed version? Better yet, bed4 only for current uses: char fileName[HDB_MAX_PATH_STRING]; safef(fileName, sizeof(fileName), "/gbdb/%s/vai/%s.bed4.bb", database, table->name); if (fileExists(fileName)) { if (retFileName != NULL) *retFileName = cloneString(fileName); return TRUE; } // Not bed4; try just .bb: safef(fileName, sizeof(fileName), "/gbdb/%s/vai/%s.bb", database, table->name); if (fileExists(fileName)) { if (retFileName != NULL) *retFileName = cloneString(fileName); return TRUE; } struct trackDb *tdb = tdbForTrack(database, table->name, &fullTrackList); if (tdb != NULL) { if (retTdb != NULL) *retTdb = tdb; return TRUE; } return FALSE; } 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", FALSE); cartMakeCheckBox(cart, "hgva_rsId", TRUE); printf("Include dbSNP rs# ID if one exists<BR>\n"); puts("<BR>"); endCollapsibleSection(); } 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); } void trackRefListToCheckboxes(struct slRef *trackRefList) { 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); printf("%s<BR>\n", tdb->longLabel); } } void selectCons(struct slRef *elTrackRefList, struct slRef *scoreTrackRefList) /* Offer checkboxes for optional Conservation scores. */ { if (elTrackRefList == NULL && scoreTrackRefList == NULL) return; if (elTrackRefList != NULL) { startCollapsibleSection("ConsEl", "Conserved elements", FALSE); trackRefListToCheckboxes(elTrackRefList); puts("<BR>"); endCollapsibleSection(); } if (scoreTrackRefList != NULL) { startCollapsibleSection("ConsScore", "Conservation scores", FALSE); trackRefListToCheckboxes(scoreTrackRefList); endCollapsibleSection(); } } void selectAnnotations() /* 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); if (dbNsfpTables == NULL && !gotSnp && elTrackRefList == NULL && scoreTrackRefList == NULL) return; puts("<BR>"); printf("<div class='sectionLiteHeader'>Select More Annotations (optional)</div>\n"); // Make wrapper table for collapsible sections: puts("<TABLE border=0 cellspacing=5 cellpadding=0 style='padding-left: 10px;'>"); selectDbNsfp(dbNsfpTables); selectDbSnp(gotSnp); selectCons(elTrackRefList, scoreTrackRefList); puts("</TABLE>"); } void selectFiltersFunc() /* Options to restrict variants based on gene region/soTerm from gpFx */ { startCollapsibleSection("filtersFunc", "Functional role", FALSE); printf("Include variants annotated as<BR>\n"); cartMakeCheckBox(cart, "hgva_include_intergenic", FALSE); printf("intergenic<BR>\n"); cartMakeCheckBox(cart, "hgva_include_upDownstream", TRUE); printf("upstream/downstream of gene<BR>\n"); cartMakeCheckBox(cart, "hgva_include_utr", TRUE); printf("5' or 3' UTR<BR>\n"); cartMakeCheckBox(cart, "hgva_include_cdsSyn", TRUE); printf("CDS - synonymous coding change<BR>\n"); cartMakeCheckBox(cart, "hgva_include_cdsNonSyn", TRUE); printf("CDS - non-synonymous (missense, stop gain/loss, frameshift etc)<BR>\n"); cartMakeCheckBox(cart, "hgva_include_intron", TRUE); printf("intron<BR>\n"); cartMakeCheckBox(cart, "hgva_include_splice", TRUE); printf("splice site or splice region<BR>\n"); cartMakeCheckBox(cart, "hgva_include_nonCodingExon", TRUE); printf("exon of non-coding gene<BR>\n"); puts("<BR>"); 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_exclude_snpMult", FALSE); printf("Exclude variants mapped to multiple genomic locations by dbSNP<BR>\n"); } if (gotCommon) { cartMakeCheckBox(cart, "hgva_exclude_snpCommon", FALSE); printf("Exclude \"common\" variants " "(uniquely mapped variants with global minor allele frequency (MAF) " "of at least 1%% according to dbSNP)<BR>\n"); } puts("<BR>"); 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("<TABLE><TR><TD>"); cartMakeCheckBox(cart, "hgva_require_consEl", FALSE); printf("</TD><TD>Include only the variants that overlap"); if (slCount(elTrackRefList) == 1) { struct trackDb *tdb = elTrackRefList->val; printf(" %s<BR>\n", tdb->longLabel); cgiMakeHiddenVar("hgva_require_consEl_track", tdb->track); puts("</TD></TR></TABLE>"); } else { puts("</TD></TR>"); char *selected = cartUsualString(cart, "hgva_require_consEl_track", ""); struct slRef *ref; for (ref = elTrackRefList; ref != NULL; ref = ref->next) { printf("<TR><TD></TD><TD>"); struct trackDb *tdb = ref->val; cgiMakeOnClickRadioButton("hgva_require_consEl_track", tdb->track, sameString(tdb->track, selected), "onclick=\"setCheckboxList('hgva_require_consEl', true);\""); printf("%s</TD></TR>\n", tdb->longLabel); } puts("</TABLE>"); } endCollapsibleSection(); } void selectFilters() /* Options to restrict output to variants with specific properties */ { puts("<BR>"); printf("<div class='sectionLiteHeader'>Define Filters</div>\n"); puts("<TABLE border=0 cellspacing=5 cellpadding=0 style='padding-left: 10px;'>"); selectFiltersFunc(); selectFiltersKnownVar(); selectFiltersCons(); puts("</TABLE>"); } 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("<BR>"); printf("<div class='sectionLiteHeader'>Configure Output</div>\n"); printf("<B>output format: </B>"); char *selected = cartUsualString(cart, "hgva_outFormat", ""); printf("<SELECT ID='hgva_outFormat' NAME='hgva_outFormat'>\n"); printOption("vepTab", selected, "Variant Effect Predictor (tab-separated text)"); printf("</SELECT><BR>\n"); char *compressType = cartUsualString(cart, "hgva_compressType", textOutCompressGzip); char *fileName = cartUsualString(cart, "hgva_outFile", ""); printf("<B>output file:</B> "); cgiMakeTextVar("hgva_outFile", fileName, 29); printf(" (leave blank to keep output in browser)<BR>\n"); printf("<B>file type returned: </B>"); 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("<BR>"); } void submitAndDisclaimer() { puts("<BR>"); puts("<div class='warn-note' style='border: 2px solid #9e5900; padding: 5px 20px; background-color: #ffe9cc;'>"); puts("<p><span style='font-weight: bold; color: #c70000;'>NOTE:</span><br>"); if (hIsPrivateHost()) puts("<span style='font-weight: bold; color: #c70000;'>THIS IS UNTESTED SOFTWARE. " "We are still working out the bugs. Feel free to play with this and tell us " "about the bugs, but treat results with extra skepticism.</span><br>"); 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("</p></div><BR>"); printf(" <img id='loadingImg' src='../images/loading.gif' />\n"); printf("<span id='loadingMsg'></span>\n"); cgiMakeButtonWithOnClick("startQuery", "Go!", "get the results of your query", "loadingImage.run(); $('#mainForm').submit();"); } /* * 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. */ { printAssemblySection(); /* Check for variant custom tracks. If there are none, tell user they need to * upload at least one. */ struct slRef *varTrackList = NULL, *varGroupList = NULL; tdbFilterGroupTrack(fullTrackList, fullGroupList, isVariantCustomTrack, NULL, &varGroupList, &varTrackList); if (varTrackList == NULL) { askUserForVariantCustomTrack(); } else { puts("<BR>"); // Make wrapper table for collapsible sections: selectVariants(varGroupList, varTrackList); selectGenes(); selectAnnotations(); selectFilters(); selectOutput(); submitAndDisclaimer(); } printf("</FORM>"); webNewSection("Using the Variant Annotation Integrator"); webIncludeHelpFile("hgVaiHelpText", FALSE); } void doUi() /* Set up globals and make web page */ { cartWebStart(cart, database, "Variant Annotation Integrator"); jsInit(); jsIncludeFile("jquery-ui.js", NULL); webIncludeResourceFile("jquery-ui.css"); jsIncludeFile("hgVarAnnogrator.js", NULL); addSomeCss(); doMainPage(); cartWebEnd(); /* Save variables. */ cartCheckout(&cart); } void checkVariantTrack(struct trackDb *tdb) /* variantTrack should be either pgSnp or VCF. */ { if (! sameString(tdb->type, "pgSnp") && ! sameString(tdb->type, "vcfTabix")) { errAbort("Expected variant track '%s' to be either pgSnp 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]; -safef(query, sizeof(query), "select fileName from %s", table); +sqlSafef(query, sizeof(query), "select fileName from %s", table); char *fileName = sqlQuickString(conn, query); hFreeConn(&conn); return fileName; } void textOpen() /* Start serving up plain text, possibly via a pipeline to gzip. */ { char *fileName = cartUsualString(cart, "hgva_outFile", ""); char *compressType = cartUsualString(cart, "hgva_compressType", textOutCompressGzip); compressPipeline = textOutInit(fileName, compressType); } struct annoGrator *gratorForSnp(char *suffix, struct annoAssembly *assembly, char *chrom, enum annoGratorOverlap overlapRule) /* Look up snpNNNsuffix; if we find it, return a grator, otherwise return NULL. */ { char *fileName = NULL; struct trackDb *tdb = NULL; if (! findSnpBed4(suffix, &fileName, &tdb)) return NULL; struct annoGrator *grator = NULL; if (fileName != NULL) { struct annoStreamer *streamer = annoStreamBigBedNew(fileName, assembly, BIGNUM); grator = annoGratorNew(streamer); grator->setOverlapRule(grator, overlapRule); } else { grator = gratorFromTrack(assembly, tdb->table, tdb, chrom, BIGNUM, NULL, overlapRule); } return grator; } void updateGratorLists(struct annoGrator *grator, struct annoGrator **pGratorList, struct annoGrator **pFirstExtra) /* If grator is non-NULL, add it to gratorList; if *pFirstExtra is NULL, set it to grator. */ { if (grator != NULL) { slAddHead(pGratorList, grator); if (pFirstExtra != NULL && *pFirstExtra == NULL) *pFirstExtra = grator; } } void doQuery() /* Translate simple form inputs into anno* components and execute query. */ { char *chrom = NULL; uint start = 0, end = 0; if (sameString(regionType, hgvaRegionTypeRange)) { char *position = cartString(cart, hgvaRange); if (! parsePosition(position, &chrom, &start, &end)) errAbort("Expected position to be chrom:start-end but got '%s'", position); } char *variantTrack = cartString(cart, "hgva_variantTrack"); char *geneTrack = cartString(cart, "hgva_geneTrack"); struct annoAssembly *assembly = getAnnoAssembly(database); struct trackDb *varTdb = tdbForTrack(database, variantTrack, &fullTrackList); if (varTdb == NULL) { if (isHubTrack(variantTrack)) warn("Can't find hub track %s; try the \"check hub\" button in " "<A href=\"%s?%s&%s=%s\">Track Data Hubs</A>.", variantTrack, hgHubConnectName(), cartSidUrlString(cart), hgHubConnectCgiDestUrl, cgiScriptName()); else warn("Can't find tdb for variant track %s", variantTrack); doUi(); return; } checkVariantTrack(varTdb); int maxVarRows = cartUsualInt(cart, "hgva_variantLimit", 10); struct annoStreamer *primary = streamerFromTrack(assembly, varTdb->table, varTdb, chrom, maxVarRows); struct trackDb *geneTdb = tdbForTrack(database, geneTrack, &fullTrackList); enum annoGratorOverlap geneOverlapRule = agoMustOverlap; struct annoGrator *gpVarGrator = gratorFromTrack(assembly, geneTdb->table, geneTdb, chrom, BIGNUM, primary->asObj, geneOverlapRule); struct annoGratorGpVarFuncFilter aggvFuncFilter; ZeroVar(&aggvFuncFilter); aggvFuncFilter.intergenic = cartUsualBoolean(cart, "hgva_include_intergenic", FALSE); aggvFuncFilter.upDownstream = cartUsualBoolean(cart, "hgva_include_upDownstream", 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); annoGratorGpVarSetFuncFilter(gpVarGrator, &aggvFuncFilter); struct annoGrator *snpGrator = NULL; if (cartBoolean(cart, "hgva_rsId")) { snpGrator = gratorForSnp("", assembly, chrom, agoNoConstraint); } // 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); // extraGrators will point to the first grator in gratorList after snpGrator; // i.e. first grator that is meant for the EXTRAS column and/or used by a filter struct annoGrator *extraGrators = NULL; if (cartUsualBoolean(cart, "hgva_exclude_snpCommon", FALSE)) { struct annoGrator *grator = gratorForSnp("Common", assembly, chrom, agoMustNotOverlap); updateGratorLists(grator, &gratorList, &extraGrators); } if (cartUsualBoolean(cart, "hgva_exclude_snpMult", FALSE)) { struct annoGrator *grator = gratorForSnp("Mult", assembly, chrom, agoMustNotOverlap); updateGratorLists(grator, &gratorList, &extraGrators); } // If we're including Conserved Elements as a filter, and it has also been selected as an // extra output value, don't make two grators for it: char *consElTrack = NULL; if (cartUsualBoolean(cart, "hgva_require_consEl", FALSE)) { struct annoGrator *grator = NULL; consElTrack = cartString(cart, "hgva_require_consEl_track"); struct trackDb *tdb = tdbForTrack(database, consElTrack, &fullTrackList); if (tdb != NULL) grator = gratorFromTrack(assembly, tdb->table, tdb, chrom, BIGNUM, NULL, agoMustOverlap); updateGratorLists(grator, &gratorList, &extraGrators); } boolean addedDbNsfpSeqChange = 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 (sameOk(consElTrack, trackName)) // We already have this as a grator because it's a filter (above): continue; struct trackDb *tdb = tdbForTrack(database, trackName, &fullTrackList); struct annoGrator *grator = NULL; if (tdb != NULL) grator = gratorFromTrack(assembly, tdb->table, tdb, chrom, BIGNUM, NULL, agoNoConstraint); else if (startsWith("dbNsfp", trackName)) { // 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. if (!addedDbNsfpSeqChange) { char *fileName = fileNameFromTable("dbNsfpSeqChange"); if (fileName == NULL) errAbort("'%s' requested, but I can't find fileName for dbNsfpSeqChange", trackName); struct annoStreamer *streamer = annoStreamBigBedNew(fileName, assembly, BIGNUM); grator = annoGratorNew(streamer); updateGratorLists(grator, &gratorList, &extraGrators); addedDbNsfpSeqChange = TRUE; } char *fileName = fileNameFromTable(trackName); if (fileName != NULL) { struct annoStreamer *streamer = annoStreamBigBedNew(fileName, assembly, BIGNUM); grator = annoGratorNew(streamer); } } updateGratorLists(grator, &gratorList, &extraGrators); } slReverse(&gratorList); struct annoFormatter *vepOut = annoFormatVepNew("stdout", primary, (struct annoStreamer *)gpVarGrator, (struct annoStreamer *)snpGrator); //#*** can all the extraItem config smarts be pulled inside annoFormatVep? struct annoStreamer *extraSource = (struct annoStreamer *)extraGrators; for (; extraSource != NULL; extraSource = extraSource->next) { char *tableName = extraSource->name; char *tag = cloneString(tableName); char *p = strrchr(tag, '/'); if (p != NULL) { // file path; strip to basenaem tableName = tag = p+1; p = strchr(tag, '.'); if (p != NULL) *p = '\0'; } p = strstr(tag, "dbNsfp"); if (p != NULL) { tableName = p; tag = p + strlen("dbNsfp"); } else { // database.table -- skip database. p = strchr(tag, '.'); if (p != NULL) tag = p+1; } touppers(tag); char *description = dbNsfpDescFromTableName(tableName); if (description == NULL) description = extraSource->name; //#*** This is where the smarts probably can't all be pulled into annoFormatVep: char *column = "ignoredVepKnowsBetterOrOverlapExcludesVariant"; if (extraSource->rowType == arWords) { if (asColumnFindIx(extraSource->asObj->columnList, "name") >= 0) column = "name"; } annoFormatVepAddExtraItem(vepOut, extraSource, tag, description, column); } // Undo the htmlPushEarlyHandlers() because after this point they make ugly text: popWarnHandler(); popAbortHandler(); textOpen(); webStartText(); struct annoGratorQuery *query = annoGratorQueryNew(assembly, primary, gratorList, vepOut); if (chrom != NULL) annoGratorQuerySetRegion(query, chrom, start, end); annoGratorQueryExecute(query); textOutClose(&compressPipeline); annoGratorQueryFree(&query); } int main(int argc, char *argv[]) /* Process command line. */ { if (hIsPrivateHost()) pushCarefulMemHandler(LIMIT_2or6GB); htmlPushEarlyHandlers(); /* Make errors legible during initialization. */ cgiSpoof(&argc, argv); oldVars = hashNew(10); setUdcCacheDir(); boolean startQuery = (cgiUsualString("startQuery", NULL) != NULL); if (startQuery) cart = cartAndCookieNoContent(hUserCookie(), excludeVars, oldVars); else cart = cartAndCookie(hUserCookie(), excludeVars, oldVars); /* Set up global variables. */ getDbAndGenome(cart, &database, &genome, oldVars); 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); #if ((defined USE_BAM || defined USE_TABIX) && defined KNETFILE_HOOKS) knetUdcInstall(); #endif//def (USE_BAM || USE_TABIX) && KNETFILE_HOOKS if (lookupPosition(cart, hgvaRange)) { initGroupsTracksTables(cart, &fullTrackList, &fullGroupList); if (startQuery) doQuery(); else doUi(); } else if (webGotWarnings()) { // We land here when lookupPosition pops up a warning box. // Reset the problematic position and show the main page. char *position = cartUsualString(cart, "lastPosition", hDefaultPos(database)); cartSetString(cart, hgvaRange, position); doMainPage(); } // If lookupPosition returned FALSE and didn't report warnings, // then it wrote HTML showing multiple position matches & links. cartCheckout(&cart); return 0; }