f93b8662afd701763c24634879d05dc08b3178de max Fri Jun 5 02:24:16 2026 -0700 Add exon search: jump to GENE exon N from position box I'm comitting this thinking that the way that we implement searches leads to duplication of code that doesn't look great to me. While this feature looks good, the code duplication across C/JS should probably get reduced with a different approach to the "quick jump" way of the page. We have currently three ways to quick jump, I think: - chr:start-end - rsxxxxx - gene symbol + autosuggest pick - HGVS? They are recognized by both the javascript and the C code with regexes. I think all of these should be probably be only implemented in the C code. The JS only sends the current string to the C code and then gets back if this can be autocompleted and to which position and what to show in the autosuggest area. For example if you type "SOD1<space>e" the C code could send back "Continue typing to jump to exon" and once you're at "SOD1<space>exon 5" the C code sends back "Hit enter to jump to chrX:123123-123213". This would work with any type of identifier and the code would stay in the C code, not more duplication and it would be much clearer to the user what is recognized in the search box. Users can now type "TP53 exon 5" or "TP53:e.5[+/-offset]" in the genome browser position/search box to navigate directly to that exon. The ":e.N" notation follows the VICC Gene Fusion Specification. An optional intronic offset (":e.5+2") lands N bases past the exon boundary, useful for splice site inspection. C (hgFind.c): findGeneExon() resolves the query against the SQL genePred tables listed in the hg.conf "geneTracks" key (default: mane, ncbiRefSeqSelect, knownGene, ncbiRefSeq, ncbiRefSeqHistorical). bigGenePred tracks (e.g. mane) are supported via bigBedOpenExtraIndex. Uses the existing exonToPos() function for strand-aware exon lookup. fixSinglePos() is called so hgp->singlePos is populated for callers. hgApi.c: new cmd=geneExonToPos returns {"pos":"chrom:start-end"} JSON so JS can navigate in place without a full page redirect to hgSearch. Direct URL links (hgTracks?position=GENE+exon+N) also work because findGeneExon() is hooked into hgPositionsFind(). JS: autocomplete.js injects a local "Jump to exon N" suggestion as soon as the exon pattern is detected, or a hint item when the query is still partial ("GENE ex"). Selecting either navigates via hgApi. hgTracks.js routes the two new autocomplete item types to the hgApi call. utils.js adds the two regexes (geneExonExp, geneExonCoordExp). query.html: documents both syntaxes; the :e.N notation links to the VICC Gene Fusion Specification at fusions.cancervariants.org. diff --git src/hg/hgApi/hgApi.c src/hg/hgApi/hgApi.c index 04e72eea7f0..2031fda41a2 100644 --- src/hg/hgApi/hgApi.c +++ src/hg/hgApi/hgApi.c @@ -1,265 +1,296 @@ /* Copyright (C) 2013 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ /* hgApi - provide a JSON based API to the browser. Required CGI parameters: db: assembly cmd: command (see below) Optional CGI parameters: jsonp: if present, the returned json is wrapped in a call to the value of the jsonp parameter (e.g. "jsonp=parseResponse"). Supported commands: defaultPos: default position for this assembly metaDb: return list of values for metaDb parameter hgt_mdbVal: return metaDb value control - see code for details tableMetadata: returns an html table with metadata for track parameter **** DEPRECATED: Not currently used in GB codonToPos: returns genomic position for given codon; parameters: codon, table and name (which is gene name). codonToPos: returns genomic position for given exon; parameters: exon, table and name (which is gene name). */ #include "common.h" #include "hdb.h" #include "mdb.h" #include "cheapcgi.h" #include "htmshell.h" #include "hPrint.h" #include "dystring.h" #include "hui.h" #include "search.h" #include "cv.h" #include "api.h" #include "chromAlias.h" #include "bigBed.h" #include "trackHub.h" #include "cart.h" +#include "hgFind.h" struct hash *oldVars = NULL; void doMiddle(struct cart *cart) { long enteredMainTime = clock1000(); struct dyString *output = dyStringNew(10000); setUdcCacheDir(); pushWarnHandler(htmlVaBadRequestAbort); pushAbortHandler(htmlVaBadRequestAbort); char *database = cgiString("db"); char *cmd = cgiString("cmd"); char *jsonp = cgiOptionalString("jsonp"); if (!trackHubDatabase(database) && !hDbExists(database)) errAbort("Invalid database '%s'", database); if (!strcmp(cmd, "defaultPos")) { dyStringPrintf(output, "{\"pos\": \"%s\"}", hDefaultPos(database)); } else if (!strcmp(cmd, "metaDb")) { // Return list of values for given metaDb var // e.g. http://genome.ucsc.edu/hgApi?db=hg18&cmd=metaDb&var=cell struct sqlConnection *conn = hAllocConn(database); boolean metaDbExists = sqlTableExists(conn, "metaDb"); if (metaDbExists) { char *var = cgiOptionalString("var"); if (!var) errAbort("Missing var parameter"); boolean fileSearch = (cgiOptionalInt("fileSearch",0) == 1); struct slPair *pairs = mdbValLabelSearch(conn, var, MDB_VAL_STD_TRUNCATION, FALSE, !fileSearch, fileSearch); struct slPair *pair; dyStringPrintf(output, "[\n"); for (pair = pairs; pair != NULL; pair = pair->next) { if (pair != pairs) dyStringPrintf(output, ",\n"); dyStringPrintf(output, "['%s','%s']", javaScriptLiteralEncode(mdbPairLabel(pair)), javaScriptLiteralEncode(mdbPairVal(pair))); } dyStringPrintf(output, "\n]\n"); } else errAbort("Assembly does not support metaDb"); } // TODO: move to lib since hgTracks and hgApi share #define METADATA_VALUE_PREFIX "hgt_mdbVal" else if (startsWith(METADATA_VALUE_PREFIX, cmd)) { // Returns metaDb value control: drop down or free text, with or without help link. // e.g. http://genome.ucsc.edu/hgApi?db=hg18&cmd=hgt_mdbVal3&var=cell // TODO: Move guts to lib, so that hgTracks::searchTracks.c and hgApi.c can share struct sqlConnection *conn = hAllocConn(database); boolean metaDbExists = sqlTableExists(conn, "metaDb"); if (metaDbExists) { char *var = cgiOptionalString("var"); if (!var) errAbort("Missing var parameter"); int ix = atoi(cmd+strlen(METADATA_VALUE_PREFIX)); // 1 based index if (ix == 0) // errAbort("Unsupported 'cmd' parameter"); enum cvSearchable searchBy = cvSearchMethod(var); char name[128]; safef(name,sizeof name,"%s%i",METADATA_VALUE_PREFIX,ix); if (searchBy == cvSearchBySingleSelect || searchBy == cvSearchByMultiSelect) { boolean fileSearch = (cgiOptionalInt("fileSearch",0) == 1); struct slPair *pairs = mdbValLabelSearch(conn, var, MDB_VAL_STD_TRUNCATION, FALSE, !fileSearch, fileSearch); if (slCount(pairs) > 0) { char *dropDownHtml = cgiMakeSelectDropList((searchBy == cvSearchByMultiSelect), name, pairs, NULL, ANYLABEL, "mdbVal", "change", "findTracksMdbValChanged(this);", "min-width: 200px; font-size: .9em;", NULL); if (dropDownHtml) { dyStringAppend(output,dropDownHtml); freeMem(dropDownHtml); } slPairFreeList(&pairs); } } else if (searchBy == cvSearchByFreeText) { dyStringPrintf(output,"<input type='text' name='%s' id='%s' value='' class='mdbVal freeText' " "style='max-width:310px; width:310px; font-size:.9em;'>", name, name); jsOnEventById("change", name, "findTracksMdbValChanged(this);"); } else if (searchBy == cvSearchByWildList) { dyStringPrintf(output,"<input type='text' name='%s' id='%s' value='' class='mdbVal wildList' " "title='enter comma separated list of values' " "style='max-width:310px; width:310px; font-size:.9em;'>", name, name); jsOnEventById("change", name, "findTracksMdbValChanged(this);"); } else if (searchBy == cvSearchByDateRange || searchBy == cvSearchByIntegerRange) { // TO BE IMPLEMENTED } else errAbort("Metadata variable not searchable"); dyStringPrintf(output,"<span id='helpLink%i'> </span>",ix); } else errAbort("Assembly does not support metaDb"); } else if (!strcmp(cmd, "tableMetadata")) { // returns an html table with metadata for a given track char *trackName = cgiOptionalString("track"); boolean showLonglabel = (NULL != cgiOptionalString("showLonglabel")); boolean showShortLabel = (NULL != cgiOptionalString("showShortLabel")); if (trackName != NULL) { // hTrackDbForTrackAndAncestors avoids overhead of getting whole track list! struct trackDb *tdb = hTrackDbForTrackAndAncestors(database, trackName); if (tdb != NULL) { char * html = metadataAsHtmlTable(database,tdb,showLonglabel,showShortLabel); if (html) { dyStringAppend(output,html); freeMem(html); } else dyStringPrintf(output,"No metadata found for track %s.",trackName); } else dyStringPrintf(output,"Track %s not found",trackName); } else dyStringAppend(output,"No track variable found"); } else if (sameString(cmd, "codonToPos") || sameString(cmd, "exonToPos")) { char query[256]; struct sqlResult *sr; char **row; struct genePred *gp = NULL; char *name = cgiString("name"); char *table = cgiString("table"); char *chrom = cgiString("chrom"); int num = cgiInt("num"); struct sqlConnection *conn = NULL; if (!trackHubDatabase(database)) conn = hAllocConn(database); struct trackDb *tdb = tdbForTrack(database, table, NULL); if (sameString(tdb->type, "genePred")) { sqlSafef(query, sizeof(query), "select name, chrom, strand, txStart, txEnd, cdsStart, cdsEnd, exonCount, exonStarts, exonEnds from %s where name = '%s' and chrom='%s'", table, name, chrom); sr = sqlGetResult(conn, query); row = sqlNextRow(sr); gp = genePredLoad(row); sqlFreeResult(&sr); } else if (sameString(tdb->type, "bigGenePred") || startsWith("bigGenePred", tdb->type)) // makes knownGene work { // TODO: what bigBed types can we even support? bigBed12 at a minimum for the blocks? // bigPsl should work maybe? // for now just support genePred and bigGenePred char *fileName = bbiNameFromSettingOrTable(tdb, conn, tdb->table); struct bbiFile *bbi = bigBedFileOpenAlias(fileName, chromAliasFindAliases); int fieldIx; struct bptFile *bpt = bigBedOpenExtraIndex(bbi, "name", &fieldIx); struct lm *lm = lmInit(0); struct bigBedInterval *bbList = bigBedNameQuery(bbi, bpt, fieldIx, name, lm); if (bbList) gp = (struct genePred *)genePredFromBigGenePred(chrom, bbList); } if (!gp) dyStringPrintf(output, "{\"error\": \"Couldn't find item: %s\"}", name); else { boolean found; int start, end; if (sameString(cmd, "codonToPos")) found = codonToPos(gp, num, &start, &end); else found = exonToPos(gp, num, &start, &end); if (found) dyStringPrintf(output, "{\"pos\": \"%s:%d-%d\"}", gp->chrom, start + 1, end); else dyStringPrintf(output, "{\"error\": \"%d is an invalid %s for this gene\"}", num, sameString(cmd, "codonToPos") ? "codon" : "exon"); } hFreeConn(&conn); } +else if (sameString(cmd, "geneExonToPos")) + { + /* Resolve "<symbol> exon <N>" or "<symbol>:e.<N>[+/-offset]" to a genomic position. + * Parameters: symbol, num, offset (optional). Returns {"pos": "chrom:start-end"} + * or {"error": "..."}. Reuses the hgFind exon search so all geneTracks tables apply. */ + char *symbol = cgiString("symbol"); + int num = cgiInt("num"); + int offset = cgiOptionalInt("offset", 0); + char term[256]; + if (offset != 0) + safef(term, sizeof term, "%s:e.%d%+d", symbol, num, offset); + else + safef(term, sizeof term, "%s exon %d", symbol, num); + /* Suppress any warn() calls (e.g. "gene has N exons") so they don't corrupt JSON. */ + pushSilentWarnHandler(); + struct hgPositions *hgp = hgPositionsFind(database, term, "", "hgApi", cart, FALSE, FALSE, NULL); + popWarnHandler(); + if (hgp && hgp->singlePos) + { + int s = hgp->singlePos->chromStart; + int e = hgp->singlePos->chromEnd; + if (s > e) { int tmp = s; s = e; e = tmp; } + char pos[256]; + safef(pos, sizeof pos, "%s:%d-%d", hgp->singlePos->chrom, s + 1, e); + dyStringPrintf(output, "{\"pos\": \"%s\"}", pos); + } + else + dyStringPrintf(output, "{\"error\": \"Exon %d of %s not found\"}", num, symbol); + freez(&hgp); + } else { warn("unknown cmd: %s",cmd); errAbort("Unsupported 'cmd' parameter"); } apiOut(dyStringContents(output), jsonp); cgiExitTime("hgApi", enteredMainTime); } /* Null terminated list of CGI Variables we don't want to save * permanently. */ char *excludeVars[] = {"fileSearch", "var", "showShortLabel", "showLongLabel", "track", "table", "name", "chrom", "cmd", "num", NULL,}; int main(int argc, char *argv[]) /* Process command line. */ { cgiSpoof(&argc, argv); cartEmptyShellNoContent(doMiddle, hUserCookie(), excludeVars, oldVars); return 0; }