a5a45be7e379b64278e667f80c75cc0cc41d9ea4 galt Thu May 8 14:43:19 2025 -0700 Simplify use of BLAT results by always creating a custom track. fixes #32751 diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c index 35db5935b93..d2ffbf54a87 100644 --- src/hg/hgc/hgc.c +++ src/hg/hgc/hgc.c @@ -3352,30 +3352,38 @@ struct bbiFile *bbi = bigBedFileOpenAlias(fileName, chromAliasFindAliases); struct lm *lm = lmInit(0); int ivStart = start, ivEnd = end; if (start == end) { // item is an insertion; expand the search range from 0 bases to 2 so we catch it: ivStart = max(0, start-1); ivEnd++; } if (cfgOptionBooleanDefault("drawDot", FALSE)) bigPslDotPlot(tdb, bbi, seqName, winStart, winEnd); boolean showEvery = sameString(item, "PrintAllSequences"); +boolean buildBigPsl = FALSE; +if (sameString(item, "buildBigPsl")) + { + buildBigPsl = TRUE; + showEvery = TRUE; + item = cloneString("PrintAllSequences"); + } + boolean showAll = trackDbSettingOn(tdb, "showAll"); unsigned seqTypeField = bbExtraFieldIndex(bbi, "seqType"); struct bigBedInterval *bb, *bbList = NULL; // If showAll is on, show all alignments with this qName, not just the // selected one. if (showEvery) { struct bbiChromInfo *chrom, *chromList = bbiChromList(bbi); for (chrom = chromList; chrom != NULL; chrom = chrom->next) { char *chromName = chrom->name; int start = 0, end = chrom->size; int itemsLeft = 0; // Zero actually means no limit.... struct bigBedInterval *intervalList = bigBedIntervalQuery(bbi, chromName, @@ -3414,30 +3422,99 @@ if (itemForUrl) printIframe(tdb, itemForUrl); printPos(seqName, ivStart, ivEnd, strand, FALSE, item); int printCount = extraFieldsPrint(tdb,NULL,extraFields, extraFieldCount); printCount += 0; } } } char *bedRow[32]; char startBuf[16], endBuf[16]; int lastChromId = -1; char chromName[bbi->chromBpt->keySize+1]; +if (buildBigPsl) + { + + char *browserUrl = hgTracksName(); + char* posStr = cartOptionalString(cart, "position"); + if (posStr != NULL) + printf("<P>Go back to <A HREF=\"%s\">%s</A> on the Genome Browser.</P>\n", browserUrl, posStr); + + printf("<FORM ACTION=\"%s?hgsid=%s&db=%s\" NAME=\"MAIN_FORM\" METHOD=%s>\n\n", + hgTracksName(), cartSessionId(cart), database, cartUsualString(cart, "formMethod", "POST")); + + cartSaveSession(cart); + + cgiMakeButton(CT_DO_REMOVE_VAR, "Remove custom track"); + cgiMakeHiddenVar(CT_SELECTED_TABLE_VAR, tdb->track); + printf("</FORM>\n"); + + + // new re-submit code with new trackname and decription + + printf("<div id=renameFormItem style='display: block'>\n"); + printf("<FORM ACTION=>\n"); + printf("<INPUT TYPE=SUBMIT NAME=Submit id='showRenameForm' VALUE=\"Rename Custom Track\">\n"); + printf("</FORM>\n"); + printf("</div>\n"); + + printf("<div id=renameForm style='display: none'>\n"); + char *hgcUrl = hgcName(); + printf( "<DIV STYLE=\"display:block;\"><FORM ACTION=\"%s\" METHOD=\"%s\" NAME=\"customTrackForm\">\n", hgcUrl,cartUsualString(cart, "formMethod", "POST")); + printf("<INPUT TYPE=\"hidden\" name=\"o\" value=\"%d\" />\n",cgiInt("o")); + printf("<INPUT TYPE=\"hidden\" name=\"t\" value=\"%d\" />\n",cgiInt("t")); + printf("<INPUT TYPE=\"hidden\" name=\"g\" value=\"%s\" />\n","buildBigPsl"); + printf("<INPUT TYPE=\"hidden\" name=\"i\" value=\"%s\" />\n",cgiString("i")); + printf("<INPUT TYPE=\"hidden\" name=\"c\" value=\"%s\" />\n",cgiString("c")); // orig psl->tName); + printf("<INPUT TYPE=\"hidden\" name=\"l\" value=\"%d\" />\n",cgiInt("l")); + printf("<INPUT TYPE=\"hidden\" name=\"r\" value=\"%d\" />\n",cgiInt("r")); + printf("<INPUT TYPE=\"hidden\" name=\"%s\" value=\"%s\" />\n", cartSessionVarName(), cartSessionId(cart)); + if (cgiOptionalString("isProt")) + printf("<INPUT TYPE=\"hidden\" name=\"isProt\" value=\"on\" />\n"); + + printf("<TABLE><TR><TD>Custom track name: "); + cgiMakeTextVar( "trackName", tdb->shortLabel, 30); + printf("</TD></TR>"); + + + printf("<TR><TD> Custom track description: "); + cgiMakeTextVar( "trackDescription", tdb->longLabel,50); + printf("</TD></TR>"); + + // remove the current blat ct so we can create a new one. + cgiMakeHiddenVar(CT_DO_REMOVE_VAR, "Remove custom track"); + cgiMakeHiddenVar(CT_SELECTED_TABLE_VAR, tdb->track); + + printf("<TR><TD><INPUT TYPE=SUBMIT NAME=Submit VALUE=\"Submit\">\n"); + puts("</TD></TR>"); + printf("</TABLE></FORM></DIV>"); + + + printf("</div>\n"); + + jsInline("$('#showRenameForm').click(function(){\n" + " $('#renameForm')[0].style.display = 'block';\n" + " $('#renameFormItem')[0].style.display = 'none';\n" + " $('#showRenameForm')[0].style.display = 'none';\n" + "return false;\n" + "});\n"); + + } + boolean firstTime = TRUE; struct hash *seqHash = hashNew(0); struct dyString *sequencesText = dyStringNew(256); int sequencesFound = 0; for (bb = bbList; bb != NULL; bb = bb->next) { bbiCachedChromLookup(bbi, bb->chromId, lastChromId, chromName, sizeof(chromName)); lastChromId=bb->chromId; bigBedIntervalToRow(bb, chromName, startBuf, endBuf, bedRow, 4); if (showEvery || sameString(bedRow[3], item)) { char *cdsStr, *seq; struct psl *psl= getPslAndSeq(tdb, chromName, bb, seqTypeField, &seq, &cdsStr); slAddHead(&pslList, psl); @@ -6601,82 +6678,178 @@ if (end != 0 && differentString(chrom,"0") && isNotEmpty(chrom)) { printf("<B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, chrom, start+1, end); printf("%s:%d-%d</A><BR>\n", chrom, start+1, end); } gbWarnFree(&gbWarn); sqlFreeResult(&sr); dyStringFree(&dy); hFreeConn(&conn); hFreeConn(&conn2); } + +void printLuckyRedirect(char *browserUrl, struct psl *psl, char *database, boolean empty) +/* Print out a very short page that redirects us. */ +{ + +char url[1024]; + +if (empty) + safef(url, sizeof(url), "%s?db=%s", + browserUrl, database); +else + safef(url, sizeof(url), "%s?position=%s:%d-%d&db=%s", + browserUrl, psl->tName, psl->tStart + 1, psl->tEnd, database); + +/* htmlStart("Redirecting"); */ +/* Odd it appears that we've already printed the Content-Typ:text/html line + but I can't figure out where... */ +htmStart(stdout, "Redirecting"); +jsInlineF("location.replace('%s');\n", url); +printf("<noscript>No javascript support:<br>Click <a href='%s'>here</a> for browser.</noscript>\n", url); +htmlEnd(); + +} + + static boolean isPslToPrintByClick(struct psl *psl, int startFirst, boolean isClicked) /* Determine if a psl should be printed based on if it was or was not the one that was clicked * on. */ { return ((psl->tStart == startFirst) && sameString(psl->tName, seqName)) == isClicked; } void printAlignmentsSimple(struct psl *pslList, int startFirst, char *hgcCommand, char *tableName, char *itemIn) /* Print list of mRNA alignments, don't add extra textual link when * doesn't honor hgcCommand. */ { struct psl *psl; int aliCount = slCount(pslList); boolean isClicked; if (pslList == NULL || tableName == NULL) return; boolean showEvery = sameString(itemIn, "PrintAllSequences"); + +boolean feelingLucky = cgiOptionalString("feelingLucky") != NULL; +if (feelingLucky) + { + // If we found something jump browser to there. + if(slCount(pslList) > 0) + printLuckyRedirect(hgTracksPathAndSettings(), pslList, database, FALSE); + // Otherwise call ourselves again not feeling lucky to print empty results. + else + { + printLuckyRedirect(hgTracksPathAndSettings(), pslList, database, TRUE); + } + } + if (!showEvery && (aliCount > 1)) printf("The alignment you clicked on is first in the table below.<BR>\n"); +char *browserHelp = "Open a Genome Browser showing this match"; +char *helpText = "Open a Genome Browser with the BLAT results, but in a new internet browser tab"; +// XX putting SVG into C code like this is ugly. define somewhere? maybe have globals for these? +char *icon = "<svg style='height:10px; padding-left:2px' xmlns='http://www.w3.org/2000/svg' viewBox='0 0 512 512'><!--!Font Awesome Free 6.5.2 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free Copyright 2024 Fonticons, Inc.--><path d='M320 0c-17.7 0-32 14.3-32 32s14.3 32 32 32h82.7L201.4 265.4c-12.5 12.5-12.5 32.8 0 45.3s32.8 12.5 45.3 0L448 109.3V192c0 17.7 14.3 32 32 32s32-14.3 32-32V32c0-17.7-14.3-32-32-32H320zM80 32C35.8 32 0 67.8 0 112V432c0 44.2 35.8 80 80 80H400c44.2 0 80-35.8 80-80V320c0-17.7-14.3-32-32-32s-32 14.3-32 32V432c0 8.8-7.2 16-16 16H80c-8.8 0-16-7.2-16-16V112c0-8.8 7.2-16 16-16H192c17.7 0 32-14.3 32-32s-14.3-32-32-32H80z'/></svg>"; printf("<PRE><TT>"); + + +// find maximum query name size for padding calculations and +// find maximum target chrom name size for padding calculations +int maxQChromNameSize = 0; +int maxTChromNameSize = 0; +for (psl = pslList; psl != NULL; psl = psl->next) + { + int qLen = strlen(psl->qName); + maxQChromNameSize = max(maxQChromNameSize,qLen); + int tLen = strlen(psl->tName); + maxTChromNameSize = max(maxTChromNameSize,tLen); + } +maxQChromNameSize = max(maxQChromNameSize, strlen("QUERY")); + +printf("BROWSER |"); +printf(" SIZE IDENTITY "); if (startsWith("chr", pslList->tName)) - printf("BROWSER | SIZE IDENTITY CHROMOSOME STRAND START END QUERY START END TOTAL\n"); + { + maxTChromNameSize = max(maxTChromNameSize, strlen("CHROMOSOME")); + spaceOut(stdout, maxTChromNameSize - strlen("CHROMOSOME")); + printf("CHROMOSOME"); + } else - printf("BROWSER | SIZE IDENTITY SCAFFOLD STRAND START END QUERY START END TOTAL\n"); -printf("-----------------------------------------------------------------------------------------------------\n"); + { + maxTChromNameSize = max(maxTChromNameSize, strlen("SCAFFOLD")); + spaceOut(stdout, maxTChromNameSize - strlen("SCAFFOLD")); + printf("SCAFFOLD"); + } +printf(" STRAND START END "); +spaceOut(stdout, maxQChromNameSize - strlen("QUERY")); +printf("QUERY"); +printf(" START END TOTAL\n"); + +printf("--------------------------------------------------------------------------------------------"); +repeatCharOut(stdout, '-', maxQChromNameSize - 5); +repeatCharOut(stdout, '-', maxTChromNameSize - 5); +printf("\n"); + +char fmt[256]; +safef(fmt, sizeof fmt, "%%5d %%5.1f%%%% %%%ds %%s %%9d %%9d %%%ds %%5d %%5d %%5d", maxTChromNameSize, maxQChromNameSize); + for (isClicked = 1; isClicked >= 0; isClicked -= 1) { for (psl = pslList; psl != NULL; psl = psl->next) { if (isPslToPrintByClick(psl, startFirst, isClicked)) { char otherString[512]; char *qName = itemIn; if (sameString(itemIn, "PrintAllSequences")) qName = psl->qName; safef(otherString, sizeof(otherString), "%d&aliTable=%s", psl->tStart, tableName); - printf("<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">browser</A> | ", - hgTracksPathAndSettings(), database, psl->tName, psl->tStart+1, psl->tEnd); + printf("<A TITLE='%s' HREF=\"%s&db=%s&position=%s%%3A%d-%d\">browser</A> ", + browserHelp, hgTracksPathAndSettings(), database, psl->tName, psl->tStart+1, psl->tEnd); + + printf("<A TITLE='%s' HREF=\"%s&db=%s&position=%s%%3A%d-%d\" TARGET=_BLANK>new tab%s</A> | ", + helpText, hgTracksPathAndSettings(), database, psl->tName, psl->tStart+1, psl->tEnd, icon); + if (psl->qSize <= MAX_DISPLAY_QUERY_SEQ_SIZE) // Only anchor if small enough hgcAnchorWindow(hgcCommand, qName, psl->tStart, psl->tEnd, otherString, psl->tName); char *displayChromName = chromAliasGetDisplayChrom(database, cart, psl->tName); - printf("%5d %5.1f%% %9s %s %9d %9d %20s %5d %5d %5d", + printf(fmt, psl->match + psl->misMatch + psl->repMatch, 100.0 - pslCalcMilliBad(psl, TRUE) * 0.1, skipChr(displayChromName), psl->strand, psl->tStart + 1, psl->tEnd, psl->qName, psl->qStart+1, psl->qEnd, psl->qSize); if (psl->qSize <= MAX_DISPLAY_QUERY_SEQ_SIZE) printf("</A>"); + + // if you modify this, also modify hgPcr.c:doQuery, which implements a similar feature + char *seq = psl->tName; + if (endsWith(seq, "_fix")) + printf(" <A target=_blank HREF=\"../FAQ/FAQdownloads.html#downloadFix\">What is chrom_fix?</A>"); + else if (endsWith(seq, "_alt")) + printf(" <A target=_blank HREF=\"../FAQ/FAQdownloads.html#downloadAlt\">What is chrom_alt?</A>"); + else if (endsWith(seq, "_random")) + printf(" <A target=_blank HREF=\"../FAQ/FAQdownloads.html#download10\">What is chrom_random?</A>"); + else if (startsWith(seq, "chrUn")) + printf(" <A target=_blank HREF=\"../FAQ/FAQdownloads.html#download11\">What is a chrUn sequence?</A>"); + printf("\n"); } } } printf("</TT></PRE>"); } void printAlignmentsExtra(struct psl *pslList, int startFirst, char *hgcCommand, char *hgcCommandInWindow, char *tableName, char *itemIn) /* Print list of mRNA alignments with special "in window" alignment function. */ { if (pslList == NULL || tableName == NULL) return; printAlignmentsSimple(pslList, startFirst, hgcCommand, tableName, itemIn); @@ -22434,38 +22607,38 @@ if (wordCount > 1) num = atoi(words[1]); if (num < 3) num = 3; footPrinterSampleClick(conn, tdb, item, start, num); } printTrackHtml(tdb); freez(&dupe); hFreeConn(&conn); } void bigPslHandlingCtAndGeneric(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start, int end) /* Special option to show all alignments for blat ct psl */ { -if (startsWith("ct_blat", tdb->track) && !sameString(item,"PrintAllSequences")) +if (startsWith("ct_blat", tdb->track) && (!(sameString(item,"PrintAllSequences") || sameString(item,"buildBigPsl")))) printf("<A href id='genericPslShowAllLink'>Show All</A>\n"); printf("<div id=genericPslShowItem style='display: block'>\n"); genericBigPslClick(NULL, tdb, item, start, end); printf("</div>\n"); -if (startsWith("ct_blat", tdb->track) && !sameString(item,"PrintAllSequences")) +if (startsWith("ct_blat", tdb->track) && (!(sameString(item,"PrintAllSequences") || sameString(item,"buildBigPsl")))) { printf("<div id=genericPslShowAll style='display: none'>\n"); genericBigPslClick(NULL, tdb, "PrintAllSequences", start, end); printf("</div>\n"); jsInline("$('#genericPslShowAllLink').click(function(){\n" " $('#genericPslShowAll')[0].style.display = 'block';\n" " $('#genericPslShowItem')[0].style.display = 'none';\n" " $('#genericPslShowAllLink')[0].style.display = 'none';\n" "return false;\n" "});\n"); } } @@ -22475,31 +22648,31 @@ char *fileName, *itemName; struct customTrack *ctList = getCtList(); struct customTrack *ct; struct bed *bed = (struct bed *)NULL; int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); char *item = cartString(cart, "i"); char *type; fileName = nextWord(&fileItem); for (ct = ctList; ct != NULL; ct = ct->next) if (sameString(trackId, ct->tdb->track)) break; if (ct == NULL) errAbort("Couldn't find '%s' in '%s'", trackId, fileName); type = ct->tdb->type; -cartWebStart(cart, database, "Custom Track: %s", ct->tdb->shortLabel); +cartWebStart(cart, database, "Custom Track: %s (%s) %s ", trackHubSkipHubName(organism), trackHubSkipHubName(database), ct->tdb->shortLabel); itemName = skipLeadingSpaces(fileItem); printf("<H2>%s</H2>\n", ct->tdb->longLabel); if (sameWord(type, "array")) doExpRatio(ct->tdb, fileItem, ct); else if ( startsWith( "longTabix", type)) doLongTabix(ct->tdb, item); else if (sameWord(type, "encodePeak")) doEncodePeak(ct->tdb, ct, fileName); else if (sameWord(type, "bigNarrowPeak")) doBigEncodePeak(ct->tdb, NULL, item); else if (sameWord(type, "bigWig")) bigWigCustomClick(ct->tdb); else if (sameWord(type, "bigChain")) genericChainClick(NULL, ct->tdb, item, start, "seq"); else if (sameWord(type, "bigPsl")) @@ -26588,31 +26761,31 @@ boolean isProt = cgiOptionalString("isProt") != NULL; char *customTextTemplate = "track type=bigPsl indelDoubleInsert=on indelQueryInsert=on pslFile=%s visibility=pack showAll=on htmlUrl=http://%s/goldenPath/help/hgUserPsl.html %s bigDataUrl=%s name=\"%s\" description=\"%s\" colorByStrand=\"0,0,0 0,0,150\" mouseOver=\"${oChromStart}-${oChromEnd} of ${oChromSize} bp, strand ${oStrand}\"\n"; char *extraForMismatch = "indelPolyA=on showDiffBasesAllScales=. baseColorUseSequence=lfExtra baseColorDefault=diffBases"; if (isProt) extraForMismatch = ""; char buffer[4096]; safef(buffer, sizeof buffer, customTextTemplate, bigBedTn.forCgi, host, extraForMismatch, bigBedTn.forCgi, trackName, trackDescription); struct customTrack *ctList = getCtList(); struct customTrack *newCts = customFactoryParse(database, buffer, FALSE, NULL, NULL); theCtList = customTrackAddToList(ctList, newCts, NULL, FALSE); customTracksSaveCart(database, cart, theCtList); -cartSetString(cart, "i", "PrintAllSequences"); +cartSetString(cart, "i", "buildBigPsl"); hgCustom(newCts->tdb->track, NULL); } void doHPRCTable(struct trackDb *tdb, char *itemName) /* Put up a generic bigBed details page, with a table of links to turn on related * * chain tracks with visibility toggles */ { int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); genericHeader(tdb, itemName); genericBigBedClick(NULL, tdb, itemName, start, end, 0); printTrackHtml(tdb); // tell the javscript to reorganize the column of assemblies: jsIncludeFile("hgc.js", NULL); jsInlineF("var doHPRCTable = true;\n");