de15ac2542d2b375ffd780b647b3ff2e217ed6d1 braney Fri Jun 10 10:06:01 2016 -0700 fix some problems in bigChain and bigMaf support #17325 diff --git src/hg/hgc/mafClick.c src/hg/hgc/mafClick.c index fe09394..a0573f2 100644 --- src/hg/hgc/mafClick.c +++ src/hg/hgc/mafClick.c @@ -1,810 +1,811 @@ /* Handle details pages for maf tracks and axt tracks. */ /* Copyright (C) 2013 The Regents of the University of California * See README in this or parent directory for licensing information. */ #include "common.h" #include "hash.h" #include "linefile.h" #include "hgc.h" #include "maf.h" #include "obscure.h" #include "cheapcgi.h" #include "genePred.h" #include "botDelay.h" #include "hgMaf.h" #include "hui.h" #include "hCommon.h" #include "hubConnect.h" #define ADDEXONCAPITAL /* Javascript to help make a selection from a drop-down * go back to the server. */ static char *autoSubmit = "onchange=\"document.gpForm.submit();\""; static void blueCapWrite(FILE *f, char *s, int size, char *r) /* Write capital letters in blue. */ { boolean isBlue = FALSE; int i; for (i=0; i<size; ++i) { if (r!=NULL && s[i]==r[i]) fprintf(f, "."); else { char c = s[i]; if (isupper(c)) { if (!isBlue) { fprintf(f, "<span style='color:#0000FF;'>"); isBlue = TRUE; } } else if (islower(c)) { if (isBlue) { fprintf(f, "</span>"); isBlue = FALSE; } } fprintf(f, "%c", c); } } if (isBlue) fprintf(f, "</span>"); } void initSummaryLine(char *summaryLine, int size, int val) /* Fill summary line with stars and null terminate */ { int i; for (i = 0; i < size; i++) summaryLine[i] = val; summaryLine[i] = 0; } void updateSummaryLine(char *summaryLine, char *referenceText, char *alignText, int size) /* Blank out columns in the summary line where this alignment * differs from the reference */ { int i; for (i=0; i<size; i++) { if (alignText[i] != referenceText[i]) summaryLine[i] = ' '; } } void mafPrettyOut(FILE *f, struct mafAli *maf, int lineSize, boolean onlyDiff, int blockNo) { int ii, ch; int srcChars = 0; struct mafComp *mc; int lineStart, lineEnd; char *summaryLine = needMem(lineSize+1); char *referenceText; int startChars, sizeChars, srcSizeChars; boolean haveInserts = FALSE; struct mafComp *masterMc = maf->components; startChars = sizeChars = srcSizeChars = 0; for (mc = maf->components; mc != NULL; mc = mc->next) { /* Figure out length of source (species) field. */ /*if (mc->size != 0)*/ { char dbOnly[128]; int len; char *org; memset(dbOnly, 0, sizeof(dbOnly)); safef(dbOnly, sizeof(dbOnly), "%s", mc->src); chopPrefix(dbOnly); if ((org = hOrganism(dbOnly)) == NULL) len = strlen(dbOnly); else len = strlen(org); if (srcChars < len) srcChars = len; len = digitsBaseTen(mc->start); if (startChars < len) startChars = len; len = digitsBaseTen(mc->size); if (sizeChars < len) sizeChars = len; len = digitsBaseTen(mc->srcSize); if (srcSizeChars < len) srcSizeChars = len; if (mc->text && (mc->rightStatus == MAF_INSERT_STATUS) && (masterMc->start + masterMc->size < winEnd)) haveInserts = TRUE; #ifdef REVERSESTRAND /* complement bases if hgTracks is on reverse strand */ if (mc->size && cartCgiUsualBoolean(cart, COMPLEMENT_BASES_VAR, FALSE)) complement(mc->text, maf->textSize); #endif } } /* first sequence in the alignment */ referenceText = maf->components->text; for (lineStart = 0; lineStart < maf->textSize; lineStart = lineEnd) { int size; lineEnd = lineStart + lineSize; if (lineEnd >= maf->textSize) lineEnd = maf->textSize; size = lineEnd - lineStart; initSummaryLine(summaryLine, size, '*'); for (mc = maf->components; mc != NULL; mc = mc->next) { char dbOnly[128], *chrom; int s = mc->start; int e = s + mc->size; char *org; char *revComp = ""; char strand = mc->strand; struct dyString *dy = newDyString(512); #ifdef REVERSESTRAND if (cartCgiUsualBoolean(cart, COMPLEMENT_BASES_VAR, FALSE)) strand = (strand == '+') ? '-' : '+'; #endif if (strand == '-') revComp = "&hgSeq.revComp=on"; dyStringClear(dy); safef(dbOnly, sizeof(dbOnly), "%s", mc->src); chrom = chopPrefix(dbOnly); if ((org = hOrganism(dbOnly)) == NULL) org = dbOnly; if (mc->strand == '-') reverseIntRange(&s, &e, mc->srcSize); if (mc->text != NULL) { if (lineStart == 0) { if (hDbIsActive(dbOnly)) { dyStringPrintf(dy, "%s Browser %s:%d-%d %c %*dbps",hOrganism(dbOnly),chrom, s+1, e, mc->strand,sizeChars, mc->size); linkToOtherBrowserTitle(dbOnly, chrom, s, e, dy->string); dyStringClear(dy); fprintf(f, "B</A> "); } else fprintf(f, " "); if (hDbExists(dbOnly)) { dyStringPrintf(dy, "Get %s DNA %s:%d-%d %c %*dbps",hOrganism(dbOnly),chrom, s+1, e, mc->strand,sizeChars, mc->size); printf("<A TITLE=\"%s\" TARGET=\"_blank\" HREF=\"%s?o=%d&g=getDna&i=%s&c=%s&l=%d&r=%d&db=%s%s\">D</A> ", dy->string,hgcName(), s, cgiEncode(chrom), chrom, s, e, dbOnly, revComp); } else fprintf(f, " "); } else { fprintf(f, " "); } dyStringClear(dy); dyStringPrintf(dy, "%s:%d-%d %c %*dbps",chrom, s+1, e, mc->strand,sizeChars, mc->size); fprintf(f, "<A TITLE=\"%s\"> %*s </A> ", dy->string, srcChars, org); updateSummaryLine(summaryLine, referenceText + lineStart, mc->text + lineStart, size); blueCapWrite(f, mc->text + lineStart, size, (onlyDiff && mc != maf->components) ? referenceText + lineStart : NULL); fprintf(f, "\n"); } else { if (((mc->leftStatus == MAF_CONTIG_STATUS) && (mc->rightStatus == MAF_CONTIG_STATUS) ) || ((mc->leftStatus == MAF_TANDEM_STATUS) && (mc->rightStatus == MAF_TANDEM_STATUS) ) || ((mc->leftStatus == MAF_INSERT_STATUS) && (mc->rightStatus == MAF_INSERT_STATUS) ) || ((mc->leftStatus == MAF_MISSING_STATUS) && (mc->rightStatus == MAF_MISSING_STATUS) )) { if (lineStart == 0) { int s = mc->start; int e = s + mc->rightLen; struct dyString *dy = newDyString(512); if (mc->strand == '-') reverseIntRange(&s, &e, mc->srcSize); if ( hDbIsActive(dbOnly)) { dyStringPrintf(dy, "%s Browser %s:%d-%d %c %d bps Unaligned",hOrganism(dbOnly),chrom, s+1, e, mc->strand, e-s); linkToOtherBrowserTitle(dbOnly, chrom, s, e, dy->string); fprintf(f,"B</A> "); dyStringClear(dy); } else fprintf(f," "); if (hDbExists(dbOnly)) { dyStringPrintf(dy, "Get %s DNA %s:%d-%d %c %d bps Unaligned",hOrganism(dbOnly),chrom, s+1, e, mc->strand, e-s); printf("<A TITLE=\"%s\" TARGET=\"_blank\" HREF=\"%s?o=%d&g=getDna&i=%s&c=%s&l=%d&r=%d&db=%s%s\">D</A> ", dy->string, hgcName(), s, cgiEncode(chrom), chrom, s, e, dbOnly,revComp); } else fprintf(f, " "); } else fprintf(f, " "); initSummaryLine(summaryLine, size, ' '); dyStringClear(dy); dyStringPrintf(dy, "%s:%d-%d %c %*dbps",chrom, s+1, e, mc->strand,sizeChars, mc->size); fprintf(f, "<A TITLE=\"%s\">%*s</A> ", dy->string, srcChars, org); ch = '-'; switch(mc->rightStatus) { case MAF_INSERT_STATUS: ch = '='; break; case MAF_MISSING_STATUS: ch = 'N'; break; case MAF_TANDEM_STATUS: case MAF_CONTIG_STATUS: ch = '-'; break; } for(ii=lineStart; ii < lineEnd ; ii++) fputc(ch,f); fprintf(f,"\n"); } } } #ifdef ADDMATCHLINE if (lineStart == 0) fprintf(f, " %-*s %s\n", srcChars, "", summaryLine); else fprintf(f, "%-*s %s\n", srcChars, "", summaryLine); #else fprintf(f, "\n"); #endif } if (haveInserts) { fprintf(f, "<B>Inserts between block %d and %d in window</B>\n",blockNo, blockNo+1); for (mc = maf->components; mc != NULL; mc = mc->next) { char dbOnly[128], *chrom; int s = mc->start + mc->size; int e = s + mc->rightLen; char *org; if (mc->text == NULL) continue; if (mc->strand == '-') reverseIntRange(&s, &e, mc->srcSize); safef(dbOnly, sizeof(dbOnly), "%s", mc->src); chrom = chopPrefix(dbOnly); if ((org = hOrganism(dbOnly)) == NULL) org = dbOnly; if (mc->rightStatus == MAF_INSERT_STATUS) { char *revComp = ""; if (hDbIsActive(dbOnly)) { char strand = mc->strand; #ifdef REVERSESTRAND if (cartCgiUsualBoolean(cart, COMPLEMENT_BASES_VAR, FALSE)) strand = (strand == '+') ? '-' : '+'; #endif if (strand == '-') revComp = "&hgSeq.revComp=on"; linkToOtherBrowser(dbOnly, chrom, s, e); fprintf(f,"B"); fprintf(f, "</A>"); fprintf(f, " "); } else fprintf(f, " "); if (hDbExists(dbOnly)) { printf("<A TARGET=\"_blank\" HREF=\"%s?o=%d&g=getDna&i=%s&c=%s&l=%d&r=%d" "&db=%s%s\">D</A> ", hgcName(), s, cgiEncode(chrom), chrom, s, e, dbOnly,revComp); } else fprintf(f, " "); fprintf(f, "%*s %dbp\n", srcChars, org,mc->rightLen); } } fprintf(f, "\n"); } freeMem(summaryLine); } static void mafLowerCase(struct mafAli *maf) /* Lower case letters in maf. */ { struct mafComp *mc; for (mc = maf->components; mc != NULL; mc = mc->next) if (mc->size != 0) tolowers(mc->text); } #ifdef ADDEXONCAPITAL static boolean findAliRange(char *ali, int aliSize, int start, int end, int *retStart, int *retEnd) /* Convert start/end in sequence coordinates to alignment * coordinates (that include dashes). Return FALSE if * no intersection. */ { int i, baseIx=0; char c; int rStart = 0, rEnd = 0; if (start >= end) return FALSE; for (i=0; i<aliSize; ++i) { c = ali[i]; if (c != '-') { if (baseIx == start) rStart = i; ++baseIx; if (baseIx == end) { rEnd = i+1; break; } } } if (rStart >= rEnd) return FALSE; *retStart = rStart; *retEnd = rEnd; return TRUE; } static void capAliTextOnTrack(struct mafAli *maf, char *db, char *chrom, char *track, boolean onlyCds) /* Capitalize exons in alignment. */ { int rowOffset; struct sqlConnection *conn = sqlConnect(db); struct mafComp *selfMc = maf->components, *mc; int start = selfMc->start; int end = start + selfMc->size; struct sqlResult *sr = hRangeQuery(conn, track, chrom, start, end, NULL, &rowOffset); char **row; while ((row = sqlNextRow(sr)) != NULL) { struct genePred *gp = genePredLoad(row+rowOffset); int i; for (i=0; i<gp->exonCount; ++i) { int s = gp->exonStarts[i]; int e = gp->exonEnds[i]; if (onlyCds) { if (s < gp->cdsStart) s = gp->cdsStart; if (e > gp->cdsEnd) e = gp->cdsEnd; } if (s < start) s = start; if (e > end) e = end; if (findAliRange(selfMc->text, maf->textSize, s-start, e-start, &s, &e)) { for (mc = maf->components; mc != NULL; mc = mc->next) if (mc->text) toUpperN(mc->text + s, e-s); } } genePredFree(&gp); } sqlFreeResult(&sr); sqlDisconnect(&conn); } static void capMafOnTrack(struct mafAli *maf, char *track, boolean onlyCds) /* Capitalize parts of maf that correspond to exons according * to given gene prediction track. */ { char dbOnly[64]; char *chrom; struct mafComp *mc = maf->components; strncpy(dbOnly, mc->src, sizeof(dbOnly)); chrom = chopPrefix(dbOnly); capAliTextOnTrack(maf, dbOnly, chrom, track, onlyCds); } #endif static struct mafAli *mafOrAxtLoadInRegion2(struct sqlConnection *conn,struct sqlConnection *conn2, struct trackDb *tdb, char *chrom, int start, int end, char *axtOtherDb, char *file) { if (axtOtherDb != NULL) { struct hash *qSizeHash = hChromSizeHash(axtOtherDb); struct mafAli *mafList = axtLoadAsMafInRegion(conn, tdb->table, chrom, start, end, database, axtOtherDb, hChromSize(database, chrom), qSizeHash); hashFree(&qSizeHash); return mafList; } else return mafLoadInRegion2(conn, conn2, tdb->table, chrom, start, end, file); } #ifdef ADDEXONCAPITAL static char *codeAll[] = { "coding", "all", }; #endif static char *showAll[] = { "all", "diff", }; static void conservationStatsLink(struct trackDb *tdb, char *label, char *table) /* write link that to display statistics of phastCons table */ { char *chrom = cartCgiUsualString(cart, "c", "chr7"); printf("<A HREF=\"%s&g=%s&i=%s&c=%s&l=%d&r=%d&o=%d&db=%s" "&parentWigMaf=%s\" TARGET=\"_blank\">%s</A>", hgcPathAndSettings(), table, table, chrom, winStart, winEnd, winStart, database, tdb->track, label); } static void mafOrAxtClick2(struct sqlConnection *conn, struct sqlConnection *conn2, struct trackDb *tdb, char *axtOtherDb, char *fileName) /* Display details for MAF or AXT tracks. */ { hgBotDelay(); if (winEnd - winStart > 30000) { printf("Zoom so that window is 30,000 bases or less to see alignments and conservation statistics\n"); } else { struct mafAli *mafList = NULL, *maf, *subList = NULL; int aliIx = 0, realCount = 0; char dbChrom[64]; char option[128]; char *capTrack; struct consWiggle *consWig, *consWiggles; struct hash *speciesOffHash = NULL; char *speciesOrder = NULL; char *speciesTarget = trackDbSetting(tdb, SPECIES_TARGET_VAR); char buffer[1024]; int useTarg = FALSE; int useIrowChains = FALSE; safef(option, sizeof(option), "%s.%s", tdb->track, MAF_CHAIN_VAR); if (cartCgiUsualBoolean(cart, option, FALSE) && trackDbSetting(tdb, "irows") != NULL) useIrowChains = TRUE; safef(buffer, sizeof(buffer), "%s.vis",tdb->track); if (useIrowChains) { if (!cartVarExists(cart, buffer) && (speciesTarget != NULL)) useTarg = TRUE; else { char *val; val = cartUsualString(cart, buffer, "useCheck"); useTarg = sameString("useTarg",val); } } if (sameString(tdb->type, "bigMaf")) { char *fileName = trackDbSetting(tdb, "bigDataUrl"); struct bbiFile *bbi = bigBedFileOpen(fileName); mafList = bigMafLoadInRegion(bbi, seqName, winStart, winEnd); } else mafList = mafOrAxtLoadInRegion2(conn,conn2, tdb, seqName, winStart, winEnd, axtOtherDb, fileName); safef(dbChrom, sizeof(dbChrom), "%s.%s", hubConnectSkipHubPrefix(database), seqName); safef(option, sizeof(option), "%s.speciesOrder", tdb->track); speciesOrder = cartUsualString(cart, option, NULL); if (speciesOrder == NULL) speciesOrder = trackDbSetting(tdb, "speciesOrder"); for (maf = mafList; maf != NULL; maf = maf->next) { int mcCount = 0; struct mafComp *mc; struct mafAli *subset; struct mafComp *nextMc; /* remove empty components and configured off components * from MAF, and ignore * the entire MAF if all components are empty * (solely for gap annotation) */ if (!useTarg) { for (mc = maf->components->next; mc != NULL; mc = nextMc) { char buf[64]; char *organism; mafSrcDb(mc->src, buf, sizeof buf); organism = hOrganism(buf); if (!organism) organism = buf; nextMc = mc->next; safef(option, sizeof(option), "%s.%s", tdb->track, buf); if (!cartUsualBoolean(cart, option, TRUE)) { if (speciesOffHash == NULL) speciesOffHash = newHash(4); hashStoreName(speciesOffHash, organism); } if (!cartUsualBoolean(cart, option, TRUE)) slRemoveEl(&maf->components, mc); else mcCount++; } } if (mcCount == 0) continue; if (speciesOrder) { int speciesCt; char *species[2048]; struct mafComp **newOrder, *mcThis; int i; mcCount = 0; speciesCt = chopLine(cloneString(speciesOrder), species); newOrder = needMem((speciesCt + 1) * sizeof (struct mafComp *)); newOrder[mcCount++] = maf->components; for (i = 0; i < speciesCt; i++) { if ((mcThis = mafMayFindCompSpecies(maf, species[i], '.')) == NULL) continue; newOrder[mcCount++] = mcThis; } maf->components = NULL; for (i = 0; i < mcCount; i++) { newOrder[i]->next = 0; slAddHead(&maf->components, newOrder[i]); } slReverse(&maf->components); } subset = mafSubsetE(maf, dbChrom, winStart, winEnd, TRUE); if (subset != NULL) { /* Reformat MAF if needed so that sequence from current * database is the first component and on the * plus strand. */ mafMoveComponentToTop(subset, dbChrom); if (subset->components->strand == '-') mafFlipStrand(subset); subset->score = mafScoreMultiz(subset); slAddHead(&subList, subset); ++realCount; } } slReverse(&subList); mafAliFreeList(&mafList); if (subList != NULL) { char *showVarName = "hgc.showMultiBase"; char *showVarVal = cartUsualString(cart, showVarName, "all"); boolean onlyDiff = sameWord(showVarVal, "diff"); #ifdef ADDEXONCAPITAL char *codeVarName = "hgc.multiCapCoding"; char *codeVarVal = cartUsualString(cart, codeVarName, "coding"); boolean onlyCds = sameWord(codeVarVal, "coding"); #endif /* add links for conservation score statistics */ consWiggles = wigMafWiggles(database, tdb); int wigCount = slCount(consWiggles); if (wigCount == 1) { conservationStatsLink(tdb, "Conservation score statistics", consWiggles->table); } else if (wigCount > 1) { /* multiple wiggles. List all that have been turned on with * checkboxes */ /* Scan for cart variables -- do any exist, are any turned on ? */ boolean wigSet = FALSE; boolean wigOn = FALSE; for (consWig = consWiggles; consWig != NULL; consWig = consWig->next) { char *wigVarSuffix = NULL; (void)wigMafWiggleVar(tdb->track, consWig, &wigVarSuffix); if (cartVarExistsAnyLevel(cart, tdb, FALSE, wigVarSuffix)) { wigSet = TRUE; if (cartBooleanClosestToHome(cart, tdb, FALSE, wigVarSuffix)) wigOn = TRUE; } } /* If there are no cart vars, turn on the first (default) wig */ if (!wigSet) { char *prefix = tdb->track; // use when setting things to the cart if (tdbIsContainerChild(tdb)) prefix = tdbGetContainer(tdb)->track; cartSetBoolean(cart, wigMafWiggleVar(prefix, consWiggles, NULL), TRUE); wigOn = TRUE; } if (wigOn) { boolean first = TRUE; for (consWig = consWiggles; consWig != NULL; consWig = consWig->next) { if (first) { printf("Conservation score statistics:"); first = FALSE; } char *wigVarSuffix = NULL; (void)wigMafWiggleVar(tdb->track, consWig, &wigVarSuffix); if (cartUsualBooleanClosestToHome(cart, tdb, FALSE, wigVarSuffix,FALSE)) { printf(" "); subChar(consWig->uiLabel, '_', ' '); conservationStatsLink(tdb, consWig->uiLabel, consWig->table); } } } } puts("</P>\n"); /* no alignment to display when in visibilities where only wiggle is shown */ char *vis = cartOptionalString(cart, tdb->track); if (vis) { enum trackVisibility tv = hTvFromStringNoAbort(vis); if (tv == tvSquish || tv == tvDense) return; } #ifdef ADDEXONCAPITAL puts("<FORM ACTION=\"../cgi-bin/hgc\" NAME=\"gpForm\" METHOD=\"GET\">"); cartSaveSession(cart); cgiContinueHiddenVar("g"); cgiContinueHiddenVar("c"); + cgiContinueHiddenVar("i"); printf("Capitalize "); cgiMakeDropListFull(codeVarName, codeAll, codeAll, ArraySize(codeAll), codeVarVal, autoSubmit); printf("exons based on "); capTrack = genePredDropDown(cart, trackHash, "gpForm", "hgc.multiCapTrack"); #endif printf("show "); cgiMakeDropListFull(showVarName, showAll, showAll, ArraySize(showAll), showVarVal, autoSubmit); printf("bases"); printf("<BR>\n"); printf("</FORM>\n"); #ifdef REVERSESTRAND /* notify if bases are complemented (hgTracks is on reverse strand) */ if (cartCgiUsualBoolean(cart, COMPLEMENT_BASES_VAR, FALSE)) puts("<EM>Alignment displayed on reverse strand</EM><BR>"); #endif puts("Place cursor over species for alignment detail. Click on 'B' to link to browser "); puts("for aligned species, click on 'D' to get DNA for aligned species.<BR>"); printf("<TT><PRE>"); /* notify if species removed from alignment */ if (speciesOffHash) { char *species; struct hashCookie hc = hashFirst(speciesOffHash); puts("<B>Components not displayed:</B> "); while ((species = hashNextName(&hc)) != NULL) printf("%s ", species); puts("<BR>"); } for (maf = subList; maf != NULL; maf = maf->next) { mafLowerCase(maf); #ifdef ADDEXONCAPITAL if (capTrack != NULL) capMafOnTrack(maf, capTrack, onlyCds); #endif printf("<B>Alignment block %d of %d in window, %d - %d, %d bps </B>\n", ++aliIx,realCount,maf->components->start + 1, maf->components->start + maf->components->size, maf->components->size); mafPrettyOut(stdout, maf, 70,onlyDiff, aliIx); } mafAliFreeList(&subList); } else { printf("No multiple alignment in browser window"); } printf("</PRE></TT>"); } } static void mafOrAxtClick(struct sqlConnection *conn, struct trackDb *tdb, char *axtOtherDb) { struct sqlConnection *conn2 = NULL; if (!isHubTrack(tdb->track)) conn2 = hAllocConn(database); // MAF file location is optionally in trackDb char *mafFile = hashFindVal(tdb->settingsHash, "mafFile"); mafOrAxtClick2(conn, conn2, tdb, axtOtherDb, mafFile); hFreeConn(&conn2); } void customMafClick(struct sqlConnection *conn, struct sqlConnection *conn2, struct trackDb *tdb) { struct hash *settings = tdb->settingsHash; char *fileName; if ((fileName = hashFindVal(settings, "mafFile")) == NULL) errAbort("cannot find custom maf file setting"); mafOrAxtClick2(conn, conn2, tdb, NULL, fileName); } void genericMafClick(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start) /* Display details for MAF tracks. */ { mafOrAxtClick(conn, tdb, NULL); } void genericAxtClick(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start, char *otherDb) /* Display details for AXT tracks. */ { mafOrAxtClick(conn, tdb, otherDb); }