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>"); } }
void extractMafs(char *file, FILE *f, struct hash *regionHash) /* extract MAFs in a file from regions specified in hash */ { char *chrom = NULL; struct bed *bed = NULL; struct mafFile *mf = mafOpen(file); struct mafAli *maf = NULL; struct mafComp *mc; char path[256]; verbose(1, "extracting from %s\n", file); maf = mafNext(mf); while (maf) { mc = maf->components; if (!chrom || differentString(chrom, chromFromSrc(mc->src))) chrom = cloneString(chromFromSrc(mc->src)); /* new chrom */ bed = (struct bed *)hashFindVal(regionHash, chrom); if (!bed) { /* no regions on this chrom -- skip to next chrom */ do mafAliFree(&maf); while (((maf = mafNext(mf)) != NULL) && sameString(chromFromSrc(maf->components->src), chrom)); continue; // start over with this maf } verbose(2, "region: %s:%d-%d\n", bed->chrom, bed->chromStart+1, bed->chromEnd); if (outDir) { if (f) endOutFile(f); safef(path, sizeof (path), "%s/%s.maf", dir, bed->name); f = startOutFile(path); } /* skip mafs before region, stopping if chrom changes */ while (maf && (mc = maf->components) && sameString(chrom, chromFromSrc(mc->src)) && (mc->start + mc->size) <= bed->chromStart) { mafAliFree(&maf); maf = mafNext(mf); } /* extract all mafs and pieces of mafs in region */ while (maf && (mc = maf->components) && sameString(chrom, chromFromSrc(mc->src)) && (bed->chromStart < mc->start + mc->size && bed->chromEnd > mc->start)) { int mafStart = mc->start; int mafEnd = mc->start + mc->size; struct mafAli *full = maf; if (mafStart < bed->chromStart || mafEnd > bed->chromEnd) { full = maf; maf = mafSubsetE(full, mc->src, bed->chromStart, bed->chromEnd, keepInitialGaps); mc = maf->components; } verbose(2, " %s:%d-%d\n", chrom, mc->start+1, mc->start + mc->size); mafWrite(f, maf); struct mafAli *nextMaf = (mafEnd > bed->chromEnd+1) ? mafSubset(full, mc->src, bed->chromEnd+1, mafEnd) : mafNext(mf); if (maf != full) mafAliFree(&maf); mafAliFree(&full); maf = nextMaf; } /* get next region */ hashRemove(regionHash, bed->chrom); if (bed->next) hashAdd(regionHash, bed->chrom, bed->next); } mafFileFree(&mf); }
struct mafAli *mafSubset(struct mafAli *maf, char *componentSource, int newStart, int newEnd) { return mafSubsetE(maf, componentSource, newStart, newEnd, FALSE); }