/* Details page for interact type tracks */ /* Copyright (C) 2018 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "obscure.h" #include "hdb.h" #include "jksql.h" #include "hgc.h" #include "customTrack.h" #include "trashDir.h" #include "hex.h" #include "jsHelper.h" #include #include "bigBed.h" #include "chromAlias.h" #include "interact.h" #include "interactUi.h" struct interactPlusRow { /* Keep field values in string format, for url processing */ struct interactPlusRow *next; struct interact *interact; char **row; }; static struct interactPlusRow *getInteractsFromTable(struct trackDb *tdb, char *chrom, int start, int end, char *name, char *foot) /* Retrieve interact items at this position from track table */ { struct sqlConnection *conn = NULL; struct customTrack *ct = lookupCt(tdb->track); char *table; if (ct != NULL) { conn = hAllocConn(CUSTOM_TRASH); table = ct->dbTableName; } else { conn = hAllocConnTrack(database, tdb); table = tdb->table; } if (conn == NULL) return NULL; struct interactPlusRow *iprs = NULL; char **row; int offset; struct sqlResult *sr = hRangeQuery(conn, table, chrom, start, end, NULL, &offset); int fieldCount = 0; while ((row = sqlNextRow(sr)) != NULL) { struct interact *inter = interactLoadAndValidate(row+offset); // got one, save object and row representation struct interactPlusRow *ipr; AllocVar(ipr); ipr->interact = inter; char **fieldVals; if (fieldCount == 0) fieldCount = sqlCountColumns(sr); AllocArray(fieldVals, fieldCount); int i; for (i = 0; i < fieldCount; i++) fieldVals[i] = cloneString(row[i]); ipr->row = fieldVals; slAddHead(&iprs, ipr); } sqlFreeResult(&sr); hFreeConn(&conn); return iprs; } static struct interactPlusRow *getInteractsFromFile(char *file, char *chrom, int start, int end, char *name, char *foot) /* Retrieve interact items at this position from big file */ { struct bbiFile *bbi = bigBedFileOpenAlias(file, chromAliasFindAliases); struct lm *lm = lmInit(0); struct bigBedInterval *bb, *bbList = bigBedIntervalQuery(bbi, chrom, start, end, 0, lm); struct interactPlusRow *iprs = NULL; for (bb = bbList; bb != NULL; bb = bb->next) { char startBuf[16], endBuf[16]; int maxFields = 32; char *row[maxFields]; // big enough ? int fieldCount = bigBedIntervalToRow(bb, chrom, startBuf, endBuf, row, maxFields); struct interact *inter = interactLoadAndValidate(row); if (inter == NULL) continue; // got one, save object and row representation struct interactPlusRow *ipr; AllocVar(ipr); ipr->interact = inter; char **fieldVals; AllocArray(fieldVals, fieldCount); int i; for (i = 0; i < fieldCount; i++) fieldVals[i] = cloneString(row[i]); ipr->row = fieldVals; slAddHead(&iprs, ipr); } return iprs; } static struct interactPlusRow *getInteractions(struct trackDb *tdb, char *chrom, int start, int end, char *name, char *foot, int *retStart, int *retEnd) /* Retrieve interact items at this position or name. * Also any others with the same endpoint, if endpoint clicked on. * Return full extent of included interactions in returned start, end */ // NOTE: Consider sortable table of matching interactions { struct interactPlusRow *ipr, *iprs = NULL, *next, *filtered = NULL; char *file = trackDbSetting(tdb, "bigDataUrl"); char *clusterMode = interactUiClusterMode(cart, tdb->track, tdb); if (file != NULL) iprs = getInteractsFromFile(file, chrom, start, end, name, foot); else iprs = getInteractsFromTable(tdb, chrom, start, end, name, foot); int minStart = 999999999; int maxEnd = 0; for (ipr = iprs; ipr; ipr = next) { struct interact *inter = ipr->interact; next = ipr->next; if (!name || sameString(name, ".")) { if (inter->chromStart != start || inter->chromEnd != end) continue; } else { char *match = inter->name; if (clusterMode) match = sameString(clusterMode, INTERACT_CLUSTER_SOURCE) ? inter->sourceName : inter->targetName; if (differentString(name, match)) { if (clusterMode || !foot) continue; // if clicked on foot, look at endpoint names if (differentString(name, inter->sourceName) && differentString(name, inter->targetName)) continue; } } minStart = inter->chromStart < minStart ? inter->chromStart : minStart; maxEnd = inter->chromEnd > maxEnd ? inter->chromEnd : maxEnd; slAddHead(&filtered, ipr); } *retStart = minStart; *retEnd = maxEnd; // consider sorting on score or position return filtered; } static char *makeInteractRegionFile(char *name, struct interact *inters, int padding, char **retCustomText) /* Create bed file in trash directory with end coordinates for multi-region mode, * and a custom track for display showing regions */ { struct tempName mrTn; trashDirFile(&mrTn, "hgt", "custRgn_interact", ".bed"); FILE *f = fopen(mrTn.forCgi, "w"); if (f == NULL) errAbort("can't create temp file %s", mrTn.forCgi); char regionInfo[1024]; safef(regionInfo, sizeof regionInfo, "#padding %d\n", padding); mustWrite(f, regionInfo, strlen(regionInfo)); safef(regionInfo, sizeof regionInfo, "#shortDesc %s\n", name); mustWrite(f, regionInfo, strlen(regionInfo)); struct interact *inter = NULL; struct bed *region, *regions = NULL; struct hash *uniqRegions = hashNew(0); struct dyString *ds = dyStringNew(0); dyStringPrintf(ds, "track name='Multi Regions' description='Interact regions for %s' " "itemRgb=On labelOnFeature=on\n", name); for (inter = inters; inter != NULL; inter = inter->next) { char buf[256]; safef(buf, sizeof buf, "%s:%d-%d", inter->sourceChrom, inter->sourceStart, inter->sourceEnd); if (!hashLookup(uniqRegions, buf)) { hashAdd(uniqRegions, cloneString(buf), NULL); AllocVar(region); region->chrom = inter->sourceChrom; region->chromStart = inter->sourceStart; region->chromEnd = inter->sourceEnd; slAddHead(®ions, region); } safef(buf, sizeof buf, "%s:%d-%d", inter->targetChrom, inter->targetStart, inter->targetEnd); if (!hashLookup(uniqRegions, buf)) { hashAdd(uniqRegions, cloneString(buf), NULL); AllocVar(region); region->chrom = inter->targetChrom; region->chromStart = inter->targetStart; region->chromEnd = inter->targetEnd; slAddHead(®ions, region); } } slSort(®ions, bedCmp); struct bed *prevRegion = NULL; // alternate item colors char *colorLight = "184,201,255"; char *colorDark = "0,0,0"; boolean doLightColor = TRUE; // print regions to BED file and custom track for (region = regions; region != NULL; region = region->next) { // filter out nested regions if (prevRegion == NULL || differentString(region->chrom, prevRegion->chrom) || region->chromStart >= prevRegion->chromEnd) { char *localChromName = chromAliasFindNative(region->chrom); if (localChromName == NULL) localChromName = region->chrom; // For some reason, aliases don't (or don't always) include the native names safef(regionInfo, sizeof regionInfo, "%s\t%d\t%d\n", localChromName, region->chromStart, region->chromEnd); mustWrite(f, regionInfo, strlen(regionInfo)); int start = max(region->chromStart - padding, 0); int end = min(region->chromEnd + padding, hChromSize(database, localChromName)); char *color = doLightColor ? colorLight : colorDark; doLightColor = !doLightColor; dyStringPrintf(ds, "%s\t%d\t%d\t" "%s:%d+%d_bp\t" "0\t.\t%d\t%d\t%s\n", region->chrom, start, end, region->chrom, start+1, end-start, start, end, color); } prevRegion = region; } fclose(f); // create SHA1 file; used to see if file has changed unsigned char hash[SHA_DIGEST_LENGTH]; SHA1((const unsigned char *)regionInfo, strlen(regionInfo), hash); char newSha1[(SHA_DIGEST_LENGTH + 1) * 2]; hexBinaryString(hash, SHA_DIGEST_LENGTH, newSha1, (SHA_DIGEST_LENGTH + 1) * 2); char sha1File[1024]; safef(sha1File, sizeof sha1File, "%s.sha1", mrTn.forCgi); f = mustOpen(sha1File, "w"); mustWrite(f, newSha1, strlen(newSha1)); carefulClose(&f); // post custom track if (retCustomText != NULL) *retCustomText = dyStringCannibalize(&ds); // return BED filename return cloneString(mrTn.forCgi); } static void multiRegionLink(struct trackDb *tdb, char *name, struct interact *inters) // Print link to multi-region view of ends if appropriate // (or provide a link to remove if already in this mode) { char *setting = trackDbSetting(tdb, "interactMultiRegion"); if (!setting || sameString(setting, "off")) return; int padding = 200; if (differentString(setting, "on") && differentString(setting, "true")) padding = (int)strtol(setting, NULL, 10); if (inters->next == NULL && interactEndsOverlap(inters)) return; char *virtShortDesc = cartOptionalString(cart, "virtShortDesc"); boolean isVirtMode = cartUsualBoolean(cart, "virtMode", FALSE); if (isVirtMode && virtShortDesc && sameString(virtShortDesc, name)) { printf("
Show interaction%s in " "" " normal browser view (exit multi-region view)", inters->next != NULL ? "s" : ""); } else { char *customText = NULL; char *regionFile = makeInteractRegionFile(name, inters, padding, &customText); printf("
Show interaction ends in " "" " multi-region view (custom regions mode)", name, cgiEncode(regionFile), CT_CUSTOM_TEXT_VAR, cgiEncode(customText)); if (isVirtMode) { printf(" or " "" " normal browser view"); } else { printf("   "); printf("(Help)\n"); printf("
    Note: all interactions will display in "pack" mode\n"); } } } void doInteractRegionDetails(struct trackDb *tdb, struct interact *inter) { /* print info for both regions */ /* Use different labels: 1) directional (source/target) 2) non-directional same chrom (lower/upper) 3) non-directional other chrom (this/other) */ char startBuf[1024], endBuf[1024], sizeBuf[1024]; printf("Interaction region: "); if (interactOtherChrom(inter)) printf("across chromosomes
"); else { sprintLongWithCommas(startBuf, inter->chromStart+1); sprintLongWithCommas(endBuf, inter->chromEnd); sprintLongWithCommas(sizeBuf, inter->chromEnd - inter->chromStart); printf("%s:%s-%s", inter->chrom, inter->chromStart, inter->chromEnd, inter->chrom, startBuf, endBuf); printf("  %s bp
\n", sizeBuf); } printf("
"); char *region1Label = "Source"; char *region1Chrom = inter->sourceChrom; int region1Start = inter->sourceStart; int region1End = inter->sourceEnd; char *region1Name = inter->sourceName; if (isEmptyTextField(inter->sourceName)) region1Name = ""; char *region2Label = "Target"; char *region2Chrom = inter->targetChrom; int region2Start = inter->targetStart; int region2End = inter->targetEnd; char *region2Name = inter->targetName; if (isEmptyTextField(inter->targetName)) region2Name = ""; if (!interactUiDirectional(tdb)) { if (interactOtherChrom(inter)) { region1Label = "This"; region2Label = "Other"; } else { region1Label = "Lower"; region2Label = "Upper"; } } // format and print sprintLongWithCommas(startBuf, region1Start + 1); sprintLongWithCommas(endBuf, region1End); sprintLongWithCommas(sizeBuf, region1End - region1Start); printf("%s region: %s  " "%s:%s-%s %s", region1Label, region1Name, region1Chrom, region1Start+1, region1End, region1Chrom, startBuf, endBuf, inter->sourceStrand[0] == '.' ? "" : inter->sourceStrand); printf("  %s bp
\n", sizeBuf); sprintLongWithCommas(startBuf, region2Start+1); sprintLongWithCommas(endBuf, region2End); sprintLongWithCommas(sizeBuf, region2End - region2Start); printf("%s region: %s  " "%s:%s-%s %s", region2Label, region2Name, region2Chrom, region2Start+1, region2End, region2Chrom, startBuf, endBuf, inter->targetStrand[0] == '.' ? "" : inter->targetStrand); printf("  %s bp
\n", sizeBuf); int distance = interactRegionDistance(inter); if (distance > 0) { // same chrom sprintLongWithCommas(sizeBuf, distance); printf("Distance between midpoints: %s bp
\n", sizeBuf); } } void doInteractItemDetails(struct trackDb *tdb, struct interactPlusRow *ipr, char *item, boolean isMultiple) /* Details of interaction item */ { struct interact *inter = ipr->interact; struct slPair *fields = getFields(tdb, ipr->row); printCustomUrlWithFields(tdb, inter->name, inter->name, TRUE, fields); if (!isEmptyTextField(inter->name)) printf("Interaction: %s
\n", inter->name); printf("Score: %d
\n", inter->score); printf("Value: %0.3f
\n", inter->value); if (!isEmptyTextField(inter->exp)) printf("Experiment: %s
\n", inter->exp); puts("

"); if (!isMultiple) { doInteractRegionDetails(tdb, inter); multiRegionLink(tdb, inter->name, inter); } } static struct interact *iprsToInters(struct interactPlusRow *iprs) /* Create list of interacts from interactPlusRows */ { struct interactPlusRow *ipr; struct interact *inters = NULL; for (ipr = iprs; ipr != NULL; ipr = ipr->next) slAddHead(&inters, ipr->interact); return inters; } void doInteractDetails(struct trackDb *tdb, char *item) /* Details of interaction items */ { char *chrom = cartString(cart, "c"); int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); char *foot = cgiOptionalString("foot"); int minStart, maxEnd; struct interactPlusRow *iprs = getInteractions(tdb, chrom, start, end, item, foot, &minStart, &maxEnd); start = minStart; end = maxEnd; if (iprs == NULL) errAbort("Can't find interaction %s", item ? item : ""); int count = slCount(iprs); char *clusterMode = interactUiClusterMode(cart, tdb->track, tdb); if (count > 1 || clusterMode) { printf("Interactions: %d

", count); struct interact *inters = iprsToInters(iprs); if (clusterMode || foot) { char startBuf[1024], endBuf[1024], sizeBuf[1024]; sprintLongWithCommas(startBuf, start + 1); sprintLongWithCommas(endBuf, end); sprintLongWithCommas(sizeBuf, end - start + 1); printf("%s interactions region:   " "%s:%s-%s ", item, chrom, start+1, end, chrom, startBuf, endBuf); printf("  %s bp
\n", sizeBuf); } else { // overlapping items, same start/end/name doInteractRegionDetails(tdb, inters); } multiRegionLink(tdb, item, inters); printf("

"); } if (count > 1) { puts(""); jsBeginCollapsibleSectionFontSize(cart, tdb->track, "interactions", "Show individual interactions", FALSE, "inherit"); } static struct interactPlusRow *ipr = NULL; for (ipr = iprs; ipr != NULL; ipr = ipr->next) { if (count > 1) printf("
\n"); doInteractItemDetails(tdb, ipr, item, count > 1); if (foot || (clusterMode && count > 1)) { struct interact *inter = ipr->interact; // just one interact (we have these in list for handling clusters earlier) inter->next = NULL; doInteractRegionDetails(tdb, inter); multiRegionLink(tdb, inter->name, inter); } if (count > 1 && !isEmptyTextField(ipr->interact->name) && sameString(ipr->interact->name, item)) printf("
\n"); } if (count > 1) { jsEndCollapsibleSection(); puts("
"); } }