95ac3b9a9a4696a6ff59dc4dc8cb057b6a43c898 kate Fri Aug 23 16:10:24 2019 -0700 Add multi-region link for all regions in interact cluster. refs #24037 diff --git src/hg/hgc/interactClick.c src/hg/hgc/interactClick.c index e12f974..3b3483f 100644 --- src/hg/hgc/interactClick.c +++ src/hg/hgc/interactClick.c @@ -1,412 +1,449 @@ /* Details page for interact type tracks */ /* Copyright (C) 2018 The Regents of the University of California * See README in this or parent directory for licensing information. */ #include "common.h" #include "obscure.h" #include "hdb.h" #include "jksql.h" #include "hgc.h" #include "trashDir.h" #include "hex.h" #include <openssl/sha.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 = bigBedFileOpen(file); 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(struct interact *inter) +static char *makeInteractRegionFile(char *name, struct interact *inters) /* Create bed file in trash directory with end coordinates for multi-region mode */ { 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]; // TODO: check chrom bounds int padding = 200; //cartSetBoolean(cart, "emAltHighlight", TRUE); safef(regionInfo, sizeof regionInfo, "#padding %d\n", padding); mustWrite(f, regionInfo, strlen(regionInfo)); //warn("%s", regionInfo); -safef(regionInfo, sizeof regionInfo, "#shortDesc %s\n", inter->name); +safef(regionInfo, sizeof regionInfo, "#shortDesc %s\n", name); mustWrite(f, regionInfo, strlen(regionInfo)); //warn("%s", regionInfo); -char *region1Chrom = inter->sourceChrom, *region2Chrom = inter->targetChrom; -int region1Start = inter->sourceStart, region1End = inter->sourceEnd; -int region2Start = inter->targetStart, region2End = inter->targetEnd; -if (sameString(inter->sourceChrom, inter->targetChrom)) - { - if (inter->sourceStart > inter->targetStart) - { - region1Start = inter->targetStart; - region1End = inter->targetEnd; - region2Start = inter->sourceStart; - region2End = inter->sourceEnd; - } + +struct interact *inter = NULL; +struct bed *region, *regions = NULL; +struct hash *uniqRegions = hashNew(0); +for (inter = inters; inter != NULL; inter = inter->next) + { + char buf[256]; + //safef(buf, sizeof buf, "%s:%d-%d", region1->chrom, region1->chromStart, region1->chromEnd); + 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); } -else - { - if (sameString(inter->chrom, inter->targetChrom)) - { - region1Chrom = inter->targetChrom; - region1Start = inter->targetStart; - region1End = inter->targetEnd; - region2Chrom = inter->sourceChrom; - region2Start = inter->sourceStart; - region2End = inter->sourceEnd; + //safef(buf, sizeof buf, "%s:%d-%d", region2->chrom, region2->chromStart, region2->chromEnd); + 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->chrom; + region->chromStart = inter->targetStart; + region->chromEnd = inter->targetEnd; + slAddHead(®ions, region); } } -safef(regionInfo, sizeof regionInfo, "%s\t%d\t%d\n" - "%s\t%d\t%d\n", - region1Chrom, region1Start, region1End, - region2Chrom, region2Start, region2End); +slSort(®ions, bedCmp); +for (region = regions; region != NULL; region = region->next) + { + safef(regionInfo, sizeof regionInfo, "%s\t%d\t%d\n", + region->chrom, region->chromStart, region->chromEnd); mustWrite(f, regionInfo, strlen(regionInfo)); //warn("%s", regionInfo); + } 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); return cloneString(mrTn.forCgi); } +static void multiRegionLink(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) +{ +if (inters->next == NULL && interactEndsOverlap(inters)) + return; +char *virtShortDesc = cartOptionalString(cart, "virtShortDesc"); +boolean isVirtMode = cartUsualBoolean(cart, "virtMode", FALSE); +//warn("virtShortDesc: %s, name: %s", virtShortDesc, name); +if (isVirtMode && virtShortDesc && sameString(virtShortDesc, name)) + { + printf("<br>Show interaction%s in " + "<a href='hgTracks?" + "virtMode=0&" + "virtModeType=default'>" + " normal browser view</a> (exit multi-region view)", + inters->next != NULL ? "s" : ""); + } +else + { + char *regionFile = makeInteractRegionFile(name, inters); + //warn("regionFile: %s", regionFile); + printf("<br>Show interaction ends in " + "<a href='hgTracks?" + "virtMode=1&" + "virtModeType=customUrl&" + "virtWinFull=on&" + "virtShortDesc=%s&" + "multiRegionsBedUrl=%s'>" + " multi-region browser view </a>(custom region mode)", + name, cgiEncode(regionFile)); + if (isVirtMode) + printf(" or " + "<a href='hgTracks?" + "virtMode=0&" + "virtModeType=default'>" + " normal browser view</a>"); + } +printf(" "); +printf("<a href=\"../goldenPath/help/multiRegionHelp.html\" target=_blank>(Help)</a>\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("<b>Interaction region:</b> "); if (interactOtherChrom(inter)) printf("across chromosomes<br>"); else { sprintLongWithCommas(startBuf, inter->chromStart+1); sprintLongWithCommas(endBuf, inter->chromEnd); sprintLongWithCommas(sizeBuf, inter->chromEnd - inter->chromStart); printf("<a href='hgTracks?position=%s:%d-%d' target='_blank'>%s:%s-%s</a>", inter->chrom, inter->chromStart, inter->chromEnd, inter->chrom, startBuf, endBuf); printf(" %s bp<br>\n", sizeBuf); } printf("<br>"); 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("<b>%s region:</b> %s " "<a href='hgTracks?position=%s:%d-%d' target='_blank'>%s:%s-%s</a> %s", region1Label, region1Name, region1Chrom, region1Start+1, region1End, region1Chrom, startBuf, endBuf, inter->sourceStrand[0] == '.' ? "" : inter->sourceStrand); printf(" %s bp<br>\n", sizeBuf); sprintLongWithCommas(startBuf, region2Start+1); sprintLongWithCommas(endBuf, region2End); sprintLongWithCommas(sizeBuf, region2End - region2Start); printf("<b>%s region:</b> %s " "<a href='hgTracks?position=%s:%d-%d' target='_blank'>%s:%s-%s</a> %s", region2Label, region2Name, region2Chrom, region2Start+1, region2End, region2Chrom, startBuf, endBuf, inter->targetStrand[0] == '.' ? "" : inter->targetStrand); printf(" %s bp<br>\n", sizeBuf); int distance = interactRegionDistance(inter); if (distance > 0) { // same chrom sprintLongWithCommas(sizeBuf, distance); printf("<b>Distance between midpoints:</b> %s bp<br>\n", sizeBuf); } - -// print link to multi-region view of ends if appropriate -// (or provide a link to remove if already in this mode) - -if (trackDbSettingOn(tdb, "interactMultiRegion") && !interactEndsOverlap(inter)) - { - char *virtShortDesc = cartOptionalString(cart, "virtShortDesc"); - //warn("virtShortDesc: %s", virtShortDesc); - if (virtShortDesc && sameString(virtShortDesc, inter->name)) - { - printf("<br><a target='_blank' " - "href='hgTracks?" - "virtMode=0&" - "virtModeType=default'>" - "Show interaction in normal browser view (exit multi-region view)</a>"); - } - else - { - char *regionFile = makeInteractRegionFile(inter); - //warn("regionFile: %s", regionFile); - printf("<br><a target='_blank' " - "href='hgTracks?" - "virtMode=1&" - "virtModeType=customUrl&" - "virtWinFull=on&" - "virtShortDesc=%s&" - "multiRegionsBedUrl=%s'>" - "Show both ends of interaction in multi-region browser view (custom region mode)</a>", - inter->name, cgiEncode(regionFile)); - } - printf(" "); - printf("<a href=\"../goldenPath/help/multiRegionHelp.html\" target=_blank>(Help)</a>\n"); - } - -#ifdef TODO /* TODO: get count and score stats of all interactions in window ?*/ -double *scores; -AllocArray(scores, count); -#endif } void doInteractItemDetails(struct trackDb *tdb, struct interactPlusRow *ipr, char *item, - boolean isMultiple) + boolean isMultiple, boolean doMultiRegion) /* 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("<b>Interaction:</b> %s<br>\n", inter->name); printf("<b>Score:</b> %d<br>\n", inter->score); printf("<b>Value:</b> %0.3f<br>\n", inter->value); if (!isEmptyTextField(inter->exp)) printf("<b>Experiment:</b> %s<br>\n", inter->exp); puts("<p>"); if (!isMultiple) + { doInteractRegionDetails(tdb, inter); + if (doMultiRegion) + multiRegionLink(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"); +boolean doMultiRegion = trackDbSettingOn(tdb, "interactMultiRegion"); 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("<b>Interactions:</b> %d<p>", 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("<b>%s interactions region:</b> " "<a href='hgTracks?position=%s:%d-%d' target='_blank'>%s:%s-%s</a> ", item, chrom, start+1, end, chrom, startBuf, endBuf); printf(" %s bp<br>\n", sizeBuf); } else { - doInteractRegionDetails(tdb, iprs->interact); + // overlapping items, same start/end/name + doInteractRegionDetails(tdb, inters); } + if (doMultiRegion) + multiRegionLink(item, inters); printf("</p>"); } -genericHeader(tdb, item); +//genericHeader(tdb, item); static struct interactPlusRow *ipr = NULL; for (ipr = iprs; ipr != NULL; ipr = ipr->next) { if (count > 1) printf("<hr>\n"); - doInteractItemDetails(tdb, ipr, item, count > 1); + doInteractItemDetails(tdb, ipr, item, count > 1, doMultiRegion); if (foot || (clusterMode && count > 1)) - doInteractRegionDetails(tdb, ipr->interact); + { + struct interact *inter = ipr->interact; + // just one interact (we have these in list for handling clusters earlier) + inter->next = NULL; + doInteractRegionDetails(tdb, inter); + if (doMultiRegion) + multiRegionLink(inter->name, inter); + } if (count > 1 && !isEmptyTextField(ipr->interact->name) && sameString(ipr->interact->name, item)) printf("<hr>\n"); } }