6f75c327bcd0cfc8bf68dfa1227aabb579120698 Merge parents 41b17ce ccb8cb2 kate Mon Dec 17 12:37:37 2018 -0800 Merge branch 'master' into interact-multiregion diff --cc src/hg/hgc/interactClick.c index 9d1e538,54cd223..87afdb5 --- src/hg/hgc/interactClick.c +++ src/hg/hgc/interactClick.c @@@ -1,331 -1,312 +1,331 @@@ /* 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 "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 = iprs->interact->chromStart; int maxEnd = iprs->interact->chromEnd; 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; } 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 + +// create bed file in trash directory with end coordinates +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); +fprintf(f, "%s\t%d\t%d\n" + "%s\t%d\t%d\n", + region1Chrom, region1Start, region1End, + region2Chrom, region2Start, region2End); +fclose(f); +printf("<br><a target='_blank' href='hgTracks?" + "virtMode=1" + "&virtModeType=customUrl" + "&multiRegionsBedUrl=%s'" + ">Show both ends of interaction in multi-region browser view</a>", + mrTn.forCgi); + #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) /* Details of interaction item */ { struct interact *inter = ipr->interact; struct slPair *fields = getFields(tdb, ipr->row); - printCustomUrlWithFields(tdb, item, item, TRUE, fields); + 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); } 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("<b>Interactions:</b> %d<p>", count); if (clusterMode || foot) { char startBuf[1024], endBuf[1024], sizeBuf[1024]; sprintLongWithCommas(startBuf, start + 1); sprintLongWithCommas(endBuf, end); sprintLongWithCommas(sizeBuf, end - start); 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); } printf("</p>"); } 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); if (foot || (clusterMode && count > 1)) doInteractRegionDetails(tdb, ipr->interact); if (count > 1 && !isEmptyTextField(ipr->interact->name) && sameString(ipr->interact->name, item)) printf("<hr>\n"); } -if (count > 1 && clusterMode) - printf("<hr>\n"); }