3f112eba0af44ffe8b5c15c7721f3e850afe9276 kate Wed Mar 28 15:14:07 2018 -0700 Expand schema to include strand for each endpoint (request by Braney and Daniel Zerbino, to enable future support of rearrangements as well as bedPE). refs #21109 diff --git src/hg/hgc/interactClick.c src/hg/hgc/interactClick.c index 412e81a..7ac27c0 100644 --- src/hg/hgc/interactClick.c +++ src/hg/hgc/interactClick.c @@ -1,206 +1,207 @@ /* 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 "hgc.h" #include "interact.h" #include "interactUi.h" static struct interact *getInteractFromTable(struct trackDb *tdb, char *item, char *chrom, int start, int end) /* Retrieve this item or items 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 interact *inters = NULL, *inter = NULL; char **row; int offset; struct sqlResult *sr = hRangeQuery(conn, table, chrom, start, end, NULL, &offset); while ((row = sqlNextRow(sr)) != NULL) { inter = interactLoad(row+offset); if (inter->chromStart != start || inter->chromEnd != end) continue; if (isNotEmpty(item) && differentString(inter->name, item)) continue; slAddHead(&inters, inter); } slSort(&inters, interactDistanceCmp); sqlFreeResult(&sr); hFreeConn(&conn); return inters; } static struct interact *getInteractFromFile(char *file, char *item, char *chrom, int start, int end) /* Retrieve interact BED item 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 interact *inters = NULL, *inter = NULL; for (bb = bbList; bb != NULL; bb = bb->next) { char startBuf[16], endBuf[16]; char *row[32]; bigBedIntervalToRow(bb, chrom, startBuf, endBuf, row, ArraySize(row)); inter = interactLoad(row); if (inter == NULL) continue; if (inter->chromStart != start || inter->chromEnd != end) continue; if (isNotEmpty(item) && differentString(inter->name, item)) continue; slAddHead(&inters, inter); } slSort(&inters, interactDistanceCmp); return inters; } static struct interact *getInteractions(struct trackDb *tdb, char *item, char *chrom, int start, int end) /* Retrieve interact BED item from track */ { struct interact *inters = NULL; char *file = trackDbSetting(tdb, "bigDataUrl"); if (file != NULL) inters = getInteractFromFile(file, item, chrom, start, end); else inters = getInteractFromTable(tdb, item, chrom, start, end); return inters; } void doInteractItemDetails(struct trackDb *tdb, struct interact *inter, char *item) /* Details of interaction item */ { char startBuf[1024], endBuf[1024], sizeBuf[1024]; if (!isEmptyTextField(inter->name)) printf("<b>Interaction name:</b> %s<br>\n", inter->name); 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("<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>"); /* 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 *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>", + "<a href='hgTracks?position=%s:%d-%d' target='_blank'>%s:%s-%s</a> %s", region1Label, region1Name, region1Chrom, region1Start+1, region1End, - region1Chrom, startBuf, endBuf); + 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>", + "<a href='hgTracks?position=%s:%d-%d' target='_blank'>%s:%s-%s</a> %s", region2Label, region2Name, region2Chrom, region2Start+1, region2End, - region2Chrom, startBuf, endBuf); + 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); } #ifdef TODO /* TODO: get count and score stats of all interactions in window ?*/ double *scores; AllocArray(scores, count); #endif } 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"); struct interact *inter = NULL; struct interact *inters = getInteractions(tdb, item, chrom, start, end); if (inters == NULL) errAbort("Can't find interaction %s", item ? item : ""); int count = slCount(inters); if (count > 1) printf("<b>Interactions:</b> %d<hr>", count); genericHeader(tdb, item); for (inter = inters; inter; inter = inter->next) { doInteractItemDetails(tdb, inter, item); printf("<hr>\n"); if (count > 1 && !isEmptyTextField(inter->name) && sameString(inter->name, item)) printf("<hr>\n"); } }