742b3553239efc01084fa74d6cb0bc87c269a4cd angie Tue Sep 14 14:29:29 2010 -0700 Fixing warning messages from gcc Ubuntu 4.4.1-4ubuntu9. diff --git src/hg/hgc/peakClusters.c src/hg/hgc/peakClusters.c index 6ad63e6..e8285b5 100644 --- src/hg/hgc/peakClusters.c +++ src/hg/hgc/peakClusters.c @@ -1,399 +1,395 @@ /* Stuff to display details on tracks that are clusters of peaks (items) in other tracks. * In particular peaks in either ENCODE narrowPeak or broadPeak settings, and residing in * composite tracks. * * These come in two main forms currently: * DNAse hypersensitive clusters - peaks clustered across cell lines stored in bed 5 * with no special type * Transcription Factor Binding Sites (TFBS) - peaks from transcription factor ChIP-seq * across a number of transcription factors and cell lines. Stored in bed 15 * plus sourceTable with type factorSource */ #include "common.h" #include "hash.h" #include "jksql.h" #include "obscure.h" #include "hCommon.h" #include "hdb.h" #include "web.h" #include "cart.h" #include "trackDb.h" #include "hui.h" #include "hgc.h" #include "encode/encodePeak.h" #include "expRecord.h" #include "bed6FloatScore.h" #include "txCluster.h" char *findGroupTagVal(struct trackDb *tdb, char *tag) /* Find value of given tag inside of subgroups field. */ { char *subGroups = trackDbSetting(tdb, "subGroups"); struct slPair *el, *list = slPairFromString(subGroups); char *val = NULL; for (el = list; el != NULL; el = el->next) { if (sameString(el->name, tag)) { val = el->val; break; } } return val; } char *mustFindGroupTagVal(struct trackDb *tdb, char *tag) /* Find value of given tag inside of subgroups field or abort with error message. */ { char *val = findGroupTagVal(tdb, tag); if (val == NULL) errAbort("Couldn't find %s in subGroups tag of %s", tag, tdb->track); return val; } char *findGroupLabel(struct trackDb *tdb, char *group) /* Given name of group, ruffle through all subGroupN tags, looking for one that * matches group */ { char *groupId = mustFindGroupTagVal(tdb, group); return compositeGroupLabel(tdb, group, groupId); } static void printClusterTableHeader(struct slName *displayGroupList) /* Print out header fields table of tracks in cluster */ { webPrintLabelCell("#"); webPrintLabelCell("signal"); struct slName *displayGroup; for (displayGroup = displayGroupList; displayGroup != NULL; displayGroup = displayGroup->next) { webPrintLabelCell(displayGroup->name); } webPrintLabelCell("description"); } static void printOutOfClusterTableHeader(struct slName *displayGroupList) /* Print out header fields for table of tracks not in cluster */ { webPrintLabelCell("#"); struct slName *displayGroup; for (displayGroup = displayGroupList; displayGroup != NULL; displayGroup = displayGroup->next) { webPrintLabelCell(displayGroup->name); } webPrintLabelCell("description"); } static void printTableInfo(struct trackDb *tdb, struct trackDb *clusterTdb, struct slName *displayGroupList) /* Print out info on table. */ { struct slName *displayGroup; for (displayGroup = displayGroupList; displayGroup != NULL; displayGroup = displayGroup->next) { char *label = findGroupLabel(tdb, displayGroup->name); char *linkedLabel = compositeLabelWithVocabLink(database, tdb, tdb, displayGroup->name, label); webPrintLinkCell(linkedLabel); } webPrintLinkCellStart(); printf("%s ", tdb->longLabel); compositeMetadataToggle(database, tdb, "...", TRUE, FALSE, trackHash); webPrintLinkCellEnd(); } static void showOnePeakOrMiss(struct trackDb *tdb, struct trackDb *clusterTdb, struct encodePeak *peakList, struct slName *displayGroupList, int *pIx) /* Show info on track and peak. Peak may be NULL in which case fewer columns will be printed. */ { struct encodePeak *peak; *pIx += 1; printf("</TR><TR>\n"); webPrintIntCell(*pIx); if (peakList) { webPrintLinkCellRightStart(); printf("%g", peakList->signalValue); for (peak = peakList->next; peak != NULL; peak = peak->next) printf(",%g", peak->signalValue); webPrintLinkCellEnd(); } printTableInfo(tdb, clusterTdb, displayGroupList); } static boolean showMatchingTrack(char *track, struct bed *cluster, struct sqlConnection *conn, struct trackDb *clusterTdb, struct slName *displayGroupList, boolean invert, int *pRowIx) /* put out a line in an html table that describes the given track. */ { struct trackDb *tdb = hashMustFindVal(trackHash, track); boolean result = FALSE; char **row; int rowOffset = 0; struct sqlResult *sr = hRangeQuery(conn, tdb->table, cluster->chrom, cluster->chromStart, cluster->chromEnd, NULL, &rowOffset); struct encodePeak *peakList = NULL; struct slDouble *slDoubleNew(double x); while ((row = sqlNextRow(sr)) != NULL) { enum encodePeakType pt = encodePeakInferTypeFromTable(database, tdb->table, tdb->type); struct encodePeak *peak = encodePeakGeneralLoad(row + rowOffset, pt); slAddTail(&peakList, peak); } if (invert) { if (!peakList) showOnePeakOrMiss(tdb, clusterTdb, NULL, displayGroupList, pRowIx); } else { if (peakList) showOnePeakOrMiss(tdb, clusterTdb, peakList, displayGroupList, pRowIx); } sqlFreeResult(&sr); return result; } static struct slName *findMatchingSubtracks(struct trackDb *tdb) /* Find subtracks that match inputTracks tags. */ { /* Just list look up tableName in inputTrackTable and return the list. */ char *inputTrackTable = trackDbRequiredSetting(tdb, "inputTrackTable"); struct sqlConnection *conn = hAllocConn(database); char query[256]; safef(query, sizeof(query), "select tableName from %s order by source", inputTrackTable); struct slName *matchTrackList = sqlQuickList(conn, query); hFreeConn(&conn); return matchTrackList; } void doPeakClusterListItemsAssayed() /* Put up a page that shows all experiments associated with a cluster track. */ { struct trackDb *clusterTdb = tdbForTableArg(); struct slName *matchTrackList = findMatchingSubtracks(clusterTdb); struct slName *matchTrack; -char title[256]; -safef(title, sizeof(title), "List of items assayed in %s", clusterTdb->shortLabel); -cartWebStart(cart, database, title); +cartWebStart(cart, database, "List of items assayed in %s", clusterTdb->shortLabel); char *inputTracksSubgroupDisplay = trackDbRequiredSetting(clusterTdb, "inputTracksSubgroupDisplay"); struct slName *displayGroupList = stringToSlNames(inputTracksSubgroupDisplay); webPrintLinkTableStart(); printOutOfClusterTableHeader(displayGroupList); int rowIx = 0; for (matchTrack = matchTrackList; matchTrack != NULL; matchTrack = matchTrack->next) { struct trackDb *tdb = hashFindVal(trackHash, matchTrack->name); showOnePeakOrMiss(tdb, clusterTdb, NULL, displayGroupList, &rowIx); } webPrintLinkTableEnd(); cartWebEnd(); } void doPeakClusters(struct trackDb *tdb, char *item) /* Display detailed info about a cluster of peaks from other tracks. */ { int start = cartInt(cart, "o"); char *table = tdb->table; int rowOffset = hOffsetPastBin(database, seqName, table); char query[256]; struct sqlResult *sr; char **row; struct bed *cluster = NULL; struct sqlConnection *conn = hAllocConn(database); -char title[256]; -safef(title, sizeof(title), "%s item details", tdb->shortLabel); -cartWebStart(cart, database, title); +cartWebStart(cart, database, "%s item details", tdb->shortLabel); safef(query, sizeof(query), "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", table, item, seqName, start); sr = sqlGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) cluster = bedLoadN(row + rowOffset, 5); sqlFreeResult(&sr); if (cluster != NULL) { /* Get list of subgroups to display */ char *inputTracksSubgroupDisplay = trackDbRequiredSetting(tdb, "inputTracksSubgroupDisplay"); struct slName *displayGroupList = stringToSlNames(inputTracksSubgroupDisplay); /* Get list of tracks that match criteria. */ struct slName *matchTrackList = findMatchingSubtracks(tdb); struct slName *matchTrack; /* Print out some information about the cluster overall. */ printf("<B>Items in Cluster:</B> %s of %d<BR>\n", cluster->name, slCount(matchTrackList)); printf("<B>Cluster Score (out of 1000):</B> %d<BR>\n", cluster->score); printPos(cluster->chrom, cluster->chromStart, cluster->chromEnd, NULL, TRUE, NULL); /* In a new section put up list of hits. */ webNewSection("List of Items in Cluster"); webPrintLinkTableStart(); printClusterTableHeader(displayGroupList); int rowIx = 0; for (matchTrack = matchTrackList; matchTrack != NULL; matchTrack = matchTrack->next) { showMatchingTrack(matchTrack->name, cluster, conn, tdb, displayGroupList, FALSE, &rowIx); } webPrintLinkTableEnd(); } printf("<A HREF=\"%s&g=htcListItemsAssayed&table=%s\" TARGET_blank>", hgcPathAndSettings(), tdb->track); printf("List all items assayed"); printf("</A><BR>\n"); webNewSection("Track Description"); printTrackHtml(tdb); cartWebEnd(); hFreeConn(&conn); } char *findFactorId(struct slName *trackList, char *label) /* Given factor label, find factor id. */ { struct slName *track; for (track = trackList; track != NULL; track = track->next) { struct trackDb *tdb = hashMustFindVal(trackHash, track->name); char *factorId = compositeGroupId(tdb, "factor", label); if (factorId != NULL) return factorId; } errAbort("Couldn't find factor labeled %s", label); return NULL; } void doFactorSource(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start) /* Display detailed info about a cluster of peaks from other tracks. */ { int rowOffset = hOffsetPastBin(database, seqName, tdb->table); char **row; struct sqlResult *sr; char query[256]; char *motifTable = NULL; #ifdef TXCLUSTER_MOTIFS_TABLE motifTable = TXCLUSTER_MOTIFS_TABLE; #endif safef(query, sizeof(query), "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", tdb->table, item, seqName, start); sr = sqlGetResult(conn, query); row = sqlNextRow(sr); struct bed *cluster = NULL; if (row != NULL) cluster = bedLoadN(row + rowOffset, 15); sqlFreeResult(&sr); if (cluster != NULL) { struct dnaMotif *motif = NULL; struct dnaSeq **seqs = NULL; struct bed6FloatScore *hits = NULL; if(motifTable != NULL && sqlTableExists(conn, motifTable)) { struct sqlResult *sr; int rowOffset; char where[256]; motif = loadDnaMotif(item, "transRegCodeMotif"); safef(where, sizeof(where), "name = '%s'", item); sr = hRangeQuery(conn, "wgEncodeRegTfbsClusteredMotifs", cluster->chrom, cluster->chromStart, cluster->chromEnd, where, &rowOffset); while ((row = sqlNextRow(sr)) != NULL) { struct bed6FloatScore *hit = NULL; AllocVar(hit); hit->chromStart = sqlUnsigned(row[rowOffset + 1]); hit->chromEnd = sqlUnsigned(row[rowOffset + 2]); hit->score = sqlFloat(row[rowOffset + 4]); hit->strand[0] = row[rowOffset + 5][0]; slAddHead(&hits, hit); } sqlFreeResult(&sr); } printf("<B>Factor:</B> %s<BR>\n", cluster->name); printf("<B>Cluster Score (out of 1000):</B> %d<BR>\n", cluster->score); if(motif != NULL && hits != NULL) { struct bed6FloatScore *hit = NULL; int i; seqs = needMem(sizeof(struct dnaSeq *) * slCount(hits)); for (hit = hits, i = 0; hit != NULL; hit = hit->next, i++) { char query[256]; float maxScore = -1; safef(query, sizeof(query), "select max(score) from %s where name = '%s'", "wgEncodeRegTfbsClusteredMotifs", item); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { if(!isEmpty(row[0])) { maxScore = sqlFloat(row[0]); } } sqlFreeResult(&sr); struct dnaSeq *seq = hDnaFromSeq(database, seqName, hit->chromStart, hit->chromEnd, dnaLower); if(hit->strand[0] == '-') reverseComplement(seq->dna, seq->size); seqs[i] = seq; printf("<B>Motif Score #%d:</B> %.2f (max: %.2f)<BR>\n", i + 1, hit->score, maxScore); } } printPos(cluster->chrom, cluster->chromStart, cluster->chromEnd, NULL, TRUE, NULL); if(seqs != NULL) { motifMultipleHitsSection(seqs, slCount(hits), motif); } /* Get list of tracks we'll look through for input. */ char *inputTrackTable = trackDbRequiredSetting(tdb, "inputTrackTable"); safef(query, sizeof(query), "select tableName from %s where factor='%s' order by source", inputTrackTable, cluster->name); struct slName *matchTrackList = sqlQuickList(conn, query); struct slName *matchTrack; /* Get list of subgroups to display */ char *inputTracksSubgroupDisplay = trackDbRequiredSetting(tdb, "inputTracksSubgroupDisplay"); struct slName *displayGroupList = stringToSlNames(inputTracksSubgroupDisplay); /* In a new section put up list of hits. */ webNewSection("List of %s Items in Cluster", cluster->name); webPrintLinkTableStart(); printClusterTableHeader(displayGroupList); int rowIx = 0; for (matchTrack = matchTrackList; matchTrack != NULL; matchTrack = matchTrack->next) { showMatchingTrack(matchTrack->name, cluster, conn, tdb, displayGroupList, FALSE, &rowIx); } webPrintLinkTableEnd(); webNewSection("List of cells assayed with %s but without hits in cluster", cluster->name); webPrintLinkTableStart(); printOutOfClusterTableHeader(displayGroupList); rowIx = 0; for (matchTrack = matchTrackList; matchTrack != NULL; matchTrack = matchTrack->next) { showMatchingTrack(matchTrack->name, cluster, conn, tdb, displayGroupList, TRUE, &rowIx); } webPrintLinkTableEnd(); webNewSection("Table of abbreviations for cells"); char *sourceTable = trackDbRequiredSetting(tdb, "sourceTable"); hPrintAbbreviationTable(conn, sourceTable, "Cell Type"); webNewSection("Track Description"); } }