480c793842e2073cc7a7a231e8dec9f37ee31d74 kent Tue Apr 26 23:26:47 2011 -0700 Making it so that the DNase clusters can get their metadata from an associated table rather than rummaging through groups and trackDb, following same pattern did for factorSource tracks. It turns out the ENCODE tracks change so much, having one depend on another just is an invitation to problems. diff --git src/hg/hgc/peakClusters.c src/hg/hgc/peakClusters.c index eb1ff69..18da418 100644 --- src/hg/hgc/peakClusters.c +++ src/hg/hgc/peakClusters.c @@ -11,30 +11,31 @@ #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 "ra.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; } @@ -131,39 +132,180 @@ } if (invert) { if (!peakList) showOnePeakOrMiss(tdb, clusterTdb, NULL, displayGroupList, pRowIx); } else { if (peakList) showOnePeakOrMiss(tdb, clusterTdb, peakList, displayGroupList, pRowIx); } sqlFreeResult(&sr); return result; } -static void printClusterTableHits(struct bed *cluster, struct sqlConnection *conn, +static double getSignalAt(char *table, struct bed *cluster) +/* Get (average) signal from table entries that overlap cluster */ +{ +struct sqlConnection *conn = hAllocConn(database); +int rowOffset; +int sqlFieldColumn(struct sqlResult *sr, char *colName); +struct sqlResult *sr = hRangeQuery(conn, table, cluster->chrom, cluster->chromStart, + cluster->chromEnd, NULL, &rowOffset); +int signalCol = sqlFieldColumn(sr, "signalValue"); +if (signalCol < 0) + internalErr(); +int count = 0; +double sum = 0; +char **row; +while ((row = sqlNextRow(sr)) != NULL) + { + count += 1; + sum += sqlDouble(row[signalCol]); + } +sqlFreeResult(&sr); +hFreeConn(&conn); + +if (count > 0) + return sum/count; +else + return 0; +} + +static void printControlledVocabFields(char **row, int fieldCount, + struct slName *fieldList, char *vocabFile, struct hash *vocabHash) +/* Print out fields from row, linking them to controlled vocab if need be. */ +{ +int i; +struct slName *field; +for (i=0, field = fieldList; i<fieldCount; ++i, field = field->next) + { + char *fieldVal = row[i]; + if (vocabFile && hashLookup(vocabHash, field->name)) + { + char *link = controlledVocabLink(vocabFile, "term", + fieldVal, fieldVal, fieldVal, ""); + webPrintLinkCell(link); + } + else + webPrintLinkCell(fieldVal); + } +} + +struct hash *getVocabHash(char *fileName) +/* Get vocabulary term hash */ +{ +struct hash *hash = raTagVals(fileName, "type"); +hashAdd(hash, "cellType", NULL); /* Will the kludge never end, no, never! */ +return hash; +} + +static void printPeakClusterTableHits(struct bed *cluster, struct sqlConnection *conn, + char *inputTrackTable, struct slName *fieldList, char *vocab) +/* Put out a lines in an html table that shows assayed sources that have hits in this + * cluster, or if invert is set, that have misses. */ +{ +char *vocabFile = NULL; +struct hash *vocabHash = NULL; +if (vocab) + { + vocabFile = cloneFirstWord(vocab); + vocabHash = getVocabHash(vocabFile); + } + +/* Make the SQL query to get the table and all other fields we want to show + * from inputTrackTable. */ +struct dyString *query = dyStringNew(0); +dyStringPrintf(query, "select tableName"); +struct slName *field; +for (field = fieldList; field != NULL; field = field->next) + dyStringPrintf(query, ",%s", field->name); +dyStringPrintf(query, " from %s", inputTrackTable); + +int displayNo = 0; +int fieldCount = slCount(fieldList); +struct sqlResult *sr = sqlGetResult(conn, query->string); +char **row; +while ((row = sqlNextRow(sr)) != NULL) + { + double signal = getSignalAt(row[0], cluster); + if (signal != 0) + { + printf("</TR><TR>\n"); + webPrintIntCell(++displayNo); + webPrintDoubleCell(signal); + printControlledVocabFields(row+1, fieldCount, fieldList, vocabFile, vocabHash); + } + } +sqlFreeResult(&sr); +freez(&vocabFile); +dyStringFree(&query); +} + +static void printPeakClusterInputs(struct sqlConnection *conn, + char *inputTrackTable, struct slName *fieldList, char *vocab) +/* Print out all input tables for clustering. */ +{ +char *vocabFile = NULL; +struct hash *vocabHash = NULL; +if (vocab) + { + vocabFile = cloneFirstWord(vocab); + vocabHash = getVocabHash(vocabFile); + } + +/* Make the SQL query to get the table and all other fields we want to show + * from inputTrackTable. */ +struct dyString *query = dyStringNew(0); +dyStringPrintf(query, "select tableName"); +struct slName *field; +for (field = fieldList; field != NULL; field = field->next) + dyStringPrintf(query, ",%s", field->name); +dyStringPrintf(query, " from %s", inputTrackTable); + +int displayNo = 0; +int fieldCount = slCount(fieldList); +struct sqlResult *sr = sqlGetResult(conn, query->string); +char **row; +while ((row = sqlNextRow(sr)) != NULL) + { + printf("</TR><TR>\n"); + webPrintIntCell(++displayNo); + printControlledVocabFields(row+1, fieldCount, fieldList, vocabFile, vocabHash); + } + + +sqlFreeResult(&sr); +freez(&vocabFile); +dyStringFree(&query); +} + +static void printFactorSourceTableHits(struct bed *cluster, struct sqlConnection *conn, char *sourceTable, char *inputTrackTable, struct slName *fieldList, boolean invert, char *vocab) /* Put out a lines in an html table that shows assayed sources that have hits in this * cluster, or if invert is set, that have misses. */ { char *vocabFile = NULL; +struct hash *vocabHash = NULL; if (vocab) + { vocabFile = cloneFirstWord(vocab); + vocabHash = getVocabHash(vocabFile); + } + /* Make the monster SQL query to get all assays*/ struct dyString *query = dyStringNew(0); dyStringPrintf(query, "select %s.id,%s.name", sourceTable, sourceTable); struct slName *field; for (field = fieldList; field != NULL; field = field->next) dyStringPrintf(query, ",%s.%s", inputTrackTable, field->name); dyStringPrintf(query, " from %s,%s ", inputTrackTable, sourceTable); dyStringPrintf(query, " where %s.source = %s.description", inputTrackTable, sourceTable); dyStringPrintf(query, " and factor='%s' order by %s.source", cluster->name, inputTrackTable); int displayNo = 0; int fieldCount = slCount(fieldList); struct sqlResult *sr = sqlGetResult(conn, query->string); char **row; while ((row = sqlNextRow(sr)) != NULL) @@ -205,96 +347,138 @@ /* 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(); +cartWebStart(cart, database, "List of items assayed in %s", clusterTdb->shortLabel); +struct sqlConnection *conn = hAllocConn(database); + +char *inputTracksSubgroupDisplay = trackDbSetting(clusterTdb, "inputTracksSubgroupDisplay"); +char *inputTableFieldDisplay = trackDbSetting(clusterTdb, "inputTableFieldDisplay"); +webPrintLinkTableStart(); +if (inputTracksSubgroupDisplay) + { struct slName *matchTrackList = findMatchingSubtracks(clusterTdb); struct slName *matchTrack; -cartWebStart(cart, database, "List of items assayed in %s", clusterTdb->shortLabel); - -char *inputTracksSubgroupDisplay = trackDbRequiredSetting(clusterTdb, "inputTracksSubgroupDisplay"); struct slName *displayGroupList = stringToSlNames(inputTracksSubgroupDisplay); -webPrintLinkTableStart(); printClusterTableHeader(displayGroupList, FALSE, TRUE, FALSE); int rowIx = 0; for (matchTrack = matchTrackList; matchTrack != NULL; matchTrack = matchTrack->next) { struct trackDb *tdb = hashFindVal(trackHash, matchTrack->name); showOnePeakOrMiss(tdb, clusterTdb, NULL, displayGroupList, &rowIx); } + } +else if (inputTableFieldDisplay) + { + struct slName *fieldList = stringToSlNames(inputTableFieldDisplay); + printClusterTableHeader(fieldList, FALSE, FALSE, FALSE); + char *vocab = trackDbSetting(clusterTdb, "controlledVocabulary"); + char *inputTrackTable = trackDbRequiredSetting(clusterTdb, "inputTrackTable"); + printPeakClusterInputs(conn, inputTrackTable, fieldList, vocab); + } +else + errAbort("Missing required trackDb setting %s or %s for track %s", + "inputTracksSubgroupDisplay", "inputTableFieldDisplay", clusterTdb->track); webPrintLinkTableEnd(); +hFreeConn(&conn); 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); 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"); + char *inputTracksSubgroupDisplay = trackDbSetting(tdb, "inputTracksSubgroupDisplay"); + char *inputTableFieldDisplay = trackDbSetting(tdb, "inputTableFieldDisplay"); + if (inputTracksSubgroupDisplay != NULL) + { 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, FALSE, TRUE, TRUE); int rowIx = 0; for (matchTrack = matchTrackList; matchTrack != NULL; matchTrack = matchTrack->next) { showMatchingTrack(matchTrack->name, cluster, conn, tdb, displayGroupList, FALSE, &rowIx); } + } + else if (inputTableFieldDisplay != NULL) + { + struct slName *fieldList = stringToSlNames(inputTableFieldDisplay); + char *vocab = trackDbSetting(tdb, "controlledVocabulary"); + char *inputTrackTable = trackDbRequiredSetting(tdb, "inputTrackTable"); + + /* Print out some information about the cluster overall. */ + printf("<B>Items in Cluster:</B> %s of %d<BR>\n", cluster->name, + sqlRowCount(conn, inputTrackTable)); + 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(fieldList, FALSE, FALSE, TRUE); + printPeakClusterTableHits(cluster, conn, inputTrackTable, fieldList, vocab); + } + else + errAbort("Missing required trackDb setting %s or %s for track %s", + "inputTracksSubgroupDisplay", "inputTableFieldDisplay", tdb->track); 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. */ { @@ -446,38 +630,38 @@ { showMatchingTrack(matchTrack->name, cluster, conn, tdb, displayGroupList, TRUE, &rowIx); } webPrintLinkTableEnd(); } else if (inputTableFieldDisplay != NULL) { struct slName *fieldList = stringToSlNames(inputTableFieldDisplay); char *vocab = trackDbSetting(tdb, "controlledVocabulary"); /* In a new section put up list of hits. */ webNewSection("List of %s Items in Cluster", cluster->name); webPrintLinkTableStart(); printClusterTableHeader(fieldList, TRUE, FALSE, TRUE); - printClusterTableHits(cluster, conn, sourceTable, + printFactorSourceTableHits(cluster, conn, sourceTable, inputTrackTable, fieldList, FALSE, vocab); webPrintLinkTableEnd(); webNewSection("List of cells assayed with %s but without hits in cluster", cluster->name); webPrintLinkTableStart(); printClusterTableHeader(fieldList, TRUE, FALSE, FALSE); - printClusterTableHits(cluster, conn, sourceTable, + printFactorSourceTableHits(cluster, conn, sourceTable, inputTrackTable, fieldList, TRUE, vocab); webPrintLinkTableEnd(); } else { errAbort("Missing required trackDb setting %s or %s for track %s", "inputTracksSubgroupDisplay", "inputTableFieldDisplay", tdb->track); } webNewSection("Table of abbreviations for cells"); hPrintAbbreviationTable(conn, sourceTable, "Cell Type"); webNewSection("Track Description"); }