void doFlyreg(struct trackDb *tdb, char *item)
/* flyreg.org: Drosophila DNase I Footprint db. */
{
struct dyString *query = newDyString(256);
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr = NULL;
char **row;
int start = cartInt(cart, "o");
int end = cartInt(cart, "t");
char fullTable[HDB_MAX_TABLE_STRING];
boolean hasBin = FALSE;
char *motifTable = "flyregMotif";
struct dnaMotif *motif = NULL;
boolean isVersion2 = sameString(tdb->table, "flyreg2");
genericHeader(tdb, item);
if (!hFindSplitTable(database, seqName, tdb->table, fullTable, sizeof fullTable, &hasBin))
errAbort("track %s not found", tdb->table);
sqlDyStringPrintf(query, "select * from %s where chrom = '%s' and ",
fullTable, seqName);
hAddBinToQuery(start, end, query);
sqlDyStringPrintf(query, "chromStart = %d and name = '%s'", start, item);
sr = sqlGetResult(conn, query->string);
if ((row = sqlNextRow(sr)) != NULL)
{
struct flyreg2 fr;
if (isVersion2)
flyreg2StaticLoad(row+hasBin, &fr);
else
flyregStaticLoad(row+hasBin, (struct flyreg *)(&fr));
printf("<B>Factor:</B> %s<BR>\n", fr.name);
printf("<B>Target:</B> %s<BR>\n", fr.target);
if (isVersion2)
printf("<B>Footprint ID:</B> %06d<BR>\n", fr.fpid);
printf("<B>PubMed ID:</B> <A HREF=\"");
printEntrezPubMedUidUrl(stdout, fr.pmid);
printf("\" TARGET=_BLANK>%d</A><BR>\n", fr.pmid);
bedPrintPos((struct bed *)(&fr), 3, tdb);
if (hTableExists(database, motifTable))
{
motif = loadDnaMotif(item, motifTable);
if (motif != NULL)
motifHitSection(NULL, motif);
}
}
else
errAbort("query returned no results: \"%s\"", query->string);
dyStringFree(&query);
sqlFreeResult(&sr);
hFreeConn(&conn);
if (motif != NULL)
webNewSection("%s",tdb->longLabel);
printTrackHtml(tdb);
}
static void doQuery(struct sqlConnection *conn, char *fullName,
struct lm *lm, struct hash *hash,
int start, int end, char * chainId, boolean isSplit)
/* doQuery- check the database for chain elements between
* start and end. Use the passed hash to resolve chain
* id's and place the elements into the right
* linkedFeatures structure
*/
{
struct sqlResult *sr = NULL;
char **row;
struct linkedFeatures *lf;
struct simpleFeature *sf;
struct dyString *query = newDyString(1024);
char *force = "";
if (isSplit)
force = "force index (bin)";
if (chainId == NULL)
dyStringPrintf(query,
"select chainId,tStart,tEnd,qStart from %sLink %s where ",
fullName, force);
else
dyStringPrintf(query,
"select chainId, tStart,tEnd,qStart from %sLink where chainId=%s and ",
fullName, chainId);
if (!isSplit)
dyStringPrintf(query, "tName='%s' and ", chromName);
hAddBinToQuery(start, end, query);
dyStringPrintf(query, "tStart<%u and tEnd>%u", end, start);
sr = sqlGetResult(conn, query->string);
/* Loop through making up simple features and adding them
* to the corresponding linkedFeature. */
while ((row = sqlNextRow(sr)) != NULL)
{
lf = hashFindVal(hash, row[0]);
if (lf != NULL)
{
lmAllocVar(lm, sf);
sf->start = sqlUnsigned(row[1]);
sf->end = sqlUnsigned(row[2]);
sf->qStart = sqlUnsigned(row[3]);
sf->qEnd = sf->qStart + (sf->end - sf->start);
slAddHead(&lf->components, sf);
}
}
sqlFreeResult(&sr);
dyStringFree(&query);
}
static void asdDoQuerySimple(struct annoStreamDb *self, char *minChrom, uint minEnd)
/* Return a sqlResult for a query on table items in position range.
* If doing a whole genome query. just select all rows from table. */
// NOTE: it would be possible to implement filters at this level, as in hgTables.
{
struct annoStreamer *streamer = &(self->streamer);
boolean hasWhere = FALSE;
struct dyString *query = self->makeBaselineQuery(self, &hasWhere);
if (!streamer->positionIsGenome)
{
if (minChrom && differentString(minChrom, streamer->chrom))
errAbort("annoStreamDb %s: nextRow minChrom='%s' but region chrom='%s'",
streamer->name, minChrom, streamer->chrom);
if (self->hasBin)
{
// Results will be in bin order, but we can restore chromStart order by
// accumulating initial coarse-bin items and merge-sorting them with
// subsequent finest-bin items which will be in chromStart order.
resetMergeState(self);
self->mergeBins = TRUE;
self->qLm = lmInit(0);
}
if (self->endFieldIndexName != NULL)
// Don't let mysql use a (chrom, chromEnd) index because that messes up
// sorting by chromStart.
sqlDyStringPrintf(query, " IGNORE INDEX (%s)", self->endFieldIndexName);
sqlDyStringAppend(query, hasWhere ? " and " : " where ");
sqlDyStringPrintf(query, "%s='%s'", self->chromField, streamer->chrom);
int chromSize = annoAssemblySeqSize(streamer->assembly, streamer->chrom);
if (streamer->regionStart != 0 || streamer->regionEnd != chromSize)
{
dyStringAppend(query, " and ");
if (self->hasBin)
hAddBinToQuery(streamer->regionStart, streamer->regionEnd, query);
sqlDyStringPrintf(query, "%s < %u and %s > %u", self->startField, streamer->regionEnd,
self->endField, streamer->regionStart);
}
if (self->notSorted)
sqlDyStringPrintf(query, " order by %s", self->startField);
}
else if (self->notSorted)
sqlDyStringPrintf(query, " order by %s,%s", self->chromField, self->startField);
if (self->maxOutRows > 0)
dyStringPrintf(query, " limit %d", self->maxOutRows);
struct sqlResult *sr = sqlGetResult(self->conn, query->string);
dyStringFree(&query);
self->sr = sr;
self->needQuery = FALSE;
}
static void testOneSql(int start, int end, char *expected)
{
struct dyString *sqlQuery;
sqlQuery = newDyString(1024);
hAddBinToQuery(start, end, sqlQuery);
if (NULL != expected)
if (differentString(sqlQuery->string,expected))
{
verbose(2,"#\tERROR: SQL incorrect at (%d, %d)\n",
start, end);
++failureCount;
}
verbose(3,"# (%d, %d):\nsql:\"%s\",\n", start, end, sqlQuery->string);
freeDyString(&sqlQuery);
}
static void asdDoQueryChunking(struct annoStreamDb *self, char *minChrom, uint minEnd)
/* Return a sqlResult for a query on table items in position range.
* If doing a whole genome query, just select all rows from table. */
{
struct annoStreamer *sSelf = &(self->streamer);
boolean hasWhere = FALSE;
struct dyString *query = self->makeBaselineQuery(self, &hasWhere);
if (sSelf->chrom != NULL && self->rowBuf.size > 0 && !self->doNextChunk)
{
// We're doing a region query, we already got some rows, and don't need another chunk:
resetRowBuf(&self->rowBuf);
self->eof = TRUE;
}
if (self->useMaxOutRows)
{
self->maxOutRows -= self->rowBuf.size;
if (self->maxOutRows <= 0)
self->eof = TRUE;
}
if (self->eof)
return;
int queryMaxItems = ASD_CHUNK_SIZE;
if (self->useMaxOutRows && self->maxOutRows < queryMaxItems)
queryMaxItems = self->maxOutRows;
if (self->hasBin)
{
// Results will be in bin order, but we can restore chromStart order by
// accumulating initial coarse-bin items and merge-sorting them with
// subsequent finest-bin items which will be in chromStart order.
if (self->doNextChunk && self->mergeBins && !self->gotFinestBin)
errAbort("annoStreamDb %s: can't continue merge in chunking query; "
"increase ASD_CHUNK_SIZE", sSelf->name);
self->mergeBins = TRUE;
if (self->qLm == NULL)
self->qLm = lmInit(0);
}
if (self->endFieldIndexName != NULL)
// Don't let mysql use a (chrom, chromEnd) index because that messes up
// sorting by chromStart.
sqlDyStringPrintf(query, " IGNORE INDEX (%s) ", self->endFieldIndexName);
if (sSelf->chrom != NULL)
{
uint start = sSelf->regionStart;
if (minChrom)
{
if (differentString(minChrom, sSelf->chrom))
errAbort("annoStreamDb %s: nextRow minChrom='%s' but region chrom='%s'",
sSelf->name, minChrom, sSelf->chrom);
if (start < minEnd)
start = minEnd;
}
if (self->doNextChunk && start < self->nextChunkStart)
start = self->nextChunkStart;
sqlDyStringAppend(query, hasWhere ? " and " : " where ");
sqlDyStringPrintf(query, "%s = '%s' and ", self->chromField, sSelf->chrom);
if (self->hasBin)
{
if (self->doNextChunk && self->gotFinestBin)
// It would be way more elegant to make a hAddBinTopLevelOnly but this will do:
dyStringPrintf(query, "bin > %d and ", self->minFinestBin);
hAddBinToQuery(start, sSelf->regionEnd, query);
}
if (self->doNextChunk)
sqlDyStringPrintf(query, "%s >= %u and ", self->startField, self->nextChunkStart);
sqlDyStringPrintf(query, "%s < %u and %s > %u ", self->startField, sSelf->regionEnd,
self->endField, start);
if (self->notSorted)
sqlDyStringPrintf(query, "order by %s ", self->startField);
sqlDyStringPrintf(query, "limit %d", queryMaxItems);
bufferRowsFromSqlQuery(self, query->string, queryMaxItems);
if (self->rowBuf.size == 0)
self->eof = TRUE;
}
else
{
// Genome-wide query: break it into chrom-by-chrom queries.
if (self->queryChrom == NULL)
self->queryChrom = self->chromList;
else if (!self->doNextChunk)
{
self->queryChrom = self->queryChrom->next;
resetMergeState(self);
}
if (minChrom != NULL)
{
// Skip chroms that precede minChrom
while (self->queryChrom != NULL && strcmp(self->queryChrom->name, minChrom) < 0)
{
self->queryChrom = self->queryChrom->next;
self->doNextChunk = FALSE;
resetMergeState(self);
}
if (self->hasBin)
{
self->mergeBins = TRUE;
if (self->qLm == NULL)
self->qLm = lmInit(0);
}
}
if (self->queryChrom == NULL)
self->eof = TRUE;
else
{
char *chrom = self->queryChrom->name;
int start = 0;
if (minChrom != NULL && sameString(chrom, minChrom))
start = minEnd;
if (self->doNextChunk && start < self->nextChunkStart)
start = self->nextChunkStart;
uint end = annoAssemblySeqSize(self->streamer.assembly, self->queryChrom->name);
sqlDyStringAppend(query, hasWhere ? " and " : " where ");
sqlDyStringPrintf(query, "%s = '%s' ", self->chromField, chrom);
if (start > 0 || self->doNextChunk)
{
dyStringAppend(query, "and ");
if (self->hasBin)
{
if (self->doNextChunk && self->gotFinestBin)
// It would be way more elegant to make a hAddBinTopLevelOnly but this will do:
dyStringPrintf(query, "bin > %d and ", self->minFinestBin);
hAddBinToQuery(start, end, query);
}
if (self->doNextChunk)
sqlDyStringPrintf(query, "%s >= %u and ", self->startField, self->nextChunkStart);
// region end is chromSize, so no need to constrain startField here:
sqlDyStringPrintf(query, "%s > %u ", self->endField, start);
}
if (self->notSorted)
sqlDyStringPrintf(query, "order by %s ", self->startField);
dyStringPrintf(query, "limit %d", queryMaxItems);
bufferRowsFromSqlQuery(self, query->string, queryMaxItems);
// If there happens to be no items on chrom, try again with the next chrom:
if (! self->eof && self->rowBuf.size == 0)
asdDoQueryChunking(self, minChrom, minEnd);
}
}
dyStringFree(&query);
}
