ceee920e8cd7b510dce7101d1338cc76287ba96e
angie
Mon Jul 30 09:38:22 2018 -0700
Just in case we someday have additional subset(s) of ncbiRefSeq such as ncbiRefSeqClinVar, instead of hardcoding Curated and Predicted, support any ncbiRefSeq* table.
diff --git src/hg/lib/annoStreamDbPslPlus.c src/hg/lib/annoStreamDbPslPlus.c
index bd73dc8..fb9e6ac 100644
--- src/hg/lib/annoStreamDbPslPlus.c
+++ src/hg/lib/annoStreamDbPslPlus.c
@@ -1,256 +1,256 @@
/* annoStreamDbPslPlus -- subclass of annoStreamer for joining PSL+CDS+seq database tables */
/* Copyright (C) 2017 The Regents of the University of California
* See README in this or parent directory for licensing information. */
#include "annoStreamDbPslPlus.h"
#include "annoStreamDb.h"
#include "hdb.h"
static char *pslPlusAutoSqlString =
"table pslPlus"
"\"transcript PSL, CDS and seq info\""
" ("
" uint match; \"Number of bases that match that aren't repeats\""
" uint misMatch; \"Number of bases that don't match\""
" uint repMatch; \"Number of bases that match but are part of repeats\""
" uint nCount; \"Number of 'N' bases\""
" uint qNumInsert; \"Number of inserts in query (transcript)\""
" int qBaseInsert; \"Number of bases inserted in query (transcript)\""
" uint tNumInsert; \"Number of inserts in target (chromosome/scaffold)\""
" int tBaseInsert; \"Number of bases inserted in target (chromosome/scaffold)\""
" char[2] strand; \"+ or - for query strand (transcript to genome orientation)\""
" string qName; \"Transcript accession\""
" uint qSize; \"Transcript sequence size\""
" uint qStart; \"Alignment start position in query (transcript)\""
" uint qEnd; \"Alignment end position in query (transcript)\""
" string tName; \"Target (chromosome/scaffold) name\""
" uint tSize; \"Target (chromosome/scaffold) size\""
" uint tStart; \"Alignment start position in target\""
" uint tEnd; \"Alignment end position in target\""
" uint blockCount; \"Number of blocks in alignment\""
" uint[blockCount] blockSizes; \"Size of each block\""
" uint[blockCount] qStarts; \"Start of each block in query.\""
" uint[blockCount] tStarts; \"Start of each block in target.\""
" string cds; \"CDS start and end in transcript (if applicable)\""
" string protAcc; \"Protein accession (if applicable)\""
" string name2; \"Gene symbolic name\""
" string path; \"Path to FASTA file containing transcript sequence\""
" uint fileOffset; \"Offset of transcript record in FASTA file\""
" uint fileSize; \"Number of bytes of transcript record in FASTA file\""
" )";
struct annoStreamDbPslPlus
{
struct annoStreamer streamer; // Parent class members & methods (external interface)
// Private members
char *gpTable; // Associated genePred (refGene, ncbiRefSeqCurated etc)
struct annoStreamer *mySource; // Internal source of PSL+CDS+seq info
struct hash *idHash; // Used to restrict PSL query result to curated/predicted
};
// select p.*, c.cds, l.protAcc, l.name, e.path, s.file_offset, s.file_size
// from (((ncbiRefSeqPsl p // NOT ANYMORE (#21770): join ncbiRefSeqCurated n on p.qName = n.name)
// left join ncbiRefSeqCds c on p.qName = c.id)
// join ncbiRefSeqLink l on p.qName = l.mrnaAcc)
// left join (seqNcbiRefSeq s left join extNcbiRefSeq e on s.extFile = e.id) on p.qName = s.acc
// where p.tName = "chr1"
// order by p.tName, p.tStart
// limit 5;
static char *ncbiRefSeqConfigJsonFormat =
"{ \"naForMissing\": false,"
" \"relatedTables\": [ { \"table\": \"ncbiRefSeqCds\","
" \"fields\": [\"cds\"] },"
" { \"table\": \"ncbiRefSeqLink\","
" \"fields\": [\"protAcc\", \"name\"] },"
" { \"table\": \"extNcbiRefSeq\","
" \"fields\": [\"path\"] },"
" { \"table\": \"seqNcbiRefSeq\","
" \"fields\": [\"file_offset\", \"file_size\"] } ] }";
//select p.*,c.name,l.protAcc,l.name,e.path,s.file_offset,s.file_size, i.version
//from refSeqAli p
// join (hgFixed.gbCdnaInfo i
// left join hgFixed.cds c on i.cds = c.id) on i.acc = p.qName
// left join (hgFixed.gbSeq s
// join hgFixed.gbExtFile e on e.id = s.gbExtFile) on s.acc = p.qName
// join hgFixed.refLink l on p.qName = l.mrnaAcc
// where p.tName = "chr1"
// order by p.tName, p.tStart
// limit 5;
static char *refSeqAliConfigJson =
"{ \"naForMissing\": false,"
" \"relatedTables\": [ { \"table\": \"hgFixed.cds\","
" \"fields\": [\"name\"] },"
" { \"table\": \"hgFixed.refLink\","
" \"fields\": [\"protAcc\", \"name\"] },"
" { \"table\": \"hgFixed.gbExtFile\","
" \"fields\": [\"path\"] },"
" { \"table\": \"hgFixed.gbSeq\","
" \"fields\": [\"file_offset\", \"file_size\"] } ] }";
struct asObject *annoStreamDbPslPlusAsObj()
/* Return an autoSql object with PSL, gene name, protein acc, CDS and sequence file info fields.
* An annoStreamDbPslPlus instance may return additional additional columns if configured, but
* these columns will always be present. */
{
return asParseText(pslPlusAutoSqlString);
}
static void asdppSetRegion(struct annoStreamer *sSelf, char *chrom, uint rStart, uint rEnd)
/* Pass setRegion down to internal source. */
{
annoStreamerSetRegion(sSelf, chrom, rStart, rEnd);
struct annoStreamDbPslPlus *self = (struct annoStreamDbPslPlus *)sSelf;
self->mySource->setRegion(self->mySource, chrom, rStart, rEnd);
}
static struct annoRow *asdppNextRow(struct annoStreamer *sSelf, char *minChrom, uint minEnd,
struct lm *lm)
/* Return next psl+ row. */
{
struct annoStreamDbPslPlus *self = (struct annoStreamDbPslPlus *)sSelf;
char **ppWords;
lmAllocArray(lm, ppWords, sSelf->numCols);
struct annoRow *ppRow;
boolean rightJoinFail = FALSE;
while ((ppRow = self->mySource->nextRow(self->mySource, minChrom, minEnd, lm)) != NULL)
{
ppWords = ppRow->data;
// If self->idHash is non-NULL, check PSL qName; skip this row if qName not found.
char *qName = ppWords[9];
if (self->idHash && ! hashLookup(self->idHash, qName))
continue;
// If there are filters, apply them, otherwise just return aRow.
if (sSelf->filters)
{
boolean fails = annoFilterRowFails(sSelf->filters, ppWords, sSelf->numCols,
&rightJoinFail);
// If this row passes the filter, or fails but is rightJoin, then we're done looking.
if (!fails || rightJoinFail)
break;
}
else
// no filtering to do, just use this row
break;
}
if (ppRow != NULL)
return annoRowFromStringArray(ppRow->chrom, ppRow->start, ppRow->end, rightJoinFail,
ppWords, sSelf->numCols, lm);
else
return NULL;
}
static void asdppClose(struct annoStreamer **pSSelf)
/* Free up state. */
{
if (pSSelf == NULL)
return;
struct annoStreamDbPslPlus *self = *(struct annoStreamDbPslPlus **)pSSelf;
freez(&self->gpTable);
self->mySource->close(&(self->mySource));
annoStreamerFree(pSSelf);
}
static struct asColumn *asColumnClone(struct asColumn *colIn)
/* Return a full clone of colIn, or NULL if colIn is NULL. */
{
if (colIn == NULL)
return NULL;
if (colIn->obType != NULL || colIn->index != NULL)
errAbort("asColumnClone: support for obType and index not implemented");
struct asColumn *colOut;
AllocVar(colOut);
colOut->name = cloneString(colIn->name);
colOut->comment = cloneString(colIn->comment);
colOut->lowType = colIn->lowType; // static struct in asParse.c
colOut->obName = cloneString(colIn->obName);
colOut->fixedSize = colIn->fixedSize;
colOut->linkedSizeName = cloneString(colIn->linkedSizeName);
colOut->linkedSize = asColumnClone(colIn->linkedSize);
colOut->isSizeLink = colIn->isSizeLink;
colOut->isList = colIn->isList;
colOut->isArray = colIn->isArray;
colOut->autoIncrement = colIn->autoIncrement;
colOut->values = slNameCloneList(colIn->values);
return colOut;
}
static void asObjAppendExtraColumns(struct asObject *asObjTarget, struct asObject *asObjSource)
/* If asObjSource has more columns than asObjTarget then clone and append those additional columns
* to asObjTarget. */
{
int tColCount = slCount(asObjTarget->columnList);
int sColCount = slCount(asObjSource->columnList);
if (tColCount < 1)
errAbort("asObjAppendExtraColumns: support for empty target columnList not implemented");
if (sColCount > tColCount)
{
struct asColumn *tCol = asObjTarget->columnList, *sCol = asObjSource->columnList;
int i;
for (i = 0; i < tColCount-1; i++)
{
tCol = tCol->next;
sCol = sCol->next;
}
while (sCol->next != NULL)
{
tCol->next = asColumnClone(sCol->next);
tCol = tCol->next;
sCol = sCol->next;
}
}
}
struct annoStreamer *annoStreamDbPslPlusNew(struct annoAssembly *aa, char *gpTable, int maxOutRows,
struct jsonElement *extraConfig)
/* Create an annoStreamer (subclass) object that streams PSL, CDS and seqFile info.
* gpTable is a genePred table that has associated PSL, CDS and sequence info
* (i.e. refGene, ncbiRefSeq, ncbiRefSeqCurated or ncbiRefSeqPredicted). */
{
char *pslTable = NULL, *configJson = NULL;
if (sameString("refGene", gpTable))
{
pslTable = "refSeqAli";
configJson = refSeqAliConfigJson;
}
else if (startsWith("ncbiRefSeq", gpTable))
{
pslTable = "ncbiRefSeqPsl";
struct dyString *dy = dyStringCreate(ncbiRefSeqConfigJsonFormat, gpTable);
configJson = dyStringCannibalize(&dy);
}
else
errAbort("annoStreamDbPslPlusNew: unrecognized table \"%s\"", gpTable);
struct annoStreamDbPslPlus *self;
AllocVar(self);
// Get internal streamer for joining PSL with other tables.
struct jsonElement *config = jsonParse(configJson);
if (extraConfig)
jsonObjectMerge(config, extraConfig);
self->mySource = annoStreamDbNew(aa->name, pslTable, aa, maxOutRows, config);
struct asObject *asObj = annoStreamDbPslPlusAsObj();
if (extraConfig)
asObjAppendExtraColumns(asObj, self->mySource->asObj);
-if (sameString("ncbiRefSeqCurated", gpTable) || sameString("ncbiRefSeqPredicted", gpTable))
+if (startsWith("ncbiRefSeq", gpTable) && differentString("ncbiRefSeq", gpTable))
{
- // Load up an ID hash to restrict PSL query results to the curated/predicted subset:
+ // Load up an ID hash to restrict PSL query results to the subset in gpTable:
struct sqlConnection *conn = hAllocConn(aa->name);
char query[1024];
sqlSafef(query, sizeof(query), "select name, 1 from %s", gpTable);
self->idHash = sqlQuickHash(conn, query);
hFreeConn(&conn);
}
// Set up external streamer interface
struct annoStreamer *streamer = &(self->streamer);
annoStreamerInit(streamer, aa, asObj, pslTable);
streamer->rowType = arWords;
self->gpTable = cloneString(gpTable);
// Override methods that need to pass through to internal source:
streamer->setRegion = asdppSetRegion;
streamer->nextRow = asdppNextRow;
streamer->close = asdppClose;
return (struct annoStreamer *)self;
}