void findGenePredOverlap(struct hash *chromHash, char **row, FILE *outFh)
/* find and output overlaps with a genePred object */
{
struct genePred *gene = genePredLoad(row);
struct binKeeper *chromBins = getChromBins(chromHash, gene->chrom,
gene->strand);
struct geneLoc *geneLocList = NULL;
struct geneLoc *geneLoc;
int iExon;
/* get any with overlaping exons */
for (iExon = 0; iExon < gene->exonCount; iExon++)
{
int exonStart = gene->exonStarts[iExon];
int exonEnd = gene->exonEnds[iExon];
if (gCdsOnly)
{
exonStart = max(exonStart, gene->cdsStart);
exonEnd = min(exonEnd, gene->cdsEnd);
}
if (exonStart < exonEnd)
findOverlapingExons(&geneLocList, chromBins, exonStart, exonEnd);
}
for (geneLoc = geneLocList; geneLoc != NULL; geneLoc = geneLoc->next)
fprintf(outFh, "%s\t%s\t%s\t%d\t%d\t%s\t%d\t%d\t%d\n",
geneLoc->chrom, geneLoc->strand,
gene->name, gene->txStart, gene->txEnd,
geneLoc->name, geneLoc->start, geneLoc->end, geneLoc->numOverlap);
geneLocUnlink(&geneLocList);
genePredFree(&gene);
}
static void wrapHgGeneLink(struct sqlConnection *conn, char *name,
char *label, char *geneTable)
/* Wrap label with link to hgGene if possible. */
{
char query[256];
struct sqlResult *sr;
char **row;
int rowOffset = hOffsetPastBin(database, seqName, "sgdGene");
sqlSafef(query, sizeof(query),
"select * from %s where name = '%s'", geneTable, name);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
{
struct genePred *gp = genePredLoad(row+rowOffset);
printf("<A HREF=\"../cgi-bin/hgGene?db=%s", database);
printf("&hgg_gene=%s", gp->name);
printf("&hgg_chrom=%s", gp->chrom);
printf("&hgg_start=%d", gp->txStart);
printf("&hgg_end=%d", gp->txEnd);
printf("\">");
printf("%s", label);
printf("</A>");
}
else
printf("%s", label);
sqlFreeResult(&sr);
}
static void chkGenePredRows(struct gbSelect* select,
struct sqlConnection* conn,
char* table, boolean isRefFlat,
struct metaDataTbls* metaDataTbls,
unsigned typeFlags)
/* check rows of genePred or refFlat table */
{
unsigned iRow = 0;
char **row;
char *geneName = NULL;
int rowOff = (isRefFlat ? 1 : 0); /* columns to skip to genePred */
if (sqlFieldIndex(conn, table, "bin") >= 0)
rowOff++;
char query[512];
sqlSafef(query, sizeof(query), "SELECT * FROM %s", table);
struct sqlResult *sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
struct genePred* gene = genePredLoad(row+rowOff);
if (isRefFlat)
geneName = row[0];
chkGenePred(gene, geneName, iRow, select->release->genome->database, table,
metaDataTbls, typeFlags);
genePredFree(&gene);
iRow++;
}
sqlFreeResult(&sr);
}
void liftGenePred(char *destFile, struct hash *liftHash, int sourceCount, char *sources[])
/* Lift a genePred files. */
{
char *row[GENEPRED_NUM_COLS];
struct lineFile* lf;
FILE* dest = mustOpen(destFile, "w");
int iSrc;
for (iSrc = 0; iSrc < sourceCount; iSrc++)
{
verbose(1, "Lifting %s\n", sources[iSrc]);
lf = lineFileOpen(sources[iSrc], TRUE);
while (lineFileChopNextTab(lf, row, ArraySize(row)))
{
struct genePred* gp = genePredLoad(row);
if (liftGenePredObj(liftHash, gp, lf))
genePredTabOut(gp, dest);
genePredFree(&gp);
}
lineFileClose(&lf);
if (dots)
verbose(1, "\n");
}
carefulClose(&dest);
}
void freen(char *chrom)
/* Test something */
{
uglyTime(NULL);
struct sqlConnection *conn = sqlConnect("hg19");
uglyTime("connect");
char query[512];
sqlSafef(query, sizeof(query), "select * from knownGene where chrom='%s'", chrom);
struct sqlResult *sr = sqlGetResult(conn, query);
uglyTime("get result");
char **row;
struct rbTree *rt = rangeTreeNew();
while ((row = sqlNextRow(sr)) != NULL)
{
struct genePred *gp = genePredLoad(row);
int i;
int exonCount = gp->exonCount;
for (i=0; i<exonCount; ++i)
rangeTreeAdd(rt, gp->exonStarts[i], gp->exonEnds[i]);
}
uglyTime("Add rows");
struct range *list = rangeTreeList(rt);
uglyTime("Did list");
uglyf("%d items in chrom %s\n", slCount(list), chrom);
}
static void showMrnaFromGenePred(struct sqlConnection *conn,
char *geneId, char *geneName)
/* Get mRNA sequence for gene from gene prediction. */
{
char *table = genomeSetting("knownGene");
struct sqlResult *sr;
char **row;
char query[256];
boolean hasBin = hIsBinned(sqlGetDatabase(conn), table);
hPrintf("<TT><PRE>");
safef(query, sizeof(query),
"select * from %s where name='%s'"
" and chrom='%s' and txStart=%d and txEnd=%d",
table, geneId, curGeneChrom, curGeneStart, curGeneEnd);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
{
struct genePred *gene = genePredLoad(row+hasBin);
struct bed *bed = bedFromGenePred(gene);
struct dnaSeq *seq = hSeqForBed(sqlGetDatabase(conn), bed);
hPrintf(">%s (%s predicted mRNA)\n", geneId, geneName);
writeSeqWithBreaks(stdout, seq->dna, seq->size, 50);
dnaSeqFree(&seq);
bedFree(&bed);
genePredFree(&gene);
}
else
errAbort("Couldn't find %s at %s:%d-%d", geneId,
curGeneChrom, curGeneStart, curGeneEnd);
sqlFreeResult(&sr);
hPrintf("</TT></PRE>");
}
static struct chromAnn* chromAnnGenePredReaderRead(struct chromAnnReader *car)
/* Read the next genePred row and create a chromAnn object row read from a
* GenePred file or table. If there is no CDS, and chromAnnCds is specified,
* it will return a record with zero-length range.*/
{
struct rowReader *rr = car->data;
if (!rowReaderNext(rr))
return NULL;
rowReaderExpectAtLeast(rr, GENEPRED_NUM_COLS);
char **rawCols = (car->opts & chromAnnSaveLines) ? rowReaderCloneColumns(rr) : NULL;
struct genePred *gp = genePredLoad(rr->row);
struct chromAnn* ca = chromAnnNew(gp->chrom, gp->strand[0], gp->name, rawCols,
strVectorWrite, strVectorFree);
if (car->opts & chromAnnRange)
{
if (car->opts & chromAnnCds)
{
if (gp->cdsStart < gp->cdsEnd)
chromAnnBlkNew(ca, gp->cdsStart, gp->cdsEnd);
}
else
chromAnnBlkNew(ca, gp->txStart, gp->txEnd);
}
else
addGenePredBlocks(ca, car->opts, gp);
chromAnnFinish(ca);
genePredFree(&gp);
return ca;
}
void readGenes(char *fileName,
struct hash **retHash, struct chromGenes **retList)
/* Read genes into a hash of chromGenes. */
{
struct lineFile *lf = lineFileOpen(fileName, TRUE);
struct hash *hash = newHash(8);
struct chromGenes *chrom, *chromList = NULL;
struct genePred *gp;
char *row[10];
int count = 0;
while (lineFileRow(lf, row))
{
gp = genePredLoad(row);
if ((chrom = hashFindVal(hash, gp->chrom)) == NULL)
{
AllocVar(chrom);
hashAddSaveName(hash, gp->chrom, chrom, &chrom->name);
slAddHead(&chromList, chrom);
}
slAddHead(&chrom->geneList, gp);
++count;
}
printf("Read %d genes in %d chromosomes in %s\n", count,
slCount(chromList), fileName);
lineFileClose(&lf);
slSort(&chromList, chromGenesCmpName);
*retHash = hash;
*retList = chromList;
}
void printBands(char *database, struct refLink *rl, FILE *f)
/* Print name of genes and bands it occurs on. */
{
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char **row;
struct genePred *gp;
char query[512];
int count = 0;
struct dyString *bands = newDyString(0);
char band[64];
sprintf(query, "select * from refGene where name = '%s'", rl->mrnaAcc);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
++count;
gp = genePredLoad(row);
if (hChromBand(database, gp->chrom, (gp->txStart + gp->txEnd)/2, band))
dyStringPrintf(bands, "%s,", band);
else
dyStringPrintf(bands, "n/a,");
}
if (count > 0)
fprintf(f, "%s\t%s\t%d\t%s\n", rl->name, rl->mrnaAcc, count, bands->string);
dyStringFree(&bands);
sqlFreeResult(&sr);
hFreeConn(&conn);
}
static struct genePred *getCurGenePred(struct sqlConnection *conn)
/* Return current gene in genePred. */
{
char *track = genomeSetting("knownGene");
char table[HDB_MAX_TABLE_STRING];
boolean hasBin;
char query[256];
struct sqlResult *sr;
char **row;
struct genePred *gp = NULL;
if (!hFindSplitTable(sqlGetDatabase(conn), curGeneChrom, track, table, sizeof table, &hasBin))
errAbort("track %s not found", track);
bool hasAttrId = sqlColumnExists(conn, table, "alignId");
sqlSafef(query, sizeof(query),
"select * from %s where name = '%s' "
"and chrom = '%s' and txStart=%d and txEnd=%d"
, table, curGeneId, curGeneChrom, curGeneStart, curGeneEnd);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
{
gp = genePredLoad(row + hasBin);
#define ALIGNIDFIELD 11 // Gencode Id
if (hasAttrId)
curAlignId = cloneString(row[ALIGNIDFIELD]);
else
curAlignId = gp->name;
}
sqlFreeResult(&sr);
if (gp == NULL)
errAbort("getCurGenePred: Can't find %s", query);
return gp;
}
struct psl *getParentAligns(struct sqlConnection *conn, struct mappingInfo *mi, char **table)
{
struct ucscRetroInfo *pg = mi->pg;
struct psl *pslList = NULL;
char query[512];
if (startsWith("August",mi->geneSet))
{
if (hTableExists(database, "augustusXAli"))
{
*table = cloneString( "augustusXAli");
pslList = loadPslRangeT(*table, mi->seqId, pg->gChrom, pg->gStart, pg->gEnd);
}
else if (hTableExists(database, "augustusX"))
{
struct sqlResult *sr;
char **row;
int targetSize = 0;
*table = cloneString( "augustusX");
sqlSafef(query, sizeof(query), "select * from augustusX where chrom = '%s' and txEnd > %d and txStart < %d and name like '%s%%'",
pg->gChrom, pg->gStart, pg->gEnd , mi->seqId );
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
{
struct genePred *gp = genePredLoad(row+1);
sqlSafef(query, sizeof(query),
"select size from chromInfo where chrom = '%s' " , gp->chrom);
sqlFreeResult(&sr);
targetSize = sqlNeedQuickNum(conn, query) ;
pslList = pslFromGenePred(gp, targetSize);
}
}
}
else if (hTableExists(database, "all_mrna"))
{
char parent[255];
char *dotPtr ;
*table = cloneString( "all_mrna");
safef(parent, sizeof(parent), "%s",pg->name);
/* strip off version and unique suffix when looking for parent gene*/
dotPtr = rStringIn(".",parent) ;
if (dotPtr != NULL)
*dotPtr = '\0';
pslList = loadPslRangeT(*table, mi->gbAcc, pg->gChrom, pg->gStart, pg->gEnd);
if (pslList == NULL)
{
*table = cloneString( "refSeqAli");
pslList = loadPslRangeT(*table, mi->gbAcc, pg->gChrom, pg->gStart, pg->gEnd);
}
}
else
printf("no all_mrna table found<br>\n");
return pslList;
}
struct genePred *readGenes(char *chrom)
/* Slurp in the genes for one chrom */
{
struct genePred *list=NULL, *el;
char query[512];
struct sqlConnection *conn = hAllocConn();
struct sqlResult *sr;
char **row;
sqlSafef(query, sizeof(query), "select * from %s where chrom='%s' ", geneTable, chrom);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
el = genePredLoad(row);
slAddHead(&list,el);
}
sqlFreeResult(&sr);
hFreeConn(&conn);
slReverse(&list); /* could possibly skip if it made much difference in speed. */
return list;
}
struct genePred *loadGeneFromTable(struct sqlConnection *conn, char *table,
char *chrom, int chromStart, int chromEnd)
/** Load all of the genes between chromstart and chromEnd */
{
struct sqlResult *sr = NULL;
char **row = NULL;
int rowOffset = -100;
struct genePred *geneList = NULL;
struct genePred *gene = NULL;
int i=0;
sr = hRangeQuery(conn, table, chrom, chromStart, chromEnd, NULL, &rowOffset);
while ((row = sqlNextRow(sr)) != NULL)
{
gene = genePredLoad(row+rowOffset);
slSafeAddHead(&geneList, gene);
}
sqlFreeResult(&sr);
slReverse(&geneList);
return geneList;
}
static void capAliTextOnTrack(struct mafAli *maf,
char *db, char *chrom,
char *track, boolean onlyCds)
/* Capitalize exons in alignment. */
{
int rowOffset;
struct sqlConnection *conn = sqlConnect(db);
struct mafComp *selfMc = maf->components, *mc;
int start = selfMc->start;
int end = start + selfMc->size;
struct sqlResult *sr = hRangeQuery(conn, track, chrom, start, end,
NULL, &rowOffset);
char **row;
while ((row = sqlNextRow(sr)) != NULL)
{
struct genePred *gp = genePredLoad(row+rowOffset);
int i;
for (i=0; i<gp->exonCount; ++i)
{
int s = gp->exonStarts[i];
int e = gp->exonEnds[i];
if (onlyCds)
{
if (s < gp->cdsStart) s = gp->cdsStart;
if (e > gp->cdsEnd) e = gp->cdsEnd;
}
if (s < start) s = start;
if (e > end) e = end;
if (findAliRange(selfMc->text, maf->textSize, s-start, e-start, &s, &e))
{
for (mc = maf->components; mc != NULL; mc = mc->next)
if (mc->text)
toUpperN(mc->text + s, e-s);
}
}
genePredFree(&gp);
}
sqlFreeResult(&sr);
sqlDisconnect(&conn);
}
void geneStarts(char *chromosome, int start, int end)
/* geneStarts - print start of genes in database. */
{
struct sqlConnection *conn = sqlConnect("hg3");
struct sqlResult *sr;
char **row;
char query[256];
struct genePred *gp;
sprintf(query,
"select * from genieKnown where chrom = '%s' and txStart >= %d and txStart < %d",
chromosome, start, end);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
gp = genePredLoad(row);
printf("%s on %s:%d-%d\n", gp->name, gp->chrom, gp->txStart, gp->txEnd);
}
sqlFreeResult(&sr);
sqlDisconnect(&conn);
}
struct genePred *loadGenePred(char *database, char *chrom, char *track, struct binKeeper *bk)
/* Load in a gene prediction track to bk. */
{
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char **row;
int rowOffset;
struct genePred *list = NULL, *el;
sr = hChromQuery(conn, track, chrom, NULL, &rowOffset);
while ((row = sqlNextRow(sr)) != NULL)
{
el = genePredLoad(row + rowOffset);
binKeeperAdd(bk, el->txStart, el->txEnd, el);
slAddHead(&list, el);
}
sqlFreeResult(&sr);
hFreeConn(&conn);
slReverse(&list);
return list;
}
void txCdsGoodBed(char *database, char *outBed, char *outCds)
/* txCdsGoodBed - Create positive example training set for SVM. This is based on
* the refSeq reviewed genes, but we fragment a certain percentage of them so as
* not to end up with a SVM that *requires* a complete transcript. */
{
struct sqlConnection *conn = sqlConnect(database);
char *refTrack = "refGene";
char *statusTable = "refSeqStatus";
if (!sqlTableExists(conn, refTrack))
errAbort("table %s doesn't exist in %s", refTrack, database);
if (!sqlTableExists(conn, statusTable))
errAbort("table %s doesn't exist in %s", statusTable, database);
FILE *fBed = mustOpen(outBed, "w");
FILE *fCds = mustOpen(outCds, "w");
char *query =
"NOSQLINJ select name,chrom,strand,txStart,txEnd,cdsStart,cdsEnd,exonCount,exonStarts,exonEnds "
"from refGene r,refSeqStatus s where r.name=s.mrnaAcc and s.status='Reviewed'";
struct sqlResult *sr = sqlGetResult(conn, query);
char **row;
double randScale = 1.0/RAND_MAX;
int id = 0;
while ((row = sqlNextRow(sr)) != NULL)
{
struct genePred *gp = genePredLoad(row);
int start = gp->txStart, end = gp->txEnd;
char *type = "refReviewed";
if (rand()*randScale < frag)
{
double midRatio = rand()*randScale;
if (midRatio > 0.5)
gpFragLimits(gp, 0, midRatio, &start, &end);
else
gpFragLimits(gp, midRatio, 1.0, &start, &end);
type = "refFrag";
}
gpPartOutAsBed(gp, start, end, fBed, type, ++id, 0);
gpPartOutAsCds(gp, start, end, fCds, type, id);
}
carefulClose(&fBed);
}
void addGenePred(struct hash *chromHash, char **row)
/* add a genePred's exons to the approriate binkeeper object in hash */
{
struct genePred *gene = genePredLoad(row);
int iExon;
struct binKeeper *chromBins = getChromBins(chromHash, gene->chrom,
gene->strand);
struct geneLoc *geneLoc = geneLocNew(chromHash->lm, gene->name, gene->chrom,
gene->strand, gene->txStart, gene->txEnd);
for (iExon = 0; iExon < gene->exonCount; iExon++)
{
int exonStart = gene->exonStarts[iExon];
int exonEnd = gene->exonEnds[iExon];
if (gCdsOnly)
{
exonStart = max(exonStart, gene->cdsStart);
exonEnd = min(exonEnd, gene->cdsEnd);
}
if (exonStart < exonEnd)
binKeeperAdd(chromBins, exonStart, exonEnd, geneLoc);
}
genePredFree(&gene);
}
struct genePred *getCurGenePred(struct sqlConnection *conn)
/* Return current gene in genePred. */
{
char *track = genomeSetting("knownGene");
char table[64];
boolean hasBin;
char query[256];
struct sqlResult *sr;
char **row;
struct genePred *gp = NULL;
hFindSplitTable(sqlGetDatabase(conn), curGeneChrom, track, table, &hasBin);
sqlSafef(query, sizeof(query),
"select * from %s where name = '%s' "
"and chrom = '%s' and txStart=%d and txEnd=%d"
, table, curGeneId, curGeneChrom, curGeneStart, curGeneEnd);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
gp = genePredLoad(row + hasBin);
sqlFreeResult(&sr);
if (gp == NULL)
errAbort("getCurGenePred: Can't find %s", query);
return gp;
}
void intronSizes(char *database, char *table)
/* intronSizes - Output list of intron sizes.. */
{
struct dyString *query = newDyString(1024);
struct sqlConnection *conn;
struct sqlResult *sr;
char **row;
struct genePred *gp;
int rowOffset;
struct bed *bedList = NULL, *bed = NULL;
hSetDb(database);
rowOffset = hOffsetPastBin(NULL, table);
conn = hAllocConn(database);
sqlDyStringPrintf(query, "select * from %s", table);
if (chromName != NULL)
dyStringPrintf(query, " where chrom = '%s'", chromName);
if (cgiBoolean("withUtr"))
{
dyStringPrintf(query, " %s txStart != cdsStart",
(chromName == NULL ? "where" : "and"));
}
sr = sqlGetResult(conn, query->string);
while ((row = sqlNextRow(sr)) != NULL)
{
gp = genePredLoad(row+rowOffset);
genePredIntrons(gp, &bedList);
slReverse(&bedList);
for (bed = bedList ; bed != NULL ; bed=bed->next)
bedTabOutN(bed,6, stdout);
bedFreeList(&bedList);
genePredFree(&gp);
}
sqlFreeResult(&sr);
hFreeConn(&conn);
}
void txCdsBadBed(char *database,
char *altSpliceBed, char *outBed)
/* txCdsBadBed - Create a bed file with regions that don't really have CDS,
* but that might look like it.. */
{
/* Open up database and make sure all the tables we want are there. */
char *refTrack = "refGene";
char *vegaPseudo = "vegaPseudoGene";
char *retroPseudo = "retroMrnaInfo";
struct sqlConnection *conn = sqlConnect(database);
if (!sqlTableExists(conn, refTrack))
errAbort("table %s doesn't exist in %s", refTrack, database);
if (!sqlTableExists(conn, vegaPseudo))
errAbort("table %s doesn't exist in %s", vegaPseudo, database);
if (!sqlTableExists(conn, retroPseudo))
errAbort("table %s doesn't exist in %s", retroPseudo, database);
/* Read in alt file and output larger retained and bleeding introns. */
struct bed *bed, *intronyList = loadRetainedAndBleeding(altSpliceBed);
FILE *f = mustOpen(outBed, "w");
for (bed = intronyList; bed != NULL; bed = bed->next)
{
int size = bed->chromEnd - bed->chromStart;
if (size > 400)
{
fprintf(f, "%s\t%d\t%d\t", bed->chrom, bed->chromStart, bed->chromEnd);
fprintf(f, "%s%d\t", bed->name, ++id);
fprintf(f, "%d\t%s\t", bed->score, bed->strand);
fprintf(f, "0\t0\t0\t1\t");
fprintf(f, "%d,\t%d,\n", bed->chromEnd - bed->chromStart, 0);
}
}
/* Read in refGene, and write out larger 3' UTRs, and occassional antisense copies. */
char query[512];
safef(query, sizeof(query), "select * from %s", refTrack);
int rowOffset = 0;
if (sqlFieldIndex(conn, refTrack, "bin") == 0)
rowOffset = 1;
struct sqlResult *sr = sqlGetResult(conn, query);
char **row;
while ((row = sqlNextRow(sr)) != NULL)
{
struct genePred *gp = genePredLoad(row + rowOffset);
int start, end;
if (gp->strand[0] == '+')
{
start = gp->cdsEnd;
end = gp->txEnd;
}
else
{
start = gp->txStart;
end = gp->cdsStart;
}
if (end - start > 400)
{
gpPartOutAsBed(gp, start, end, f, "utr", ++id, 400);
}
if (rand()%20 == 0)
{
gp->strand[0] = (gp->strand[0] == '+' ? '-' : '+');
gpPartOutAsBed(gp, gp->txStart, gp->txEnd, f, "anti", ++id, 0);
}
}
sqlFreeResult(&sr);
/* Write out vega pseudo-genes. */
safef(query, sizeof(query), "select * from %s", vegaPseudo);
rowOffset = 0;
if (sqlFieldIndex(conn, vegaPseudo, "bin") == 0)
rowOffset = 1;
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
struct genePred *gp = genePredLoad(row + rowOffset);
gpPartOutAsBed(gp, gp->txStart, gp->txEnd, f, "vega", ++id, 0);
}
/* Write out retroGenes. */
safef(query, sizeof(query), "select * from %s where score > 600", retroPseudo);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
struct bed *bed = bedLoad12(row);
char name[128];
safef(name, sizeof(name), "retro_%d_%s", ++id, bed->name);
bed->name = name;
bedTabOutN(bed, 12, f);
}
carefulClose(&f);
}
void intronEnds(char *database, char *table)
/* intronEnds - Gather stats on intron ends.. */
{
struct dyString *query = newDyString(1024);
struct sqlConnection *conn;
struct sqlResult *sr;
char **row;
struct genePred *gp;
int total = 0;
int gtag = 0;
int gcag = 0;
int atac = 0;
int ctac = 0;
DNA ends[4];
int exonIx, txStart;
struct dnaSeq *seq;
int rowOffset;
char strand;
rowOffset = hOffsetPastBin(database, NULL, table);
conn = hAllocConn(database);
sqlDyStringPrintf(query, "select * from %s", table);
if (chromName != NULL)
dyStringPrintf(query, " where chrom = '%s'", chromName);
if (cgiBoolean("withUtr"))
{
dyStringPrintf(query, " %s txStart != cdsStart",
(chromName == NULL ? "where" : "and"));
}
sr = sqlGetResult(conn, query->string);
while ((row = sqlNextRow(sr)) != NULL)
{
gp = genePredLoad(row+rowOffset);
strand = gp->strand[0];
txStart = gp->txStart;
seq = hDnaFromSeq(database, gp->chrom, txStart, gp->txEnd, dnaLower);
for (exonIx=1; exonIx < gp->exonCount; ++exonIx)
{
++total;
memcpy(ends, seq->dna + gp->exonEnds[exonIx-1] - txStart, 2);
memcpy(ends+2, seq->dna + gp->exonStarts[exonIx] - txStart - 2, 2);
if (strand == '-')
reverseComplement(ends, 4);
if (ends[0] == 'g' && ends[1] == 't' && ends[2] == 'a' && ends[3] == 'g')
++gtag;
if (ends[0] == 'g' && ends[1] == 'c' && ends[2] == 'a' && ends[3] == 'g')
++gcag;
if (ends[0] == 'a' && ends[1] == 't' && ends[2] == 'a' && ends[3] == 'c')
++atac;
if (ends[0] == 'c' && ends[1] == 't' && ends[2] == 'a' && ends[3] == 'c')
++ctac;
}
freeDnaSeq(&seq);
genePredFree(&gp);
}
sqlFreeResult(&sr);
hFreeConn(&conn);
printf("gt/ag %d (%4.2f)\n", gtag, 100.0*gtag/total);
printf("gc/ag %d (%4.2f)\n", gcag, 100.0*gcag/total);
printf("at/ac %d (%4.2f)\n", atac, 100.0*atac/total);
printf("ct/ac %d (%4.2f)\n", ctac, 100.0*ctac/total);
printf("Total %d\n", total);
}
void knownToVisiGene(char *database)
/* knownToVisiGene - Create knownToVisiGene table by riffling through various other knownTo tables. */
{
char *tempDir = ".";
FILE *f = hgCreateTabFile(tempDir, outTable);
struct sqlConnection *hConn = sqlConnect(database);
struct sqlConnection *iConn = sqlConnect(visiDb);
struct sqlResult *sr;
char **row;
struct hash *geneImageHash = newHash(18);
struct hash *locusLinkImageHash = newHash(18);
struct hash *refSeqImageHash = newHash(18);
struct hash *genbankImageHash = newHash(18);
struct hash *probeImageHash = newHash(18);
struct hash *knownToLocusLinkHash = newHash(18);
struct hash *knownToRefSeqHash = newHash(18);
struct hash *knownToGeneHash = newHash(18);
struct hash *favorHugoHash = newHash(18);
struct hash *knownToProbeHash = newHash(18);
struct hash *knownToAllProbeHash = newHash(18);
struct genePred *knownList = NULL, *known;
struct hash *dupeHash = newHash(17);
probesDb = optionVal("probesDb", database);
struct sqlConnection *probesConn = sqlConnect(probesDb);
vgProbes = sqlTableExists(probesConn,"vgProbes");
vgAllProbes = sqlTableExists(probesConn,"vgAllProbes");
/* Go through and make up hashes of images keyed by various fields. */
sr = sqlGetResult(iConn,
NOSQLINJ "select image.id,imageFile.priority,gene.name,gene.locusLink,gene.refSeq,gene.genbank"
",probe.id,submissionSet.privateUser,vgPrbMap.vgPrb,gene.id"
" from image,imageFile,imageProbe,probe,gene,submissionSet,vgPrbMap"
" where image.imageFile = imageFile.id"
" and image.id = imageProbe.image"
" and imageProbe.probe = probe.id"
" and probe.gene = gene.id"
" and image.submissionSet=submissionSet.id"
" and vgPrbMap.probe = probe.id");
while ((row = sqlNextRow(sr)) != NULL)
{
int id = sqlUnsigned(row[0]);
float priority = atof(row[1]);
int privateUser = sqlSigned(row[7]);
char vgPrb_Id[256];
safef(vgPrb_Id, sizeof(vgPrb_Id), "vgPrb_%s",row[8]);
int geneId = sqlUnsigned(row[9]);
if (privateUser == 0)
{
addPrioritizedImage(probeImageHash, id, priority, geneId, vgPrb_Id);
addPrioritizedImage(geneImageHash, id, priority, geneId, row[2]);
addPrioritizedImage(locusLinkImageHash, id, priority, geneId, row[3]);
addPrioritizedImage(refSeqImageHash, id, priority, geneId, row[4]);
addPrioritizedImage(genbankImageHash, id, priority, geneId, row[5]);
}
}
verbose(2, "Made hashes of image: geneImageHash %d, locusLinkImageHash %d, refSeqImageHash %d"
", genbankImageHash %d probeImageHash %d\n",
geneImageHash->elCount, locusLinkImageHash->elCount, refSeqImageHash->elCount,
genbankImageHash->elCount, probeImageHash->elCount);
sqlFreeResult(&sr);
/* Build up list of known genes. */
sr = sqlGetResult(hConn, NOSQLINJ "select * from knownGene");
while ((row = sqlNextRow(sr)) != NULL)
{
struct genePred *known = genePredLoad(row);
if (!hashLookup(dupeHash, known->name))
{
hashAdd(dupeHash, known->name, NULL);
slAddHead(&knownList, known);
}
}
slReverse(&knownList);
sqlFreeResult(&sr);
verbose(2, "Got %d known genes\n", slCount(knownList));
/* Build up hashes from knownGene to other things. */
if (vgProbes)
bestProbeOverlap(probesConn, "vgProbes", knownList, knownToProbeHash);
if (vgAllProbes)
bestProbeOverlap(probesConn, "vgAllProbes", knownList, knownToAllProbeHash);
foldIntoHash(hConn, "knownToLocusLink", "name", "value", knownToLocusLinkHash, NULL, FALSE);
foldIntoHash(hConn, "knownToRefSeq", "name", "value", knownToRefSeqHash, NULL, FALSE);
foldIntoHash(hConn, "kgXref", "kgID", "geneSymbol", knownToGeneHash, favorHugoHash, FALSE);
foldIntoHash(hConn, "kgAlias", "kgID", "alias", knownToGeneHash, favorHugoHash, TRUE);
foldIntoHash(hConn, "kgProtAlias", "kgID", "alias", knownToGeneHash, favorHugoHash, TRUE);
verbose(2, "knownToLocusLink %d, knownToRefSeq %d, knownToGene %d knownToProbe %d knownToAllProbe %d\n",
knownToLocusLinkHash->elCount, knownToRefSeqHash->elCount, knownToGeneHash->elCount,
knownToProbeHash->elCount, knownToAllProbeHash->elCount);
/* Try and find an image for each gene. */
for (known = knownList; known != NULL; known = known->next)
{
char *name = known->name;
struct prioritizedImage *best = NULL;
{
best = bestImage(name, knownToLocusLinkHash, locusLinkImageHash);
if (!best)
best = bestImage(name, knownToRefSeqHash, refSeqImageHash);
if (!best)
{
best = hashFindVal(genbankImageHash, name);
}
if (!best)
best = bestImage(name, knownToGeneHash, geneImageHash);
if (vgProbes && !best)
best = bestImage(name, knownToProbeHash, probeImageHash);
if (vgAllProbes && !best)
best = bestImage(name, knownToAllProbeHash, probeImageHash);
}
if (best)
{
fprintf(f, "%s\t%d\t%d\n", name, best->imageId, best->geneId);
}
}
createTable(hConn, outTable);
hgLoadTabFile(hConn, tempDir, outTable, &f);
hgRemoveTabFile(tempDir, outTable);
}
int main(int argc, char *argv[])
{
long enteredMainTime = clock1000();
struct dyString *output = newDyString(10000);
setUdcCacheDir();
cgiSpoof(&argc, argv);
pushWarnHandler(htmlVaBadRequestAbort);
pushAbortHandler(htmlVaBadRequestAbort);
char *database = cgiString("db");
char *cmd = cgiString("cmd");
char *jsonp = cgiOptionalString("jsonp");
if (!hDbExists(database))
errAbort("Invalid database '%s'", database);
if (!strcmp(cmd, "defaultPos"))
{
dyStringPrintf(output, "{\"pos\": \"%s\"}", hDefaultPos(database));
}
else if (!strcmp(cmd, "metaDb"))
{
// Return list of values for given metaDb var
// e.g. http://genome.ucsc.edu/hgApi?db=hg18&cmd=metaDb&var=cell
struct sqlConnection *conn = hAllocConn(database);
boolean metaDbExists = sqlTableExists(conn, "metaDb");
if (metaDbExists)
{
char *var = cgiOptionalString("var");
if (!var)
errAbort("Missing var parameter");
boolean fileSearch = (cgiOptionalInt("fileSearch",0) == 1);
struct slPair *pairs = mdbValLabelSearch(conn, var, MDB_VAL_STD_TRUNCATION, FALSE,
!fileSearch, fileSearch);
struct slPair *pair;
dyStringPrintf(output, "[\n");
for (pair = pairs; pair != NULL; pair = pair->next)
{
if (pair != pairs)
dyStringPrintf(output, ",\n");
dyStringPrintf(output, "['%s','%s']", javaScriptLiteralEncode(mdbPairLabel(pair)),
javaScriptLiteralEncode(mdbPairVal(pair)));
}
dyStringPrintf(output, "\n]\n");
}
else
errAbort("Assembly does not support metaDb");
}
// TODO: move to lib since hgTracks and hgApi share
#define METADATA_VALUE_PREFIX "hgt_mdbVal"
else if (startsWith(METADATA_VALUE_PREFIX, cmd))
{
// Returns metaDb value control: drop down or free text, with or without help link.
// e.g. http://genome.ucsc.edu/hgApi?db=hg18&cmd=hgt_mdbVal3&var=cell
// TODO: Move guts to lib, so that hgTracks::searchTracks.c and hgApi.c can share
struct sqlConnection *conn = hAllocConn(database);
boolean metaDbExists = sqlTableExists(conn, "metaDb");
if (metaDbExists)
{
char *var = cgiOptionalString("var");
if (!var)
errAbort("Missing var parameter");
int ix = atoi(cmd+strlen(METADATA_VALUE_PREFIX)); // 1 based index
if (ix == 0) //
errAbort("Unsupported 'cmd' parameter");
enum cvSearchable searchBy = cvSearchMethod(var);
char name[128];
safef(name,sizeof name,"%s%i",METADATA_VALUE_PREFIX,ix);
if (searchBy == cvSearchBySingleSelect || searchBy == cvSearchByMultiSelect)
{
boolean fileSearch = (cgiOptionalInt("fileSearch",0) == 1);
struct slPair *pairs = mdbValLabelSearch(conn, var, MDB_VAL_STD_TRUNCATION, FALSE,
!fileSearch, fileSearch);
if (slCount(pairs) > 0)
{
char *dropDownHtml =
cgiMakeSelectDropList((searchBy == cvSearchByMultiSelect),
name, pairs, NULL, ANYLABEL, "mdbVal",
"style='min-width: 200px; font-size: .9em;' "
"onchange='findTracksMdbValChanged(this);'");
if (dropDownHtml)
{
dyStringAppend(output,dropDownHtml);
freeMem(dropDownHtml);
}
slPairFreeList(&pairs);
}
}
else if (searchBy == cvSearchByFreeText)
{
dyStringPrintf(output,"<input type='text' name='%s' value='' class='mdbVal freeText' "
"onchange='findTracksMdbValChanged(this);' style='max-width:310px; "
"width:310px; font-size:.9em;'>", name);
}
else if (searchBy == cvSearchByWildList)
{
dyStringPrintf(output,"<input type='text' name='%s' value='' class='mdbVal wildList' "
"title='enter comma separated list of values' "
"onchange='findTracksMdbValChanged(this);' style='max-width:310px; "
"width:310px; font-size:.9em;'>", name);
}
else if (searchBy == cvSearchByDateRange || searchBy == cvSearchByIntegerRange)
{
// TO BE IMPLEMENTED
}
else
errAbort("Metadata variable not searchable");
dyStringPrintf(output,"<span id='helpLink%i'> </span>",ix);
}
else
errAbort("Assembly does not support metaDb");
}
else if (!strcmp(cmd, "tableMetadata"))
{ // returns an html table with metadata for a given track
char *trackName = cgiOptionalString("track");
boolean showLonglabel = (NULL != cgiOptionalString("showLonglabel"));
boolean showShortLabel = (NULL != cgiOptionalString("showShortLabel"));
if (trackName != NULL)
{
// hTrackDbForTrackAndAncestors avoids overhead of getting whole track list!
struct trackDb *tdb = hTrackDbForTrackAndAncestors(database, trackName);
if (tdb != NULL)
{
char * html = metadataAsHtmlTable(database,tdb,showLonglabel,showShortLabel);
if (html)
{
dyStringAppend(output,html);
freeMem(html);
}
else
dyStringPrintf(output,"No metadata found for track %s.",trackName);
}
else
dyStringPrintf(output,"Track %s not found",trackName);
}
else
dyStringAppend(output,"No track variable found");
}
else if (sameString(cmd, "codonToPos") || sameString(cmd, "exonToPos"))
{
char query[256];
struct sqlResult *sr;
char **row;
struct genePred *gp;
char *name = cgiString("name");
char *table = cgiString("table");
int num = cgiInt("num");
struct sqlConnection *conn = hAllocConn(database);
sqlSafef(query, sizeof(query), "select name, chrom, strand, txStart, txEnd, cdsStart, cdsEnd, exonCount, exonStarts, exonEnds from %s where name = '%s'", table, name);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
{
gp = genePredLoad(row);
boolean found;
int start, end;
if (sameString(cmd, "codonToPos"))
found = codonToPos(gp, num, &start, &end);
else
found = exonToPos(gp, num, &start, &end);
if (found)
dyStringPrintf(output, "{\"pos\": \"%s:%d-%d\"}", gp->chrom, start + 1, end);
else
dyStringPrintf(output, "{\"error\": \"%d is an invalid %s for this gene\"}", num, sameString(cmd, "codonToPos") ? "codon" : "exon");
}
else
dyStringPrintf(output, "{\"error\": \"Couldn't find item: %s\"}", name);
sqlFreeResult(&sr);
hFreeConn(&conn);
}
else
{
warn("unknown cmd: %s",cmd);
errAbort("Unsupported 'cmd' parameter");
}
apiOut(dyStringContents(output), jsonp);
cgiExitTime("hgApi", enteredMainTime);
return 0;
}
static void displayMappingInfo(struct sqlConnection *conn, struct mappingInfo *mi)
/* display information from a transMap table */
{
struct ucscRetroInfo *pg = mi->pg;
double wt[12]; /* weights on score function*/
char query[512];
char *name;
char alignTbl[128];
char scoreSql[128];
struct psl *psl;
float coverFactor = 0;
float maxOverlap = 0;
if (mi->suffix == NULL)
{
safef(alignTbl, sizeof(alignTbl), "%s%sAli", mi->tblPre, mi->geneSet);
sqlSafef(scoreSql, sizeof(scoreSql), "select max(score) from %s%sInfo", mi->tblPre, mi->geneSet);
}
else
{
safef(alignTbl, sizeof(alignTbl), "%s%sAli%s", mi->tblPre, mi->geneSet, mi->suffix);
sqlSafef(scoreSql, sizeof(scoreSql), "select max(score) from %s%sInfo%s", mi->tblPre, mi->geneSet, mi->suffix);
}
printf("<TABLE class=\"transMap\">\n");
printf("<H3>Retrogene Statistics:</H3>\n");
printf("<THEAD>\n");
printf("<TR><TH>Feature<TH>Value </TR>\n");
printf("</THEAD><TBODY>\n");
if (sameString(pg->type, "singleExon"))
printf("<TR><TH>Type of Parent<TD>%s</tr>\n",pg->type);
else
printf("<TR><TH>Expression of Retrogene<TD>%s</TR>\n",pg->type);
printf("<TR><TH>Score <TD>%d (range from 0 - %d)</TR>\n",
pg->score,
sqlQuickNum(conn, scoreSql) );
printf("<TR><TH>Parent Gene Alignment Coverage (Bases Matching Parent) <TD>%d %% (%d bp) </TR>\n", pg->coverage, pg->matches);
printf("<TR><TH>Introns Processed Out <TD>%d out of %d (%d exons covered)\n", pg->processedIntrons, (pg->parentSpliceCount/2), pg->exonCover);
printf("<TR><TH>Possible Introns or Gaps in Retrogene<TD>%d,%d\n", pg->intronCount, pg->alignGapCount);
printf("<TR><TH>Conserved Splice Sites<TD>%d</TR>\n", pg->conservedSpliceSites);
printf("<TR><TH>Parent Splice Sites<TD>%d</TR>\n", pg->parentSpliceCount);
psl = getAlignments(conn, alignTbl, mi->pg->name);
if (psl != NULL)
{
maxOverlap = (float)pg->maxOverlap/(float)(psl->match+psl->misMatch+psl->repMatch) ;
coverFactor = ((float)(psl->qSize-psl->qEnd)/(float)psl->qSize);
}
else
{
maxOverlap = 0;
}
wt[0] = 0; wt[1] = 0.85; wt[2] = 0.2; wt[3] = 0.3; wt[4] = 0.8;
wt[5] = 1; wt[6] = 1 ; wt[7] = 0.5; wt[8] = 0.5; wt[9] = 1; wt[10] = 1;
#ifdef debug
char table[512];
struct psl *pslList = getParentAligns(conn, mi, &table);
if (psl != NULL)
{
printf("<TR><TH>Blocks in retro:gap%%/intronsSpliced <TD>\n");
printBlocks(psl, MAXBLOCKGAP, pslList);
printf("</td></TR>\n");
}
if (pslList != NULL)
{
printf("<TR><TH>Exons in parent:gap%% <TD>\n");
printBlocks(pslList, MAXBLOCKGAP, NULL);
printf("</td></TR>\n");
pslFreeList(&pslList);
}
#endif
printf("<TR><TH>Length of PolyA Tail<TD>%d As out of %d bp </TR><TR><TH>%% A's from Parent PolyA tail (Position)<TD>%5.1f %%\n",pg->polyA,pg->polyAlen, (float)pg->polyA*100/(float)pg->polyAlen);
if (pg->polyAstart < 0)
printf(" (%d bp before end of retrogene)<br>\n",-(pg->polyAstart));
else
printf(" (%d bp past end of retrogene)<br>\n",pg->polyAstart);
printf("<tr><th>mRNA Expression Evidence<td>");
if (!sameString(pg->overName, "none"))
printf("%s (overlap: %d bp)\n", pg->overName, pg->maxOverlap);
else
printf("No overlapping");
printf("<TR><TH>BESTORF Score (>50 is good)<TD>%4.0f</td></TR>\n",pg->posConf);
#ifdef score
printf("<TR><TH>score function<TD>1:xon %d %4.1f conSS %d 2: ax %4.1f 3: pA %4.1f 4: net + %4.1f max (%d, %d) 5: procIntrons %d %4.1f 6:in.cnt %d -%4.1f 7:overlap - %4.1f 8:cov %d*(qe %d- qsz %d)/%d=%4.1f 9:tRep - %4.1f 10:oldintron %d %4.1f </td></TR>\n",
pg->exonCover,
wt[1]*(log(pg->exonCover+1)/log(2))*200 ,
pg->conservedSpliceSites,
wt[2]*(((log(pg->axtScore>0?pg->axtScore:1)/log(2))*170)-1000),
wt[3]*(log(pg->polyAlen+2)*200) ,
wt[4]*overlapOrtholog*10 , pg->overlapMouse, pg->overlapDog,
pg->processedIntrons,
wt[5]*(((log(pg->processedIntrons > 0 ? pg->processedIntrons : 1))/log(2))*600) ,
pg->intronCount,
wt[6]*pow(pg->intronCount,0.5)*750 ,
wt[7]*(maxOverlap*300),
pg->coverage, pg->qEnd, pg->qSize , pg->qSize,
wt[8]*((pg->coverage/100.0)*(1.0-coverFactor)*300.0),
wt[9]*(pg->tReps*10),
pg->alignGapCount,
wt[10]*pg->alignGapCount);
printf("<TR><TH>score function<TD>%4.1f+ %4.1f+ %4.1f+ %4.1f+ %4.1f - %4.1f - %4.1f+ %4.1f - %4.1f - %4.1f</td></TR>\n",
wt[1]*(log(pg->exonCover+1)/log(2))*200 ,
wt[2]*(((log(pg->axtScore>0?pg->axtScore:1)/log(2))*170)-1000),
wt[3]*(log(pg->polyAlen+2)*200) ,
wt[4]*overlapOrtholog*10 ,
wt[5]*(((log(pg->processedIntrons > 0 ? pg->processedIntrons : 1))/log(2))*600) ,
(float)wt[6]*pow(pg->intronCount,0.5)*750 ,
(float)wt[7]*(maxOverlap*300),
wt[8]*((pg->coverage/100.0)*(1.0-coverFactor)*300.0),
wt[9]*(pg->tReps*10),
wt[10]*pg->alignGapCount);
if (pg->kaku > 0 && pg->kaku < 1000000)
printf("<TR><TH>KA/KU mutation rate in non-syn sites vs utr with repect to parent gene<TD>%4.2f</TR>\n", pg->kaku);
#endif
#ifdef xxx
sqlSafef(query, sizeof(query), "select * from refGene where chrom = '%d' and txEnd > %d and txStart %d and name = '%s'",
pg->chrom, pg->gStart, pg->gEnd , pg->overName );
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
overlappingGene = genePredLoad(row);
if (overlappingGene != NULL)
{
printf ("CDS exons %d ",genePredcountCdsExons(overlappingGene));
}
#endif
printf("</tr>\n");
if ( differentString("none",pg->overName) &&
sqlFieldIndex(conn, "refGene", "exonFrames") != -1)
{
sqlSafef(query, sizeof(query),
"select concat(exonFrames,'(',cdsStart,')') from refGene where name = '%s' and chrom = '%s'" ,
pg->overName, pg->chrom);
if (sqlQuickString(conn, query) != NULL)
printf("<TR><TH>Frame of retro %s (start)<TD>%s</TR>\n",
pg->overName, sqlQuickString(conn, query));
}
name = cloneString(pg->name);
chopSuffix(name);
sqlSafef(query, sizeof(query),
"select concat(exonFrames,'(',cdsStart,')') from rbRetroParent where name like '%s%%' and chrom = '%s'" ,
name, pg->chrom);
if (hTableExists(database, "rbRetroParent"))
{
if ( sqlQuickString(conn, query) != NULL)
printf("<TR><TH>Frames of mapped parent %s (start)<TD>%s</TR>\n",
name, sqlQuickString(conn, query));
}
printf("</TBODY></TABLE>\n");
}
struct annoRow *annoGratorGpVarIntegrate(struct annoGrator *gSelf,
struct annoStreamRows *primaryData,
boolean *retRJFilterFailed, struct lm *callerLm)
// integrate a variant and a genePred, generate as many rows as
// needed to capture all the changes
{
struct annoGratorGpVar *self = (struct annoGratorGpVar *)gSelf;
lmCleanup(&(self->lm));
self->lm = lmInit(0);
// Temporarily tweak primaryRow's start and end to find upstream/downstream overlap:
struct annoRow *primaryRow = primaryData->rowList;
int pStart = primaryRow->start, pEnd = primaryRow->end;
if (primaryRow->start <= GPRANGE)
primaryRow->start = 0;
else
primaryRow->start -= GPRANGE;
primaryRow->end += GPRANGE;
struct annoRow *rows = annoGratorIntegrate(gSelf, primaryData, retRJFilterFailed, self->lm);
primaryRow->start = pStart;
primaryRow->end = pEnd;
if (self->variantFromRow == NULL)
setVariantFromRow(self, primaryData);
if (self->curChromSeq == NULL || differentString(self->curChromSeq->name, primaryRow->chrom))
{
dnaSeqFree(&self->curChromSeq);
struct twoBitFile *tbf = self->grator.streamer.assembly->tbf;
self->curChromSeq = twoBitReadSeqFragLower(tbf, primaryRow->chrom, 0, 0);
}
// TODO Performance improvement: instead of creating the transcript sequence for each
// variant that intersects the transcript, cache transcript sequence; possibly
// an slPair with a concatenation of {chrom, txStart, txEnd, cdsStart, cdsEnd,
// exonStarts, exonEnds} as the name, and sequence as the val. When something in
// the list is no longer in the list of rows from the internal annoGratorIntegrate call,
// drop it.
// BETTER YET: make a callback for gpFx to get CDS sequence only when it needs it.
char *refAllele = getGenomicSequence(self->curChromSeq->dna, primaryRow->start, primaryRow->end,
self->lm);
struct variant *variant = self->variantFromRow(self, primaryRow, refAllele);
if (rows == NULL)
{
// No genePreds means that the primary variant is intergenic.
if (self->funcFilter != NULL && self->funcFilter->intergenic)
return aggvIntergenicRow(self, variant, retRJFilterFailed, callerLm);
else if (retRJFilterFailed && self->gpVarOverlapRule == agoMustOverlap)
*retRJFilterFailed = TRUE;
return NULL;
}
if (retRJFilterFailed && *retRJFilterFailed)
return NULL;
struct annoRow *outRows = NULL;
int hasFrames = (asColumnFindIx(gSelf->mySource->asObj->columnList, "exonFrames") >= 0);
for(; rows; rows = rows->next)
{
char **inWords = rows->data;
// work around genePredLoad's trashing its input
char *saveExonStarts = lmCloneString(self->lm, inWords[8]);
char *saveExonEnds = lmCloneString(self->lm, inWords[9]);
struct genePred *gp = hasFrames ? genePredExtLoad(inWords, GENEPREDX_NUM_COLS) :
genePredLoad(inWords);
inWords[8] = saveExonStarts;
inWords[9] = saveExonEnds;
struct annoRow *outRow = aggvGenRows(self, variant, gp, rows, callerLm);
if (outRow != NULL)
{
slReverse(&outRow);
outRows = slCat(outRow, outRows);
}
genePredFree(&gp);
}
slReverse(&outRows);
// If all rows failed the filter, and we must overlap, set *retRJFilterFailed.
if (outRows == NULL && retRJFilterFailed && self->gpVarOverlapRule == agoMustOverlap)
*retRJFilterFailed = TRUE;
return outRows;
}
