void maskFeatures(char *database, struct sqlConnection *conn, char *chrom, int chromSize, Bits *maskBits)
/* Mask out bits we're not interested in for conservation. */
{
fbOrTableBits(database, maskBits, "gap", chrom, chromSize, conn);
fbOrTableBits(database, maskBits, "refGene:exon:12", chrom, chromSize, conn);
fbOrTableBits(database, maskBits, "mrna:exon:12", chrom, chromSize, conn);
fbOrTableBits(database, maskBits, "ensGene:exon:12", chrom, chromSize, conn);
fbOrTableBits(database, maskBits, "softberryGene:exon:12", chrom, chromSize, conn);
fbOrTableBits(database, maskBits, "twinscan:exon:12", chrom, chromSize, conn);
fbOrTableBits(database, maskBits, "xenoMrna:exon:12", chrom, chromSize, conn);
fbOrTableBits(database, maskBits, "intronEst:exon:12", chrom, chromSize, conn);
fbOrTableBits(database, maskBits, "anyMrnaCov", chrom, chromSize, conn);
fbOrTableBits(database, maskBits, "rmsk", chrom, chromSize, conn);
printf("%s: %d bits masked\n", chrom, bitCountRange(maskBits, 0, chromSize));
}
void explainSome(char *database, Bits *h**o, Bits *once, Bits *bits, char *chrom, int chromSize,
struct sqlConnection *conn, char *trackSpec, char *homologyTrack)
/* Explain some of homology. */
{
int trackSize = 0, homoSize = 0, andSize = 0, cumSize = 0, newSize = 0;
homoSize = bitCountRange(h**o, 0, chromSize);
bitClear(bits, chromSize);
if (trackSpec != NULL)
{
fbOrTableBits(database, bits, trackSpec, chrom, chromSize, conn);
trackSize = bitCountRange(bits, 0, chromSize);
bitAnd(bits, h**o, chromSize);
andSize = bitCountRange(bits, 0, chromSize);
bitAnd(bits, once, chromSize);
newSize = bitCountRange(bits, 0, chromSize);
bitNot(bits, chromSize);
bitAnd(once, bits, chromSize);
cumSize = homoSize - bitCountRange(once, 0, chromSize);
}
else
{
trackSpec = homologyTrack;
trackSize = andSize = homoSize;
cumSize = newSize = 0;
}
printf("%-21s %8d %8d %5.2f%% %6.2f%% %6.2f%% %5.2f%% %5.2f%%\n",
trackSpec, trackSize, andSize,
100.0*trackSize/chromSize,
100.0*andSize/trackSize,
100.0*andSize/homoSize,
100.0*newSize/homoSize,
100.0*cumSize/homoSize);
}
void whyConserved(char *database, char *chrom, char *homologyTrack)
/* whyConserved - Try and analyse why a particular thing is conserved. */
{
struct sqlConnection *conn;
int chromSize;
Bits *h**o = NULL;
Bits *bits = NULL;
Bits *once = NULL;
hSetDb(database);
conn = hAllocConn();
chromSize = hChromSize(chrom);
h**o = bitAlloc(chromSize);
bits = bitAlloc(chromSize);
once = bitAlloc(chromSize);
/* Get homology bitmap and set once mask to be the same. */
fbOrTableBits(h**o, homologyTrack, chrom, chromSize, conn);
bitOr(once, h**o, chromSize);
/* printHeader */
printf("%-21s %8s %8s %5s %6s %6s %5s %5s \n",
"Track Specification", "track", "overlap",
"track", "mus", "track", "new", "cum");
printf("%-21s %8s %8s %5s %6s %6s %5s %5s \n",
"", "size", "size",
"geno", "track", "mus", "mus", "mus");
printf("-----------------------------------------------------------------------------\n");
/* Whittle awway at homology... */
explainSome(h**o, once, bits, chrom, chromSize, conn, NULL, homologyTrack);
explainSome(h**o, once, bits, chrom, chromSize, conn, "simpleRepeat", NULL);
explainSome(h**o, once, bits, chrom, chromSize, conn, "rmsk", NULL);
explainSome(h**o, once, bits, chrom, chromSize, conn, "sanger22:CDS:10", NULL);
explainSome(h**o, once, bits, chrom, chromSize, conn, "refGene:CDS:10", NULL);
explainSome(h**o, once, bits, chrom, chromSize, conn, "sanger22:exon:10", NULL);
explainSome(h**o, once, bits, chrom, chromSize, conn, "refGene:exon:10", NULL);
explainSome(h**o, once, bits, chrom, chromSize, conn, "ensGene:exon:10", NULL);
explainSome(h**o, once, bits, chrom, chromSize, conn, "rnaGene", NULL);
explainSome(h**o, once, bits, chrom, chromSize, conn, "mrna:exon:10", NULL);
explainSome(h**o, once, bits, chrom, chromSize, conn, "intronEst:exon:10", NULL);
explainSome(h**o, once, bits, chrom, chromSize, conn, "xenoMrna:exon:10", NULL);
explainSome(h**o, once, bits, chrom, chromSize, conn, "xenoEst:exon:10", NULL);
explainSome(h**o, once, bits, chrom, chromSize, conn, "genscan:exon:10", NULL);
explainSome(h**o, once, bits, chrom, chromSize, conn, "genscanSubopt", NULL);
explainSome(h**o, once, bits, chrom, chromSize, conn, "psu:exon:10", NULL);
explainSome(h**o, once, bits, chrom, chromSize, conn, "sanger22:upstream:200", NULL);
explainSome(h**o, once, bits, chrom, chromSize, conn, "refGene:upstream:200", NULL);
explainSome(h**o, once, bits, chrom, chromSize, conn, "mrna:upstream:200", NULL);
explainSome(h**o, once, bits, chrom, chromSize, conn, "est", NULL);
hFreeConn(&conn);
}
void statsOnSpan(char *database, struct sqlConnection *conn, struct region *r,
char *axtBestDir, struct stats *stats, FILE *f,
struct scoredWindow **pWinList)
/* Gather region info on one chromosome/region. */
{
char *chrom = r->chrom;
int chromSize = hChromSize(database, chrom);
Bits *maskBits = bitAlloc(chromSize);
Bits *aliBits = bitAlloc(chromSize);
Bits *matchBits = bitAlloc(chromSize);
Bits *geneBits = bitAlloc(chromSize);
/* Set up aliBits and matchBits for to be turned on
* where bases align, and where bases align and match.
* Zero both bitmaps in areas that are transcribed. */
setAliBits(axtBestDir, chrom, chromSize, aliBits, matchBits);
maskFeatures(database, conn, chrom, chromSize, maskBits);
bitNot(maskBits, chromSize);
bitAnd(aliBits, maskBits, chromSize);
bitAnd(matchBits, maskBits, chromSize);
/* Set up maskBits to have 0's on gaps in genome */
bitClear(maskBits, chromSize);
fbOrTableBits(database, maskBits, "gap", chrom, chromSize, conn);
bitNot(maskBits, chromSize);
/* Set up bitmap for Ensemble or mRNA. */
fbOrTableBits(database, geneBits, "ensGene", chrom, chromSize, conn);
fbOrTableBits(database, geneBits, "mrna", chrom, chromSize, conn);
/* Calculate various stats on windows. */
addToStats(stats, aliBits, matchBits, geneBits, maskBits, r, f, pWinList);
/* Cleanup */
bitFree(&geneBits);
bitFree(&maskBits);
bitFree(&aliBits);
bitFree(&matchBits);
}
void trackOverlap(char *database, char *chrom, char *homologyTrack, char *specFile)
/* trackOverlap - Correlate a track with a series of tracks specified in specFile. */
{
struct lineFile *lf = NULL;
char *line = NULL;
struct sqlConnection *conn;
int chromSize;
Bits *h**o = NULL;
Bits *bits = NULL;
Bits *once = NULL;
lf = lineFileOpen(specFile, TRUE);
conn = hAllocConn(database);
chromSize = hChromSize(database, chrom);
h**o = bitAlloc(chromSize);
bits = bitAlloc(chromSize);
once = bitAlloc(chromSize);
/* Get homology bitmap and set once mask to be the same. */
fbOrTableBits(database, h**o, homologyTrack, chrom, chromSize, conn);
bitOr(once, h**o, chromSize);
/* printHeader */
printf("%-21s %8s %8s %5s %6s %6s %5s %5s \n",
"Track Specification", "track", "overlap",
"track", "cov", "track", "new", "cum");
printf("%-21s %8s %8s %5s %6s %6s %5s %5s \n",
"", "size", "size",
"geno", "track", "cov", "cov", "cov");
printf("-----------------------------------------------------------------------------\n");
/* Whittle awway at homology... */
explainSome(database, h**o, once, bits, chrom, chromSize, conn, NULL, homologyTrack);
while(lineFileNextReal(lf, &line))
{
explainSome(database, h**o, once, bits, chrom, chromSize, conn, line, NULL);
}
lineFileClose(&lf);
hFreeConn(&conn);
}
