void txInfoAssemble(char *txBedFile, char *cdsEvFile, char *txCdsPredictFile, char *altSpliceFile,
char *exceptionFile, char *sizePolyAFile, char *pslFile, char *flipFile, char *outFile)
/* txInfoAssemble - Assemble information from various sources into txInfo table.. */
{
/* Build up hash of evidence keyed by transcript name. */
struct hash *cdsEvHash = hashNew(18);
struct cdsEvidence *cdsEv, *cdsEvList = cdsEvidenceLoadAll(cdsEvFile);
for (cdsEv = cdsEvList; cdsEv != NULL; cdsEv = cdsEv->next)
hashAddUnique(cdsEvHash, cdsEv->name, cdsEv);
verbose(2, "Loaded %d elements from %s\n", cdsEvHash->elCount, cdsEvFile);
/* Build up hash of bestorf structures keyed by transcript name */
struct hash *predictHash = hashNew(18);
struct cdsEvidence *predict, *predictList = cdsEvidenceLoadAll(txCdsPredictFile);
for (predict = predictList; predict != NULL; predict = predict->next)
hashAddUnique(predictHash, predict->name, predict);
verbose(2, "Loaded %d predicts from %s\n", predictHash->elCount, txCdsPredictFile);
/* Build up structure for random access of retained introns */
struct bed *altSpliceList = bedLoadNAll(altSpliceFile, 6);
verbose(2, "Loaded %d alts from %s\n", slCount(altSpliceList), altSpliceFile);
struct hash *altSpliceHash = bedsIntoHashOfKeepers(altSpliceList);
/* Read in exception info. */
struct hash *selenocysteineHash, *altStartHash;
genbankExceptionsHash(exceptionFile, &selenocysteineHash, &altStartHash);
/* Read in polyA sizes */
struct hash *sizePolyAHash = hashNameIntFile(sizePolyAFile);
verbose(2, "Loaded %d from %s\n", sizePolyAHash->elCount, sizePolyAFile);
/* Read in psls */
struct hash *pslHash = hashNew(20);
struct psl *psl, *pslList = pslLoadAll(pslFile);
for (psl = pslList; psl != NULL; psl = psl->next)
hashAdd(pslHash, psl->qName, psl);
verbose(2, "Loaded %d from %s\n", pslHash->elCount, pslFile);
/* Read in accessions that we flipped for better splice sites. */
struct hash *flipHash = hashWordsInFile(flipFile, 0);
/* Open primary gene input and output. */
struct lineFile *lf = lineFileOpen(txBedFile, TRUE);
FILE *f = mustOpen(outFile, "w");
/* Main loop - process each gene */
char *row[12];
while (lineFileRow(lf, row))
{
struct bed *bed = bedLoad12(row);
verbose(3, "Processing %s\n", bed->name);
/* Initialize info to zero */
struct txInfo info;
ZeroVar(&info);
/* Figure out name, sourceAcc, and isRefSeq from bed->name */
info.name = bed->name;
info.category = "n/a";
if (isRfam(bed->name) || stringIn("tRNA", bed->name) != NULL)
{
info.sourceAcc = cloneString(bed->name);
}
else
{
info.sourceAcc = txAccFromTempName(bed->name);
}
info.isRefSeq = startsWith("NM_", info.sourceAcc);
if (startsWith("antibody.", info.sourceAcc)
|| startsWith("CCDS", info.sourceAcc) || isRfam(info.sourceAcc)
|| stringIn("tRNA", info.sourceAcc) != NULL)
{
/* Fake up some things for antibody frag and CCDS that don't have alignments. */
info.sourceSize = bedTotalBlockSize(bed);
info.aliCoverage = 1.0;
info.aliIdRatio = 1.0;
info. genoMapCount = 1;
}
else
{
/* Loop through all psl's associated with our RNA. Figure out
* our overlap with each, and pick best one. */
struct hashEl *hel, *firstPslHel = hashLookup(pslHash, info.sourceAcc);
if (firstPslHel == NULL)
errAbort("%s is not in %s", info.sourceAcc, pslFile);
int mapCount = 0;
struct psl *psl, *bestPsl = NULL;
int coverage, bestCoverage = 0;
boolean isFlipped = (hashLookup(flipHash, info.sourceAcc) != NULL);
for (hel = firstPslHel; hel != NULL; hel = hashLookupNext(hel))
{
psl = hel->val;
mapCount += 1;
coverage = pslBedOverlap(psl, bed);
if (coverage > bestCoverage)
{
bestCoverage = coverage;
bestPsl = psl;
}
/* If we flipped it, try it on the opposite strand too. */
if (isFlipped)
{
psl->strand[0] = (psl->strand[0] == '+' ? '-' : '+');
coverage = pslBedOverlap(psl, bed);
if (coverage > bestCoverage)
{
bestCoverage = coverage;
bestPsl = psl;
}
psl->strand[0] = (psl->strand[0] == '+' ? '-' : '+');
}
}
if (bestPsl == NULL)
errAbort("%s has no overlapping alignments with %s in %s",
bed->name, info.sourceAcc, pslFile);
/* Figure out and save alignment statistics. */
int polyA = hashIntValDefault(sizePolyAHash, bed->name, 0);
info.sourceSize = bestPsl->qSize - polyA;
info.aliCoverage = (double)bestCoverage / info.sourceSize;
info.aliIdRatio = (double)(bestPsl->match + bestPsl->repMatch)/
(bestPsl->match + bestPsl->misMatch + bestPsl->repMatch);
info. genoMapCount = mapCount;
}
/* Get orf size and start/end complete from cdsEv. */
if (bed->thickStart < bed->thickEnd)
{
cdsEv = hashFindVal(cdsEvHash, bed->name);
if (cdsEv != NULL)
{
info.orfSize = cdsEv->end - cdsEv->start;
info.startComplete = cdsEv->startComplete;
info.endComplete = cdsEv->endComplete;
}
}
/* Get score from prediction. */
predict = hashFindVal(predictHash, bed->name);
if (predict != NULL)
info.cdsScore = predict->score;
/* Figure out nonsense-mediated-decay from bed itself. */
info.nonsenseMediatedDecay = isNonsenseMediatedDecayTarget(bed);
/* Figure out if retained intron from bed and alt-splice keeper hash */
info.retainedIntron = hasRetainedIntron(bed, altSpliceHash);
info.strangeSplice = countStrangeSplices(bed, altSpliceHash);
info.atacIntrons = countAtacIntrons(bed, altSpliceHash);
info.bleedIntoIntron = addIntronBleed(bed, altSpliceHash);
/* Look up selenocysteine info. */
info.selenocysteine = (hashLookup(selenocysteineHash, bed->name) != NULL);
/* Loop through bed looking for small gaps indicative of frame shift/stop */
int i, lastBlock = bed->blockCount-1;
int exonCount = 1;
for (i=0; i < lastBlock; ++i)
{
int gapStart = bed->chromStarts[i] + bed->blockSizes[i];
int gapEnd = bed->chromStarts[i+1];
int gapSize = gapEnd - gapStart;
switch (gapSize)
{
case 1:
case 2:
info.genomicFrameShift = TRUE;
break;
case 3:
info.genomicStop = TRUE;
break;
default:
exonCount += 1;
break;
}
}
info.exonCount = exonCount;
/* Write info, free bed. */
txInfoTabOut(&info, f);
bedFree(&bed);
}
/* Clean up and go home. */
carefulClose(&f);
}
void txGeneSeparateNoncoding(char *inBed, char *inInfo,
char *outCoding, char *outNearCoding, char *outNearCodingJunk,
char *outAntisense, char *outNoncoding, char *outInfo)
/* txGeneSeparateNoncoding - Separate genes into four piles - coding,
* non-coding that overlap coding, antisense to coding, and independent non-coding. */
{
/* Read in txInfo into a hash keyed by transcript name */
struct hash *infoHash = hashNew(16);
struct txInfo *info, *infoList = txInfoLoadAll(inInfo);
for (info = infoList; info != NULL; info = info->next)
hashAdd(infoHash, info->name, info);
verbose(2, "Read info on %d transcripts from %s\n", infoHash->elCount,
inInfo);
/* Read in bed, and sort so we can process it easily a
* strand of one chromosome at a time. */
struct bed *inBedList = bedLoadNAll(inBed, 12);
slSort(&inBedList, bedCmpChromStrandStart);
/* Open up output files. */
FILE *fCoding = mustOpen(outCoding, "w");
FILE *fNearCoding = mustOpen(outNearCoding, "w");
FILE *fNearCodingJunk = mustOpen(outNearCodingJunk, "w");
FILE *fNoncoding = mustOpen(outNoncoding, "w");
FILE *fAntisense = mustOpen(outAntisense, "w");
/* Go through input one chromosome strand at a time. */
struct chrom *chrom, *chromList = chromsForBeds(inBedList);
for (chrom = chromList; chrom != NULL; chrom = chrom->next)
{
verbose(2, "chrom %s\n", chrom->name);
/* Do the separation. */
struct bed *codingList, *nearCodingList, *nearCodingJunkList, *antisenseList, *noncodingList;
separateChrom(chrom, infoHash, &codingList, &nearCodingList,
&nearCodingJunkList, &antisenseList, &noncodingList);
verbose(2, "%d coding, %d near, %d anti, %d non\n",
slCount(codingList), slCount(nearCodingList), slCount(antisenseList), slCount(noncodingList));
/* Write lists to respective files. */
writeBedList(codingList, fCoding);
writeBedList(nearCodingList, fNearCoding);
writeBedList(nearCodingJunkList, fNearCodingJunk);
writeBedList(antisenseList, fAntisense);
writeBedList(noncodingList, fNoncoding);
}
carefulClose(&fCoding);
carefulClose(&fNearCoding);
carefulClose(&fNearCodingJunk);
carefulClose(&fNoncoding);
carefulClose(&fAntisense);
verbose(1, "coding %d, codingJunk %d, nearCoding %d, junk %d, antisense %d, noncoding %d\n",
codingCount, codingJunkCount, nearCodingCount, junkCount, antisenseCount, noncodingCount);
/* Write out updated info file */
FILE *f = mustOpen(outInfo, "w");
for (info = infoList; info != NULL; info = info->next)
{
txInfoTabOut(info, f);
}
carefulClose(&f);
}
