void pslRecalcMatch(char *inName, char *targetName, char *queryName,
char *outName)
/* pslRecalcMatch - Recalculate match,mismatch,repMatch columns in psl file.
* This can be useful if the psl went through pslMap, or if you've added
* lower-case repeat masking after the fact. */
{
struct nibTwoCache *tCache = nibTwoCacheNew(targetName);
struct dnaSeq *qSeqList = dnaLoadAll(queryName);
struct hash *qHash = dnaSeqHash(qSeqList);
struct psl *psl;
struct lineFile *lf = pslFileOpen(inName);
FILE *f = mustOpen(outName, "w");
while ((psl = pslNext(lf)) != NULL)
{
int tSize;
struct dnaSeq *tSeqPart = nibTwoCacheSeqPart(tCache,
psl->tName, psl->tStart, psl->tEnd - psl->tStart, &tSize);
struct dnaSeq *qSeq = hashMustFindVal(qHash, getQName(psl->qName));
recalcMatches(psl, tSeqPart, psl->tStart, qSeq);
pslTabOut(psl, f);
dnaSeqFree(&tSeqPart);
}
carefulClose(&f);
lineFileClose(&lf);
}
void txgAnalyze(char *inTxg, char *dnaPath, char *outFile)
/* txgAnalyze - Analyse transcription graph for alt exons, alt 3', alt 5',
* retained introns, alternative promoters, etc.. */
{
struct lineFile *lf = lineFileOpen(inTxg, TRUE);
FILE *f = mustOpen(outFile, "w");
char *row[TXGRAPH_NUM_COLS];
struct nibTwoCache *ntc = nibTwoCacheNew(dnaPath);
struct dnaSeq *chrom = NULL;
while (lineFileRow(lf, row))
{
struct txGraph *txg = txGraphLoad(row);
if (chrom == NULL || !sameString(chrom->name, txg->tName))
{
dnaSeqFree(&chrom);
chrom = nibTwoCacheSeq(ntc, txg->tName);
verbose(2, "Loaded %s into %s\n", txg->tName, chrom->name);
}
struct range *exonsWithIntrons = retainedIntrons(txg, f);
cassetteExons(txg, f);
altThreePrime(txg, exonsWithIntrons, f);
altFivePrime(txg, exonsWithIntrons, f);
altPromoter(txg, f);
strangeSplices(txg, chrom, f);
bleedsIntoIntrons(txg, f);
refSeparateButJoined(txg, f);
if (fConst != NULL)
constExons(txg, fConst);
slFreeList(&exonsWithIntrons);
txGraphFree(&txg);
}
carefulClose(&f);
}
void netToAxt(char *netName, char *chainName, char *tNibDir, char *qNibDir, char *axtName)
/* netToAxt - Convert net (and chain) to axt.. */
{
Bits *usedBits = findUsedIds(netName);
struct hash *chainHash;
struct chainNet *net;
struct lineFile *lf = lineFileOpen(netName, TRUE);
FILE *f = mustOpen(axtName, "w");
struct dnaSeq *tChrom = NULL;
struct nibTwoCache *qNtc = nibTwoCacheNew(qNibDir);
char *gapFileName = optionVal("gapOut", NULL);
FILE *gapFile = NULL;
if (gapFileName)
gapFile = mustOpen(gapFileName, "w");
lineFileSetMetaDataOutput(lf, f);
chainHash = chainReadUsedSwap(chainName, qChain, usedBits);
bitFree(&usedBits);
while ((net = chainNetRead(lf)) != NULL)
{
verbose(1, "Processing %s\n", net->name);
tChrom = nibTwoLoadOne(tNibDir, net->name);
if (tChrom->size != net->size)
errAbort("Size mismatch on %s. Net/nib out of sync or possibly nib dirs swapped?",
tChrom->name);
rConvert(net->fillList, tChrom, qNtc, qNibDir, chainHash, f, gapFile);
freeDnaSeq(&tChrom);
chainNetFree(&net);
}
nibTwoCacheFree(&qNtc);
}
void doIt(char *inName, char *tNibDirOr2bit, char *qNibDirOr2bit, char *outName)
/* chainToAxt - Convert from chain to axt file. */
{
struct lineFile *lf = lineFileOpen(inName, TRUE);
struct nibTwoCache *tSeqCache = nibTwoCacheNew(tNibDirOr2bit);
struct nibTwoCache *qSeqCache = nibTwoCacheNew(qNibDirOr2bit);
struct chain *chain = NULL;
FILE *f = mustOpen(outName, "w");
while ((chain = chainRead(lf)) != NULL)
{
if (chain->score >= minScore)
doAChain(chain, tSeqCache, qSeqCache, f);
chainFree(&chain);
}
lineFileClose(&lf);
carefulClose(&f);
}
static struct seqReader *seqReaderNew(char *seqSpec)
/* construct a new seqReader object */
{
struct seqReader *seqReader;
AllocVar(seqReader);
seqReader->spec = cloneString(seqSpec);
if (endsWith(seqSpec, ".fa") || endsWith(seqSpec, ".fa.gz") || endsWith(seqSpec, ".fa.Z") || endsWith(seqSpec, ".fa.bz2"))
seqReaderLoadFasta(seqReader);
else
seqReader->nibTwo = nibTwoCacheNew(seqSpec);
return seqReader;
}
