void readAllSts(FILE *asf)
/* Read in current sequences for sts markers */
{
struct dnaSeq *ds;
struct sts *s;
char *words[8], *acc=NULL, *line;
int wordCount;
while (faReadMixedNext(asf, 0, "default", TRUE, &line, &ds))
{
/* Determine the UCSC id */
wordCount = chopByWhite(line, words, ArraySize(words));
stripString(words[0], ">");
if (wordCount == 3)
acc = cloneString(words[2]);
else
acc = NULL;
/* Find the record and attach */
if (hashLookup(stsHash, ds->name))
{
s = hashMustFindVal(stsHash, ds->name);
s->fa = ds;
s->faAcc = acc;
s->si->sequence = 1;
}
else
{
dnaSeqFree(&ds);
freez(&line);
if (acc != NULL)
freez(&acc);
}
}
}
struct dnaSeq *readSeqFromFaPos(struct seqFilePos *sfp, FILE *f)
/* Read part of FA file. */
{
struct dnaSeq *seq;
fseek(f, sfp->pos, SEEK_SET);
if (!faReadMixedNext(f, TRUE, "", TRUE, NULL, &seq))
errAbort("Couldn't faReadNext on %s in %s\n", sfp->name, sfp->file);
return seq;
}
boolean faReadNext(FILE *f, char *defaultName, boolean mustStartWithComment,
char **retCommentLine, struct dnaSeq **retSeq)
/* Read next sequence from .fa file. Return sequence in retSeq.
* If retCommentLine is non-null
* return the '>' line in retCommentLine.
* The whole thing returns FALSE at end of file.
* DNA chars are mapped to lower case.*/
{
return faReadMixedNext(f, 0, defaultName, mustStartWithComment,
retCommentLine, retSeq);
}
void readDbstsFa(FILE *dff)
/* Read in sequences from dbSTS.fa and add, if possible */
{
struct dnaSeq *ds;
struct sts *s;
struct gb *gb;
char name[256], *line;
while (faReadMixedNext(dff, 0, "default", TRUE, &line, &ds))
{
/* Determine the UCSC id */
if (hashLookup(gbAccHash, ds->name))
{
/* Determine if this is linked to a marker */
gb = hashMustFindVal(gbAccHash, ds->name);
if (gb->s != NULL)
{
/* If no recorded sequence, then add */
s = gb->s;
if (s->fa == NULL)
{
s->faAcc = cloneString(ds->name);
safef(name, ArraySize(name), "%d", s->si->identNo);
ds->name = cloneString(name);
s->fa = ds;
s->si->sequence = 1;
}
/* If no accession recorded, see if sequences are the same */
else if (s->faAcc == NULL)
{
if (sameString(s->fa->dna, ds->dna))
{
s->faAcc = cloneString(ds->name);
s->si->sequence = 1;
}
freeDnaSeq(&ds);
}
/* If same accession as recorded, the update sequence */
else if (sameString(s->faAcc, ds->name))
{
ds->name = cloneString(s->fa->name);
freeDnaSeq(&s->fa);
s->fa = ds;
s->si->sequence = 1;
}
else
freeDnaSeq(&ds);
}
else
freeDnaSeq(&ds);
}
}
}
void axtChain(char *axtIn, char *tNibDir, char *qNibDir, char *chainOut)
/* axtChain - Chain together axt alignments.. */
{
struct hash *pairHash = newHash(0); /* Hash keyed by qSeq<strand>tSeq */
struct seqPair *spList = NULL, *sp;
FILE *f = mustOpen(chainOut, "w");
char *qName = "", *tName = "";
struct dnaSeq *qSeq = NULL, *tSeq = NULL;
char qStrand = 0, tStrand = 0;
struct chain *chainList = NULL, *chain;
FILE *details = NULL;
struct dnaSeq *seq, *seqList = NULL;
struct hash *faHash = newHash(0);
struct hash *tFaHash = newHash(0);
FILE *faF;
boolean qIsTwoBit = twoBitIsFile(qNibDir);
boolean tIsTwoBit = twoBitIsFile(tNibDir);
axtScoreSchemeDnaWrite(scoreScheme, f, "axtChain");
if (detailsName != NULL)
details = mustOpen(detailsName, "w");
/* Read input file and divide alignments into various parts. */
if (optionExists("psl"))
spList = readPslBlocks(axtIn, pairHash, f);
else
spList = readAxtBlocks(axtIn, pairHash, f);
if (optionExists("faQ"))
{
faF = mustOpen(qNibDir, "r");
while ( faReadMixedNext(faF, TRUE, NULL, TRUE, NULL, &seq))
{
hashAdd(faHash, seq->name, seq);
slAddHead(&seqList, seq);
}
fclose(faF);
}
if (optionExists("faT"))
{
faF = mustOpen(tNibDir, "r");
while ( faReadMixedNext(faF, TRUE, NULL, TRUE, NULL, &seq))
{
hashAdd(tFaHash, seq->name, seq);
slAddHead(&seqList, seq);
}
fclose(faF);
}
for (sp = spList; sp != NULL; sp = sp->next)
{
slReverse(&sp->blockList);
removeExactOverlaps(&sp->blockList);
verbose(1, "%d blocks after duplicate removal\n", slCount(sp->blockList));
if (optionExists("faQ"))
{
assert (faHash != NULL);
loadFaSeq(faHash, sp->qName, sp->qStrand, &qName, &qSeq, &qStrand);
}
else
{
loadIfNewSeq(qNibDir, qIsTwoBit, sp->qName, sp->qStrand,
&qName, &qSeq, &qStrand);
}
if (optionExists("faT"))
{
assert (tFaHash != NULL);
loadFaSeq(tFaHash, sp->tName, '+', &tName, &tSeq, &tStrand);
}
else
{
loadIfNewSeq(tNibDir, tIsTwoBit, sp->tName, '+',
&tName, &tSeq, &tStrand);
}
chainPair(sp, qSeq, tSeq, &chainList, details);
}
slSort(&chainList, chainCmpScore);
for (chain = chainList; chain != NULL; chain = chain->next)
{
assert(chain->qStart == chain->blockList->qStart
&& chain->tStart == chain->blockList->tStart);
chainWrite(chain, f);
}
carefulClose(&f);
}
void doChainScore(char *chainIn, char *tNibDir, char *qNibDir, char *chainOut)
{
char qStrand = 0, tStrand = 0;
struct dnaSeq *qSeq = NULL, *tSeq = NULL;
char *qName = "", *tName = "";
FILE *f = mustOpen(chainOut, "w");
struct chain *chainList = NULL, *chain;
struct chain *inputChains, *next;
FILE *details = NULL;
struct lineFile *lf = NULL;
struct dnaSeq *seq, *seqList = NULL;
struct hash *faHash = newHash(0);
struct hash *chainHash = newHash(0);
char comment[1024];
FILE *faF;
struct seqPair *spList = NULL, *sp;
struct dyString *dy = newDyString(512);
struct lineFile *chainsLf = lineFileOpen(chainIn, TRUE);
while ((chain = chainRead(chainsLf)) != NULL)
{
dyStringClear(dy);
dyStringPrintf(dy, "%s%c%s", chain->qName, chain->qStrand, chain->tName);
sp = hashFindVal(chainHash, dy->string);
if (sp == NULL)
{
AllocVar(sp);
slAddHead(&spList, sp);
hashAddSaveName(chainHash, dy->string, sp, &sp->name);
sp->qName = cloneString(chain->qName);
sp->tName = cloneString(chain->tName);
sp->qStrand = chain->qStrand;
}
slAddHead(&sp->chain, chain);
}
slSort(&spList, seqPairCmp);
lineFileClose(&chainsLf);
if (optionExists("faQ"))
{
faF = mustOpen(qNibDir, "r");
while ( faReadMixedNext(faF, TRUE, NULL, TRUE, NULL, &seq))
{
hashAdd(faHash, seq->name, seq);
slAddHead(&seqList, seq);
}
fclose(faF);
}
for (sp = spList; sp != NULL; sp = sp->next)
{
if (optionExists("faQ"))
{
assert (faHash != NULL);
loadFaSeq(faHash, sp->qName, sp->qStrand, &qName, &qSeq, &qStrand);
}
else
loadIfNewSeq(qNibDir, sp->qName, sp->qStrand, &qName, &qSeq, &qStrand);
loadIfNewSeq(tNibDir, sp->tName, '+', &tName, &tSeq, &tStrand);
scorePair(sp, qSeq, tSeq, &chainList, sp->chain);
}
slSort(&chainList, chainCmpScore);
for (chain = chainList; chain != NULL; chain = chain->next)
{
assert(chain->qStart == chain->blockList->qStart
&& chain->tStart == chain->blockList->tStart);
chainWrite(chain, f);
}
carefulClose(&f);
}
