void reTraceFixMaf(char *mafFileName, char *qaFileName, char *newMafFileName)
/* reTraceFixMaf - Add quality line and recompute chrom line in maf. */
{
struct mafFile *mFile = mafReadAll(mafFileName);
struct qaSeq *qaList = qaRead(qaFileName);
struct hash *qaHash = makeQaHash(qaList);
struct mafAli *ali;
for (ali = mFile->alignments; ali != NULL; ali = ali->next)
{
if (!ali->components || !ali->components->next)
errAbort("Something's up with the maf.");
else
{
struct mafComp *secondSrc = ali->components->next;
struct qaSeq *qas = hashMustFindVal(qaHash, secondSrc->src);
int i, offset;
int length = strlen(secondSrc->text);
if (secondSrc->strand == '-')
reverseBytes(qas->qa, qas->size);
offset = secondSrc->start;
AllocArray(secondSrc->quality, length+1);
for (i = 0; i < length; i++)
{
if (secondSrc->text[i] == '-')
secondSrc->quality[i] = '-';
else
{
int q = (int)qas->qa[offset++];
char c = 'F';
if ((q >= 0) && (q < 45))
{
q = q / 5;
c = '0' + q;
}
else if ((q >= 45) && (q < 98))
c = '9';
else if (q == 99)
c = '0';
else
c = 'F';
secondSrc->quality[i] = c;
}
}
secondSrc->quality[length] = '\0';
if (secondSrc->strand == '-')
reverseBytes(qas->qa, qas->size);
}
}
mafWriteAll(mFile, newMafFileName);
hashFree(&qaHash);
qaSeqFreeList(&qaList);
mafFileFree(&mFile);
}
void txCdsPredict(char *inFa, char *outCds, char *nmdBed, char *mafFile, boolean anyStart)
/* txCdsPredict - Somewhat simple-minded ORF predictor using a weighting scheme.. */
{
struct dnaSeq *rna, *rnaList = faReadAllDna(inFa);
verbose(2, "Read %d sequences from %s\n", slCount(rnaList), inFa);
/* Make up hash of bed records for NMD analysis. */
struct hash *nmdHash = hashNew(18);
if (nmdBed != NULL)
{
struct bed *bed, *bedList = bedLoadNAll(nmdBed, 12);
for (bed = bedList; bed != NULL; bed = bed->next)
hashAdd(nmdHash, bed->name, bed);
verbose(2, "Read %d beds from %s\n", nmdHash->elCount, nmdBed);
}
/* Make up hash of maf records for conservation analysis. */
struct hash *mafHash = hashNew(18);
int otherSpeciesCount = 0;
if (mafFile != NULL)
{
struct mafFile *mf = mafReadAll(mafFile);
struct mafAli *maf;
for (maf = mf->alignments; maf != NULL; maf = maf->next)
hashAdd(mafHash, maf->components->src, maf);
verbose(2, "Read %d alignments from %s\n", mafHash->elCount, mafFile);
struct hash *uniqSpeciesHash = hashNew(0);
for (maf = mf->alignments; maf != NULL; maf = maf->next)
{
struct mafComp *comp;
for (comp = maf->components->next; comp != NULL; comp = comp->next)
hashStore(uniqSpeciesHash, comp->src);
}
otherSpeciesCount = uniqSpeciesHash->elCount;
verbose(2, "%d other species in %s\n", otherSpeciesCount, mafFile);
}
FILE *f = mustOpen(outCds, "w");
for (rna = rnaList; rna != NULL; rna = rna->next)
{
verbose(3, "%s\n", rna->name);
struct cdsEvidence *orfList = orfsOnRna(rna, nmdHash, mafHash, otherSpeciesCount, anyStart);
if (orfList != NULL)
{
slSort(&orfList, cdsEvidenceCmpScore);
cdsEvidenceTabOut(orfList, f);
}
cdsEvidenceFreeList(&orfList);
}
carefulClose(&f);
}
void mafToSnpBed(char *database, char *mafIn, char *gpIn, char *bedOut)
/* mafToSnpBed - finds SNPs in MAF and builds a bed with their functional consequence. */
{
struct mafFile *mafFile = mafReadAll(mafIn);
struct genePred *genePred = genePredLoadAll(gpIn);
FILE *f = mustOpen(bedOut, "w");
struct genePred *gp, *next;
for(gp = genePred; gp; gp = next)
{
next = gp->next;
gp->next = NULL;
parseOneGp(database, mafFile->alignments, gp, f);
}
}
