void snpMaskGenes(char *nibFile, char *outFile)
/* snpMaskGenes - Print gene sequence, exons only,
using IUPAC codes for single base substitutions. */
{
struct genePred *genes = NULL;
struct genePred *gene = NULL;
struct dnaSeq *seq;
char *ptr;
struct snpSimple *snps = NULL;
struct snpSimple *snp = NULL;
int snpPos = 0;
int size = 0;
FILE *fileHandle = mustOpen(outFile, "w");
genes = readGenes(chromName);
for (gene = genes; gene != NULL; gene = gene->next)
{
verbose(4, "gene = %s\n", gene->name);
snps = readSnpsFromGene(gene, chromName);
size = gene->txEnd - gene->txStart;
assert(size > 0);
AllocVar(seq);
seq->dna = needLargeMem(size+1);
seq = nibLoadPartMasked(NIB_MASK_MIXED, nibFile, gene->txStart, size);
ptr = seq->dna;
/* do substitutions */
/* including introns; doesn't take much time, keeps code clean */
for (snp = snps; snp != NULL; snp = snp->next)
{
snpPos = snp->chromStart - gene->txStart;
assert(snpPos >= 0);
verbose(5, "before substitution %c\n", ptr[snpPos]);
ptr[snpPos] = iupac(snp->name, snp->observed, ptr[snpPos]);
verbose(5, "after substitution %c\n", ptr[snpPos]);
}
printExons(gene, seq, fileHandle);
snpSimpleFreeList(&snps);
dnaSeqFree(&seq);
}
geneFreeList(&genes);
if (fclose(fileHandle) != 0)
errnoAbort("fclose failed");
}
struct axt *netFillToAxt(struct cnFill *fill, struct dnaSeq *tChrom , int tSize,
struct hash *qChromHash, char *nibDir,
struct chain *chain, boolean swap)
/* Convert subset of chain as defined by fill to axt. swap query and target if swap is true*/
{
struct dnaSeq *qSeq;
boolean isRev = (chain->qStrand == '-');
struct chain *subChain, *chainToFree;
int qOffset;
struct axt *axtList = NULL , *axt;
struct nibInfo *nib = hashFindVal(qChromHash, fill->qName);
/* Get query sequence fragment. */
{
if (nib == NULL)
{
char path[512];
AllocVar(nib);
safef(path, sizeof(path), "%s/%s.nib", nibDir, fill->qName);
nib->fileName = cloneString(path);
nibOpenVerify(path, &nib->f, &nib->size);
hashAdd(qChromHash, fill->qName, nib);
}
qSeq = nibLoadPartMasked(NIB_MASK_MIXED, nib->fileName,
fill->qStart, fill->qSize);
if (isRev)
{
reverseComplement(qSeq->dna, qSeq->size);
qOffset = nib->size - (fill->qStart + fill->qSize);
}
else
qOffset = fill->qStart;
}
chainSubsetOnT(chain, fill->tStart, fill->tStart + fill->tSize,
&subChain, &chainToFree);
if (subChain != NULL)
{
axtList = chainToAxt(subChain, qSeq, qOffset, tChrom, fill->tStart, 100, BIGNUM);
if (swap)
{
for (axt = axtList ; axt != NULL ; axt = axt->next)
axtSwap(axt, tSize, nib->size);
}
}
chainFree(&chainToFree);
freeDnaSeq(&qSeq);
return axtList;
}
void createFastaFilesForBits(char *root, struct genomeBit *gbList, boolean addDummy)
/* load all of the fasta records for the bits in the genome list into one
fasta file. Uses .nib files as they are much more compact and allow random access. */
{
struct dnaSeq *seq = NULL;
struct genomeBit *gb = NULL;
FILE *faOut = NULL;
char *faFile = NULL;
char *nibFile = NULL;
int totalBp = 0;
assert(gbList);
faFile = fileNameFromGenomeBit(outputRoot, ".fa", gbList);
faOut = mustOpen(faFile, "w");
for(gb = gbList; gb != NULL; gb = gb->next)
{
char buff[256];
snprintf(buff, sizeof(buff), "%s:%u-%u", gb->chrom, gb->chromStart, gb->chromEnd);
nibFile = nibFileFromChrom(root, gb->chrom);
seq = nibLoadPartMasked(NIB_MASK_MIXED, nibFile, gb->chromStart, gb->chromEnd-gb->chromStart);
totalBp += strlen(seq->dna);
faWriteNext(faOut, buff, seq->dna, seq->size);
dnaSeqFree(&seq);
freez(&nibFile);
}
/* Add a dummy fasta record so that avid will order and orient things for us.. */
if(addDummy)
faWriteNext(faOut, "garbage", "nnnnnnnnnn", 10);
carefulClose(&faOut);
/** This bit is commented out as we are now using nnnn's as repeat masking */
/* if(slCount(gbList) > 1) */
/* repeatMaskFile(outputRoot, gbList); */
/* else */
/* fakeRepeatMaskFile(outputRoot, gbList); */
freez(&faFile);
}
