struct dnaSeq *stickyEnd(struct cutter *enz)
/* Return the sticky end sequence of an enzyme. Strand is unspecified. Free this. */
{
struct dnaSeq *ret = NULL;
if (!enz)
return NULL;
if (enz->overhang > 0)
{
char *seq = cloneStringZ(enz->seq + enz->cut, enz->overhang);
ret = newDnaSeq(seq, enz->overhang, "sticky");
}
else if (enz->overhang < 0)
{
int size = intAbs(enz->overhang);
char *seq = cloneStringZ(enz->seq + enz->cut - size, size);
complement(seq, strlen(seq));
ret = newDnaSeq(seq, strlen(seq), "sticky");
}
return ret;
}
struct dnaSeq *gffReadDnaSeq(char *fileName)
/* Open gff file and read DNA sequence from it. */
{
struct gff gff;
struct dnaSeq *seq = NULL;
if (!gffOpen(&gff, fileName))
return NULL;
if (gffReadDna(&gff))
{
seq = newDnaSeq(gff.dna, gff.dnaSize, gff.dnaName);
gff.dna = NULL;
}
gffClose(&gff);
return seq;
}
static struct dnaSeq *seqReaderTblGet(struct seqReader *seqReader, char *seqName, int start, int end,
int *retFullSeqSize)
/* get a sequence from the seqTbl */
{
struct dnaSeq *fullSeq = hashFindVal(seqReader->seqTbl, seqName);
if (fullSeq == NULL)
errAbort("can't find sequence %s in %s", seqName, seqReader->spec);
if (end > fullSeq->size)
errAbort("range %d-%d longer than sequence %s length %d in %s",
start, end, seqName, fullSeq->size, seqReader->spec);
if (retFullSeqSize != NULL)
*retFullSeqSize = fullSeq->size;
int len = (end-start);
struct dnaSeq *seq = newDnaSeq(cloneStringZ(fullSeq->dna+start, len), len, seqName);
if (!gMasked)
tolowers(seq->dna);
return seq;
}
boolean faReadMixedNext(FILE *f, boolean preserveCase, 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.
* Contains parameter to preserve mixed case. */
{
char lineBuf[1024];
int lineSize;
char *words[1];
int c;
off_t offset = ftello(f);
size_t dnaSize = 0;
DNA *dna, *sequence;
char *name = defaultName;
if (name == NULL)
name = "";
dnaUtilOpen();
if (retCommentLine != NULL)
*retCommentLine = NULL;
*retSeq = NULL;
/* Skip first lines until it starts with '>' */
for (;;)
{
if(fgets(lineBuf, sizeof(lineBuf), f) == NULL)
{
if (ferror(f))
errnoAbort("read of fasta file failed");
return FALSE;
}
lineSize = strlen(lineBuf);
if (lineBuf[0] == '>')
{
if (retCommentLine != NULL)
*retCommentLine = cloneString(lineBuf);
offset = ftello(f);
chopByWhite(lineBuf, words, ArraySize(words));
name = words[0]+1;
break;
}
else if (!mustStartWithComment)
{
if (fseeko(f, offset, SEEK_SET) < 0)
errnoAbort("fseek on fasta file failed");
break;
}
else
offset += lineSize;
}
/* Count up DNA. */
for (;;)
{
c = fgetc(f);
if (c == EOF || c == '>')
break;
if (isalpha(c))
{
++dnaSize;
}
}
if (dnaSize == 0)
{
warn("Invalid fasta format: sequence size == 0 for element %s",name);
}
/* Allocate DNA and fill it up from file. */
dna = sequence = needHugeMem(dnaSize+1);
if (fseeko(f, offset, SEEK_SET) < 0)
errnoAbort("fseek on fasta file failed");
for (;;)
{
c = fgetc(f);
if (c == EOF || c == '>')
break;
if (isalpha(c))
{
/* check for non-DNA char */
if (ntChars[c] == 0)
{
*dna++ = preserveCase ? 'N' : 'n';
}
else
{
*dna++ = preserveCase ? c : ntChars[c];
}
}
}
if (c == '>')
ungetc(c, f);
*dna = 0;
*retSeq = newDnaSeq(sequence, dnaSize, name);
if (ferror(f))
errnoAbort("read of fasta file failed");
return TRUE;
}
