def _read_seqrecords(fhands, file_format=GUESS_FORMAT):
'It returns an iterator of seqrecords'
seq_iters = []
for fhand in fhands:
if file_format == GUESS_FORMAT or file_format is None:
fmt = guess_format(fhand)
else:
fmt = file_format
fmt = remove_multiline(fmt)
if fmt in ('fasta', 'qual') or 'fastq' in fmt:
title = title2ids
if fmt == 'fasta':
seq_iter = FastaIterator(fhand, title2ids=title)
elif fmt == 'qual':
seq_iter = QualPhredIterator(fhand, title2ids=title)
elif fmt == 'fastq' or fmt == 'fastq-sanger':
seq_iter = FastqPhredIterator(fhand, title2ids=title)
elif fmt == 'fastq-solexa':
seq_iter = FastqSolexaIterator(fhand, title2ids=title)
elif fmt == 'fastq-illumina':
seq_iter = FastqIlluminaIterator(fhand, title2ids=title)
else:
seq_iter = parse_into_seqrecs(fhand, fmt)
seq_iters.append(seq_iter)
return chain.from_iterable(seq_iters)
def _read_seqrecords(fhands, file_format=GUESS_FORMAT):
'It returns an iterator of seqrecords'
seq_iters = []
for fhand in fhands:
if file_format == GUESS_FORMAT or file_format is None:
fmt = guess_format(fhand)
else:
fmt = file_format
fmt = remove_multiline(fmt)
if fmt in ('fasta', 'qual') or 'fastq' in fmt:
title = title2ids
if fmt == 'fasta':
seq_iter = FastaIterator(fhand, title2ids=title)
elif fmt == 'qual':
seq_iter = QualPhredIterator(fhand, title2ids=title)
elif fmt == 'fastq' or fmt == 'fastq-sanger':
seq_iter = FastqPhredIterator(fhand, title2ids=title)
elif fmt == 'fastq-solexa':
seq_iter = FastqSolexaIterator(fhand, title2ids=title)
elif fmt == 'fastq-illumina':
seq_iter = FastqIlluminaIterator(fhand, title2ids=title)
else:
seq_iter = parse_into_seqrecs(fhand, fmt)
seq_iters.append(seq_iter)
return chain.from_iterable(seq_iters)
def _read_seqrecords(fhands):
'It returns an iterator of seqrecords'
seq_iters = []
for fhand in fhands:
fmt = get_format(fhand)
if fmt in ('fasta', 'qual') or 'fastq' in fmt:
title = title2ids
if fmt == 'fasta':
seq_iter = FastaIterator(fhand, title2ids=title)
elif fmt == 'qual':
seq_iter = QualPhredIterator(fhand, title2ids=title)
elif fmt == 'fastq' or fmt == 'fastq-sanger':
seq_iter = FastqPhredIterator(fhand, title2ids=title)
elif fmt == 'fastq-solexa':
seq_iter = FastqSolexaIterator(fhand, title2ids=title)
elif fmt == 'fastq-illumina':
seq_iter = FastqIlluminaIterator(fhand, title2ids=title)
else:
seq_iter = parse_into_seqrecs(fhand, fmt)
seq_iters.append(seq_iter)
return chain.from_iterable(seq_iters)
def _read_seqrecords(fhands):
'It returns an iterator of seqrecords'
seq_iters = []
for fhand in fhands:
fmt = get_format(fhand)
if fmt in ('fasta', 'qual') or 'fastq' in fmt:
title = title2ids
if fmt == 'fasta':
seq_iter = FastaIterator(fhand, title2ids=title)
elif fmt == 'qual':
seq_iter = QualPhredIterator(fhand, title2ids=title)
elif fmt == 'fastq' or fmt == 'fastq-sanger':
seq_iter = FastqPhredIterator(fhand, title2ids=title)
elif fmt == 'fastq-solexa':
seq_iter = FastqSolexaIterator(fhand, title2ids=title)
elif fmt == 'fastq-illumina':
seq_iter = FastqIlluminaIterator(fhand, title2ids=title)
else:
seq_iter = parse_into_seqrecs(fhand, fmt)
seq_iters.append(seq_iter)
return chain.from_iterable(seq_iters)
def _get_lengths(fhand):
lengths = {}
for seq in parse_into_seqrecs(fhand, 'fasta'):
lengths[seq.id] = len(seq)
return lengths
def _get_lengths(fhand):
lengths = {}
for seq in parse_into_seqrecs(fhand, 'fasta'):
lengths[seq.id] = len(seq)
return lengths