def read_sequences(seqfilename, qualityfilename, colorspace, fileformat):
"""
Read sequences and (if available) quality information from either:
* seqfilename in FASTA format (qualityfilename must be None)
* seqfilename in FASTQ format (qualityfilename must be None)
* seqfilename in .csfasta format and qualityfilename in .qual format
(SOLiD color space)
Return a generator over tuples (description, sequence, qualities).
qualities is None if no qualities are available.
qualities are ASCII-encoded (chr(quality) + 33).
"""
#if ftype == 'FASTQ' and qualityfilename is not None:
#raise ValueError("If a FASTQ file is given, no quality file can be provided.")
if qualityfilename is not None:
if colorspace:
# read from .(CS)FASTA/.QUAL
return seqio.ColorspaceFastaQualReader(seqfilename,
qualityfilename)
else:
return seqio.FastaQualReader(seqfilename, qualityfilename)
else:
# read from FASTA or FASTQ
return seqio.SequenceReader(seqfilename, colorspace, fileformat)
def test_sequence_reader():
# test the autodetection
with seqio.SequenceReader("tests/data/simple.fastq") as f:
reads = list(f)
assert reads == simple_fastq
with seqio.SequenceReader("tests/data/simple.fasta") as f:
reads = list(f)
assert reads == simple_fasta
with open("tests/data/simple.fastq") as f:
reads = list(seqio.SequenceReader(f))
assert reads == simple_fastq
# make the name attribute unavailable
f = StringIO(open("tests/data/simple.fastq").read())
reads = list(seqio.SequenceReader(f))
assert reads == simple_fastq
f = StringIO(open("tests/data/simple.fasta").read())
reads = list(seqio.SequenceReader(f))
assert reads == simple_fasta
def test_context_manager():
filename = "tests/data/simple.fasta"
with open(filename) as f:
assert not f.closed
reads = list(seqio.SequenceReader(f))
assert not f.closed
assert f.closed
with seqio.FastaReader(filename) as sr:
tmp_sr = sr
assert not sr.fp.closed
reads = list(sr)
assert not sr.fp.closed
assert tmp_sr.fp.closed