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_invalid_quality_value():
fasta = StringIO(">name\nACG")
qual = StringIO(">name\n3 xx 7")
list(seqio.FastaQualReader(fasta, qual))
def test_mismatching_read_names():
fasta = StringIO(">name\nACG")
qual = StringIO(">nome\n3 5 7")
list(seqio.FastaQualReader(fasta, qual))