def test_write_to_file_like_object(self):
sio = StringIO()
with FastaWriter(sio) as fw:
fw.write(Sequence("name", "CCATA"))
fw.write(Sequence("name2", "HELLO"))
assert sio.getvalue() == '>name\nCCATA\n>name2\nHELLO\n'
assert not fw._file.closed
def test_write_to_file_like_object(self):
sio = StringIO()
with FastqWriter(sio) as fq:
fq.writeseq("name", "CCATA", "!#!#!")
fq.writeseq("name2", "HELLO", "&&&!&&")
assert sio.getvalue(
) == '@name\nCCATA\n+\n!#!#!\n@name2\nHELLO\n+\n&&&!&&\n'
def test_write_to_file_like_object(self):
sio = StringIO()
with FastaWriter(sio) as fw:
fw.write(Sequence("name", "CCATA"))
fw.write(Sequence("name2", "HELLO"))
assert sio.getvalue() == '>name\nCCATA\n>name2\nHELLO\n'
assert not fw._file.closed
def test(self):
reads = [(Sequence('A/1 comment', 'TTA',
'##H'), Sequence('A/2 comment', 'GCT', 'HH#')),
(Sequence('B/1', 'CC', 'HH'), Sequence('B/2', 'TG', '#H'))]
sio = StringIO()
with InterleavedSequenceWriter(sio) as writer:
for read1, read2 in reads:
writer.write(read1, read2)
assert sio.getvalue(
) == '@A/1 comment\nTTA\n+\n##H\n@A/2 comment\nGCT\n+\nHH#\n@B/1\nCC\n+\nHH\n@B/2\nTG\n+\n#H\n'
def test(self):
reads = [
(Sequence('A/1 comment', 'TTA', '##H'),
Sequence('A/2 comment', 'GCT', 'HH#')),
(Sequence('B/1', 'CC', 'HH'),
Sequence('B/2', 'TG', '#H'))
]
sio = StringIO()
with InterleavedSequenceWriter(sio) as writer:
for read1, read2 in reads:
writer.write(read1, read2)
assert sio.getvalue() == '@A/1 comment\nTTA\n+\n##H\n@A/2 comment\nGCT\n+\nHH#\n@B/1\nCC\n+\nHH\n@B/2\nTG\n+\n#H\n'
def test(self):
with FastaReader("tests/data/simple.fasta") as f:
reads = list(f)
assert reads == simple_fasta
fasta = StringIO(">first_sequence\nSEQUENCE1\n>second_sequence\nSEQUENCE2\n")
reads = list(FastaReader(fasta))
assert reads == simple_fasta
def test_wrong_fasta_format():
fasta = StringIO(
dedent("""
# a comment
# another one
unexpected
>first_sequence
SEQUENCE1
>second_sequence
SEQUENCE2
"""))
reads = list(seqio.FastaReader(fasta))
def test_fastareader_with_comments():
fasta = StringIO(
dedent("""
# a comment
# another one
>first_sequence
SEQUENCE1
>second_sequence
SEQUENCE2
"""))
reads = list(seqio.FastaReader(fasta))
assert reads == simple_fasta
def test_sequence_reader():
# test the autodetection
with seqio.open("tests/data/simple.fastq") as f:
reads = list(f)
assert reads == simple_fastq
with seqio.open("tests/data/simple.fasta") as f:
reads = list(f)
assert reads == simple_fasta
with open("tests/data/simple.fastq") as f:
reads = list(seqio.open(f))
assert reads == simple_fastq
# make the name attribute unavailable
f = StringIO(open("tests/data/simple.fastq").read())
reads = list(seqio.open(f))
assert reads == simple_fastq
f = StringIO(open("tests/data/simple.fasta").read())
reads = list(seqio.open(f))
assert reads == simple_fasta
def test_quiet_is_quiet():
captured_standard_output = StringIO()
captured_standard_error = StringIO()
old_stdout = sys.stdout
old_stderr = sys.stderr
try:
sys.stdout = captured_standard_output
sys.stderr = captured_standard_error
cutadapt.main(['-o', '/dev/null', '--quiet', '-a', 'XXXX', datapath('illumina.fastq.gz')])
finally:
sys.stdout = old_stdout
sys.stderr = old_stderr
assert captured_standard_output.getvalue() == ''
assert captured_standard_error.getvalue() == ''
def test_fastq_incomplete():
fastq = StringIO("@name\nACGT+\n")
with seqio.FastqReader(fastq) as fq:
list(fq)
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))
def test_write_zero_length_sequence(self):
sio = StringIO()
with FastaWriter(sio) as fw:
fw.write(Sequence("name", ""))
assert sio.getvalue() == '>name\n\n', '{0!r}'.format(
sio.getvalue())
def test_incorrectly_paired(self):
s = StringIO('@r1/1\nACG\n+\nHHH\n@wrong_name\nTTT\n+\nHHH')
list(InterleavedSequenceReader(s))
def test_missing_partner(self):
s = StringIO('@r1\nACG\n+\nHHH')
list(InterleavedSequenceReader(s))
