def test_split_paired_reads_2_mixed_fq_orphans_to_file():
# test input file
infile = utils.copy_test_data('paired-mixed-2.fq')
in_dir = os.path.dirname(infile)
outfile = utils.get_temp_filename('out.fq')
script = 'split-paired-reads.py'
args = ['-0', outfile, infile]
status, out, err = utils.runscript(script, args, in_dir)
assert status == 0
assert "split 6 sequences (3 left, 3 right, 5 orphans)" in err, err
n_orphans = len([1 for record in screed.open(outfile)])
assert n_orphans == 5
n_left = len([1 for record in screed.open(infile + '.1')])
assert n_left == 3
n_right = len([1 for record in screed.open(infile + '.2')])
assert n_right == 3
for filename in [outfile, infile + '.1', infile + '.2']:
fp = gzip.open(filename)
try:
fp.read()
except IOError as e:
assert "Not a gzipped file" in str(e), str(e)
fp.close()
def test_split_paired_reads_2_mixed_fq_orphans_to_file():
# test input file
infile = utils.copy_test_data('paired-mixed-2.fq')
in_dir = os.path.dirname(infile)
outfile = utils.get_temp_filename('out.fq')
script = 'split-paired-reads.py'
args = ['-0', outfile, infile]
status, out, err = utils.runscript(script, args, in_dir)
assert status == 0
assert "split 6 sequences (3 left, 3 right, 5 orphans)" in err, err
n_orphans = len([1 for record in screed.open(outfile)])
assert n_orphans == 5
n_left = len([1 for record in screed.open(infile + '.1')])
assert n_left == 3
n_right = len([1 for record in screed.open(infile + '.2')])
assert n_right == 3
for filename in [outfile, infile + '.1', infile + '.2']:
fp = gzip.open(filename)
try:
fp.read()
except IOError as e:
assert "Not a gzipped file" in str(e), str(e)
fp.close()
def test_split_paired_reads_2_mixed_fq_broken_pairing_format():
# test input file
infile = utils.copy_test_data('paired-mixed-broken.fq')
in_dir = os.path.dirname(infile)
script = 'split-paired-reads.py'
args = [infile]
status, out, err = utils.runscript(script, args, in_dir, fail_ok=True)
assert status == 1
assert "Unpaired reads found starting at 895:1:37:17593:9954" in err, err
def test_split_paired_reads_2_mixed_fq():
# test input file
infile = utils.copy_test_data('paired-mixed-2.fq')
in_dir = os.path.dirname(infile)
script = 'split-paired-reads.py'
args = ['-0', '/dev/null', infile]
status, out, err = utils.runscript(script, args, in_dir)
assert status == 0
assert "split 6 sequences (3 left, 3 right, 5 orphans)" in err, err
def test_split_paired_reads_2_mixed_fq_require_pair():
# test input file
infile = utils.copy_test_data('paired-mixed.fq')
in_dir = os.path.dirname(infile)
script = 'split-paired-reads.py'
args = [infile]
status, out, err = utils.runscript(script, args, in_dir, fail_ok=True)
assert status == 1, status
assert "Unpaired reads found" in err
def test_split_paired_reads_2_mixed_fq_broken_pairing_format():
# test input file
infile = utils.copy_test_data('paired-mixed-broken.fq')
in_dir = os.path.dirname(infile)
script = 'split-paired-reads.py'
args = [infile]
status, out, err = utils.runscript(script, args, in_dir, fail_ok=True)
assert status == 1
assert "Unpaired reads found starting at 895:1:37:17593:9954" in err, err
def test_split_paired_reads_2_mixed_fq():
# test input file
infile = utils.copy_test_data('paired-mixed-2.fq')
in_dir = os.path.dirname(infile)
script = 'split-paired-reads.py'
args = ['-0', '/dev/null', infile]
status, out, err = utils.runscript(script, args, in_dir)
assert status == 0
assert "split 6 sequences (3 left, 3 right, 5 orphans)" in err, err
def test_split_paired_reads_2_mixed_fq_require_pair():
# test input file
infile = utils.copy_test_data('paired-mixed.fq')
in_dir = os.path.dirname(infile)
script = 'split-paired-reads.py'
args = [infile]
status, out, err = utils.runscript(script, args, in_dir, fail_ok=True)
assert status == 1, status
assert "Unpaired reads found" in err
def test_split_paired_reads_2_mixed_fq_gzfile():
# test input file
infile = utils.copy_test_data('paired-mixed-2.fq')
in_dir = os.path.dirname(infile)
outfile = utils.get_temp_filename('out.fq')
script = 'split-paired-reads.py'
args = ['-0', outfile, '--gzip', infile]
status, out, err = utils.runscript(script, args, in_dir)
assert status == 0
assert "split 6 sequences (3 left, 3 right, 5 orphans)" in err, err
n_orphans = len([1 for record in screed.open(outfile)])
assert n_orphans == 5
n_left = len([1 for record in screed.open(infile + '.1')])
assert n_left == 3
n_right = len([1 for record in screed.open(infile + '.2')])
assert n_right == 3
for filename in [outfile, infile + '.1', infile + '.2']:
fp = gzip.open(filename)
fp.read() # this will fail if not gzip file.
fp.close()
def test_split_paired_reads_2_mixed_fq_gzfile():
# test input file
infile = utils.copy_test_data('paired-mixed-2.fq')
in_dir = os.path.dirname(infile)
outfile = utils.get_temp_filename('out.fq')
script = 'split-paired-reads.py'
args = ['-0', outfile, '--gzip', infile]
status, out, err = utils.runscript(script, args, in_dir)
assert status == 0
assert "split 6 sequences (3 left, 3 right, 5 orphans)" in err, err
n_orphans = len([1 for record in screed.open(outfile)])
assert n_orphans == 5
n_left = len([1 for record in screed.open(infile + '.1')])
assert n_left == 3
n_right = len([1 for record in screed.open(infile + '.2')])
assert n_right == 3
for filename in [outfile, infile + '.1', infile + '.2']:
fp = gzip.open(filename)
fp.read() # this will fail if not gzip file.
fp.close()