def test_sample_seq(self):
sample_seq = os.path.join(BIN_DIR, 'sample_seqs')
assert 'usage' in check_output([sample_seq, '-h'])
fasta_fhand = NamedTemporaryFile()
fasta_fhand.write('>seq\nACTA\n>seq2\nACTA\n>seq3\nACTA\n')
fasta_fhand.flush()
# random sample
result = check_output([sample_seq, '-n', '1', fasta_fhand.name])
assert count_seqs(read_seqs([StringIO(result)]))['num_seqs'] == 1
# random sample
result = check_output([sample_seq, '-n', '2', fasta_fhand.name])
assert count_seqs(read_seqs([StringIO(result)]))['num_seqs'] == 2
# random sample
try:
stderr = NamedTemporaryFile()
check_output([sample_seq, '-n', '10', fasta_fhand.name],
stderr=stderr)
except CalledProcessError:
assert 'larger' in open(stderr.name).read()
# random sample with stdin
result = check_output([sample_seq, '-n', '2'],
stdin=open(fasta_fhand.name))
assert count_seqs(read_seqs([StringIO(result)]))['num_seqs'] == 2
def test_sample_seq(self):
sample_seq = os.path.join(BIN_DIR, 'sample_seqs')
assert 'usage' in check_output([sample_seq, '-h'])
fasta_fhand = NamedTemporaryFile()
fasta_fhand.write('>seq\nACTA\n>seq2\nACTA\n>seq3\nACTA\n')
fasta_fhand.flush()
# random sample
result = check_output([sample_seq, '-n', '1', fasta_fhand.name])
assert count_seqs(read_seqs([StringIO(result)]))['num_seqs'] == 1
# random sample
result = check_output([sample_seq, '-n', '2', fasta_fhand.name])
assert count_seqs(read_seqs([StringIO(result)]))['num_seqs'] == 2
# random sample
try:
stderr = NamedTemporaryFile()
check_output([sample_seq, '-n', '10', fasta_fhand.name],
stderr=stderr)
except CalledProcessError:
assert 'larger' in open(stderr.name).read()
# random sample with stdin
result = check_output([sample_seq, '-n', '2'],
stdin=open(fasta_fhand.name))
assert count_seqs(read_seqs([StringIO(result)]))['num_seqs'] == 2
def test_count_seqs():
in_fhands = []
for val in range(1, 6):
fhand = open(join(TEST_DATA_DIR, 'pairend{0}.sfastq'.format(val)))
in_fhands.append(fhand)
seqs = read_seqs(in_fhands, prefered_seq_classes=[SEQRECORD])
counts = count_seqs(seqs)
assert counts == {'total_length': 96, 'num_seqs': 24}
def test_count_seqs():
in_fhands = []
for val in range(1, 6):
fhand = open(join(TEST_DATA_DIR, 'pairend{0}.sfastq'.format(val)))
in_fhands.append(fhand)
seqs = read_seqs(in_fhands, prefered_seq_classes=[SEQRECORD])
counts = count_seqs(seqs)
assert counts == {'total_length': 96, 'num_seqs': 24}
def test_sample_seq(self):
'It tests the seq head'
sample_seq = os.path.join(BIN_DIR, 'sample_seqs')
assert 'usage' in check_output([sample_seq, '-h'])
fasta_fhand = NamedTemporaryFile()
fasta_fhand.write('>seq\nACTA\n>seq2\nACTA\n>seq3\nACTA\n')
fasta_fhand.flush()
# random sample
result = check_output([sample_seq, '-n', '1', fasta_fhand.name])
assert count_seqs(read_seqs([StringIO(result)]))['num_seqs'] == 1
# random sample
result = check_output([sample_seq, '-n', '2', fasta_fhand.name])
assert count_seqs(read_seqs([StringIO(result)]))['num_seqs'] == 2
# random sample with stdin
result = check_output([sample_seq, '-n', '2'],
stdin=open(fasta_fhand.name))
assert count_seqs(read_seqs([StringIO(result)]))['num_seqs'] == 2
def test_sample_seq(self):
'It tests the seq head'
sample_seq = os.path.join(BIN_DIR, 'sample_seqs')
assert 'usage' in check_output([sample_seq, '-h'])
fasta_fhand = NamedTemporaryFile()
fasta_fhand.write('>seq\nACTA\n>seq2\nACTA\n>seq3\nACTA\n')
fasta_fhand.flush()
# random sample
result = check_output([sample_seq, '-n', '1', fasta_fhand.name])
assert count_seqs(read_seqs([StringIO(result)]))['num_seqs'] == 1
# random sample
result = check_output([sample_seq, '-n', '2', fasta_fhand.name])
assert count_seqs(read_seqs([StringIO(result)]))['num_seqs'] == 2
# random sample with stdin
result = check_output([sample_seq, '-n', '2'],
stdin=open(fasta_fhand.name))
assert count_seqs(read_seqs([StringIO(result)]))['num_seqs'] == 2