def setUp(self):
"""Setup"""
self.configuration_file = 'tests/data/application.cfg'
self.meme_fasta = 'tests/data/expected_out/macsPeak.fasta'
self.pipeline = Pipeline(self.configuration_file)
class TestPipeline(unittest.TestCase):
"""Test pipeline """
def setUp(self):
"""Setup"""
self.configuration_file = 'tests/data/application.cfg'
self.meme_fasta = 'tests/data/expected_out/macsPeak.fasta'
self.pipeline = Pipeline(self.configuration_file)
def test_meme(self):
"""Test meme runner"""
if os.path.exists('tests/data/generated_out/meme_analysis'):
shutil.rmtree('tests/data/generated_out/meme_analysis')
meme_args = self.pipeline.get_meme_default_params
output = self.pipeline.run_meme(fasta_in=self.meme_fasta,
out_dir='tests/data/generated_out/meme_analysis',
strargs=meme_args.replace(' -p {}'.format(get_cpu_count()), ''))
#TODO Check if meme.txt is same and created
#TODO This check is too stringent, specially if logos are being produced.
#MEME installation leads to hard coded paths
print output
assert output['exitcode'] == 0
meme_record = read_memefile('tests/data/generated_out/meme_analysis/meme.txt')
assert meme_record['total_motifs'] == 5
motif_record1 = meme_record['motif_records'][0]
motif_record2 = meme_record['motif_records'][1]
motif_record3 = meme_record['motif_records'][2]
assert motif_record1.consensus == 'CAGAACGCTGCTGCCAACCCGACCT'
assert motif_record2.consensus == 'AGCAGA'
assert motif_record3.consensus == 'CAGTTT'
def test_fimo(self):
"""Test fimo runner"""
fimo_output = self.pipeline.run_fimo(motif_file='tests/data/expected_out/meme_analysis/meme.txt',
motif_num=1,
sequence_file=self.meme_fasta,
out_dir='tests/data/generated_out/fimo_analysis',
strargs=None)
assert fimo_output['exitcode'] == 0
def test_fimotosites(self):
"""Test fimo_to_sites"""
fimo_file = 'tests/data/expected_out/fimo_analysis/fimo.txt'
record_dict = SeqIO.to_dict(SeqIO.parse(open(self.meme_fasta), 'fasta'))
fimo_df = fimo_to_sites(os.path.abspath(fimo_file))
for _, row in fimo_df.iterrows():
record_id = row['sequence name']
fimo_sequence = row['matched sequence']
start = row['start']-1 # 0-based start
end = row['stop'] # 1-based end
strand = row['strand']
fasta_sequence = record_dict[record_id].seq
if strand == '+':
assert str(fasta_sequence)[start:end] == fimo_sequence
else:
assert str(fasta_sequence[start:end].reverse_complement()) == fimo_sequence
def test_fimostd(self):
"""Test fimo to sites with
standard sequence names"""
fimo_file = 'tests/data/fimo.std.txt'
fimo_df = fimo_to_sites(os.path.abspath(fimo_file))
for _, row in fimo_df.iterrows():
record_id = row['sequence name']
fimo_sequence = row['matched sequence']
start = row['start']
end = row['stop'] # 1-based end
strand = row['strand']
assert start-1 == row['motifStartZeroBased']
assert end == row['motifEndOneBased']
def test_shuffler(self):
"""Smoke test for shuffler"""
fasta_in = 'tests/data/expected_out/macsPeak.fasta'
fasta_out = 'tests/data/generated_out/macsPeak.shuffled.fastsa'
output = self.pipeline.run_fasta_shuffler(fasta_in=fasta_in, fasta_out=fasta_out)
print output
with open(fasta_out) as f:
assert 'chr1' in f.readline()
