def test_parse_orthofinder(self):
"""Test parsing OrthoFinder results.
"""
launch_orthofinder(self.proteomes_dir, 1)
date = time.strftime("%c").split()
day = date[2]
if int(day) < 10:
day = "0%s" % day
results_dir = join(
self.proteomes_dir, "Results_%s%s" % (date[1], day),
"WorkingDirectory")
species_ids, sequence_ids, orthogroups_act =\
parse_orthofinder(results_dir)
species_ids_exp = {'1': 'seqs_prot_2.fasta', '0': 'seqs_prot_1.fasta'}
seq_ids_exp = {'1_2': 'YP_004590028.1', '1_1': 'YP_004590123.1',
'1_0': 'YP_004590122.1', '0_2': 'YP_002468032.1',
'0_0': 'YP_002468181.1', '0_1': 'YP_002468184.1'}
orthogroups_exp = [['0_0', '1_0'], ['0_1', '1_1'], ['0_2', '1_2']]
self.assertDictEqual(species_ids, species_ids_exp)
self.assertDictEqual(sequence_ids, seq_ids_exp)
orthogroups_act_sorted = [sorted(group) for group in orthogroups_act]
orthogroups_exp_sorted = [sorted(group) for group in orthogroups_exp]
orthogroups_act_sorted_2 = sorted(orthogroups_act_sorted)
orthogroups_exp_sorted_2 = sorted(orthogroups_exp_sorted)
self.assertListEqual(orthogroups_act_sorted_2,
orthogroups_exp_sorted_2)
def test_launch_orthofinder(self):
"""Test running OrthoFinder.
"""
launch_orthofinder(self.proteomes_dir, 1, verbose=True)
date = time.strftime("%c").split()
day = date[2]
if int(day) < 10:
day = "0%s" % day
results_dir = join(
self.proteomes_dir, "Results_%s%s" % (date[1], day))
orthogroups_exp = [['YP_002468181.1', 'YP_004590122.1'],
['YP_004590123.1', 'YP_002468184.1'],
['YP_002468032.1', 'YP_004590028.1']]
orthogroups_act = []
with open(join(results_dir, "OrthologousGroups.txt"), 'r') as o:
orthogroups_act = [line.split()[1:] for line in o]
orthogroups_act_sorted = [sorted(group) for group in orthogroups_act]
orthogroups_exp_sorted = [sorted(group) for group in orthogroups_exp]
orthogroups_act_sorted_2 = sorted(orthogroups_act_sorted)
orthogroups_exp_sorted_2 = sorted(orthogroups_exp_sorted)
self.assertListEqual(orthogroups_act_sorted_2,
orthogroups_exp_sorted_2)
