def test_exe_mafft(self):
"""Tests that the Mafft executor module calls mafft"""
extra_aln = am.MAFFT(self.filepath + os.sep + 'multiFasta.fasta')
aln_path = extra_aln.run()
self.assertTrue(os.path.exists(aln_path))
am.clean_alignment(aln_path, cache=False)
self.assertFalse(os.path.exists(aln_path))
def pipe(self):
"""
Queries the OMA database, Mafft and Rate4Site in sequence to get the
Returns:
A dictionary containing the various statistical scores mapped to each amino acid, depending
on which inputs were selected.
"""
old_dir = os.getcwd()
directory = old_dir + os.sep + 'Sequence_Alignments'
if not os.path.isdir(directory):
os.makedirs(directory)
os.chdir(directory)
msa = directory + os.sep + '%s.aln' % (self.name)
if os.path.isfile(msa):
aln = msa
self.call_rate4site(aln)
else:
orth = self.call_orthologs()
aln = self.call_alignment(orth)
self.call_rate4site(aln)
os.remove(os.getcwd() + os.sep + "%s.orth" % (self.name))
aminoCons.clean_alignment(aln, self.cache)
os.chdir(old_dir)
if not self.cache and not os.listdir(directory):
os.rmdir(directory)
return self.scores
def test_clean_alignment(self):
"""Tests to see that alignment file and the folder created are deleted
after calling clean argument"""
extra_aln = am.build_alignment(self.filepath + os.sep +
'multiFasta.fasta')
self.assertTrue(os.path.exists(extra_aln))
am.clean_alignment(extra_aln, cache=False)
self.assertFalse(os.path.exists(extra_aln))
def test_call_alignment(self, mock_aln):
"""tests that call_alignment calls the correct methods and generates the correct output"""
mock_aln.return_value = self.filepath + os.sep + 'multiFasta.aln'
tester = self.CDC48A.call_alignment(self.filepath + os.sep +
'multiFasta.fasta')
self.assertTrue(mock_aln.called)
self.assertTrue(os.path.isfile(tester))
self.assertTrue('multiFasta.aln' in tester)
am.clean_alignment(tester, cache=False)
def tearDownClass(cls):
am.clean_alignment(os.getcwd() + os.sep + 'multiFasta.aln',
cache=False)