def test_detect_and_output_transporters_via_signalp_when_no_sigpeps(self):
"""
Test optional transporter prediction is generated even if
abortion of script due to no signal peptides
"""
test_fas_no_sigpep = os.path.join(self.tmp_dir, 'test_no_sigpep.fas')
tmp_dir_to_test_removal = os.path.join(self.tmp_dir, 'intermediate_tmp_2')
os.mkdir(tmp_dir_to_test_removal)
rename_mappings = {'KGQ972831Candidaalbicans': 'KGQ972831Candidaalbicans'}
with self.assertRaises(SystemExit):
_, _, _ = utils.signalp(test_fas_no_sigpep,
tmp_dir_to_test_removal,
rename_mappings,
'actual',
trans=2)
self.assertFalse(os.path.exists(tmp_dir_to_test_removal))
expected_transporters = os.path.join(self.tmp_dir,
'expected_no_sigpep_transporters.fas')
actual_transporters = 'actual_predicted_transporters.fas'
self.assertTrue(actual_transporters)
self.compare_files(actual_transporters, expected_transporters)
def test_signalp_func(self):
"""
Test that the signalp function correctly parses signalp output
"""
expected_accessions_with_sig_pep = ['PM50_trimmed_paired_qual32_contig_10408',
'R1qual32.paired_(paired)_contig_1567',
'PM50_trimmed_paired_qual32_contig_16575',
'PM50_trimmed_paired_qual32_contig_18412',
'PM50_trimmed_paired_qual32_contig_12144',
'R1qual32.paired_(paired)_contig_2534']
expected_mature_seq_fp = os.path.join(self.tmp_dir, 'expected_signalp_mature_seqs.fasta')
expected_full_sequences_with_sigpep_fp = os.path.join(self.tmp_dir,
'expected_signalp_full_seqs_with_sigpep.fasta')
actual_mature_seqs_fp, \
actual_accessions_with_sig_pep, \
actual_full_sequences_with_sigpep_fp = utils.signalp(self.test_fas, '', '', '')
self.assertEqual(actual_accessions_with_sig_pep, expected_accessions_with_sig_pep)
self.compare_files(actual_full_sequences_with_sigpep_fp,
expected_full_sequences_with_sigpep_fp)
self.compare_files(actual_mature_seqs_fp, expected_mature_seq_fp)
def test_pipe_aborts_in_signalp_step_when_no_sigpeps(self):
"""
Test execution abortion if there are no signal peptides detected
"""
test_fas_no_sigpep = os.path.join(self.tmp_dir, 'test_no_sigpep.fas')
tmp_dir_to_test_removal = os.path.join(self.tmp_dir, 'intermediate_tmp')
os.mkdir(tmp_dir_to_test_removal)
with self.assertRaises(SystemExit):
_, _, _ = utils.signalp(test_fas_no_sigpep,
tmp_dir_to_test_removal,
'',
'')
self.assertFalse(os.path.exists(tmp_dir_to_test_removal))
def main(argv):
"""
Main execution of the program in the proper order
input: argv from arg parser
"""
utils.check_dependencies(check_run=argv.check, verbose=argv.verbose)
input_file = argv.input_file
if argv.run_name is False:
basename = os.path.basename(input_file)
run_name = os.path.splitext(basename)[0]
else:
run_name = argv.run_name
tmp_dir = os.path.join(os.getcwd(), 'intermediate_outputs_' + run_name)
try:
os.makedirs(tmp_dir)
except OSError:
if os.path.exists(tmp_dir):
warnings.warn('\n\nintermediate output dir: {0} exists '
'overwriting contents\n'.format(tmp_dir))
else:
raise OSError('Error creating intermediate '
'output dir: {0}'.format(tmp_dir))
rename_mappings, formatted_fasta_fp = utils.format_fasta(
input_file, tmp_dir, verbose=argv.verbose)
mature_seqs_fp, \
accessions_with_sig_pep, \
full_sequences_with_sigpep_fp = utils.signalp(formatted_fasta_fp,
tmp_dir,
rename_mappings,
run_name,
trans=argv.trans,
verbose=argv.verbose)
if argv.trans:
utils.detect_and_output_transporters(formatted_fasta_fp,
rename_mappings,
tmp_dir,
run_name,
mature_seqs=mature_seqs_fp,
verbose=argv.verbose,
tm_threshold=argv.trans)
accesions_no_tm_in_mature_seq = utils.tmhmm(mature_seqs_fp,
verbose=argv.verbose)
secreted_accessions = utils.targetp(full_sequences_with_sigpep_fp,
plant=False,
verbose=argv.verbose)
extracellular_accessions = utils.wolfpsort(formatted_fasta_fp,
verbose=argv.verbose)
if argv.permissive:
conservative_flag = False
else:
conservative_flag = True
secretome_accessions = utils.secretome(accessions_with_sig_pep,
accesions_no_tm_in_mature_seq,
secreted_accessions,
extracellular_accessions,
conservative=conservative_flag,
verbose=argv.verbose)
utils.generate_output(formatted_fasta_fp,
secretome_accessions,
rename_mappings,
run_name,
conservative=conservative_flag,
verbose=argv.verbose)
if not argv.nocleanup:
shutil.rmtree(tmp_dir)
def main(argv):
"""
Main execution of the program in the proper order
input: argv from arg parser
"""
utils.check_dependencies(check_run=argv.check,
verbose=argv.verbose)
input_file = argv.input_file
if argv.run_name is False:
basename = os.path.basename(input_file)
run_name = os.path.splitext(basename)[0]
else:
run_name = argv.run_name
tmp_dir = os.path.join(os.getcwd(), 'intermediate_outputs_'+run_name)
try:
os.makedirs(tmp_dir)
except OSError:
if os.path.exists(tmp_dir):
warnings.warn('\n\nintermediate output dir: {0} exists '
'overwriting contents\n'.format(tmp_dir))
else:
raise OSError('Error creating intermediate '
'output dir: {0}'.format(tmp_dir))
rename_mappings, formatted_fasta_fp = utils.format_fasta(input_file,
tmp_dir,
verbose=argv.verbose)
mature_seqs_fp, \
accessions_with_sig_pep, \
full_sequences_with_sigpep_fp = utils.signalp(formatted_fasta_fp,
tmp_dir,
rename_mappings,
run_name,
trans=argv.trans,
verbose=argv.verbose)
if argv.trans:
utils.detect_and_output_transporters(formatted_fasta_fp,
rename_mappings,
tmp_dir,
run_name,
mature_seqs=mature_seqs_fp,
verbose=argv.verbose,
tm_threshold=argv.trans)
accesions_no_tm_in_mature_seq = utils.tmhmm(mature_seqs_fp,
verbose=argv.verbose)
secreted_accessions = utils.targetp(full_sequences_with_sigpep_fp,
plant=False,
verbose=argv.verbose)
extracellular_accessions = utils.wolfpsort(formatted_fasta_fp,
verbose=argv.verbose)
if argv.permissive:
conservative_flag = False
else:
conservative_flag = True
secretome_accessions = utils.secretome(accessions_with_sig_pep,
accesions_no_tm_in_mature_seq,
secreted_accessions,
extracellular_accessions,
conservative=conservative_flag,
verbose=argv.verbose)
utils.generate_output(formatted_fasta_fp,
secretome_accessions,
rename_mappings,
run_name,
conservative=conservative_flag,
verbose=argv.verbose)
if not argv.nocleanup:
shutil.rmtree(tmp_dir)