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 test_check_dependencies(self):
"""
Make sure the dependency checking function works
"""
ret = utils.check_dependencies('dependencies/bin')
self.assertIs(True, ret)
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)
