def main(args):
"""
Prints a human readable output of a genome properties assignment file.
:param args: The command line arguments.
"""
genome_property_flat_file_path = sanitize_cli_path(
args.input_genome_properties_flat_file)
json_output_path = sanitize_cli_path(args.output_file_path)
assignment_file_paths = (
sanitize_cli_path(path)
for path in args.input_genome_properties_assignment_files)
with open(genome_property_flat_file_path) as genome_property_file:
genome_properties_tree = parse_genome_property_file(
genome_property_file)
leaf_assignments = []
for path in assignment_file_paths:
with open(path) as assignment_file:
leaf_assignments.append(
parse_genome_property_longform_file(assignment_file))
results = GenomePropertiesResults(
*leaf_assignments, genome_properties_tree=genome_properties_tree)
with open(json_output_path, 'w') as json_file:
results.to_json(json_file)
def main(args):
"""
Creates a JSON file representing genome property assignments.
:param args: The command line arguments.
"""
genome_property_flat_file_path = sanitize_cli_path(
args.input_genome_properties_flat_file)
json_output_path = sanitize_cli_path(args.output_file_path)
interproscan_file_path = (sanitize_cli_path(path)
for path in args.input_interproscan_tsv_files)
with open(genome_property_flat_file_path) as genome_property_file:
genome_properties_tree = parse_genome_property_file(
genome_property_file)
interproscan_assignments = []
for path in interproscan_file_path:
with open(path) as interproscan_file:
interproscan_assignments.append(
parse_interproscan_file(interproscan_file))
results = GenomePropertiesResults(
*interproscan_assignments,
genome_properties_tree=genome_properties_tree)
with open(json_output_path, 'w') as json_file:
results.to_json(json_file)
def test_parse_genome_property_file(self):
"""Test if a physical genome properties file can be parsed."""
genome_property_flat_file_path = 'pygenprop/testing/test_constants/test_genome_properties.txt'
with open(genome_property_flat_file_path) as genome_property_file:
properties = parse_genome_property_file(genome_property_file)
self.assertEqual(len(properties), 4)
def main(args):
"""
Prints a human readable output of a genome properties flat file.
:param args: The command line arguments.
"""
genome_property_flat_file_path = sanitize_cli_path(args.input_genome_properties_file)
with open(genome_property_flat_file_path) as genome_property_file:
properties = parse_genome_property_file(genome_property_file)
if properties is not None:
print(str(len(properties)) + ' properties have been parsed.')
else:
print('Properties parsing has failed.')
sys.exit(1)
def setUpClass(cls):
"""Set up testing data for testing."""
with open('pygenprop/testing/test_constants/C_chlorochromatii_CaD3.txt'
) as assignment_file_one:
properties_one = parse_genome_property_longform_file(
assignment_file_one)
with open('pygenprop/testing/test_constants/C_luteolum_DSM_273.txt'
) as assignment_file_two:
properties_two = parse_genome_property_longform_file(
assignment_file_two)
with open(
'pygenprop/testing/test_constants/test_genome_properties_two.txt'
) as test_genome_properties_file:
genome_properties_tree = parse_genome_property_file(
test_genome_properties_file)
cls.test_genome_property_results = [properties_one, properties_two]
cls.test_tree = genome_properties_tree