def main(input_filepath, output_mappings_filepath, output_curation_filepath,
filters, zooma_host, oxo_target_list, oxo_distance):
logger.info('Started parsing trait names')
trait_names_list = parse_trait_names(input_filepath)
trait_names_counter = Counter(trait_names_list)
logger.info("Loaded {} trait names".format(len(trait_names_counter)))
with open(output_mappings_filepath, "w", newline='') as mapping_file, \
open(output_curation_filepath, "wt") as curation_file:
mapping_writer = csv.writer(mapping_file, delimiter="\t")
mapping_writer.writerow(["#clinvar_trait_name", "uri", "label"])
curation_writer = csv.writer(curation_file, delimiter="\t")
logger.info('Processing trait names in parallel')
trait_list = [
Trait(trait_name, freq)
for trait_name, freq in trait_names_counter.items()
]
trait_process_pool = multiprocessing.Pool(processes=12)
processed_trait_list = [
trait_process_pool.apply(process_trait,
args=(trait, filters, zooma_host,
oxo_target_list, oxo_distance))
for trait in trait_list
]
for trait in processed_trait_list:
output_trait(trait, mapping_writer, curation_writer)
logger.info('Finished processing trait names')
def main(input_filepath, output_mappings_filepath, output_curation_filepath, filters, zooma_host, oxo_target_list,
oxo_distance):
logger.info('Started parsing trait names')
trait_list = parse_trait_names(input_filepath)
logger.info("Loaded {} trait names".format(len(trait_list)))
with open(output_mappings_filepath, "w", newline='') as mapping_file, \
open(output_curation_filepath, "wt") as curation_file:
mapping_writer = csv.writer(mapping_file, delimiter="\t")
mapping_writer.writerow(["#clinvar_trait_name", "uri", "label"])
curation_writer = csv.writer(curation_file, delimiter="\t")
logger.info('Processing trait names in parallel')
trait_process_pool = multiprocessing.Pool(processes=24)
processed_trait_list = [
trait_process_pool.apply(
process_trait,
args=(trait, filters, zooma_host, oxo_target_list, oxo_distance)
)
for trait in trait_list
]
logger.info('Writing output with the processed traits')
for trait in processed_trait_list:
# Remove non-specific trait names which should never be output
if trait.name.lower() not in ClinVarTrait.NONSPECIFIC_TRAITS:
output_trait(trait, mapping_writer, curation_writer)
logger.info('Finished processing trait names')
def test_trait_names_parsing(self):
# Test file contains two records: one with a Pathogenic variant another with a Benign one. Trait names
# from *both* records must be parsed and returned.
test_filename = os.path.join(
os.path.dirname(__file__),
'../evidence_string_generation/resources/test_clinvar_record.xml.gz'
)
trait_names = [
trait.name
for trait in trait_names_parsing.parse_trait_names(test_filename)
]
self.assertEqual(trait_names, ['leber congenital amaurosis 13'])
def test_trait_names_parsing(self):
# Test file contains two records: one with a Pathogenic variant another with a Benign one. Only trait names
# from the Pathogenic one should get into the
test_filename = os.path.join(os.path.dirname(__file__),
'resources/variant_summary.tsv.gz')
trait_names = [
trait.name
for trait in trait_names_parsing.parse_trait_names(test_filename)
]
self.assertEqual(
sorted(trait_names),
sorted([
'breast-ovarian cancer, familial 1',
'hereditary breast and ovarian cancer syndrome',
'hereditary cancer-predisposing syndrome', 'not provided'
]))
def main(input_filepath, output_mappings_filepath, output_curation_filepath, filters, zooma_host,
oxo_target_list, oxo_distance):
trait_names_list = parse_trait_names(input_filepath)
trait_names_counter = Counter(trait_names_list)
with open(output_mappings_filepath, "w", newline='') as mapping_file, \
open(output_curation_filepath, "wt") as curation_file:
mapping_writer = csv.writer(mapping_file, delimiter="\t")
mapping_writer.writerow(["#clinvar_trait_name", "uri", "label"])
curation_writer = csv.writer(curation_file, delimiter="\t")
bar = progressbar.ProgressBar(max_value=len(trait_names_counter),
widgets=[progressbar.AdaptiveETA(samples=1000)])
for trait_name, freq in bar(trait_names_counter.items()):
trait = Trait(trait_name, freq)
trait = process_trait(trait, filters, zooma_host, oxo_target_list,
oxo_distance)
output_trait(trait, mapping_writer, curation_writer)
def main(input_filepath, output_mappings_filepath, output_curation_filepath,
filters, zooma_host, oxo_target_list, oxo_distance):
trait_names_list = parse_trait_names(input_filepath)
trait_names_counter = Counter(trait_names_list)
with open(output_mappings_filepath, "w", newline='') as mapping_file, \
open(output_curation_filepath, "wt") as curation_file:
mapping_writer = csv.writer(mapping_file, delimiter="\t")
mapping_writer.writerow(["#clinvar_trait_name", "uri", "label"])
curation_writer = csv.writer(curation_file, delimiter="\t")
bar = progressbar.ProgressBar(
max_value=len(trait_names_counter),
widgets=[progressbar.AdaptiveETA(samples=1000)])
for trait_name, freq in bar(trait_names_counter.items()):
trait = Trait(trait_name, freq)
trait = process_trait(trait, filters, zooma_host, oxo_target_list,
oxo_distance)
output_trait(trait, mapping_writer, curation_writer)