def create_cases(config_data, jsons):
'''Create cases from list of jsons.'''
print("== Create cases from new json format ==")
case_objs = progress_bar("Create cases")(lambda json_file: case.Case(
json_file, vcf_path=config_data.input["vcf"]))(jsons)
print("Correcting transcripts with mutalyzer")
case_objs = multiprocess("Fetch hgvs", touch_hgvs, case_objs)
MUTALYZER_INST.correct_reference_transcripts(case_objs)
print("Creating pickle.")
if config_data.dump_intermediate:
with open('case_cleaned.p', 'wb') as pfile:
pickler.CasePickler(pfile).dump(case_objs, )
return case_objs
def save_vcfs(config_data, qc_cases):
'''Create VCF files from genetic information and create a config.yml
listing all vcf files.
'''
simulated = config_data.output["simulated_vcf_path"]
realvcf = config_data.output["real_vcf_path"]
config_path = config_data.output["vcf_config_file"]
progress_bar("Generate VCF")(
lambda x: x.put_hgvs_vcf(simulated, recreate=False))(
[case for (valid, _), case in qc_cases if valid])
print("Pickling vcf cases")
if config_data.dump_intermediate:
with open('qc_case_with_simulated_vcf.p', 'wb') as pfile:
pickler.CasePickler(pfile).dump(qc_cases)
create_config(config_path, simulated, realvcf)
return qc_cases