def setUp(self):
input_file = os.path.join(INPUT_PATH, "cases", "normal.json")
loaded_correct = json.NewJson.from_file(input_file)
self.case = case.Case(loaded_correct)
self.phenomizer = phenomizer.PhenomizerService(config=CONFIG)
self.omim_obj = omim.Omim(api_key=CONFIG.omim['api_key'],
mimdir=INPUT_PATH,
use_cached=False)
def main():
'''Query list of phenotypic omim ids'''
config_data = config.ConfigManager("config.ini")
omim_internal = omim.Omim(config=config_data)
r = omim_internal.construct_phenotypic_series_mapping()
print(r)
def create_cases(args, config_data, jsons):
print("== Create cases from new json format ==")
error_fixer = errorfixer.ErrorFixer(config=config_data)
omim_obj = omim.Omim(config=config_data)
case_objs = yield_cases(jsons, error_fixer, omim_obj,
config_data.preprocess["exclude_normal_variants"])
mutalyzer.correct_reference_transcripts(case_objs)
if config_data.general['dump_intermediate'] and not args.single:
pickle.dump(case_objs, open('case_cleaned.p', 'wb'))
return case_objs
def setUpClass(cls):
super().setUpClass()
cls.error_fixer = errorfixer.ErrorFixer(config=cls.config,
version=ERROR_VERSION)
cls.omim = omim.Omim(config=cls.config)
def test_init(self):
omim_obj = omim.Omim(mimdir=self.input_path)
self.assertIsNotNone(omim_obj)
def setUpClass(cls):
super().setUpClass()
cls.omim = omim.Omim(mimdir=cls.input_path)
def get_qc_cases(config_data, cases):
'''Get qc results for all cases.'''
omim_obj = omim.Omim(config=config_data)
return {c.case_id: (c.check(omim_obj), c) for c in cases}
def convert_to_old_format(args, config_data, cases):
print("== Mapping to old json format ==")
destination = args.output or config_data.conversion["output_path"]
omim_obj = omim.Omim(config=config_data)
return yield_old_json(cases, destination, omim_obj)
}
# cases have to pass vcf check
qc_passed = {
case_id: case
for case_id, case in qc_passed.items() if qc_vcf[case_id][0]
}
# Cases with mutations marked as benign excluded from analysis
qc_benign_passed = {
k: v
for k, v in {k: v.get_benign_excluded()
for k, v in qc_passed.items()}.items() if v > 0
}
omim_obj = omim.Omim(config=config_data)
# Cases where pathogenic diagnosed mutation is not in geneList
@progress_bar("Get pathogenic genes in geneList")
def pathogenic_genes_process(cases):
for case_id, case_obj in cases.items():
yield case_id, case_obj.pathogenic_gene_in_gene_list(omim_obj)
qc_pathongenic_passed = dict(c for c in pathogenic_genes_process(qc_passed)
if not c[1][0])
# Compiled stats to be dumped into a json file
qc_output = {
"failed": qc_failed_msg,
"benign_excluded": qc_benign_passed,
"pathogenic_missing": qc_pathongenic_passed,
from lib.api import mutalyzer, jannovar, omim, phenomizer, aws_download, lab from lib import errorfixer MUTALYZER_INST = mutalyzer.Mutalyzer() JANNOVAR_INST = jannovar.JannovarClient() OMIM_INST = omim.Omim() PHENOMIZER_INST = phenomizer.PhenomizerService() ERRORFIXER_INST = errorfixer.ErrorFixer() AWS_INST = aws_download.AWSBucket() LAB_INST = lab.Lab()
