logging.debug(record)
raise
for record_mapped in _map_line_to_json(record_parsed, hg19):
yield record_mapped
def load_data(data_folder, version):
# try to get logger from uploader
import logging as loggingmod
global logging
logging = loggingmod.getLogger("clinvar_upload")
import_clinvar_lib(data_folder)
files = glob.glob(os.path.join(data_folder, GLOB_PATTERN))
assert len(
files) == 1, "Expecting only one file matching '%s', got: %s" % (
GLOB_PATTERN, files)
input_file = files[0]
data_generator = rcv_feeder(input_file, version == "hg19")
data_list = list(data_generator)
# TODO: why do we sort this list ? this prevent from using yield/iterator
data_list_sorted = sorted(data_list, key=lambda k: k['_id'])
data_merge_rcv = merge_rcv_accession(data_list_sorted)
return data_merge_rcv
if __name__ == "__main__":
from biothings.utils.mongo import get_data_folder
data_folder = get_data_folder("clinvar")
load_data(data_folder=data_folder)
continue
try:
record_parsed = clinvar.parseString(record, silence=1)
except:
logging.debug(record)
raise
for record_mapped in _map_line_to_json(record_parsed, hg19):
yield record_mapped
def load_data(data_folder, version):
# try to get logger from uploader
import logging as loggingmod
global logging
logging = loggingmod.getLogger("clinvar_upload")
import_clinvar_lib(data_folder)
files = glob.glob(os.path.join(data_folder,GLOB_PATTERN))
assert len(files) == 1, "Expecting only one file matching '%s', got: %s" % (GLOB_PATTERN,files)
input_file = files[0]
data_generator = rcv_feeder(input_file, version == "hg19")
data_list = list(data_generator)
# TODO: why do we sort this list ? this prevent from using yield/iterator
data_list_sorted = sorted(data_list, key=lambda k: k['_id'])
data_merge_rcv = merge_rcv_accession(data_list_sorted)
return data_merge_rcv
if __name__ == "__main__":
from biothings.utils.mongo import get_data_folder
data_folder = get_data_folder("clinvar")
load_data(data_folder=data_folder)