INNER CODE UNIT · Python
__init__
pha4ge/hAMRonization · hAMRonization/AmrFinderPlusIO.py:61
def __init__(self, source, metadata):
metadata["analysis_software_name"] = "amrfinderplus"
metadata["reference_database_name"] = "NCBI Reference Gene Database"
self.metadata = metadata
# We pass None for the field_map as it differs depending on
# whether we return a nucleotide or protein variant detection.
# TODO: refactor field_map out of super's constructor, and make
# it a parameter on super's hARMonize().
super().__init__(source, None, self.metadata)
def parse(self, handle):
"""
Read each and return it
"""
skipped_truncated = 0
reader = csv.DictReader(handle, delimiter="\t")
for result in reader: