INNER CODE UNIT · Python
AmrPlusPlusIterator
pha4ge/hAMRonization · hAMRonization/AmrPlusPlusIO.py:14
class AmrPlusPlusIterator(hAMRonizedResultIterator):
def __init__(self, source, metadata):
metadata["analysis_software_name"] = "amrplusplus"
metadata["reference_database_name"] = "megares"
metadata["genetic_variation_type"] = GENE_PRESENCE
self.metadata = metadata
self.field_mapping = {
# Sample Gene Hits Gene Fraction
"Sample": "input_file_name",
"Gene": None,
"Gene Fraction": "coverage_percentage",
# following will be extacted from gene
"_reference_accession": "reference_accession",
"_gene_name": "gene_name",
"_gene_symbol": "gene_symbol",
"_drug_class": "drug_class",
}