INNER CODE UNIT · Python

AbricateIterator

pha4ge/hAMRonization · hAMRonization/AbricateIO.py:10

class AbricateIterator(hAMRonizedResultIterator):
    def __init__(self, source, metadata):
        metadata["analysis_software_name"] = "abricate"
        metadata["genetic_variation_type"] = GENE_PRESENCE
        self.metadata = metadata

        self.field_mapping = {
            "#FILE": "input_file_name",
            "SEQUENCE": "input_sequence_id",
            "START": "input_gene_start",
            "END": "input_gene_stop",
            "STRAND": "strand_orientation",
            "GENE": "gene_symbol",
            "PRODUCT": "gene_name",
            "%COVERAGE": "coverage_percentage",
            "COVERAGE": None,
            "%IDENTITY": "sequence_identity",
            "DATABASE": "reference_database_name",

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