SraxIO.py

#!/usr/bin/env python

import csv
from .Interfaces import hAMRonizedResultIterator
from hAMRonization.constants import GENE_PRESENCE

required_metadata = [
    "analysis_software_version",
    "reference_database_version",
    "reference_database_name",
    "input_file_name",
]


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

        self.field_mapping = {
            "Locus ID": None,
            "# Sequences": None,
            "ARG": "gene_symbol",
            "Coverage (%)": "coverage_percentage",
            "Identity (%)": "sequence_identity",
            "Drug class": "drug_class",
            "Gene accession ID": "reference_accession",
            "Gene description": "gene_name",
            "AMR detection model": None,
        }

        super().__init__(source, self.field_mapping, self.metadata)

    def parse(self, handle):
        """
        Read each and return it
        """
        # skip any manually specified fields for later
        reader = csv.DictReader(handle, delimiter="\t")
        for result in reader:
            yield self.hAMRonize(result, self.metadata)