Srst2IO.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",
    "input_file_name",
]


class Srst2Iterator(hAMRonizedResultIterator):
    def __init__(self, source, metadata):
        metadata["analysis_software_name"] = "srst2"
        metadata["genetic_variation_type"] = GENE_PRESENCE
        self.metadata = metadata

        self.field_mapping = {
            "Sample": "input_file_name",
            "DB": "reference_database_name",
            "gene": "gene_symbol",
            "allele": "gene_name",
            "coverage": "coverage_percentage",
            "depth": "coverage_depth",
            "diffs": None,
            "uncertainty": None,
            "divergence": None,
            # needs checked if this is correct
            "length": "reference_gene_length",
            "maxMAF": None,
            "clusterid": None,
            "seqid": "reference_accession",
            "annotation": 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)