/
AbricateIO.py
43 lines (36 loc) · 1.42 KB
/
AbricateIO.py
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#!/usr/bin/env python
import csv
from .Interfaces import hAMRonizedResultIterator
from hAMRonization.constants import GENE_PRESENCE
required_metadata = ["analysis_software_version", "reference_database_version"]
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",
"ACCESSION": "reference_accession",
"RESISTANCE": "drug_class",
"COVERAGE_MAP": None,
"GAPS": 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)