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Result.py
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Result.py
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"""AntimicrobialResistanceResult class.
"""
import json
DEFAULTAMRRESULT = {
'input_file_name': '',
'contig': '',
'start': 0,
'stop': 0,
'strand_orientation': '',
'resistance_gene_symbol': '',
'resistance_gene_name': '',
'resistance_gene_allele': '',
'coverage_positions': '',
'coverage_depth': 0.0,
'coverage_percent': 0.0,
'sequence_identity': 0.0,
'reference_database': '',
'reference_database_version': '',
'reference_accession': '',
'reference_length': 0,
'target_length': 0,
'drug_class': '',
'antimicrobial_agent': '',
'analysis_software_name': '',
'analysis_software_version': '',
'resistance_mechanism': '',
}
class AntimicrobialResistanceResult():
"""Class for the management of antimicrobial resistance analysis results."""
def __init__(self, input=None):
"""Initialize the class."""
self.input_file_name = ''
self.contig = ''
self.start = 0
self.stop = 0
self.strand_orientation = 0
self.resistance_gene_symbol = ''
self.resistance_gene_name = ''
self.resistance_gene_allele = ''
self.coverage_positions = ''
self.coverage_depth = 0.0
self.coverage_percent = 0.0
self.sequence_identity = 0.0
self.reference_database = ''
self.reference_database_version = ''
self.reference_accession = ''
self.reference_length = 0
self.target_length = 0
self.drug_class = ''
self.antimicrobial_agent = ''
self.analysis_software_name = ''
self.analysis_software_version = ''
self.resistance_mechanism = ''
if input:
self.read(input)
else:
self.read(DEFAULTAMRRESULT)
def __repr__(self):
return json.dumps(self.__dict__)
def read(self, input):
# TODO: There must be a less verbose way to do this...
try:
self.input_file_name = input['input_file_name']
except KeyError as e:
pass
try:
self.contig = input['contig']
except KeyError as e:
pass
try:
self.start = input['start']
except KeyError as e:
pass
try:
self.stop = input['stop']
except KeyError as e:
pass
try:
self.strand_orientation = input['strand_orientation']
except KeyError as e:
pass
try:
self.resistance_gene_symbol = input['resistance_gene_symbol']
except KeyError as e:
pass
try:
self.resistance_gene_name = input['resistance_gene_name']
except KeyError as e:
pass
try:
self.resistance_gene_allele = input['resistance_gene_allele']
except KeyError as e:
pass
try:
self.coverage_positions = input['coverage_positions']
except KeyError as e:
pass
try:
self.coverage_depth = input['coverage_depth']
except KeyError as e:
pass
try:
self.coverage_percent = input['coverage_percent']
except KeyError as e:
pass
try:
self.sequence_identity = input['sequence_identity']
except KeyError as e:
pass
try:
self.reference_database = input['reference_database']
except KeyError as e:
pass
try:
self.reference_database_version = input['reference_database_version']
except KeyError as e:
pass
try:
self.reference_accession = input['reference_accession']
except KeyError as e:
pass
try:
self.reference_length = input['reference_length']
except KeyError as e:
pass
try:
self.target_length = input['target_length']
except KeyError as e:
pass
try:
self.drug_class = input['drug_class']
except KeyError as e:
pass
try:
self.antimicrobial_agent = input['antimicrobial_agent']
except KeyError as e:
pass
try:
self.analysis_software_name = input['analysis_software_name']
except KeyError as e:
pass
try:
self.analysis_software_version = input['analysis_software_version']
except KeyError as e:
pass
try:
self.resistance_mechanism = input['resistance_mechanism']
except KeyError as e:
pass