def test_amrplusplus():
metadata = {
"analysis_software_version": "0.0.1",
"reference_database_version": "2019-Jul-28",
'input_file_name': 'Dummy'
}
parsed_report = hAMRonization.parse("dummy/amrplusplus/gene.tsv", metadata,
"amrplusplus")
for result in parsed_report:
# assert mandatory fields
assert result.input_file_name == 'Dummy'
assert result.gene_symbol == 'OQXA'
assert result.gene_name == 'Drug_and_biocide_RND_efflux_pumps'
assert result.reference_database_id == 'megares'
assert result.reference_database_version == '2019-Jul-28'
assert result.reference_accession == 'MEG_4334'
assert result.analysis_software_name == 'amrplusplus'
assert result.analysis_software_version == '0.0.1'
# optional fields - present in dummy dataset
assert result.coverage_percentage == 96.7687
assert result.drug_class == 'Drug_and_biocide_resistance'
# missing data in report
assert result.sequence_identity is None
assert result.input_sequence_id is None
assert result.input_gene_start is None
assert result.input_gene_stop is None
assert result.strand_orientation is None
assert result.reference_gene_length is None
assert result.input_gene_length is None
assert result.antimicrobial_agent is None
assert result.reference_protein_length is None
assert result.coverage_depth is None
assert result.coverage_ratio is None
assert result.input_protein_length is None
assert result.resistance_mechanism is None
assert result.input_protein_start is None
assert result.input_protein_stop is None
assert result.reference_protein_start is None
assert result.reference_protein_stop is None
assert result.reference_gene_start is None
assert result.reference_gene_stop is None
def test_rgi():
metadata = {
"analysis_software_version": "5.1.0",
"reference_database_version": "2019-Jul-28",
"input_file_name": "Dummy"
}
parsed_report = hAMRonization.parse("dummy/rgi/rgi.txt", metadata, "rgi")
for result in parsed_report:
# assert mandatory fields
assert result.input_file_name == 'Dummy'
assert result.gene_symbol == 'oqxA'
assert result.gene_name == 'resistance-nodulation-cell division (RND) antibiotic efflux pump'
assert result.reference_database_id == 'CARD'
assert result.reference_database_version == '2019-Jul-28'
assert result.reference_accession == '3003922'
assert result.analysis_software_name == 'rgi'
assert result.analysis_software_version == '5.1.0'
# optional fields - present in dummy dataset
assert result.input_sequence_id == 'NZ_LR792628.1_1289'
assert result.input_gene_start == 1333608
assert result.input_gene_stop == 1334783
assert result.strand_orientation == '-'
assert result.drug_class == 'fluoroquinolone antibiotic; glycylcycline; tetracycline antibiotic; diaminopyrimidine antibiotic; nitrofuran antibiotic'
assert result.sequence_identity == 99.49
assert result.coverage_percentage == 100
assert result.resistance_mechanism == 'antibiotic efflux'
# missing data in report
assert result.reference_gene_length is None
assert result.coverage_depth is None
assert result.input_gene_length is None
assert result.antimicrobial_agent is None
assert result.reference_protein_length is None
assert result.coverage_ratio is None
assert result.input_protein_length is None
assert result.input_protein_start is None
assert result.input_protein_stop is None
assert result.reference_protein_start is None
assert result.reference_protein_stop is None
assert result.reference_gene_start is None
assert result.reference_gene_stop is None
def test_resfinder():
metadata = {
"analysis_software_version": "0.0.1",
"reference_database_version": "2019-Jul-28"
}
parsed_report = hAMRonization.parse("dummy/resfinder/data_resfinder.json",
metadata, "resfinder")
for result in parsed_report:
# assert mandatory fields
assert result.input_file_name == 'Dummy'
assert result.gene_symbol == 'oqxA'
assert result.gene_name == 'oqxA_1_EU370913'
assert result.reference_database_id == 'resfinder'
assert result.reference_database_version == '2019-Jul-28'
assert result.reference_accession == 'EU370913'
assert result.analysis_software_name == 'resfinder.py' # drop the .py?
assert result.analysis_software_version == '0.0.1'
# optional fields - present in dummy dataset
assert result.input_sequence_id == 'NZ_LR792628.1 Klebsiella pneumoniae isolate SB5881 chromosome SB5881_omosome'
assert result.input_gene_start == 1333608
assert result.input_gene_stop == 1334783
assert result.strand_orientation == '+'
assert result.drug_class == 'Quinolone resistance'
assert result.sequence_identity == 99.57
assert result.reference_gene_length == 1176
assert result.coverage_depth is None
assert result.coverage_percentage == 100
# missing data in report
assert result.input_gene_length is None
assert result.antimicrobial_agent is None
assert result.reference_protein_length is None
assert result.coverage_ratio is None
assert result.input_protein_length is None
assert result.resistance_mechanism is None
assert result.input_protein_start is None
assert result.input_protein_stop is None
assert result.reference_protein_start is None
assert result.reference_protein_stop is None
assert result.reference_gene_start is None
assert result.reference_gene_stop is None
def test_mykrobe():
metadata = {}
parsed_report = hAMRonization.parse("dummy/mykrobe/mykrobe.json", metadata, "mykrobe")
for result in parsed_report:
# assert mandatory fields
assert result.input_file_name == 'mykrobe.json'
assert result.gene_symbol == 'rpoB'
assert result.gene_name == 'rpoB'
assert result.reference_database_id == 'tb/tb-species-170421.fasta.gz;tb/tb-hunt-probe-set-jan-03-2019.fasta.gz;tb/tb.lineage.20200930.probes.fa.gz'
assert result.reference_database_version == 'v0.10.0'
assert result.reference_accession == 'NC_000962.3'
assert result.analysis_software_name == 'mykrobe'
assert result.analysis_software_version == 'v0.10.0'
assert result.genetic_variation_type == 'protein_variant'
# optional fields - present in dummy dataset
assert result.drug_class == 'Rifampicin' # TODO: this is not following the spec as this is not an ARO term, what to do?
assert result.coverage_percentage == 100
assert result.coverage_depth == 60
assert result.protein_mutation == "p.Ser450Leu"
assert result.variant_frequency == 0.6 # TODO: confirm with tool authors that this is correct calculation
# assert result.nucleotide_mutation == "" # TODO: this is not working yet
# missing data in report
assert result.sequence_identity is None
assert result.reference_gene_length is None
assert result.input_gene_length is None
assert result.input_sequence_id is None
assert result.input_gene_start is None
assert result.input_gene_stop is None
assert result.strand_orientation is None
assert result.antimicrobial_agent is None
assert result.reference_protein_length is None
assert result.coverage_ratio is None
assert result.input_protein_length is None
assert result.resistance_mechanism is None
assert result.input_protein_start is None
assert result.input_protein_stop is None
assert result.reference_protein_start is None
assert result.reference_protein_stop is None
assert result.reference_gene_start is None
assert result.reference_gene_stop is None
def test_csstar():
metadata = {"analysis_software_version": "0.0.1", "reference_database_version": "2019-Jul-28",
"input_file_name": "Dummy", "reference_database_id": 'ResFinder'}
parsed_report = hAMRonization.parse("dummy/sstar/report.tsv", metadata, "csstar")
for result in parsed_report:
# assert mandatory fields
assert result.input_file_name == 'Dummy'
assert result.gene_symbol == 'oqxA'
assert result.gene_name == 'oqxA'
assert result.reference_database_id == 'ResFinder'
assert result.reference_database_version == '2019-Jul-28'
assert result.reference_accession == 'oqxA'
assert result.analysis_software_name == 'csstar'
assert result.analysis_software_version == '0.0.1'
# optional fields - present in dummy dataset
assert result.reference_gene_length == 1176
assert result.input_gene_length == 1176
assert result.sequence_identity == 99.575
assert result.input_sequence_id == 'NZ_LR792628.1'
# missing data in report
assert result.coverage_percentage is None
assert result.coverage_depth is None
assert result.drug_class is None
assert result.input_gene_start is None
assert result.input_gene_stop is None
assert result.strand_orientation is None
assert result.antimicrobial_agent is None
assert result.reference_protein_length is None
assert result.coverage_ratio is None
assert result.input_protein_length is None
assert result.resistance_mechanism is None
assert result.input_protein_start is None
assert result.input_protein_stop is None
assert result.reference_protein_start is None
assert result.reference_protein_stop is None
assert result.reference_gene_start is None
assert result.reference_gene_stop is None
assert result.variant_frequency is None
assert result.genetic_variation_type is None
def test_amrfinder():
metadata = {"analysis_software_version": "3.6.10", "reference_database_version": "2019-Jul-28",
'input_file_name': 'Dummy'}
parsed_report = hAMRonization.parse("dummy/amrfinder/report.tsv", metadata, "amrfinderplus")
for result in parsed_report:
# assert mandatory fields
assert result.input_file_name == 'Dummy'
assert result.gene_symbol == 'oqxA'
assert result.gene_name == 'multidrug efflux RND transporter periplasmic adaptor subunit OqxA'
assert result.reference_database_id == 'NCBI Reference Gene Database'
assert result.reference_database_version == '2019-Jul-28'
assert result.reference_accession == 'WP_002914189.1'
assert result.analysis_software_name == 'amrfinderplus'
assert result.analysis_software_version == '3.6.10'
# optional fields - present in dummy dataset
assert result.sequence_identity == 99.49
assert result.input_sequence_id == 'NZ_LR792628.1'
assert result.input_gene_start == 1333611
assert result.input_gene_stop == 1334783
assert result.strand_orientation == '-'
assert result.coverage_percentage == 100
assert result.drug_class == 'PHENICOL/QUINOLONE'
assert result.antimicrobial_agent == 'PHENICOL/QUINOLONE'
assert result.reference_protein_length == 391
assert result.input_protein_length == 391
# missing data in report
assert result.reference_gene_length == None
assert result.input_gene_length == None
assert result.coverage_depth is None
assert result.coverage_ratio is None
assert result.resistance_mechanism is None
assert result.input_protein_start is None
assert result.input_protein_stop is None
assert result.reference_protein_start is None
assert result.reference_protein_stop is None
assert result.reference_gene_start is None
assert result.reference_gene_stop is None
assert result.variant_frequency is None
assert result.genetic_variation_type is None
def test_groot():
metadata = {"analysis_software_version": "0.0.1", "reference_database_version": "2019-Jul-28",
"input_file_name": "Dummy", 'reference_database_id': "argannot"}
parsed_report = hAMRonization.parse("dummy/groot/groot_report.tsv", metadata, "groot")
for result in parsed_report:
# assert mandatory fields
assert result.input_file_name == 'Dummy'
assert result.gene_symbol == 'OqxA'
assert result.gene_name == 'OqxA.3003470.EU370913'
assert result.reference_database_id == 'argannot'
assert result.reference_database_version == '2019-Jul-28'
assert result.reference_accession == 'OqxA.3003470.EU370913.4407527-4408202.4553'
assert result.analysis_software_name == 'groot'
assert result.analysis_software_version == '0.0.1'
# optional fields - present in dummy dataset
assert result.reference_gene_length == 1176
assert result.coverage_depth == 266
# missing data in report
assert result.input_sequence_id is None
assert result.input_gene_start is None
assert result.input_gene_stop is None
assert result.strand_orientation is None
assert result.resistance_mechanism is None
assert result.input_gene_length is None
assert result.antimicrobial_agent is None
assert result.reference_protein_length is None
assert result.coverage_ratio is None
assert result.input_protein_length is None
assert result.input_protein_start is None
assert result.input_protein_stop is None
assert result.reference_protein_start is None
assert result.reference_protein_stop is None
assert result.reference_gene_start is None
assert result.reference_gene_stop is None
assert result.drug_class is None
assert result.sequence_identity is None
assert result.coverage_percentage is None
assert result.variant_frequency is None
assert result.genetic_variation_type is None
def test_deeparg():
metadata = {"analysis_software_version": "0.0.1", "reference_database_version": "2019-Jul-28",
'input_file_name': 'Dummy'}
parsed_report = hAMRonization.parse("dummy/deepARG/output.mapping.ARG.", metadata, "deeparg")
for result in parsed_report:
# assert mandatory fields
assert result.input_file_name == 'Dummy'
assert result.gene_symbol == 'OQXA'
assert result.gene_name == 'YP_001693237.1|FEATURES|oqxA|multidrug|oqxA'
assert result.reference_database_id == 'deeparg_db'
assert result.reference_database_version == '2019-Jul-28'
assert result.reference_accession == 'YP_001693237.1'
assert result.analysis_software_name == 'deeparg'
assert result.analysis_software_version == '0.0.1'
# optional fields - present in dummy dataset
assert result.drug_class == 'multidrug'
assert result.sequence_identity == 94.6
assert result.input_sequence_id == "SNL153:124:HLM5WBCXX:1:2207:7453:53826"
assert result.input_gene_start == 49
assert result.input_gene_stop == 84
# missing data in report
assert result.coverage_percentage is None
assert result.strand_orientation is None
assert result.reference_gene_length is None
assert result.input_gene_length is None
assert result.antimicrobial_agent is None
assert result.reference_protein_length is None
assert result.coverage_depth is None
assert result.coverage_ratio is None
assert result.input_protein_length is None
assert result.resistance_mechanism is None
assert result.input_protein_start is None
assert result.input_protein_stop is None
assert result.reference_protein_start is None
assert result.reference_protein_stop is None
assert result.reference_gene_start is None
assert result.reference_gene_stop is None
assert result.variant_frequency is None
assert result.genetic_variation_type is None
def test_srax():
metadata = {"analysis_software_version": "5.1.0", "reference_database_version": "2019-Jul-28",
"input_file_name": "Dummy", 'reference_database_id': "resfinder"}
parsed_report = hAMRonization.parse("dummy/srax/sraX_detected_ARGs.tsv", metadata, "srax")
for result in parsed_report:
# assert mandatory fields
assert result.input_file_name == 'Dummy'
assert result.gene_symbol == 'oqxA'
assert result.gene_name == 'RND efflux pump conferring resistance to fluoroquinolone'
assert result.reference_database_id == 'resfinder'
assert result.reference_database_version == '2019-Jul-28'
assert result.reference_accession == 'NG_048024.1'
assert result.analysis_software_name == 'srax'
assert result.analysis_software_version == '5.1.0'
# optional fields - present in dummy dataset
assert result.drug_class == 'Fluoroquinolone'
assert result.sequence_identity == 99.7
assert result.coverage_percentage == 100
# missing data in report
assert result.input_sequence_id is None
assert result.input_gene_start is None
assert result.input_gene_stop is None
assert result.strand_orientation is None
assert result.resistance_mechanism is None
assert result.reference_gene_length is None
assert result.coverage_depth is None
assert result.input_gene_length is None
assert result.antimicrobial_agent is None
assert result.reference_protein_length is None
assert result.coverage_ratio is None
assert result.input_protein_length is None
assert result.input_protein_start is None
assert result.input_protein_stop is None
assert result.reference_protein_start is None
assert result.reference_protein_stop is None
assert result.reference_gene_start is None
assert result.reference_gene_stop is None
assert result.variant_frequency is None
assert result.genetic_variation_type is None
def test_kmerresistance():
metadata = {"analysis_software_version": "0.0.1", "reference_database_version": "2019-Jul-28",
'input_file_name': 'Dummy'}
parsed_report = hAMRonization.parse("dummy/kmerresistance/results.res", metadata, "kmerresistance")
for result in parsed_report:
# assert mandatory fields
assert result.input_file_name == 'Dummy'
assert result.gene_symbol == 'oqxA'
assert result.gene_name == 'oqxA_1'
assert result.reference_database_id == 'resfinder'
assert result.reference_database_version == '2019-Jul-28'
assert result.reference_accession == 'oqxA_1_EU370913'
assert result.analysis_software_name == 'kmerresistance'
assert result.analysis_software_version == '0.0.1'
# optional fields - present in dummy dataset
assert result.sequence_identity == 99.57
assert result.reference_gene_length == 1176
assert result.coverage_depth == 96.31
assert result.coverage_percentage == 100
# missing data in report
assert result.input_sequence_id is None
assert result.input_gene_start is None
assert result.input_gene_stop is None
assert result.strand_orientation is None
assert result.drug_class is None
assert result.input_gene_length is None
assert result.antimicrobial_agent is None
assert result.reference_protein_length is None
assert result.coverage_ratio is None
assert result.input_protein_length is None
assert result.resistance_mechanism is None
assert result.input_protein_start is None
assert result.input_protein_stop is None
assert result.reference_protein_start is None
assert result.reference_protein_stop is None
assert result.reference_gene_start is None
assert result.reference_gene_stop is None
assert result.variant_frequency is None
assert result.genetic_variation_type is None
def test_ariba():
metadata = {"analysis_software_version": "0.0.1", "reference_database_version": "2019-Jul-28",
'input_file_name': 'Dummy', 'reference_database_id': 'ncbi'}
parsed_report = hAMRonization.parse("dummy/ariba/report.tsv", metadata, "ariba")
for result in parsed_report:
# assert mandatory fields
assert result.input_file_name == 'Dummy'
assert result.gene_symbol == 'oqxA'
assert result.gene_name == 'oqxA.3003922.EU370913.1.46651_47827.5460'
assert result.reference_database_id == 'ncbi'
assert result.reference_database_version == '2019-Jul-28'
assert result.reference_accession == 'oqxA.3003922.EU370913.1.46651_47827.5460'
assert result.analysis_software_name == 'ariba'
assert result.analysis_software_version == '0.0.1'
# optional fields - present in dummy dataset
assert result.sequence_identity == 99.57
assert result.input_sequence_id == 'oqxA.l15.c17.ctg.1'
assert result.reference_gene_length == 1176
assert result.coverage_depth == 64.2
# missing data in report
assert result.input_gene_start is None
assert result.input_gene_stop is None
assert result.strand_orientation is None
assert result.coverage_percentage is None
assert result.drug_class is None
assert result.input_gene_length is None
assert result.antimicrobial_agent is None
assert result.reference_protein_length is None
assert result.coverage_ratio is None
assert result.input_protein_length is None
assert result.resistance_mechanism is None
assert result.input_protein_start is None
assert result.input_protein_stop is None
assert result.reference_protein_start is None
assert result.reference_protein_stop is None
assert result.reference_gene_start is None
assert result.reference_gene_stop is None
assert result.variant_frequency is None
assert result.genetic_variation_type is None
def test_abricate():
metadata = {"analysis_software_version": "0.9.8", "reference_database_version": "2019-Jul-28"}
parsed_report = hAMRonization.parse("dummy/abricate/report.tsv", metadata, "abricate")
for result in parsed_report:
# assert mandatory fields
assert result.input_file_name == 'Dummy'
assert result.gene_symbol == 'oqxA'
assert result.gene_name == 'multidrug efflux RND transporter periplasmic adaptor subunit OqxA'
assert result.reference_database_id == 'ncbi'
assert result.reference_database_version == '2019-Jul-28'
assert result.reference_accession == 'NG_048024.1'
assert result.analysis_software_name == 'abricate'
assert result.analysis_software_version == '0.9.8'
# optional fields - present in dummy dataset
assert result.sequence_identity == 99.58
assert result.input_sequence_id == 'NZ_LR792628.1'
assert result.input_gene_start == 1333608
assert result.input_gene_stop == 1334783
assert result.strand_orientation == '-'
assert result.coverage_percentage == 100
assert result.drug_class == 'PHENICOL;QUINOLONE'
# missing data in report
assert result.coverage_depth is None
assert result.coverage_ratio is None
assert result.reference_gene_length is None
assert result.reference_protein_length is None
assert result.input_gene_length is None
assert result.input_protein_length is None
assert result.antimicrobial_agent is None
assert result.resistance_mechanism is None
assert result.input_protein_start is None
assert result.input_protein_stop is None
assert result.reference_protein_start is None
assert result.reference_protein_stop is None
assert result.reference_gene_start is None
assert result.reference_gene_stop is None
assert result.variant_frequency is None
assert result.genetic_variation_type is None
def test_srst2():
metadata = {"analysis_software_version": "0.0.1", "reference_database_version": "2019-Jul-28",
"input_file_name": "Dummy"}
parsed_report = hAMRonization.parse("dummy/srst2/report.tsv", metadata, "srst2")
for result in parsed_report:
# assert mandatory fields
assert result.input_file_name == 'Dummy'
assert result.gene_symbol == 'oqxA'
assert result.gene_name == 'oqxA'
assert result.reference_database_id == 'ResFinder'
assert result.reference_database_version == '2019-Jul-28'
assert result.reference_accession == '1995'
assert result.analysis_software_name == 'srst2'
assert result.analysis_software_version == '0.0.1'
# optional fields - present in dummy dataset
assert result.coverage_percentage == 100
assert result.reference_gene_length == 660
assert result.coverage_depth == 75.852
# missing data in report
assert result.drug_class is None
assert result.sequence_identity is None
assert result.input_sequence_id is None
assert result.input_gene_start is None
assert result.input_gene_stop is None
assert result.strand_orientation is None
assert result.input_gene_length is None
assert result.antimicrobial_agent is None
assert result.reference_protein_length is None
assert result.coverage_ratio is None
assert result.input_protein_length is None
assert result.resistance_mechanism is None
assert result.input_protein_start is None
assert result.input_protein_stop is None
assert result.reference_protein_start is None
assert result.reference_protein_stop is None
assert result.reference_gene_start is None
assert result.reference_gene_stop is None
def generic_cli_interface():
"""
Generate a generic tool report parser that passes to the tool specific
parser
"""
parser = argparse.ArgumentParser(description="Convert AMR gene detection "
"tool output(s) to "
"hAMRonization specification"
" format",
prog='hamronize',
usage='hamronize <tool> <options>')
parser.add_argument('-v',
'--version',
action='version',
version=f"%(prog)s {hAMRonization.__version__}")
# add tool specific parsers
subparser = parser.add_subparsers(title="Tools with hAMRonizable reports",
help='',
dest='analysis_tool')
for analysis_tool in hAMRonization._RequiredToolMetadata.keys():
subparser = generate_tool_subparser(subparser, analysis_tool)
# add summarize subparser
# not very pretty to have this tied into the analysis tools list
# but there still doesn't seem a good way to group subparsers in
# the argparse library
description = "Concatenate and summarize AMR detection reports"
usage = "hamronize summarize <options> <list of reports>"
summarize_help = "Provide a list of paths to the reports you wish "\
"to summarize"
summarize_subparser = subparser.add_parser("summarize",
description=description,
usage=usage,
help=summarize_help)
summarize_subparser.add_argument("-t",
"--summary_type",
choices=['tsv', 'json', 'interactive'],
default='tsv',
help="Which summary report format to "
"generate")
summarize_subparser.add_argument("-o",
"--output",
type=str,
default=None,
help="Output file path for summary")
summarize_subparser.add_argument("hamronized_reports",
nargs="+",
help="list of hAMRonized reports")
args = parser.parse_args()
if args.analysis_tool and args.analysis_tool != 'summarize':
required_mandatory_metadata = \
hAMRonization._RequiredToolMetadata[args.analysis_tool]
metadata = {
field: getattr(args, field)
for field in required_mandatory_metadata
}
# parse reports and write as appropriate (only first report with head
# in tsv mode)
# check number of reports and append correctly if >1
total_report_count = len(args.report)
for report_number, report in enumerate(args.report):
parsed_report = hAMRonization.parse(report, metadata,
args.analysis_tool)
parsed_report.write(report_number=report_number,
total_report_count=total_report_count,
output_location=args.output,
output_format=args.format)
elif args.analysis_tool == 'summarize':
hAMRonization.summarize.summarize_reports(args.hamronized_reports,
args.summary_type,
args.output)
exit(0)
else:
parser.print_help()
exit(1)
