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#!/usr/bin/env python3
"""
This script modifies the ARGannot_clustered80_r3.csv file (comes with SRST2) for use with
Kleborate. Specifically, it does two things:
1) Add beta-lactamase description and class columns
2) Removes some genes not suitable for inclusion in Kleborate
It takes two arguments:
1) SRST2's copy of the ARGannot_clustered80_r3.csv file
2) the table made by bla_info.py
Usage:
./make_argannot_csv.py path/to/srst2/data/ARGannot_clustered80_r3.csv bla_info_table > ARGannot_clustered80_r3.csv
"""
import sys
argannot_csv_filename = sys.argv[1]
bla_parse_output_filename = sys.argv[2]
descriptions = {}
bla_classes = {}
with open(bla_parse_output_filename, 'rt') as bla_parse_output_file:
for line in bla_parse_output_file:
allele, description, bla_class = line.strip().split('\t')
descriptions[allele] = description
bla_classes[allele] = bla_class
new_csv_lines = []
with open(argannot_csv_filename, 'rt') as argannot_csv_file:
for line in argannot_csv_file:
stripped_line = line.rstrip()
if stripped_line.startswith('clusterid,queryID'):
print(stripped_line + ',bla_description,bla_class')
continue
# Fix verbose gene name
stripped_line = stripped_line.replace('NimB_Nitroimidazole_Gene', 'NimB')
# Fix resistance class capitalisation
stripped_line = stripped_line.replace(',Agly,', ',AGly,')
line_parts = stripped_line.split(',')
res_class = line_parts[2]
gene = line_parts[3]
allele = line_parts[4]
# Skip some genes not relevant for Kleborate.
if gene == 'OqxB' or gene == 'OqxA' or gene == 'Far1' or gene == 'OptrA':
continue
# Fix Colistin class name to just three letters.
if res_class == 'Colistin':
stripped_line = stripped_line.replace(',Colistin,', ',Col,')
if line_parts[2] == 'Bla' and allele in bla_classes:
new_csv_lines.append(stripped_line + ',' + descriptions[allele] + ',' + bla_classes[allele])
else:
new_csv_lines.append(stripped_line + ',NA,NA')
# Sort so 'TEM-2' will come before 'TEM-10', etc.
new_csv_lines = sorted(new_csv_lines, key=lambda x: (int(x.split(',')[0]), int(x.split(',')[5])))
for line in new_csv_lines:
print(line)
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