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#!/usr/bin/env python3
"""
This script modifies the ARGannot_r3.fasta file (comes with SRST2) for use with Kleborate.
Specifically, it removes alleles which are not in the ARGannot_clustered80_r3.csv file.
It takes two arguments:
1) SRST2's copy of ARGannot_r3.fasta
2) the ARGannot_clustered80_r3.csv file made by make_argannot_csv.py
Usage:
./make_argannot_fasta.py path/to/srst2/data/ARGannot_r3.fasta ARGannot_clustered80_r3.csv > ARGannot_r3.fasta
"""
import sys
def main():
argannot_fasta_filename = sys.argv[1]
argannot_csv_filename = sys.argv[2]
allele_names = set()
with open(argannot_csv_filename, 'rt') as argannot_csv_file:
for line in argannot_csv_file:
allele_names.add(line.split(',')[4])
fasta_seqs = load_fasta(argannot_fasta_filename)
fasta_seqs = sorted(fasta_seqs, key=fasta_sorting_key)
for name, seq in fasta_seqs:
name = name.replace('NimB_Nitroimidazole_Gene', 'NimB') # fix verbose gene name
name = name.replace('_Colistin__', '_Col__') # colistin class name to just three letters
name = name.replace('_Agly__', '_AGly__') # fix capitalisation
allele_name = name.split('__')[2]
if allele_name in allele_names:
print('>' + name)
print(seq, end='')
def load_fasta(filename):
"""Returns the names and sequences for the given fasta file."""
fasta_seqs = []
with open(filename, 'rt') as fasta_file:
name = ''
sequence = ''
for line in fasta_file:
stripped_line = line.strip()
if not stripped_line:
continue
if stripped_line[0] == '>': # Header line = start of new contig
if name:
fasta_seqs.append((name, sequence))
sequence = ''
name = stripped_line[1:]
else:
sequence += line
if name:
fasta_seqs.append((name, sequence))
return fasta_seqs
def fasta_sorting_key(fasta_record):
"""
This function defines a sorting key for fasta so 'TEM-2' will come before 'TEM-10', etc.
"""
name_parts = fasta_record[0].split()[0].split('__')
return int(name_parts[0]), int(name_parts[3])
if __name__ == '__main__':
main()
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