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amrfinder_wrapper.py
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amrfinder_wrapper.py
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#!/usr/bin/env python
__version__ = "0.0.1"
import os
import sys
import re
import argparse
import textwrap
import pandas as pd
class AMR_Finder:
'''
'''
def __init__(self, assembly):
self.cwd = os.getcwd()
self.assembly = assembly
basename = os.path.basename(self.assembly)
self.sample_name = re.sub('[_.].*', '', basename)
def tab_to_excel(self, tab_file):
excel_file = tab_file.replace('tab', 'xlsx')
df = pd.read_csv(tab_file, sep='\t')
df.to_excel(excel_file)
def run(self,):
sample_name = self.sample_name
os.mkdir("amrfinder")
os.chdir("amrfinder")
print("\n*** Running amrfinder...")
if os.path.isabs(self.assembly):
assembly = f'{self.assembly}'
else:
assembly = f'{self.cwd}/{self.assembly}'
# os.system(f'amrfinder.pl -n {assembly} >> {sample_name}-amrfinder.tab')
os.system(f'amrfinder --nucleotide {assembly} --output {sample_name}-amrfinder.tab')
self.tab_to_excel(f'{sample_name}-amrfinder.tab')
self.amrfinder_file = f'{self.cwd}/amrfinder/{sample_name}-amrfinder.tab'
os.chdir(self.cwd)
self.version = os.popen("amrfinder --version").readlines()[0].split()[0]
if __name__ == "__main__": # execute if directly access by the interpreter
parser = argparse.ArgumentParser(prog='PROG', formatter_class=argparse.RawDescriptionHelpFormatter, description=textwrap.dedent('''\
---------------------------------------------------------
Place description
'''), epilog='''---------------------------------------------------------''')
parser.add_argument('-a', '--assembly', action='store', dest='assembly', required=True, help='FASTA assembly file')
parser.add_argument('-v', '--version', action='version', version=f'{os.path.basename(__file__)}: version {__version__}')
args = parser.parse_args()
print(f'\n{os.path.basename(__file__)} SET ARGUMENTS:')
print(args)
print("\n")
amr_finder = AMR_Finder(args.assembly)
amr_finder.run()
# Created March 2020 by Tod Stuber