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run_prokka_forall.py
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run_prokka_forall.py
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#!/user/bin/env python3
"""
Author: Gustavo Tamasco
Script to run:
The script takes:
Run the code by: ex_p5.py <reference_fasta_file> <related_fasta_file>
"""
# import statements
from sys import argv
import os.path
import subprocess
# functions and classes
def get_file(path):
"""This function creates the path for all your files
input: is a string with the path to your folder containing all files
Out: is a list of strings containing the path of all files
"""
files = []
for r, d, f in os.walk(path):
for file in f:
if '.fasta' in file:
files.append(os.path.join(r,file))
return files
def run_prokka(files):
for file in files:
out_name = file.split("/")[-1][0:-6]
prokka_out = "prokka_{0}".format(out_name)
if os.path.exists(prokka_out):
print("{0} already exists".format(prokka_out))
else:
cmd_prokka = "prokka --kingdom Bacteria --outdir prokka_{0} {1}".format(out_name, file)
exit_message = subprocess.check_call(cmd_prokka, shell=True)
print("Exit status: {0}".format(exit_message))
print("{0} was created".format(out_name))
def main():
"""Main code of the script"""
# only thing that need to be changed is the location folder
#path = "/Users/gustavotamasco/pantoea_pangenome/all_genomes2"
dirpath = os.getcwd()
os.chdir(dirpath)
files = get_file(dirpath)
run_prokka(files)
# main
if __name__ == '__main__':
main()