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run_mummer.py
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run_mummer.py
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#!/user/bin/env python3
"""
Author: Gustavo Tamasco
Script to run:
The script takes:
"""
# 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' and 'ref' in file:
files.append(os.path.join(r,file))
return files
def run_mummer(files,bb):
for file in files:
out_name = file.split("/")[-1]
mummer_out = "mummer_{0}".format(out_name)
if os.path.exists(mummer_out):
print("{0} already exists".format(mummer_out))
else:
cmd_mummer = "nucmer {0} {1}".format(file, bb)
exit_message = subprocess.check_call(cmd_mummer, 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/PycharmProjects/tcc"
bb_file = '/Users/gustavotamasco/PycharmProjects/tcc/33_1.fasta'
#dirpath = os.getcwd()
#os.chdir(dirpath)
files = get_file(path)
run_mummer(files, bb_file)
# main
if __name__ == '__main__':
main()