fasta_cleanner.py

#!/usr/bin/env python3
# -*- coding: utf-8 -*-

###############################################################################
#### Goal: remove "-" from begining of lines in FASTA files                 
#### Usage: python fasta_cleaner.py /path/to/directory_wt_all_files/ 
#### Note: provide full path!                                          
###############################################################################

import argparse
import fileinput
import os, sys

parser=argparse.ArgumentParser(
    description='''Goal: remove "-" from begining of lines in FASTA files.''')

__file__ = "orf_annotation.py"
__author__ = 'Sandra Godinho Silva (sandragodinhosilva@gmail.com)'
__version__ = '0.2'
__date__ = '05-12-2020'

parser.add_argument('inputDirectory', 
		help='Specify the directory containing *.fa files')

# Execute parse_args()
args = parser.parse_args()

inputDirectory = sys.argv[1]
###############################################################################
curdir = inputDirectory
os.chdir(curdir)

entries = os.listdir(curdir)

print("Starting...")

for filename in entries:
    if ".fa" in filename:
        filepath = os.path.join(curdir, filename)
        with fileinput.FileInput(filepath, inplace=True) as file: 
            for line in file:
                if line.strip().startswith("-"):
                    line = line.replace("-", "")
                sys.stdout.write(line)
            fileinput.close()
            
print("Removed '-' from the beginning of all lines that started with it.")

###############################################################################