#!/usr/bin/env python
"""
Script for erasing annoying sequences from FASTA files.
Use `erase_annoying_sequences.py -h` to see an auto-generated description of advanced options.
"""
import argparse
from yamda.sequences import load_fasta_sequences, save_fasta, erase_subsequences
def get_args():
parser = argparse.ArgumentParser(description="Train model.",
epilog='\n'.join(__doc__.strip().split('\n')[1:]).strip(),
formatter_class=argparse.RawTextHelpFormatter)
parser.add_argument('-i', '--input', required=True,
help='Input FASTA file', type=str)
parser.add_argument('-o', '--output', default=None,
help='Output FASTA file of negative sequences', type=str)
args = parser.parse_args()
return args
def main():
args = get_args()
fasta_file = args.input
output_file = args.output
print('Loading sequences from FASTA')
seqs, keys = load_fasta_sequences(fasta_file, return_keys=True)
annoying_subsequences = [
'AAAAAA',
'TTTTTT',
'CCCGCCC',
'GGGCGGG'
]
seqs = erase_subsequences(seqs, annoying_subsequences)
save_fasta(output_file, seqs, keys)
if __name__ == '__main__':
main()
