FAfilterByLenght.py

#!/usr/bin/env python
# -*- coding: utf-8 -*-
from Bio import SeqIO

def FAfilterByLength(sequence, lengths, output_fasta):
    """Well exclude some ids from a multifasta file
    """
    fasta_seq = SeqIO.parse(sequence, 'fasta')
    buffer_seqs = []
    for record in fasta_seq:
        if str(len(record.seq)) in lengths:
            buffer_seqs.append(record)
    SeqIO.write(buffer_seqs, output_fasta, "fasta")

if __name__ == "__main__":
    import argparse
    parser = argparse.ArgumentParser()#pylint: disable=invalid-name
    parser.add_argument("-s", "--sequence", help="Sequence file (.fasta)", required=True)
    parser.add_argument("-l", "--lenghts", help="Exclude some ids", action='append')
    parser.add_argument("-o", "--output", help="Output file name (.fasta format)", required=True)
    args = parser.parse_args()#pylint: disable=invalid-name
    FAfilterByLength(args.sequence, args.lenghts, args.output)