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FAextractFirstN.py
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FAextractFirstN.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
from Bio import SeqIO
def FAextractN(sequence, n, output):
"""Well exclude some ids from a multifasta file
"""
fasta_seq = SeqIO.parse(sequence, 'fasta')
buffer_seqs =[]
for i in range(n):
record = fasta_seq.next()
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("-n", "--number", help="Filter n first sequences", type=int, required=True)
parser.add_argument("-o", "--output", help="Output file name (.fasta format)", required=True)
args = parser.parse_args()#pylint: disable=invalid-name
FAextractN(args.sequence, args.number, args.output)