#/usr/bin/python

from Bio import SeqIO

import sys

arg1=sys.argv[1]

arg2=sys.argv[2]

arg3=sys.argv[3]

filename = arg1

reads_dict=SeqIO.to_dict(SeqIO.parse(arg2, "fasta"))

with open(arg3, "w") as output_file:

n=0

for record in SeqIO.parse(filename, "fasta"):

if record.id in reads_dict:

#n=n+1

SeqIO.write(record, output_file, "fasta")

else:

#SeqIO.write(record, output_file, "fasta")

n=n+1

print(n)