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#!/usr/bin/python3
import sys
from Bio import SeqIO
if len(sys.argv) < 4:
print("Usage:", sys.argv[0], "<contigs_file> <file with names> <output> [<operation mode>]")
print("Operation mode is \"retain\" (default) or \"remove\"")
sys.exit(1)
f_n = sys.argv[1]
names_f = open(sys.argv[2], "r")
names = set(l.strip() for l in names_f.readlines())
input_seq_iterator = SeqIO.parse(open(f_n, "r"), "fasta")
filtered_iterator = (record for record in input_seq_iterator \
if record.name in names)
if (len(sys.argv) == 5):
if sys.argv[4] == "remove":
filtered_iterator = (record for record in input_seq_iterator \
if record.name not in names)
else:
if sys.argv[4] != "retain":
print("Wrong operation mode")
output_handle = open(sys.argv[3], "w")
SeqIO.write(filtered_iterator, output_handle, "fasta")
output_handle.close()
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