#!/usr/bin/env python

from Bio.Seq import Seq

from Bio.Alphabet import IUPAC

from Bio import SeqIO

from Bio.SeqRecord import SeqRecord

from Bio.SeqFeature import SeqFeature, FeatureLocation

import random

import os

import subprocess

import re

import getopt

import sys

import signal

from math import ceil

opts, arguments = getopt.getopt(sys.argv[1:], "f:",

["fasta"])

for option, argument in opts:

if option in ("-f", "--fasta"):

fasta_file = argument

record_dict = SeqIO.index(argument, "fasta")

pwd = os.getcwd()

def find_cds ():

return 0

def write_file(object_name, file_name, mode):

handle.close()

i = 1

check = 0

for keys in record_dict:

print i

check = find_cds()

if check == 0:

write_file(record_dict[keys].id, "/error_sequences.txt", "a" )

else:

pass

i +=1