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prep.py
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prep.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
# @Time : 2016/12/8 17:01
# @Author : Runsheng
# @File : prep.py
import os
import shutil
from Bio import SeqIO
from utils import myexe
from glob import glob
def check_depend():
"""
todo: check the required software needed for mitovar
:return:
"""
pass
def fasta_shuffle(ref_file, out_file, file_type="fasta"):
ref_dict=SeqIO.to_dict(SeqIO.parse(ref_file, file_type))
fw=open(out_file, "w")
k_used_set=set()
for k in ref_dict.keys():
if "shuffled" in k:
k_used_set.add(k.replace("_shuffled", ""))
for k,v in ref_dict.iteritems():
if "shuffled" in k or k in k_used_set:
fw.write(">" + k + "\n")
fw.write(str(v.seq))
fw.write("\n")
else:
v_str=str(v.seq)
v_new=v_str[len(v)/2:]+v_str[:len(v)/2]
k_new=str(k)+"_shuffled"
fw.write(">"+k+"\n")
fw.write(v_str)
fw.write("\n")
fw.write(">"+k_new+"\n")
fw.write(v_new)
fw.write("\n")
fw.close()
return out_file
if __name__=="__main__":
pass