new_contents: # -*- coding: utf-8 -*-
  """
  Created on Fri Jun  3 15:18:42 2016
  
  @author: Ahmed
  
  Given a 
  echo <file> | python phageblast.py <genome> > <output>
  where:
  <file> is the name of a fasta file containing protein sequences of the antiCRISPR genes of interest
  <genome> is the name of a file containing the bacterial genome of interest 
  <output> is the name of the (xml) file you'd like to write the results to  
  
  http://www.ncbi.nlm.nih.gov/books/NBK279675/ 
  ^ see Table C5 for other tblastn options 
  
  DEPENDENCIES:
  Biopython
  blast+
  """
  
  from Bio.Blast.Applications import NcbitblastnCommandline 
  import sys
  import subprocess 
  
  genome = sys.argv[-1]
  
  #loads input file
  seq = [l.strip() for l in sys.stdin if l.strip()]
  seq = ''.join(seq)
  
  #builds command line string 
  tblastn_obj = NcbitblastnCommandline(cmd = 'tblastn', query=seq, subject=genome.read(), 
                                       evalue=10, outfmt = 5)
  
  tblastn_cline = str(tblastn_obj) 
  
  #executes command line string in bash 
  subprocess.call(tblastn_cline, shell=True) 
  
subject: Create anticrisprblast.py