new_contents: #!/usr/bin/env python
  
  """
  
  Name: bedassle_from_genotypes.py 
  
  Author: Michael G. Harvey
  Date: 26 February 2014
  
  Convert genotype probabilities file output by Tom White's post-UNEAK processing scripts to allale
  and sample size input files for BEDASSLE (Bradburd et al. 2013).
  
  Usage: 	python bedassle_from_genotypes.py in_file a_outfile s_outfile sample_size
  
  Ex.: python bedassle_from_genotypes.py HapMapPairedFilt.txt \
  		HapMapPairedFiltBedassleA.txt HapMapPairedFiltBedassleB.txt 73
  
  
  """
  
  
  import os
  import sys
  import argparse
  
  
  def get_args():
  	parser = argparse.ArgumentParser(
  			description="""Program description""")
  	parser.add_argument(
  			"genotype_file",
  			type=str,
  			help="""The input genotype probabilities file from Tom White's scripts"""
  		)
  	parser.add_argument(
  			"a_outfile",
  			type=str,
  			help="""The file name"""
  		)
  	parser.add_argument(
  			"s_outfile",
  			type=str,
  			help="""The file name"""
  		)
  	parser.add_argument(
  			"sample_size",
  			type=str,
  			help="""The number of samples/individuals in file"""
  		)
  	return parser.parse_args()
  		
  		
  def read_samples(infile, sample_size):
  	samples = list()
  	first_line = infile.readline()
  	parts = first_line.split()
  	for i in range(int(sample_size)):
  		parts2 = parts[4+i]
  		parts3 = parts2.split('_')
  		samples.append(parts3[0])	
  	return samples
  
  
  def process_alleles(infile, sample_size):	
  	aarray = list()
  	sarray = list()
  	for line in infile:
  		parts = line.split()
  		alleles = str(parts[3]).split('/')
  		a1 = alleles[0]
  		a2 = alleles[1]
  		aseq = list() # allele list		
  		sseq = list() # sample size list
  		for i in range(int(sample_size)):
  			if parts[4+i] == "NA":
  				aseq.append("0")
  				sseq.append("0")
  			else:
  				counts = str(parts[4+i]).split(',')
  				aseq.append("{0}".format(counts.count('1')))
  				sseq.append('2')
  		aarray.append(aseq)
  		sarray.append(sseq)
  	return aarray, sarray
  
  
  def main():
  	args = get_args()
  	infile = open("{0}".format(args.genotype_file), 'r')
  	a_outfile = open("{0}".format(args.a_outfile), 'wb')
  	s_outfile = open("{0}".format(args.s_outfile), 'wb')
  	samples = read_samples(infile, args.sample_size)
  	arrays = process_alleles(infile, args.sample_size)
  	aarray = arrays[0]
  	sarray = arrays[1]
  	aalignment = zip(*aarray)
  	salignment = zip(*sarray)
  	i = 0
  	a_outfile.write("Ind")	
  	for j in range(len(aalignment[0])):
  		a_outfile.write("\tloc{0}".format(j+1))
  	a_outfile.write("\n")
  	s_outfile.write("Ind")	
  	for j in range(len(salignment[0])):
  		s_outfile.write("\tloc{0}".format(j+1))
  	s_outfile.write("\n")
  	for k, sample in enumerate(samples): # Loop through samples
  		a_outfile.write("{0}".format(sample))
  		s_outfile.write("{0}".format(sample))
  		for j in range(len(aalignment[0])):
  			acount = str(aalignment[i][j])
  			scount = str(salignment[i][j])
  			a_outfile.write("\t{0}".format(acount))
  			s_outfile.write("\t{0}".format(scount))
  		a_outfile.write("\n")
  		s_outfile.write("\n")
  		i += 1
  	infile.close()
  	a_outfile.close()
  	s_outfile.close()
  
  if __name__ == '__main__':
      main()
subject: add script for bedassle format