Convert impute2 to PEDMAP

Documentation

Converts from legend and haplotype file of impute2 (https://mathgen.stats.ox.ac.uk/impute/impute_v2.html) to PED and MAP files (http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped)

Parameters:

• chromosome: string, the chromosome.
• legend_file: string, the legend filename.
• haplotypes_file: string, the hap filename.
• sample_names : a Python list with the names of the samples in the haplotypes file. (Optional, if not set the default value is: 0,1,2,3, ..).
• sample_names_filename : filename with one sample name per line (Optional).
• family_id: a Python list with the family ids of the samples. (Optional, if not set the default value is: 1 for all the samples).
• family_id_filename : filename with one family id per line (Optional).
• p_id: a Python list with the paternal id. (Optional, if not set the default value is: 0 for all the samples).
• p_id_filename : filename with one parent_id per line (Optional).
• m_id: a Python list with the maternal id. (Optional, if not set the default value is: 0 for all the samples).
• m_id_filename: filename with one maternal_id per line (Optional).
• gender: a Python list with the gender id. (Optional, if not set the default value is: 3 for all the samples).
• gender_filenane: filename with one gender id per line (Optional)
• pheno: a Python list with the pheno id. (Optional, if not set the default value is: 0 for all the samples).
• pheno_filename: filename with one pheno id per line (Optional)
• output: The prefix of the output filenames. i.e. if output is "results" then the output files will be output.ped and output.map. If not defined then the basename of the legend_file will be used.

For more info about the famility_id, p_id, m_id, gender and pheno values check the definition of the PED format: http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped

Parameters

<inputs>
</inputs>

Return

A tuple with the filenames if the generated ped and map files.

See also

• User articles: Convert_impute2_to_PEDMAP_user_Kantale

Code

import os

def Convert_impute2_to_PEDMAP(
	chromosome = None, 
	legend_file = None, 
	haplotypes_file = None, 
	sample_names = None,
	sample_names_filename = None,
	family_id = None,
	family_id_filename = None,
	p_id = None,
	p_id_filename = None,
	m_id = None,
	m_id_filename = None,
	gender = None,
	gender_filename = None,
	pheno = None,
	pheno_filename = None,
	output = None, 
	):
	
	legend = open(legend_file).readlines()[1:] # Skip first line from legend
	haplotypes = open(haplotypes_file).readlines()
	
	snps = len(legend)
	
	if not output:
		output = os.path.splitext(legend_file)[0]
	
	map_filename = output + ".map"
	ped_filename = output + ".ped"
	
	map_file = open(map_filename, "w")
	ped = {}
	
	read_filename_lines = lambda filename : [x.replace("\n", "") for x in open(filename, 'U').readlines()] if filename else None
	if not sample_names: sample_names = read_filename_lines(sample_names_filename)
	if not family_id: family_id = read_filename_lines(family_id_filename)
	if not p_id: p_id = read_filename_lines(p_id_filename)
	if not m_id: m_id = read_filename_lines(m_id_filename)
	if not gender: gender = read_filename_lines(gender_filename)
	if not pheno: phrno = read_filename_lines(pheno_filename)
	
	print "Saving map file.."
	for snp_index, pair in enumerate(zip(legend, haplotypes)):
		l_splitted = [x for x in pair[0].replace("\n", "").split() if len(x) > 0]
		h_splitted = [x for x in pair[1].replace("\n", "").split() if len(x) > 0]
		
		for individual_id, genotype in [(index/2, (h_splitted[index], h_splitted[index+1])) for index, value in enumerate(h_splitted) if index % 2 == 0]:
			if not ped.has_key(individual_id):
				ped[individual_id] = {}
				if family_id:
					ped[individual_id]["family_id"] = family_id[individual_id]
				else:
					ped[individual_id]["family_id"] = 1
					
				if sample_names:
					ped[individual_id]["ind_id"] = sample_names[individual_id]
				else:
					ped[individual_id]["ind_id"] = individual_id
				
				if p_id:
					ped[individual_id]["p_id"] = p_id[individual_id]
				else:
					ped[individual_id]["p_id"] = 0
					
				if m_id:
					ped[individual_id]["m_id"] = m_id[individual_id]
				else:
					ped[individual_id]["m_id"] = 0
					
				if gender:
					ped[individual_id]["gender"] = gender[individual_id]
				else:
					ped[individual_id]["gender"] = 3
				
				if pheno:
					ped[individual_id]["pheno"] = pheno[individual_id]
				else:
					ped[individual_id]["pheno"] = 0
					
				ped[individual_id]["geno"] = []
	 	
			if genotype[0] == "0":
				allele1 = l_splitted[2]
			elif genotype[0] == "1":
				allele1 = l_splitted[3]
			else:
				raise Exception("Invalid format in phased file")
			
			if genotype[1] == "0":
				allele2 = l_splitted[2]
			elif genotype[1] == "1":
				allele2 = l_splitted[3]
			else:
				raise Exception("Invalid format in phased file")
	 		
			ped[individual_id]["geno"] += [ allele1, allele2 ]
	 
		if not snp_index % 1000: print snp_index, "/", snps 
	 
		map_file.write( str.join("\t", [str(chromosome), l_splitted[0], "0", l_splitted[1]]) + "\n") 
	map_file.close()
	print "..DONE saving map file"
	
	print "Saving ped file.."
	individuals = len(ped)
	ped_file = open(ped_filename, "w")
	for ind, value in ped.iteritems():
		print "Writing individual:", ind, "/", individuals
		ped_file.write(str.join("\t", [str(x) for x in [value["family_id"], value["ind_id"], value["p_id"], value["m_id"], value["gender"], value["pheno"]] + value["geno"]]) + "\n")
	ped_file.close()
	print "..DONE saving ped file"
	
	return (ped_filename, map_filename)

Unit Tests

def uni1():
	return True

Development Code

def Convert_impute2_to_PEDMAP():
	pass

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