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# This is a converter for common LMM formats, so as to keep file
# reader complexity outside the main routines.
# Copyright (C) 2015 Pjotr Prins (pjotr.prins@thebird.nl)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Affero General Public License for more details.
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
from __future__ import print_function
from optparse import OptionParser
import sys
import os
import numpy as np
# from lmm import LMM, run_other
# import input
import plink
usage = """
python convertlmm.py [--plink] [--prefix out_basename] [--kinship kfile] [--pheno pname] [--geno gname]
Convert files for runlmm.py processing. Writes to stdout by default.
try --help for more information
Examples:
python ./my_pylmm/pyLMM/convertlmm.py --plink --pheno data/test_snps.132k.clean.noX.fake.phenos > test.pheno
python ./my_pylmm/pyLMM/convertlmm.py --plink --pheno data/test_snps.132k.clean.noX.fake.phenos --geno data/test_snps.132k.clean.noX > test.geno
"""
# if len(args) == 0:
# print usage
# sys.exit(1)
option_parser = OptionParser(usage=usage)
option_parser.add_option("--kinship", dest="kinship",
help="Parse a kinship file. This is an nxn plain text file and can be computed with the pylmmKinship program")
option_parser.add_option("--pheno", dest="pheno",
help="Parse a phenotype file (use with --plink only)")
option_parser.add_option("--geno", dest="geno",
help="Parse a genotype file (use with --plink only)")
option_parser.add_option("--plink", dest="plink", action="store_true", default=False,
help="Parse PLINK style")
# option_parser.add_option("--kinship",action="store_false", dest="kinship", default=True,
# help="Parse a kinship file. This is an nxn plain text file and can be computed with the pylmmKinship program.")
option_parser.add_option("--prefix", dest="prefix",
help="Output prefix for output file(s)")
option_parser.add_option("-q", "--quiet",
action="store_false", dest="verbose", default=True,
help="don't print status messages to stdout")
option_parser.add_option("-v", "--verbose",
action="store_true", dest="verbose", default=False,
help="Print extra info")
(options, args) = option_parser.parse_args()
writer = None
num_inds = None
snp_names = []
ind_names = []
def msg(s):
sys.stderr.write("INFO: ")
sys.stderr.write(s)
sys.stderr.write("\n")
def wr(s):
if writer:
writer.write(s)
else:
sys.stdout.write(s)
def wrln(s):
wr(s)
wr("\n")
if options.pheno:
if not options.plink:
raise Exception("Use --plink switch")
# Because plink does not track size we need to read the whole thing first
msg("Converting pheno "+options.pheno)
phenos = []
count = 0
count_pheno = None
for line in open(options.pheno,'r'):
count += 1
list = line.split()
pcount = len(list)-2
assert(pcount > 0)
if count_pheno == None:
count_pheno = pcount
assert(count_pheno == pcount)
row = [list[0]]+list[2:]
phenos.append(row)
writer = None
if options.prefix:
writer = open(options.prefix+".pheno","w")
wrln("# Phenotype format version 1.0")
wrln("# Individuals = "+str(count))
wrln("# Phenotypes = "+str(count_pheno))
for i in range(count_pheno):
wr("\t"+str(i+1))
wr("\n")
for i in range(count):
wr("\t".join(phenos[i]))
wr("\n")
num_inds = count
msg(str(count)+" pheno lines written")
if options.kinship:
is_header = True
count = 0
msg("Converting kinship "+options.kinship)
writer = None
if options.prefix:
writer = open(options.prefix+".kin","w")
for line in open(options.kinship,'r'):
count += 1
if is_header:
size = len(line.split())
wrln("# Kinship format version 1.0")
wrln("# Size="+str(size))
for i in range(size):
wr("\t"+str(i+1))
wr("\n")
is_header = False
wr(str(count))
wr("\t")
wr("\t".join(line.split()))
wr("\n")
num_inds = count
msg(str(count)+" kinship lines written")
if options.geno:
msg("Converting geno "+options.geno+'.bed')
if not options.plink:
raise Exception("Use --plink switch")
if not num_inds:
raise Exception("Can not figure out the number of individuals, use --pheno or --kinship")
bim_snps = plink.readbim(options.geno+'.bim')
num_snps = len(bim_snps)
writer = None
if options.prefix:
writer = open(options.prefix+".geno","w")
wrln("# Genotype format version 1.0")
wrln("# Individuals = "+str(num_inds))
wrln("# SNPs = "+str(num_snps))
wrln("# Encoding = HAB")
for i in range(num_inds):
wr("\t"+str(i+1))
wr("\n")
m = []
def out(i,x):
# wr(str(i)+"\t")
# wr("\t".join(x))
# wr("\n")
m.append(x)
snps = plink.readbed(options.geno+'.bed',num_inds, ('A','H','B','-'), out)
msg("Write transposed genotype matrix")
for g in range(num_snps):
wr(bim_snps[g][1]+"\t")
for i in range(num_inds):
wr(m[g][i])
wr("\n")
msg(str(count)+" geno lines written (with "+str(snps)+" snps)")
msg("Converting done")
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