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# This is a converter for common LMM formats, so as to keep 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 optparse import OptionParser
import sys
import os
import numpy as np
# from lmm import LMM, run_other
import input
usage = """
python convertlmm.py [--kinship kfile]
Convert files for runlmm.py processing. Writes to stdout.
try --help for more information
"""
# 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("--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()
if options.kinship:
is_header = True
count = 0
sys.stderr.write("Converting "+options.kinship+"\n")
for line in open(options.kinship,'r'):
count += 1
if is_header:
size = len(line.split())
print "# Kinship format version 1.0"
print "# Size=",size
for i in range(size):
sys.stdout.write("\t"+str(i+1))
sys.stdout.write("\n")
is_header = False
sys.stdout.write(str(count))
sys.stdout.write("\t")
sys.stdout.write("\t".join(line.split()))
sys.stdout.write("\n")
sys.stderr.write("Converting done\n")
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