1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
|
# 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
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
"""
# 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
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.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")
msg(str(count)+" kinship lines written")
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")
msg(str(count)+" pheno lines written")
if options.geno:
if not options.plink:
raise Exception("Use --plink switch")
# msg("Converting geno "+options.geno)
# plink.readbim(options.geno+'.bim')
msg("Converting geno "+options.geno+'.bed')
plink.readbed(options.geno+'.bed',1000,8)
msg("Converting done")
|
