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
|
#!/bin/bash
# This script runs checks on ProbABEL's pacoxph module
# These are almost identical to the checks in test_cox.sh, but this
# time without covariate data (see bug #1266).
echo "Analysing Cox model without covariates..."
scriptdir=$(dirname $0)
if [ -z ${PA_BINDIR} ]; then
PA_BINDIR="${scriptdir}/../src/"
fi
if [ -z ${srcdir} ]; then
srcdir="."
PA_BINDIR=${scriptdir}/../src/
fi
. ${scriptdir}/run_diff.sh
inputdir=${scriptdir}/inputfiles
pacoxph=${PA_BINDIR}/pacoxph
# Redirect all output to file descriptor 3 to /dev/null except if
# the first argument is "verbose" then redirect handle 3 to stdout
exec 3>/dev/null
if [ "$1" = "verbose" ]; then
echo "Verbose mode ON"
exec 3>&1
fi
$pacoxph \
-p ${inputdir}/coxph_data_nocovar.txt \
-d ${inputdir}/test.mldose \
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 \
-o coxph_dose_nocovar \
>& 3
$pacoxph \
-p ${inputdir}/coxph_data_nocovar.txt \
-d ${inputdir}/test.dose.fvi \
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 \
-o coxph_dose_nocovar_fv \
>& 3
run_diff coxph_dose_nocovar_add.out.txt coxph_dose_nocovar_fv_add.out.txt \
"pacoxph check: dose vs. dose_fv"
$pacoxph \
-p ${inputdir}/coxph_data_nocovar.txt \
-d ${inputdir}/test.mlprob \
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
--ngpreds=2 \
-c 19 \
-o coxph_prob_nocovar \
>& 3
run_diff coxph_dose_nocovar_add.out.txt coxph_prob_nocovar_add.out.txt \
"pacoxph check: dose vs. prob" -I SNP
$pacoxph \
-p ${inputdir}/coxph_data_nocovar.txt \
-d ${inputdir}/test.prob.fvi \
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
--ngpreds=2 \
-c 19 \
-o coxph_prob_nocovar_fv \
>& 3
for model in add domin recess over_domin 2df; do
run_diff coxph_prob_nocovar_${model}.out.txt \
coxph_prob_nocovar_fv_${model}.out.txt \
"pacoxph check ($model model): prob vs. prob_fv"
done
|
