-
Notifications
You must be signed in to change notification settings - Fork 4
/
Copy pathscr
71 lines (59 loc) · 2.19 KB
/
scr
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
#!/bin/bash
export JAVA_HOME="/booleanfs/sahoo/softwares/java/jdk1.8.0_45"
export PATH=$JAVA_HOME/bin:$PATH
export CLASSPATH="./stepminer-1.1.jar"
stepminer="java -cp $CLASSPATH -Xms64m -Xmx10G tools.CustomAnalysis"
stepminer1="java -cp $CLASSPATH -Xms64m -Xmx10G tools.Analyze"
export PERL_HASH_SEED=0
#git clone https://github.com/sahoo00/Hegemon
#javac Hegemon/tools/*.java
#perl analyze.pl data-download PLP10 data/arijs-2018-uc
#perl analyze.pl toidx data/arijs-2018-uc-expr.txt > data/arijs-2018-uc-idx.txt
#
#for i in data/arijs-2018-uc-expr.txt
#do
# P=${i/-expr.txt/}
# echo $P
# rm -f "$P-thr.txt" "$P-info.txt" "$P-vinfo.txt" "$P-bv.txt"
# if [[ ! -f "$P-thr.txt" ]]; then
# perl analyze.pl thr $i 2 70000 0.5 > "$P-thr.txt"
# fi
# if [[ ! -f "$P-info.txt" ]]; then
# perl analyze.pl Info $P > $P-info.txt
# fi
# if [[ ! -f "$P-vinfo.txt" ]]; then
# perl analyze.pl VInfo $P > $P-vinfo.txt
# fi
# if [[ ! -f "$P-bv.txt" ]]; then
# perl analyze.pl bv $P > $P-bv.txt
# fi
#done
#FILE=results/ibd-network
#rm -f $FILE.rl
#${stepminer}
#${stepminer} boolean bitMatrix $FILE.rl \
# data/peters-2017-ibd-bv.txt \
# $FILE.ph All 0.1 2.5 0.05
#cp $FILE.rl $FILE-1.rl
#${stepminer} boolean bitMatrixFill $FILE-1.rl
#${stepminer} boolean bitMatrixFillStats $FILE-1.rl
#${stepminer} boolean bitMatrixPrint $FILE-1.rl > $FILE-res.txt
#
#FILE=results/ibd-network-2
#rm -f $FILE.rl
#${stepminer}
#${stepminer} boolean bitMatrix $FILE.rl \
# data/arijs-2018-uc-bv.txt \
# $FILE.ph All 0.1 2.5 0.05
#cp $FILE.rl $FILE-1.rl
#${stepminer} boolean bitMatrixFill $FILE-1.rl
#${stepminer} boolean bitMatrixFillStats $FILE-1.rl
#${stepminer} boolean bitMatrixPrint $FILE-1.rl > $FILE-res.txt
#Building Clustered Boolean Implication Network:
#PERL_HASH_SEED=0 perl analyze.pl ibd eq > results/ibd-network-g-eq-4.txt
#PERL_HASH_SEED=0 perl analyze.pl ibd eq-corr > results/ibd-network-g-eq-4-corr.txt
#PERL_HASH_SEED=0 perl analyze.pl ibd cls > results/ibd-network-g-eq-cls-4.txt
#PERL_HASH_SEED=0 perl analyze.pl ibd g-cls > results/ibd-network-g-eq-g-4.txt
#Identifying Paths:
#perl analyze.pl ibd genes > results/path-1.json
#perl analyze.pl ibd genes C21orf33 NCF2 > results/path-2.json