-
Notifications
You must be signed in to change notification settings - Fork 0
/
mustache.sh
147 lines (106 loc) · 5.7 KB
/
mustache.sh
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
143
144
145
146
147
#!/bin/bash
touch mustache.log
wget -P ./../ https://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63525/suppl/GSE63525_GM12878_insitu_primary_30.hic &
wget -P ./../ https://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63525/suppl/GSE63525_GM12878_insitu_replicate_30.hic &
wget -P ./../ https://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63525/suppl/GSE63525_K562_combined_30.hic &
wait
exec > mustache.log 2>&1
#===================================================
#=======================Primary=====================
#===================================================
start=$(date +%s)
mustache -f ./../GSE63525_GM12878_insitu_primary_30.hic -r 5kb -o mustache_primary_chr1_5K.tsv -ch 1
end=$(date +%s)
echo "At 5K primary chr 1 Elapsed Time: $(($end-$start)) seconds"
start=$(date +%s)
mustache -f ./../GSE63525_GM12878_insitu_primary_30.hic -r 5kb -o mustache_primary_chr6_5K.tsv -ch 6
end=$(date +%s)
echo "At 5K primary chr 6 Elapsed Time: $(($end-$start)) seconds"
start=$(date +%s)
mustache -f ./../GSE63525_GM12878_insitu_primary_30.hic -r 10kb -o mustache_primary_chr1_10K.tsv -ch 1
end=$(date +%s)
echo "At 10K primary chr 1 Elapsed Time: $(($end-$start)) seconds"
start=$(date +%s)
mustache -f ./../GSE63525_GM12878_insitu_primary_30.hic -r 10kb -o mustache_primary_chr6_10K.tsv -ch 6
end=$(date +%s)
echo "At 10K primary chr 6 Elapsed Time: $(($end-$start)) seconds"
#===================================================
#=======================Replicate===================
#===================================================
start=$(date +%s)
mustache -f ./../GSE63525_GM12878_insitu_replicate_30.hic -r 5kb -o mustache_replicate_chr1_5K.tsv -ch 1
end=$(date +%s)
echo "At 5K replicate chr 1 Elapsed Time: $(($end-$start)) seconds"
start=$(date +%s)
mustache -f ./../GSE63525_GM12878_insitu_replicate_30.hic -r 5kb -o mustache_replicate_chr6_5K.tsv -ch 6
end=$(date +%s)
echo "At 5K replicate chr 6 Elapsed Time: $(($end-$start)) seconds"
start=$(date +%s)
mustache -f ./../GSE63525_GM12878_insitu_replicate_30.hic -r 10kb -o mustache_replicate_chr1_10K.tsv -ch 1
end=$(date +%s)
echo "At 10K replicate chr 1 Elapsed Time: $(($end-$start)) seconds"
start=$(date +%s)
mustache -f ./../GSE63525_GM12878_insitu_replicate_30.hic -r 10kb -o mustache_replicate_chr6_10K.tsv -ch 6
end=$(date +%s)
echo "At 10K replicate chr 6 Elapsed Time: $(($end-$start)) seconds"
#===================================================
#=======================K562========================
#===================================================
start=$(date +%s)
mustache -f ./../GSE63525_K562_combined_30.hic -r 5kb -o mustache_K562_chr1_5K.tsv -ch 1
end=$(date +%s)
echo "At 5K K562 chr 1 Elapsed Time: $(($end-$start)) seconds"
start=$(date +%s)
mustache -f ./../GSE63525_K562_combined_30.hic -r 5kb -o mustache_K562_chr6_5K.tsv -ch 6
end=$(date +%s)
echo "At 5K K562 chr 6 Elapsed Time: $(($end-$start)) seconds"
start=$(date +%s)
mustache -f ./../GSE63525_K562_combined_30.hic -r 10kb -o mustache_K562_chr1_10K.tsv -ch 1
end=$(date +%s)
echo "At 10K K562 chr 1 Elapsed Time: $(($end-$start)) seconds"
start=$(date +%s)
mustache -f ./../GSE63525_K562_combined_30.hic -r 10kb -o mustache_K562_chr6_10K.tsv -ch 6
end=$(date +%s)
echo "At 10K K562 chr 6 Elapsed Time: $(($end-$start)) seconds"
#===================================================
#====================Normalized=====================
#===================================================
#!/bin/bash
exec > mustache_normKR.log 2>&1
start=$(date +%s)
mustache -f /storage/store/mohit/data/kr_norm/GM12878_primary_30_KR_5000.cool -o GM12878_primary_KR_chr1_5k.mustache.tsv -ch 1 -r 5kb
end=$(date +%s)
echo "primary chr1 @5k primary, Elapsed Time: $(($end-$start)) seconds"
start=$(date +%s)
mustache -f /storage/store/mohit/data/kr_norm/GM12878_primary_30_KR_10000.cool -o GM12878_primary_KR_chr1_10k.mustache.tsv -ch 1 -r 10kb
end=$(date +%s)
echo "primary chr1 @10k primary, Elapsed Time: $(($end-$start)) seconds"
start=$(date +%s)
mustache -f /storage/store/mohit/data/kr_norm/GM12878_primary_30_KR_5000.cool -o GM12878_primary_KR_chr6_5k.mustache.tsv -ch 6 -r 5kb
end=$(date +%s)
echo "primary chr6 @5k primary, Elapsed Time: $(($end-$start)) seconds"
start=$(date +%s)
mustache -f /storage/store/mohit/data/kr_norm/GM12878_primary_30_KR_10000.cool -o GM12878_primary_KR_chr6_10k.mustache.tsv -ch 6 -r 10kb
end=$(date +%s)
echo "primary chr6 @10k primary, Elapsed Time: $(($end-$start)) seconds"
#===================================================
#====================Replicate======================
#===================================================
#!/bin/bash
exec > mustache_replicate.log 2>&1
start=$(date +%s)
mustache -f /storage/store/mohit/data/replicate/GM12878_replicate_KR_5000.cool -o GM12878_replicate_KR_chr1_5k.mustache.tsv -ch 1 -r 5kb
end=$(date +%s)
echo "replicate chr1 @5k replicate, Elapsed Time: $(($end-$start)) seconds"
start=$(date +%s)
mustache -f /storage/store/mohit/data/replicate/GM12878_replicate_KR_10000.cool -o GM12878_replicate_KR_chr1_10k.mustache.tsv -ch 1 -r 10kb
end=$(date +%s)
echo "replicate chr1 @10k replicate, Elapsed Time: $(($end-$start)) seconds"
start=$(date +%s)
mustache -f /storage/store/mohit/data/replicate/GM12878_replicate_KR_5000.cool -o GM12878_replicate_KR_chr6_5k.mustache.tsv -ch 6 -r 5kb
end=$(date +%s)
echo "replicate chr6 @5k replicate, Elapsed Time: $(($end-$start)) seconds"
start=$(date +%s)
mustache -f /storage/store/mohit/data/replicate/GM12878_replicate_KR_10000.cool -o GM12878_replicate_KR_chr6_10k.mustache.tsv -ch 6 -r 10kb
end=$(date +%s)
echo "replicate chr6 @10k replicate, Elapsed Time: $(($end-$start)) seconds"