forked from arq5x/gemini
-
Notifications
You must be signed in to change notification settings - Fork 0
Expand file tree
/
Copy pathtest-effstring.sh
More file actions
91 lines (88 loc) · 4.13 KB
/
Copy pathtest-effstring.sh
File metadata and controls
91 lines (88 loc) · 4.13 KB
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
####################################################################
# 1. Test variant_impacts table for the impact columns
####################################################################
echo " effstring.t01...\c"
echo "gene impact impact_severity biotype is_exonic is_coding is_lof
FAM138A downstream LOW protein_coding 0 0 0
FAM138A downstream LOW processed_transcript 0 0 0
MIR1302-10 downstream LOW miRNA 0 0 0
MIR1302-10 intron LOW antisense 0 0 0
MIR1302-10 intron LOW antisense 0 0 0
WASH7P upstream LOW unprocessed_pseudogene 0 0 0
WASH7P upstream LOW unprocessed_pseudogene 0 0 0
WASH7P upstream LOW unprocessed_pseudogene 0 0 0
WASH7P upstream LOW unprocessed_pseudogene 0 0 0
WASH7P upstream LOW unprocessed_pseudogene 0 0 0
OR4F5 synonymous_coding LOW protein_coding 1 1 0
OR4F5 non_syn_coding MED protein_coding 1 1 0
SAMD11 downstream LOW protein_coding 0 0 0
SAMD11 downstream LOW protein_coding 0 0 0
NOC2L downstream LOW protein_coding 0 0 0
NOC2L downstream LOW processed_transcript 0 0 0
NOC2L downstream LOW processed_transcript 0 0 0
SAMD11 frame_shift HIGH protein_coding 1 1 1
SAMD11 upstream LOW processed_transcript 0 0 0
SAMD11 upstream LOW processed_transcript 0 0 0
SAMD11 upstream LOW retained_intron 0 0 0
SAMD11 upstream LOW retained_intron 0 0 0
NOC2L downstream LOW processed_transcript 0 0 0
SAMD11 downstream LOW processed_transcript 0 0 0
SAMD11 downstream LOW processed_transcript 0 0 0
SAMD11 downstream LOW retained_intron 0 0 0
SAMD11 downstream LOW retained_intron 0 0 0
NOC2L exon LOW processed_transcript 0 0 0
NOC2L exon LOW processed_transcript 0 0 0
SAMD11 UTR_3_prime LOW protein_coding 1 0 0
NOC2L UTR_3_prime LOW protein_coding 1 0 0
HES4 start_gain LOW protein_coding 1 0 0
HES4 upstream LOW protein_coding 0 0 0
HES4 upstream LOW protein_coding 0 0 0
HES4 upstream LOW processed_transcript 0 0 0
MRPL20 downstream LOW protein_coding 0 0 0
MRPL20 downstream LOW processed_transcript 0 0 0
MRPL20 downstream LOW processed_transcript 0 0 0
MRPL20 downstream LOW processed_transcript 0 0 0
RP4-758J18.5.1 downstream LOW processed_transcript 0 0 0
CCNL2 exon LOW processed_transcript 0 0 0
CCNL2 intron LOW protein_coding 0 0 0
CCNL2 intron LOW protein_coding 0 0 0
CCNL2 intron LOW nonsense_mediated_decay 0 0 0
CCNL2 intron LOW nonsense_mediated_decay 0 0 0
CCNL2 intron LOW nonsense_mediated_decay 0 0 0
CCNL2 intron LOW nonsense_mediated_decay 0 0 0
CCNL2 splice_acceptor HIGH nonsense_mediated_decay 0 0 0
CCNL2 upstream LOW processed_transcript 0 0 0
CCNL2 upstream LOW processed_transcript 0 0 0
CCNL2 upstream LOW processed_transcript 0 0 0
CCNL2 upstream LOW retained_intron 0 0 0
RP4-758J18.2.1 upstream LOW processed_transcript 0 0 0
RP4-758J18.2.1 upstream LOW processed_transcript 0 0 0
RP4-758J18.2.1 upstream LOW processed_transcript 0 0 0
RP4-758J18.2.1 upstream LOW processed_transcript 0 0 0
RP4-758J18.3.1 upstream LOW processed_transcript 0 0 0" > exp
gemini query -q "select gene, impact, impact_severity, biotype, \
is_exonic, is_coding, is_lof from variant_impacts" \
--header \
test1.snpeff.db \
> obs
check obs exp
rm obs exp
####################################################################
# 2. Test variants table for severe_impact columns
####################################################################
echo " effstring.t02...\c"
echo "anno_id gene transcript impact impact_severity biotype is_exonic is_coding is_lof
1 FAM138A ENST00000417324 downstream LOW protein_coding 0 0 0
1 OR4F5 ENST00000335137 synonymous_coding LOW protein_coding 1 1 0
1 OR4F5 ENST00000335137 non_syn_coding MED protein_coding 1 1 0
6 SAMD11 ENST00000342066 frame_shift HIGH protein_coding 1 1 1
8 SAMD11 ENST00000342066 UTR_3_prime LOW protein_coding 1 0 0
1 HES4 ENST00000428771 start_gain LOW protein_coding 1 0 0
13 CCNL2 ENST00000488340 splice_acceptor HIGH nonsense_mediated_decay 0 0 0" > exp
gemini query -q "select anno_id, gene, transcript, impact, impact_severity, biotype, \
is_exonic, is_coding, is_lof from variants" \
--header \
test1.snpeff.db \
> obs
check obs exp
rm obs exp