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1#! /bin/bash
2
3# Note: if you use this with the -i option, the output will be
4# the input plus a new column with the alternate mapped xrefs.
5# Warning: the -i option is currently unable to retain headers
6# and comments from the input.
7
8# Inputs with a single column:
9
10echo $'1234\n1235\n' |\
11 ./bin/bridgedb xrefs -f "tsv" \
12 "Homo sapiens" "Entrez Gene" 0 \
13 uniprot
14
15echo $'1234\n1235\n' |\
16 ./bin/bridgedb xrefs -f "tsv" \
17 "Homo sapiens" "Entrez Gene" 0 \
18 ensembl uniprot
19
20./bin/bridgedb xrefs -f "tsv" \
21 "Homo sapiens" "Entrez Gene" 0 \
22 <<< $'1234\n1235\n'
23
24echo $'1234\n1235\n' |\
25 ./bin/bridgedb xrefs -f "tsv" \
26 "Homo sapiens" "Entrez Gene" 0
27
28echo $'1234\n1235\n' | \
29 ./bin/bridgedb xrefs -f "tsv" -i 1 \
30 "Homo sapiens" "Entrez Gene" 0 \
31 ensembl
32
33echo $'1234\n1235\n' | \
34 ./bin/bridgedb xrefs -f "tsv" -i 0 \
35 "Homo sapiens" "Entrez Gene" 0 \
36 ensembl
37
38./bin/bridgedb xrefs -f "csv" \
39 "Homo sapiens" "Entrez Gene" 0 \
40 < test/xrefIdentifiers.csv
41
42# Inputs with multiple columns:
43
44echo $'Entrez Gene\t1234\nEntrez Gene\t1235\n' | \
45 ./bin/bridgedb xrefs -f "tsv" \
46 "Homo sapiens" 0 1 \
47 ensembl
48
49echo $'Entrez Gene\t1234\nEntrez Gene\t1235\n' | \
50 ./bin/bridgedb xrefs -f "tsv" -i 2 \
51 "Homo sapiens" 0 1
52
53echo $'Entrez Gene\t1234\nEntrez Gene\t1235\n' | \
54 ./bin/bridgedb xrefs -f "tsv" -i 2 \
55 "Homo sapiens" 0 1 \
56 ensembl uniprot
57
58echo $'Entrez Gene\t1234\nEntrez Gene\t1235\n' | \
59 ./bin/bridgedb xrefs -f "tsv" -i 1 \
60 "Homo sapiens" 0 1 \
61 ensembl
62
63./bin/bridgedb xrefs -f "tsv" \
64 "Homo sapiens" "Entrez Gene" 0 \
65 <<< $'1234\n1235\n'
66
67echo $'gene\n1234\n1235\n' |\
68 ./bin/bridgedb xrefs -f "tsv" \
69 --headers=true \
70 "Homo sapiens" "Entrez Gene" "gene"
71
72./bin/bridgedb xrefs -f "tsv" \
73 "Homo sapiens" "Entrez Gene" 0 \
74 < test/xrefIdentifiers.csv
75
76./bin/bridgedb xrefs -f "csv" \
77 "Homo sapiens" 0 1 \
78 < test/xrefDataSourcesAndIdentifiers.csv
79
80./bin/bridgedb xrefs -f "csv" \
81 "Homo sapiens" "Entrez Gene" 1 \
82 < test/xrefIdentifiersInSecondColumn.csv
83
84./bin/bridgedb xrefs -f "tsv" --headers=true -i 3 \
85 "Homo sapiens" "Entrez Gene" "Gene" \
86 ensembl \
87 < test/RefSeqSample.tsv