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
|
Notes on how to test tabix
──────────────────────────
The tabix package contains example data to test the tabix program. It is
already compressed and indexed. The following instruction decompress,
recompress, re-index and test the example data.
# Create a temporary file
TABIXDATA=$(mktemp)
# Uncompress example data
zcat /usr/share/doc/tabix/examples/example.gtf.gz > $TABIXDATA
# Compress example data with bgzip
bgzip $TABIXDATA
# Index with tabix
tabix $TABIXDATA.gz
# Extract with tabix the he features on chromosome 1 whose coordinates overlap
# the interval 150,309–150,309.
tabix $TABIXDATA.gz chr1:150309-150309 > $TABIXDATA.out
# Reference result at the bottom of this file
grep H\AVANA /usr/share/doc/tabix/README.test > $TABIXDATA.ref
# No difference ?
diff $TABIXDATA.ref $TABIXDATA.out
# Clean
rm $TABIXDATA.gz $TABIXDATA.gz.tbi $TABIXDATA.out $TABIXDATA.ref
This sequence of tests is also implemented debian/tests/with-example-data
in the source package.
-- Charles Plessy <plessy@debian.org> Fri, 22 Jun 2012 13:11:36 +0900
chr1 HAVANA exon 150309 150553 . + . gene_id "ENSG00000241599"; transcript_id "ENST00000496488"; gene_type "processed_transcript"; gene_status "KNOWN"; gene_name "AL627309.12"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "AL627309.12-201"; level 2; havana_gene "OTTHUMG00000002525"; havana_transcript "OTTHUMT00000007169";
chr1 HAVANA gene 150309 151388 . + . gene_id "ENSG00000241599"; transcript_id "ENSG00000241599"; gene_type "processed_transcript"; gene_status "KNOWN"; gene_name "AL627309.12"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "AL627309.12"; level 2; havana_gene "OTTHUMG00000002525";
chr1 HAVANA transcript 150309 151388 . + . gene_id "ENSG00000241599"; transcript_id "ENST00000496488"; gene_type "processed_transcript"; gene_status "KNOWN"; gene_name "AL627309.12"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "AL627309.12-201"; level 2; havana_gene "OTTHUMG00000002525"; havana_transcript "OTTHUMT00000007169";
|
