1 Notes on how to test tabix
2 ──────────────────────────
4 The tabix package contains example data to test the tabix program. It is
5 already compressed and indexed. The following instruction decompress,
6 recompress, re-index and test the example data.
8 # Create a temporary file
11 # Uncompress example data
12 zcat /usr/share/doc/tabix/examples/example.gtf.gz > $TABIXDATA
14 # Compress example data with bgzip
20 # Extract with tabix the he features on chromosome 1 whose coordinates overlap
21 # the interval 150,309–150,309.
22 tabix $TABIXDATA.gz chr1:150309-150309 > $TABIXDATA.out
24 # Reference result at the bottom of this file
25 grep H\AVANA /usr/share/doc/tabix/README.test > $TABIXDATA.ref
28 diff $TABIXDATA.ref $TABIXDATA.out
31 rm $TABIXDATA.gz $TABIXDATA.gz.tbi $TABIXDATA.out $TABIXDATA.ref
33 -- Charles Plessy <plessy@debian.org> Tue, 10 May 2011 19:12:19 +0900
37 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";
38 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";
39 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";