From 115f4508fb71ad7e60fa333ffe49de8c8d1bbd8c Mon Sep 17 00:00:00 2001 From: Charles Plessy Date: Tue, 10 May 2011 19:13:26 +0900 Subject: [PATCH] Notes on how to test tabix. --- debian/README.test | 39 +++++++++++++++++++++++++++++++++++++++ debian/docs | 1 + 2 files changed, 40 insertions(+) create mode 100644 debian/README.test diff --git a/debian/README.test b/debian/README.test new file mode 100644 index 0000000..a7b2e86 --- /dev/null +++ b/debian/README.test @@ -0,0 +1,39 @@ +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 + + -- Charles Plessy Tue, 10 May 2011 19:12:19 +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"; diff --git a/debian/docs b/debian/docs index edc0071..c3f0f84 100644 --- a/debian/docs +++ b/debian/docs @@ -1 +1,2 @@ NEWS +debian/README.test -- 2.30.2