Notes on how to test tabix
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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";