[Bioperl-l] Bio::*Taxonomy* changes

Sendu Bala bix at sendu.me.uk
Tue Jul 18 08:43:43 UTC 2006

Sendu Bala wrote:
[snip proposed changes to Bio::DB::Taxonomy::* and Bio::Taxonomy::Node]
> If anyone can see a problem with any of these changes, let me know asap.

I've just realised that there are currently no tests for 
Bio::DB::Taxonomy::flatfile, and that the ones for entrez get skipped. 
Node doesn't get an especially thorough work-out either (in the skipped 

I'm guessing it's not feasible to include the full taxdump from NCBI 
(~40MB) in t/data... do people think it would be reasonable to create 
some sort of small subset of the data? I could just pull out the lines 
from names.dmp and nodes.dmp relevant to a few example organisms. Say, 
for human and a tricky bacteria and virus?
For the purposes of running the test, where should the index files be 
kept? In t/data with the .dmp files or in /tmp? Should the test script 
delete them afterwards, or leave them be?

The entrez tests are skipped to 'avoid blocking', but the test only 
makes 2 entrez queries with a sleep(3) in-between. Basically, I don't 
think there's ever any reason to skip. Shall I remove the skip? Lots of 
other database-accessing tests in the test suite just go right ahead and 
access their database, no problem.


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