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