[Bioperl-l] t/entrezgene, t/protgraph and t/FeatureIO
cjfields at uiuc.edu
Mon Aug 7 10:35:25 EDT 2006
On Aug 7, 2006, at 9:04 AM, Sendu Bala wrote:
> Chris Fields wrote:
>> Brian already knows about the 'pseudohash' issue with protgraph.
> With entrezgene you mean?
Yes, sorry. Lack of coffee.
> Do you get the same test fails for protgraph on Windows that I get
The tests all pass on Mac OS X; Ill try Windows today, but if memory
serves there were problems with this a few months back
Okay, found it on the gmane lists:
This part of the thread details the issues. Linux and WinXP fails
similar tests, Mac OS X (Tiger) passes (Heikki and I ran the tests).
My feeling: could be OS-specific, could be Clone.pm, could be perl
>> I think it's a weird ref call or construct that tripping the perl
>> warnings. I don't think perl 5.6 does this; the pseudohash warning
>> was added in perl 5.8.
>> I really wouldn't worry about the other tests throwing warnings. You
>> have your hands full with Taxonomy now; focus on getting that up and
>> running before you move on to other ventures.
> As far as I'm concerned I'm more or less finished with Taxonomy. I'm
> just waiting for your confirmed 'vote' on what species() should
> and at least one other vote.
> Might also be waiting to find out how get_lca should really work as
> well. But in any case, I'm just waiting, which isn't that hard ;)
> FYI I'm actually moving on to the previously mooted hmmpfam plugin for
Cool! The only problem I saw with the way you wanted to go about it
was you would have to preparse the report since everything is
reported as 1 hsp/hit. They usually aren't long, so that shouldn't
be a problem.
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign
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