[Bioperl-l] Bio::DB::GFF/Postgres test failures

[Chris Fields]

Scott, 

I'll try documenting the Pg error for SF::Store in the next hour.  Had my hands full with the GSoC onslaught of emails and local $job stuff.  Would like to get it fixed for the CPAN release.

chris

On Apr 8, 2011, at 12:58 PM, Scott Cain wrote:

> OK, I'll take it out and move on to the next problem.
> 
> Thanks,
> Scott
> 
> 
> On Fri, Apr 8, 2011 at 1:51 PM, Lincoln Stein <lincoln.stein at gmail.com> wrote:
>> Oh right. The Bio::DB::GFF adaptor has that broken behavior and it is too
>> late to change it now. (Bio::DB::SeqFeature::Store had better not!) Best to
>> remove the test altogether.
>> Lincoln
>> 
>> On Fri, Apr 8, 2011 at 1:18 PM, Scott Cain <scott at scottcain.net> wrote:
>>> 
>>> Hi Lincoln,
>>> 
>>> Yes, apparently, it does.  It does this for both the memory and the
>>> postgres adaptors.  I looked at how the data was stored in the feature
>>> object with Data::Dumper and that is how it is represented in the hash
>>> too.  Perhaps this test should be calling the "absolute" method first?
>>> 
>>> Scott
>>> 
>>> 
>>> On Fri, Apr 8, 2011 at 1:10 PM, Lincoln Stein <lincoln.stein at gmail.com>
>>> wrote:
>>>> Do start() and end() flip values for minus strand features? This isn't
>>>> supposed to happen.
>>>> Lincoln
>>>> 
>>>> On Fri, Apr 8, 2011 at 11:41 AM, Scott Cain <scott at scottcain.net> wrote:
>>>>> 
>>>>> Hi Lincoln,
>>>>> 
>>>>> I've been looking into some test failures with the postgres adaptor
>>>>> for Bio::DB::GFF and I wanted to check with you that I'm interpreting
>>>>> this correctly.  In t/LocalDB/BioDBGFF.t there are these lines:
>>>>> 
>>>>>  @features = sort {$a->start<=>$b->start} @features;
>>>>> 
>>>>>  is($features[0]->type,'Component:reference');
>>>>>  is($features[-1]->type,'exon:confirmed');
>>>>> 
>>>>> So that the features in the data set are sorted by their start values
>>>>> and the beginning and end of the list are checked.  The test refers to
>>>>> the test.gff data file, that contains among others these lines:
>>>>> 
>>>>> Contig1 confirmed   transcript      30001   31000   .   -   .
>>>>> Transcript trans-2; Gene "xyz-2"; Note "Terribly interesting"
>>>>> Contig1 confirmed   exon    30001   30100   .   -   .   Transcript
>>>>> trans-2; Gene "abc-1"; Note "function unknown"
>>>>> Contig1 confirmed   exon    30701   30800   .   -   .   Transcript
>>>>> trans-2
>>>>> Contig1 confirmed   exon    30801   31000   .   -   .   Transcript
>>>>> trans-2
>>>>> 
>>>>> Since this transcript and its exons are on the minus strand, the
>>>>> values that the start and stop method return will be reversed, so that
>>>>> start for the transcript will be 31000 and stop will be 30001.  The
>>>>> problem with this test is since the last exon and the transcript share
>>>>> a start value (31000), you can't really be sure which one will be at
>>>>> the bottom of the list after sorting, right?  In the case of the
>>>>> postgres adaptor, it fails this test on my machine because the
>>>>> transcript is at the bottom of the list.  The test for the beginning
>>>>> of the list similarly could fail though it didn't in my case, as other
>>>>> features that have 1 as a start are of type "Component:clone".
>>>>> 
>>>>> So, my question is this: am I missing something, and the postgres
>>>>> adaptor is not behaving as expected, or are these tests ambiguous?
>>>>> 
>>>>> Thanks,
>>>>> Scott
>>>>> 
>>>>> 
>>>>> --
>>>>> 
>>>>> ------------------------------------------------------------------------
>>>>> Scott Cain, Ph. D.                                   scott at scottcain
>>>>> dot net
>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>>> Ontario Institute for Cancer Research
>>>> 
>>>> 
>>>> 
>>>> --
>>>> Lincoln D. Stein
>>>> Director, Informatics and Biocomputing Platform
>>>> Ontario Institute for Cancer Research
>>>> 101 College St., Suite 800
>>>> Toronto, ON, Canada M5G0A3
>>>> 416 673-8514
>>>> Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
>>>> 
>>> 
>>> 
>>> 
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain
>>> dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>> 
>> 
>> 
>> --
>> Lincoln D. Stein
>> Director, Informatics and Biocomputing Platform
>> Ontario Institute for Cancer Research
>> 101 College St., Suite 800
>> Toronto, ON, Canada M5G0A3
>> 416 673-8514
>> Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
>> 
> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
> 
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