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

[Scott Cain]

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