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

[Lincoln Stein]

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>