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

[Lincoln Stein]

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>