[Gmod-help] Bio::DB::SeqFeature::Store issue

[Scott Cain]

Hi Ian,

That is rather bizarre behavior you're describing.  I have a few
questions to get us started:

Is there a line that describes what ctgA is (either a
##sequence-region line or a GFF line)?

Does the file start with ##gff-version 3 ?  I think the seqfeature
loader is somewhat particular about this.

Scott


On Thu, Mar 19, 2009 at 2:29 PM, Ian Holmes <ihh at berkeley.edu> wrote:
> Hi, not sure if GMOD is the right place to direct this query, apologies
> if not.
>
> I'm having some problems with Bio::DB::SeqFeature::Store and I hoped
> someone better-versed in the internals might be able to help.
>
> The following GFF file seems to work fine with the "features" method of
> Bio::DB::SeqFeature::Store (NB there is a tab at the end of each line,
> denoting an empty group field; I have also attached this as a GFF file)
>
> ctgA    bed2gff feature 1659    1984    .       .       .
> ctgA    bed2gff feature 3014    6130    .       .       .
> ctgA    bed2gff feature 1       50000   .       .       .
>
> For example, the following Perl correctly calculates & prints the total
> number of features in the file (3):
>
> use Bio::DB::SeqFeature::Store;
> my $db = Bio::DB::SeqFeature::Store->new
>  (-adaptor => "memory",
>  -dsn => "testbed.gff");
> my @features = $db->features (-seqid => "ctgA");
> print @features+0;
>
>
>
> However, if I delete the last line of the GFF file (i.e. the feature
> from 1 to 50000), it doesn't work (it thinks there are zero features in
> the file). It also doesn't seem to mind if I change the coordinates of
> the last feature, as long as the endpoint is vaguely "large" (e.g. 49000
> works, but 7000 doesn't).
>
>
> Anyone have any ideas? Is this something to do with binning and/or
> default start/endpoints in the feature query method?
>
>
> Ian
>
> ctgA    bed2gff feature 1659    1984    .       .       .
> ctgA    bed2gff feature 3014    6130    .       .       .
> ctgA    bed2gff feature 1660    7000    .       .       .
>
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research