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

[Ian Holmes]

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
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