This is bizarre behavior. I'll try to reproduce it.<br><br>Lincoln<br><br><div class="gmail_quote">On Thu, Mar 19, 2009 at 2:29 PM, Ian Holmes <span dir="ltr"><<a href="mailto:ihh@berkeley.edu">ihh@berkeley.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi, not sure if GMOD is the right place to direct this query, apologies<br>
if not.<br>
<br>
I'm having some problems with Bio::DB::SeqFeature::Store and I hoped<br>
someone better-versed in the internals might be able to help.<br>
<br>
The following GFF file seems to work fine with the "features" method of<br>
Bio::DB::SeqFeature::Store (NB there is a tab at the end of each line,<br>
denoting an empty group field; I have also attached this as a GFF file)<br>
<br>
ctgA bed2gff feature 1659 1984 . . .<br>
ctgA bed2gff feature 3014 6130 . . .<br>
ctgA bed2gff feature 1 50000 . . .<br>
<br>
For example, the following Perl correctly calculates & prints the total<br>
number of features in the file (3):<br>
<br>
use Bio::DB::SeqFeature::Store;<br>
my $db = Bio::DB::SeqFeature::Store->new<br>
(-adaptor => "memory",<br>
-dsn => "testbed.gff");<br>
my @features = $db->features (-seqid => "ctgA");<br>
print @features+0;<br>
<br>
<br>
<br>
However, if I delete the last line of the GFF file (i.e. the feature<br>
from 1 to 50000), it doesn't work (it thinks there are zero features in<br>
the file). It also doesn't seem to mind if I change the coordinates of<br>
the last feature, as long as the endpoint is vaguely "large" (e.g. 49000<br>
works, but 7000 doesn't).<br>
<br>
<br>
Anyone have any ideas? Is this something to do with binning and/or<br>
default start/endpoints in the feature query method?<br>
<font color="#888888"><br>
<br>
Ian<br>
</font><br>ctgA bed2gff feature 1659 1984 . . .<br>
ctgA bed2gff feature 3014 6130 . . .<br>
ctgA bed2gff feature 1660 7000 . . .<br>
<br></blockquote></div><br><br clear="all"><br>-- <br>Lincoln D. Stein<br>Director, Informatics and Biocomputing Platform<br>Ontario Institute for Cancer Research<br>101 College St., Suite 800<br>Toronto, ON, Canada M5G0A3<br>
416 673-8514<br>Assistant: Renata Musa <<a href="mailto:Renata.Musa@oicr.on.ca">Renata.Musa@oicr.on.ca</a>><br>