[Bioperl-l] SeqFeatureCollection issue

[Jason Stajich]

Did you try passing in a filename with -file => '/tmp/myfile.idx'?

 Title   : new
 Usage   : my $obj = new Bio::SeqFeature::Collection();
 Function: Builds a new Bio::SeqFeature::Collection object
 Returns : Bio::SeqFeature::Collection
 Args    :

           -minbin        minimum value to use for binning
                          (default is 100,000,000)
           -maxbin        maximum value to use for binning
                          (default is 1,000)
           -file          filename to store/read the
                          BTREE from rather than an in-memory structure
                          (default is false and in-memory).
           -keep          boolean, will not remove index file on
                          object destruction.
           -features      Array ref of features to add initially

No idea where the /var/tmp is going...

This *should* work but I haven't done much with it/used it for quite a
while so I don't know if there are things that don't work...

If it is really not working you can always go the -> to GFF -> load in
Bio::DB::GFF route using the in-memory adaptor - I wanted to merge the
interface so that SeqFeature::Collection used the same method names but
never got around to it.  If someone is using the module would be a nice
thing to have...

-jason


On Wed, 14 Jul 2004, Wiepert, Mathieu wrote:

> Hi,
>
>
>
> I was trying to use the seqfeature collection to pull out features in a range I was interested in.  I have two problems (maybe because I am loading features form a contig?)
>
>
>
> In the first case, I ended up running out of space on /var/tmp.  We have about .5 GB there I am.  Code is like
>
> my $in1  = Bio::SeqIO->new('-file' => $contig.'.gb' , '-format' => 'Genbank');
>
> while (my $seq = $in1->next_seq) {
>
>             my @feat_ary = $seq->get_SeqFeatures();
>
>             my $col = new Bio::SeqFeature::Collection();
>
>             # add these features to the object
>
>             my $totaladded = $col->add_features(\@feat_ary);
>
> }
>
>
>
> I end up filling /var/tmp to 100%, as I said.
>
>
>
> So I tried to initialize the collection like
>
> my $col = new Bio::SeqFeature::Collection(-features => \@feat_ary);
>
>
>
> but that gave an error:
>
>
>
> "Can't call method "put" on an undefined value at /usr/local/biotools/perl/5.8.2/lib/site_perl/5.8.2/Bio/SeqFeature/Collection.pm line 225, <GEN0> line 95373."
>
>
>
> That looked like the _btree wasn't set, but not sure.
>
>
>
> I am told we have plenty of room in /tmp, so I should change my tmp dir, but the docs said that it was all in memory by default, is that not the case?  I tried to export a new tmp dir, but that didn't fix the problem...
>
>
>
>
>
> -mat
>
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>
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>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu