[Bioperl-l] Bio::DB::SeqFeature::Store problem with transcripts
Sendu Bala
bix at sendu.me.uk
Tue Feb 13 16:09:09 UTC 2007
I have some raw sequences in a Bio::DB::SeqFeature::Store mysql database
and wanted to associated some basic information with them, like exon
positions. I thought of creating Bio::SeqFeature::Gene::Transcript
objects and storing them so I could later use features() to see what
other features overlapped exons. I ran into a fatal error that can be
replicated with the following simplified one-liner:
perl -MBio::DB::SeqFeature::Store -MBio::SeqFeature::Gene::Transcript -e
'$db = Bio::DB::SeqFeature::Store->new(-adaptor => "DBI::mysql", -dsn =>
"dbi:mysql:test"); $trans =
Bio::SeqFeature::Gene::Transcript->new(-start => 1, -end => 2, -seq_id
=> "test"); $db->store($trans); @trans = $db->features(-seqid => $id,
-type => "transcript"); print "@trans\n";'
code sub {
package Bio::SeqFeature::Generic;
use strict 'refs';
my $self = shift @_;
foreach my $f (@{[] unless $$self{'_gsf_sub_array'};}) {
$f = undef;
}
$$self{'_gsf_seq'} = undef;
foreach my $t (keys %{{} unless $$self{'_gsf_tag_hash'};}) {
$$self{'_gsf_tag_hash'}{$t} = undef;
delete $$self{'_gsf_tag_hash'}{$t};
}
} did not evaluate to a subroutine reference, at
/.../Bio/DB/SeqFeature/Store.pm line 2280
Is this a bug? Or am I taking the wrong approach?
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