[Bioperl-l] Bio::DB::SeqFeature::Segment problem
Jon Flowers
jonathanmflowers at gmail.com
Thu Apr 30 16:40:42 UTC 2009
Dear colleagues,
I have set up a mySQL database and loaded a GFF3 and fasta file using
Bio::DB::SeqFeature::Store::GFF3Loader. Everything appears to be working
normally except when I attempt to create a Bio::DB::SeqFeature::Segment
object.
The following works as expected:
my $db = Bio::DB::SeqFeature::Store->new(-adaptor => 'DBI::mysql',
-dsn => 'dbi:mysql:foo',
-user => 'myuser',
-pass => 'mypassword',
-write => '1');
my @features = $db->features(-seq_id=>'chr1',
-start=>1,
-end=>10000,
-types=>['gene']);
However, when I try to create a segment object using either of the two
following method calls I get an error:
my $segment = $db->segment('chr1',1=>10000);
my $segment = $db->segment( -seq_id => 'chr1', -start => '1', -end =>
'10000');
-------------------------------- EXCEPTION
------------------------------------
MSG: segment() called in a scalar context but multiple features match.
Either call in a list context or narrow your search using the -types or
-class arguments
STACK Bio::DB::SeqFeature::Store::segment
/usr/share/perl5/Bio/DB/SeqFeature/Store.pm:1178
STACK toplevel trial.pl:42
-------------------------------------------------------
Calling in list context (which is not defined in the documentation) produces
an array of 22 identical scalars = 'chr1:1..10000'.
Any ideas?
Thanks
Jonathan
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