BioPerl Question

tucano has asked for the wisdom of the Perl Monks concerning the following question:

I have alittle program that try to connect to a database with this f... module and structure called Bio::DB::GFF.

#!/usr/bin/perl

use strict;
use Bio::DB::GFF;

my $db  = Bio::DB::GFF->new(-user        => 'bio',
                -pass        => 'bio',
                -dsn         => 'elegans',
                            -aggregators => 'gene_model{coding_exon,5_
+UTR,3_UTR/CDS}');

my $gene_stream = $db->get_seq_stream('gene_model:curated');

while (my $gene = $gene_stream->next_seq) {
  print $gene->name,"\n";
  for my $part ($gene->get_SeqFeatures) {
    print "\t",join("\t",$part->method,$part->start,$part->end),"\n";
  }
  print "\n";
}
[download]

When I execute it, i have this error:

2L52.1

------------- EXCEPTION Bio::Root::NotImplemented -------------
MSG: Abstract method "Bio::FeatureHolderI::get_SeqFeatures" is not imp
+lemented by package Bio::DB::GFF::Feature.
This is not your fault - author of Bio::DB::GFF::Feature should be bla
+med!
[download]

Any Idea / suggestion monks?

Comment on BioPerl Question Select or Download Code

Replies are listed 'Best First'.
Re: BioPerl Question by duff (Parson) on Jun 03, 2004 at 15:54 UTC
Implement that method yourself or harangue the module author until he complies to implement it. :-) duff	[reply]
Re^2: BioPerl Question by tucano (Scribe) on Jun 03, 2004 at 15:56 UTC
Better i implement another mod. ach .. a lot of work :-(	[reply]
Re: BioPerl Question by stajich (Chaplain) on Jun 04, 2004 at 15:20 UTC
You'll get better answers from Lincoln or others if you post the question to the bioperl list. If what you are trying to do is get the exons which should be subfeatures as made by the gene aggregator, then you call the old method sub_SeqFeature `for my $exon ( $gene->sub_SeqFeature ) { }` [download] get_SeqFeatures is part of the newer bioperl interface and I don't think Lincoln has updated the DB::GFF code to implement the additions to the interface.	[reply] [d/l]
Re^2: BioPerl Question by tucano (Scribe) on Jun 05, 2004 at 11:30 UTC
Great and impressive. But the bioperl list is outside this site? where i can find it? AnyWAy i take the terrible decision to cut off the BIO::DB::GFF from my system and try to make another connection module starting from zero. So now my task is the module DBI for conection to a mySQL server. Thanks for help anyway, probably i will ask more Bio::Perl questions to you	[reply]
Re^3: BioPerl Question by stajich (Chaplain) on Jun 05, 2004 at 13:36 UTC
The mailing list is mentioned in the POD for every single module. Try the main website Bioperl Site. I would strongly suggest trying out the existing code that is used in production environments as part of GMOD before reinventing this from scratch. You get a LOT for free if you use the existing schemas including a Genome Browser.	[reply]
Re^4: BioPerl Question by tucano (Scribe) on Jun 07, 2004 at 16:50 UTC