[Bioperl-l] Bio::Cluster::Family

[Shawn]

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Subject: Re: [Bioperl-l] Bio::Cluster::Family
From: Shawn <shawnh@fugu-sg.org>
To: Jason Stajich <jason@cgt.mc.duke.edu>
In-Reply-To:
	<Pine.LNX.4.33.0210011455040.18014-100000@tenero.genetics.duke.edu>
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	<Pine.LNX.4.33.0210011455040.18014-100000@tenero.genetics.duke.edu>
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Date: 02 Oct 2002 09:40:06 +0800
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<Combining my replies to Hilmar and Jason>

Sounds good. There was a Bio::Cluster::UniGeneI so wasn't sure whether
to have a Bio::Cluster::FamilyI as well. I guess we expect to have
different kinds of families? Just curious, is the convention to have a
Bio::ClusterI one level up in namespace or Bio::Cluster::ClusterI as u
proposed?

the methods look good and kinda what i had in mind. I can work on an
interface and propose it to the list.

shawn


On Wed, 2002-10-02 at 02:57, Jason Stajich wrote:
> 
> Just an idea, let me know if you guys like it better?
> 
> Bio::Cluster::ClusterI
> 
> my @hs_members = $cluster->get_members(-species => 'homo sapiens');
> my @all_members = $cluster->get_members();
> my $size = $cluster->size();
> my $desc = $cluster->description();
> 
> 
> -jason
> 
> On Tue, 1 Oct 2002, Hilmar Lapp wrote:
> 
> > Looks good. Species is an object property though, not a string.
> > (Also, use -display_id instead of -id, which is ambiguous has been
> > deprecated a while ago I believe)
> >
> > Do you want to propose an interface Bio::Cluster::FamilyI which can
> > then be implemented by different modules? Also, I just realize there
> > is no Bio::ClusterI yet, which Bio::Cluster::Family will want to
> > implement.
> >
> > If someone feels up to propose the methods of this that'd be great.
> > Any volunteers?
> >
> > 	-hilmar
> >
> > On Monday, September 30, 2002, at 05:33 AM, Shawn wrote:
> >
> > > Hi folks,
> > >
> > > 	I'm currently working on a protein clustering pipeline and am
> > > proposing
> > > the following object for storing of families. It is simple and
> > > works for
> > > me right now. Proposed usage:
> > >
> > >
> > > use Bio::Cluster::Family;
> > >
> > > my $prot1 = Bio::Seq->new(-id=>"Q8W551",
> > >                                -alphabet=>"protein",
> > > 			       -species=>"homo sapiens",
> > >                                -desc=>"POLYUBIQUITIN");
> > > my $prot2 = Bio::Seq->new(-id=>"Q92332",
> > >                                -alphabet=>"protein",
> > >                                -species=>"Mus musculus",
> > >                                -desc=>"POLYUBIQUITIN");
> > > my $prot3 = Bio::Seq->new(-id=>"Q94EA5",
> > >                                -alphabet=>"protein",
> > >                                -species=>"Fugu rubripes",
> > >                                -desc=>"H01 26 protein");
> > >
> > > my $family = Bio::Cluster::Family->new(-family_id=>"TribeFamily",
> > > 				       -members=>[$prot1, $prot2 						,$prot3],
> > > 				       -description=>"POLYUBIQUITIN",
> > >                                        -annotation_score=>60);
> > >
> > > print $family->size."\n";
> > > print $family->description."\n";
> > > print $family->annotation_score."\n"; #the confidence in which the
> > > 				      #consensus
> > >                                  #description is assigned to the family
> > >                                  #by TribeMCl
> > >
> > > my @members = $family->get_members_by_species("homo sapiens");
> > >
> > >
> > > foreach my $seq ($family->members){
> > > 	print $seq->desc."\n";
> > > }
> > >
> > >
> > > Currently, I have ported over the Ensembl Logic of generating family
> > > consensus descriptions to the TribeMCL wrapper. It will also be nice to
> > > add a SimpleAlign get/set for storing multiple alignments. The name
> > > space can also be changed to TribeFamily if Family alone is too
> > > encompassing.
> > >
> > > all comments welcomed.
> > >
> > >
> > > cheers,
> > > shawn
> > >
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l@bioperl.org
> > > http://bioperl.org/mailman/listinfo/bioperl-l
> > >
> > --
> > -------------------------------------------------------------
> > Hilmar Lapp                            email: lapp at gnf.org
> > GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> > -------------------------------------------------------------
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> >
> 
> -- 
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
> 


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