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

[Hilmar Lapp]

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
>
>
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--
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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