[Bioperl-l] phylogeny-trait association methods into BioPerl

Jason Stajich jason at bioperl.org
Wed Sep 10 13:44:25 EDT 2008


Those are just take from Bio::SeqFeature::Generic tag manipulation  
methods so please feel free to add a better one - maybe can propagate  
that new method to Bio::SeqFeature::Generic as well?

Would be nice to see those other methods add as well so am glad to see  
them.

-jason
On Sep 10, 2008, at 4:32 AM, Heikki Lehvaslaiho wrote:

> FYI,
>
> I've been recently writing code to analyse phylogeny-trait  
> associations. These
> traits are typically geographical location of the sequence but they  
> can be any
> phenotypic characters associated with the sequences.
>
> This involves trees, i.e. Bio::Tree::Tree and Bio::Tree::Node  
> objects and
> strings describing the traits. I've been using tags to store trait  
> values
> within nodes. The tag methods are:
>
> Bio::Tree::Node::add_tag_value
> Bio::Tree::Node::get_all_tags
> Bio::Tree::Node::get_tag_values
> Bio::Tree::Node::has_tag
> Bio::Tree::Node::remove_all_tags
> Bio::Tree::Node::remove_tag
>
> Question: Is  there any particular reason why there is no
> set_tag_value(scalar|@array) method?
>
> I am getting tired of writing:
>  $node->remove_tag($key);
>  map {$node->add_tag_value($key)} @values ;
> so I am going to implement that unless there is are strong objections.
>
> Otherwise it has been smooth sailing. I am going to add
> Bio::Tree::TreeFunctions::is_binary() and start populating
> Bio::Tree::Statistics soon with these methods:
>
> ps() - Parsimony Score (PS) from Fitch 1971
> ai() - Association index (AI) of Whang et al. 2001
> mc() - Monophyletic Clade (MC) size statistics by Salemi at al. 2005
> cherries() - number of leaf node pairs
>
> If you have any comments, please feel free to post them here.
>
>    -Heikki
>
> -- 
> ______ _/      _/_____________________________________________________
>      _/      _/
>     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
>    _/_/_/_/_/  Senior Scientist    skype: heikki_lehvaslaiho
>   _/  _/  _/  SANBI, South African National Bioinformatics Institute
>  _/  _/  _/  University of Western Cape, South Africa
>     _/      Phone: +27 21 959 2096   FAX: +27 21 959 2512
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>
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Jason Stajich
jason at bioperl.org





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