[Bioperl-l] extract taxonomy from Bio::Tree::NodeI objects...

Chris Fields cjfields at illinois.edu
Tue Jul 13 08:58:41 EDT 2010


Change to the following:

{ print $nodelet->scientific_name() . "\t" ;  }

chris

On Jul 13, 2010, at 5:47 AM, mark alston (TGAC) wrote:

> Hi,
> BioPerl newbie question coming up...
> I want to feed my BioPerl program the name of a bug and extract taxonomic information. Simples.
> Here's my script after days of effort (I joke not):
> #########################################################################
> use Bio::DB::Taxonomy ;
> my $entrez_dbh = new Bio::DB::Taxonomy (-source => 'entrez');
> 
> my $entrezBug = $entrez_dbh->get_taxon(-name => 'Cronobacter sakazakii ATCC BAA-894') ;
> my $bugTree = Bio::Tree::Tree->new(-node => $entrezBug) ;
> 
> my @taxa = $bugTree->get_nodes ;                       ### returns an array of Bio::Tree:NodeI objects
> 
> foreach my $nodelet (@taxa)
> { print $nodelet->to_string() . "\t" ;  }
> #########################################################################
> 
> This outputs:
> 131567 2              1224       1236       91347    543         413496 28141    290339
> 
> If I feed these to the NCBI taxonomy browser as 'taxonomy id' they make sense because
> 2 corresponds to: bacteria (superkingdom)
> 1224  corresponds to: proteobacteria (phylum)
> etc etc
> 290339 corresponds to: Cronobacter sakazakii ATCC BAA-894 (species)
> 
> 
> But how can I get the things I've underlined out via BioPerl?
> Many thanks,
> Mark
> 
> ################################################
> Dr Mark Alston,
> Computer Biologist,
> The Genome Analysis Centre,
> Norwich Research Park,
> Colney Lane, Norwich, NR4 7UH, UK.
> 
> tel                +44 (0)1603 450910
> e-mail         mark.alston at bbsrc.ac.uk<mailto:mark.alston at bbsrc.ac.uk>
> web            http://www.tgac.bbsrc.ac.uk<http://www.tgac.bbsrc.ac.uk/>
> ################################################
> 
> 
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