[Bioperl-l] extract taxonomy from Bio::Tree::NodeI objects...
mark alston (TGAC)
mark.alston at BBSRC.AC.UK
Tue Jul 13 10:47:04 UTC 2010
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
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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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