[Bioperl-l] Taxonomy and entrez

Nathan Haigh n.haigh at sheffield.ac.uk
Mon Sep 4 06:02:34 EDT 2006


I'm trying write a script that parses a BLAST report and retrieves the
taxanomic information from entrez and prints the binomial name for each hit.

I'm new to these objects so I started with the classify_hits_kingdom
script from the script directory in CVS. However, I have problems with
things that are subspecies etc

I have a script that uses the following objects:

my $taxdb = Bio::DB::Taxonomy->new(-source => 'entrez');
my $node = $taxdb->get_Taxonomy_Node($taxid);
print $node->binomial;

However, I get warnings such as:
-------------------- WARNING ---------------------
MSG: can't create a species object for Brassica rapa subsp. pekinensis
(bai cai) because it isn't a species but is a 'subspecies' instead
---------------------------------------------------

I've had a look around and it appears that there has been an overhaul of
species, taxonomy etc since 1.5.1. I was wondering if someone could
point me in the right direction for doing this with bioperl-live?

Thanks
Nathan



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