[Bioperl-l] Taxonomy and get_taxaid

[Jason Stajich]

However - you won't be able to do this code because Salmonella is not a
species and the data returned by NCBI is not rich enough to build a full
Bio::Species object.

This is in part why we are trying to build a generation of Taxonomy
objects but really need more people pitching in to develop the objects and
connecting this to the data retrieval systems.

So basically this isn't going to work every when you fix the syntax
problem below.

-jason

On Wed, 7 May 2003 anthony.underwood at hpa.org.uk wrote:

> Hi All,
>
>
> I'm getting a problem with the taxonomy module when I write this script:
>
> use Bio::DB::Taxonomy;
> my $db=new Bio::DB::Taxonomy(-source=>'entrez');
> my $taxaid=$db->get_taxaid("Salmonella");
> my $species=$db->get_Taxonomy_Node(-taxaid=>$taxaid);
> print $species->species->genus;
>
>
>
> The error I get is Can't call method "children" on an undefined value at
> /usr/lib/perl5/site_perl/5.6.1/Bio/DB/Taxonomy/entrez.pm line 167.
> I think this is when the get_taxaid routine is called
>
>
> Can anyone advise on this. Thanks in advance,
>
> Anthony
>
> Dr Anthony Underwood
> Bioinformatics Unit
> Central Public Health Laboratory
> Health Protection Agency
> 61 Colindale Avenue
> London
> NW9 5HT
> t:    0208 2004400 ext. 3618
> f:    0208 3583138
> e: anthony.underwood at hpa.org.uk
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu