[Bioperl-l] Taxonomy and get_taxaid

[Jason Stajich]

Sorry this module is still very new - I had changed the API a little
without fixing the docs.  See below.


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);
                                     ^^^^^^^
my $species=$db->get_Taxonomy_Node($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