[Bioperl-l] Taxonomy and get_taxaid

[anthony.underwood at hpa.org.uk]

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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