[Bioperl-l] Taxonomy and get_taxaid

anthony.underwood at hpa.org.uk anthony.underwood at hpa.org.uk
Wed May 7 10:26:58 EDT 2003


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

**************************************************************************
The information contained in the EMail and any attachments is
confidential
and intended solely and for the attention and use of the named
addressee(s).
It may not be disclosed to any other person without the express
authority of
the HPA, or the intended recipient, or both. If you are not the
intended
recipient, you must not disclose, copy, distribute or retain this
message or
any part of it.

For information on how to send data to the HPA in encrypted form via
E.Mail, visit www.HPA.org.uk.

This footnote also confirms that this EMail has been swept for computer
viruses, but please re-sweep any attachments before opening or saving.

HTTP://www.HPA.org.uk
**************************************************************************



More information about the Bioperl-l mailing list