[Bioperl-l] Help with taxonomy db

Brian Osborne brian_osborne at cognia.com
Fri Apr 1 12:26:01 EST 2005


I'm just guessing here but is "flatfile" really the correct value for
'source'? Shouldn't this be an actual file name?

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of
zhoujie at fudan.edu.cn
Sent: Thursday, March 31, 2005 10:45 PM
To: bioperl-l at portal.open-bio.org
Subject: [Bioperl-l] Help with taxonomy db

Hi all,
Would you please help me with this error message in using local
taxonomy db?

My test code is here:
use Bio::DB::Taxonomy;
my $db = new Bio::DB::Taxonomy(-source    => 'flatfile',
			       -nodesfile => 'nodes.dmp',
			       -namesfile => 'names.dmp',
			       -directory => 'index');

my $id = $db->get_taxonid('Homo sapiens');
print "id is $id for Homo sapiens\n";

The code generates three files in the index
directory: 'nodes','names2id','id2names'.

but after that I get an error message:

------------- EXCEPTION  -------------
MSG: No such file or directory index/nodes
STACK Bio::DB::Taxonomy::flatfile::_db_connect
STACK Bio::DB::Taxonomy::flatfile::new
STACK Bio::DB::Taxonomy::new c:/Perl/site/lib/Bio/DB/Taxonomy.pm:104
STACK toplevel local_taxonomy_query.pl:10

I'm quite confused with this error, because the nodes file is just in
there, but why "No such file"?

Can anyone tell me what happening? Any suggestion is appreciated.

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