[Bioperl-l] Help with taxonomy db

zhoujie at fudan.edu.cn zhoujie at fudan.edu.cn
Thu Mar 31 22:44:49 EST 2005

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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