[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
c:/Perl/site/lib/Bio\DB\Taxonomy\
flatfile.pm:325
STACK Bio::DB::Taxonomy::flatfile::new
c:/Perl/site/lib/Bio\DB\Taxonomy\flatfile
.pm:138
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.
J Z
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