[Bioperl-l] Help with taxonomy db

[Brian Osborne]

Jason,

OK, in which case the Taxonomy.pm module is wrong, it says "localfile" not
"flatfile". I'll correct this ....

Brian O.

-----Original Message-----
From: Jason Stajich [mailto:jason.stajich at duke.edu]
Sent: Friday, April 01, 2005 12:51 PM
To: Brian Osborne
Cc: zhoujie at fudan.edu.cn; bioperl-l at portal.open-bio.org
Subject: Re: [Bioperl-l] Help with taxonomy db


The source => 'flatfile' is right you can either use 'flatfile' or
'entrez' as the source.

I think there may have been bugs in one of the released versions of the
module where it doesn't properly re-open the index.  I know I fixed
something in this after the 1.4 release but I don't remember what was
the exact problem.

I'd see if bioperl 1.5.0 code still gives the problem.

-jason
--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/

On Apr 1, 2005, at 12:26 PM, Brian Osborne wrote:

> J,
>
> 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
> 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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