[Bioperl-l] A question about flatting taxonomy database

[zhoujie at fudan.edu.cn]

Sorry, probably the first mail I replyed was lost, so I send it agian 
here.

My conmmand line is:

perl bp_local_taxonomydb_query.pl --nodes nodes.dmp --names names.dmp

I only changed one thing: the directory in the script, I changed it 
to './index' , and it generates the right thing in that directory. But 
when it finished, the script throw out an exception: 

------------------- EXCEPTION  ----------------
MSG: No such file or directory ./index/nodes  
STACK Bio::DB::Taxonomy::flatfile::_db_connect 
C:/Perl/site/lib/Bio\DBTaxonomy\flatfile.pm:325
STACK Bio::DB::Taxonomy::flatfile::new 
C:/Perl/site/lib/Bio\Bio\DB\Taxonomy\flatfile.pm:138
STACK Bio::DB::Taxonomy::new C:/Perl/site/lib/Bio/DB/Taxonomy.pm:104
STACK toplevel bp_local_taxonomy_query.pl:22
-----------------------------------------------

I think I have already told the script the location, by the -directory 
parameter in the new method of Bio::DB::Taxonomy, at line 25 of the 
script.

Is there anything wrong with my process?

J Z

----- Ô­Óʼþ -----
´Ó: Jason Stajich <jason.stajich at duke.edu>
ÈÕÆÚ: ÐÇÆÚÒ», ÈýÔÂ 28ÈÕ, 2005 ÉÏÎç6:58
Ö÷Ìâ: Re: [Bioperl-l] A question about flatting taxonomy database

> Can you show the command line argument that you passing in? You 
> need to tell 
> the script where to find these files.
> 
> -jason
> -- 
> Jason Stajich
> jason.stajich at duke.edu
> http://www.duke.edu/~jes12/
> 
> 
> Quoting zhoujie at fudan.edu.cn:
> 
> > Hi all,
> > 
> > When I'm using "bp_local_taxonomydb_query.pl" to build a local 
> > taxonomy database and query it, I always get a exception 
> saying:"no 
> > such file or directory ***, STACK ***", it seems that the nodes 
> file, 
> > id2names and names2id files are already created, but how does 
> the 
> > error MSG arise? I have already installed the BerkeleyDB module 
> by 
> > ppm. Is there anything else that I need to do?
> > 
> > Thanks very much for you help.
> > 
> > J Z
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> > 
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