[Bioperl-l] Flat databases

[S.Paul]

Thanks Lincoln; I'm using bioperl version 1.4

I'll try it with the Berkeley DB also and see how it works

Sujoy Paul
Sujoy Paul, PRISE Centre, UniS, s.paul at surrey.ac.uk
----- Original Message ----- 
From: "Lincoln Stein" <lstein at cshl.edu>
To: "S.Paul" <s.paul at surrey.ac.uk>; "Bioperl" <bioperl-l at bioperl.org>
Sent: Wednesday, July 14, 2004 11:19 AM
Subject: Re: [Bioperl-l] Flat databases


> By the way, I advise that you use the Berkeley DB interface, if 
> possible.  The "flat" indexing scheme is quite slow.
> 
> Lincoln
> 
> On Wednesday 14 July 2004 05:35 pm, S.Paul wrote:
> > Hi Everybody:
> >
> > I was trying to follow the HowTo for Flat databases and try to run
> > the following command: bp_bioflat_index.pl -c -l
> > c:\research\perl\genbank -d g
> > enbank -i flat -f genbank data/*.gbk
> >
> > I installed the bioflat_index.pls script and then tried to run the
> > above command but am getting the following error message:
> >
> > *******************************************************************
> >***
> >
> > C:\research\perl\genbank>bp_bioflat_index.pl -c -l
> > c:\research\perl\genbank -d g enbank -i flat -f genbank data/*.gbk
> >
> > ------------- EXCEPTION  -------------
> > MSG: Can't locate Bio/DB/Flat/Flat/genbank.pm in @INC (@INC
> > contains: C:/Perl/li b C:/Perl/site/lib .) at (eval 4) line 2.
> > BEGIN failed--compilation aborted at (eval 4) line 2.
> >
> > STACK Bio::DB::Flat::new C:/Perl/site/lib/Bio/DB/Flat.pm:140
> > STACK toplevel C:\research\perl\genbank\bp_bioflat_index.pl:89
> >
> > *******************************************************************
> >**********
> >
> > Thanks in advance for the help
> >
> > Sujoy
> >
> >
> >
> > Sujoy Paul, PRISE Centre, UniS, s.paul at surrey.ac.uk
> 
> -- 
> Lincoln D. Stein
> Cold Spring Harbor Laboratory
> 1 Bungtown Road
> Cold Spring Harbor, NY 11724
>