[Bioperl-l] indexing and accessing local database

[Jason Stajich]

What is the full version of perl i.e.
% perl -v

What version of bioperl?
(if you don't know do this)
% perldoc -m Bio::Seq | grep VERSION

I'll guess that DB_File must not be installed correctly or something as
this works on most linux+perl distributions out of the box.

What version of DB_File?
(do this)
% perldoc -m DB_File | grep VERSION

Are you getting a segfault or just an exception from bioperl?


-jason

On Tue, 9 Jul 2002, Qunfeng Dong wrote:

> It's Linux and perl 5 (and when I install bioperl, perl is also installed)
>
>
> > What operating system are you using and version of Perl?
> >
> > On Tue, 9 Jul 2002, Qunfeng Dong wrote:
> >
> > > Hi,
> > >
> > > I am trying to follow the sample code from
> > > http://bioperl.org/Core/POD/bptutorial.html#III_1_1_Accessing_remote_databas
> > >
> > > to build a local fasta sequence database
> > >  #!/usr/bin/perl -w
> > >  #scriptName - BuildIndex.pl
> > >   use Bio::Index::Fasta; # using fasta file format
> > >   $Index_File_Name = shift;
> > >   $inx = Bio::Index::Fasta->new(
> > >       -filename => $Index_File_Name,
> > >       -write_flag => 1);
> > >   $inx->make_index(@ARGV);
> > >
> > >
> > > then I ran the script BuildIndex.pl as
> > > % BuildIndex.pl indexName FastaSeqName
> > > and I got Segmentation fault. Any idea why?
> > >
> > > Qunfeng Dong
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l@bioperl.org
> > > http://bioperl.org/mailman/listinfo/bioperl-l
> > >
> >
> > --
> > Jason Stajich
> > Duke University
> > jason at cgt.mc.duke.edu
> >
> >
>
>
> Qunfeng Dong, Ph.D
> ZmDB Manager
> 2104 Molecular Biology Building
> Iowa State University
> Ames, IA 50010
>
>
>
>
>
>

-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu