[Bioperl-l] indexing and accessing local database

[Brian Osborne]

Qunfeng,

I'm also seeing a segmentation fault on my Cygwin/Windows machine with code
like yours, using Bio::Index::Fasta. But I'm surprised that I can index
using Bio::DB::Fasta. If you don't care which indexing module you're using
then I suggest you try something like this and see what happens:

use Bio::DB::Fasta;
$File_Name = shift;
$inx = Bio::DB::Fasta->new($File_Name);
$seq = $inx->get_Seq_by_id("P8413");
print $seq->seq;


Brian O.

-----Original Message-----
From: bioperl-l-admin@bioperl.org [mailto:bioperl-l-admin@bioperl.org]On
Behalf Of Qunfeng Dong
Sent: Tuesday, July 09, 2002 12:44 PM
To: Jason Stajich
Cc: bioperl-l@bioperl.org
Subject: Re: [Bioperl-l] indexing and accessing local database

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






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