[Bioperl-l] indexing and accessing local database

[Lincoln Stein]

I don't have any insight as to why Bio::DB::Fasta works and Bio::Index::Fasta 
doesn't.  Internally they use much the same code.

Lincoln

On Tuesday 09 July 2002 01:42 pm, Brian Osborne wrote:
> 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_databa
>s
>
> > > 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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-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
========================================================================