[Bioperl-l] indexing and accessing local database

[Qunfeng Dong]

Cool! It works with  "use strict" with the big file I have here!!! Thanks a lot
Jason! 

Qunfeng

> okay I can reproduce it with a real file, let's see what is going on.
> 
> First off - the tutorial needs to be revamped to reflect this - always
> 'use strict';
> 
> If I use strict and turn warnings on, I have no problem.
> Do that first.
> 
> I'm not sure why this is failing so horribly with strict off but it works
> when I do that and use 'my' to declare the variables.
> 
> -jason
> 
> On Tue, 9 Jul 2002, Jason Stajich wrote:
> 
> > I can reproduce this if the file FastaSeqName is empty.
> >
> > Make sure it is not an empty file.
> >
> > Bugreport added that Index::Fasta will segfault when one tries to index an
> > empty file.
> >
> > -jason
> > 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
> 
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> 


Qunfeng Dong, Ph.D
ZmDB Manager 
2104 Molecular Biology Building
Iowa State University
Ames, IA 50010