[Bioperl-l] indexing and accessing local database

[Qunfeng Dong]

No, it's not an empty file. It's 165,518 maize EST sequences (98 MB). Is it too
large for Bioperl? Thanks for your patient help, Jason

Qunfeng


> 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
> 
> 


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