[Bioperl-l] (no subject)

[Jason Stajich]

thanks for the report - the tutorial needs to be updated to use a platform
independent way of creating filenames (which we support through
Bio::Root::IO).
I'll add a bug report for this.

As for your last question - we support connection to nt dbs
through Bio::DB::EMBL and Bio::DB::GenBank if you mean remote databases.
Otherwise you can read in local 'databases' of nucleotide data that are
stored in flatfiles with the Bio::SeqIO system.

-jason

On Fri, 11 Oct 2002, Wu, Liangtang wrote:

> Hello,
>
>
> I try Bioperl in windows 2000 with Apatche2 sever installed in PC. I try to
> run demo "bptutorial.pl". I got something like this:
>
>
>
> F:\>perl -w c:\bioperl-1.0.2\bptutorial.pl  9
>
> Beginning blast.pm parser example...
>
> -------------------- WARNING ---------------------
> MSG: Bio::Tools::BLAST is deprecated, use Bio::SearchIO system or
> Bio::Tools:
> lite
> ---------------------------------------------------
>
> ------------- EXCEPTION  -------------
> MSG: File is empty or non-existent: t\data\blast.report
> STACK Bio::Root::IOManager::file C:/Perl/lib/Bio/Root/IOManager.pm:231
> STACK Bio::Root::Object::file C:/Perl/lib/Bio/Root/Object.pm:1595
> STACK Bio::Root::Utilities::create_filehandle
> C:/Perl/lib/Bio/Root/Utilities.
> 787
> STACK Bio::Root::Utilities::get_newline
> C:/Perl/lib/Bio/Root/Utilities.pm:856
> STACK Bio::Tools::Blast::_parse_blast_stream
> C:/Perl/lib/Bio/Tools/Blast.pm:1
>
> STACK Bio::Tools::Blast::parse C:/Perl/lib/Bio/Tools/Blast.pm:1474
> STACK Bio::Tools::SeqAnal::_initialize C:/Perl/lib/Bio/Tools/SeqAnal.pm:282
> STACK Bio::Root::Object::new C:/Perl/lib/Bio/Root/Object.pm:463
> STACK Bio::Tools::Blast::new C:/Perl/lib/Bio/Tools/Blast.pm:1077
> STACK main::__ANON__ c:\bioperl-1.0.2\bptutorial.pl:3045
> STACK toplevel c:\bioperl-1.0.2\bptutorial.pl:3900
>
> --------------------------------------
>
> F:\>perl -w c:\bioperl-1.0.2\bptutorial.pl  4
>
> Beginning sequence_manipulations and SeqIO example...
>
> ------------- EXCEPTION  -------------
> MSG: Could not open t\data\dna1.fa for reading: No such file or directory
> STACK Bio::Root::IO::_initialize_io C:/Perl/lib/Bio/Root/IO.pm:244
> STACK Bio::SeqIO::_initialize C:/Perl/lib/Bio/SeqIO.pm:381
> STACK Bio::SeqIO::new C:/Perl/lib/Bio/SeqIO.pm:314
> STACK Bio::SeqIO::new C:/Perl/lib/Bio/SeqIO.pm:327
> STACK main::__ANON__ c:\bioperl-1.0.2\bptutorial.pl:2689
> STACK toplevel c:\bioperl-1.0.2\bptutorial.pl:3895
>
> --------------------------------------
>
>
> It semms to me there is no link to romote DNA database at all. How to solve
> this? Any suggestion?
>
> Thanks.
>
> Liangtang Wu
>
> _______________________________________________
> 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