[Bioperl-l] Re: ask for help!

[Heikki Lehvaslaiho]

Liangtang,

I am forwading this to the bioperl mailing list so that Windows users
can comment.

I use only unix and "perl bptutorial 9" works for me.

Yours,
	-Heikki


Peter & other bioperlers,

bptutorial inn biopelr-live gives:
 
  syntax error at bptutorial.pl line 2820, near "print"

Maybe it is time to update it for 1.2 release.

	-H

On Fri, 2002-10-11 at 17:55, Wu, Liangtang wrote:
> Hello,
> 
> 
> You may use bioperl in your work.
> 
> 
> I try it in windows 2000 with Aptche2 server installered.
> 
> 
> I run demo bptutorial.pl. I got message 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 seems to me that there is no connection with romote DNA database. How do
> I solve this? Any suggestions?
> 
> 
> Thanks.
> 
> 
> Liangtang Wu  
-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
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