[Bioperl-l] (no subject)

[Wu, Liangtang]

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