[Bioperl-l] RE: Question: How do I run SwissPfam within Bioperl ?

[Brian Osborne]

Misaki,

What the error message is saying is that the Perl module DB_File isn't
installed, you'll need to install it. This module serves as an interface to
the Berkeley DB package, you'll need to install this as well. I've always
downloaded Berkeley DB from www.sleepycat.com.

Brian O.


-----Original Message-----
From: Misaki Sato [mailto:misaki at sfc.keio.ac.jp]
Sent: Wednesday, October 06, 2004 2:37 AM
To: jason at bioperl.org; brian_osborne at cognia.com; heikki at ebi.ac.uk
Subject: Question: How do I run SwissPfam within Bioperl ?

Dear all,

I found a basic structure of SwissPfam like below on some web-sites, but
still have some questions.

1, What file format does this recommend ?
        I tried using FASTA format file "test", but failed like below.
        Content of "swissPfam.pl" is at the bottom of this mail.
% perl swissPfam.pl test
------------- EXCEPTION  -------------
MSG: Can't open 'DB_File' dbm file 'test' :
STACK Bio::Index::Abstract::open_dbm
/usr/lib/perl5/site_perl/5.8.3/Bio/Index/Abstract.pm:389
STACK Bio::Index::Abstract::new
/usr/lib/perl5/site_perl/5.8.3/Bio/Index/Abstract.pm:150
STACK toplevel swissPfam.pl:7
--------------------------------------
%

2, Are there any additional things for running this module ?

3, Could you show me an example to use this module?


--------Content of swissPfam.pl-----------------------
#!/usr/bin/perl -w
   use Bio::Index::SwissPfam;
   use strict;
   my $Index_File_Name = shift;
   my $inx = Bio::Index::SwissPfam->new('-filename' => $Index_File_Name,
                                        '-write_flag' => 'WRITE');
   $inx->make_index(@ARGV);
   use Bio::Index::SwissPfam;
   use strict;
   my $Index_File_Name = shift;
   my $inx = Bio::Index::SwissPfam->new('-filename' => $Index_File_Name);
   foreach my $id (@ARGV) {
        my $seq = $inx->fetch($id); # Returns stream
        while( <$seq> ) {
                if(/^>/) {
                        print; last;
                }
        }
   }
-------------------------------------------
From: http://doc.bioperl.org/releases/bioperl-1.2/Bio/Index/SwissPfam.html


Waiting for your reply.
Thank you.

Misaki Sato
-------------------------------
Keio Univ. SFC
Institute for Advanced Biosciences
                     Misaki Sato
         misaki at sfc.keio.ac.jp
-------------------------------