[Bioperl-l] problems converting bsml to another file type

[Clancy, Kevin]

Dear All
I am working with BioPerl-1.2.1, with ActiveState Perl 5.6.1, build 635 on Windows 2000. I am running the code snippet, which is included in the Bio::SeqIO::bsml pod, that tests the conversion of  a file of a particular type to bsml and back again. I am simply using data files from the BioPerl t/data directory.
 
When I run the snippet, the conversion to bsml is fine - the expected out.bsml file is created and looks like it is compliant with the standard. However, the script is unable to reverse the process, and produces the following error message:
Can't locate object method "create_sequence" via package "Bio::Seq::Seqfactory"
(perhaps you forgot to load "Bio::Seq::SeqFactory"?) at D:/Perl/site/lib/Bio|SeqIO\bsml.pm line 181, <GEN0> line 78.
 
Looking at the line in bsml.pm, it is part of subroutine next_seq() and has the following code at that line:
my $bioSeq = $self->sequence_factory->create(-verbose =>$self->verbose());
 
Running perl -w bptutorial.pl 100 Bio::SeqIO::bsml, there is no sign of a create_sequence method in bsml.pm or any of its dependent modules.
 
I am including the code snippet for reference below. Any help would be appreciated.
 
Sincerely
Kevin Clancy
 
Kevin Clancy, PhD
Senior Bioinformatics Scientist
InforMax: Invitrogen Life Science Software
phone: 720 746 3707
email: kclancy at informaxinc.com
433 Park Point Drive, Suite 275
Golden, CO 80401
 
#!/usr/bin/perl
use strict;
use Bio::SeqIO;
 # Tests preservation of details during round-trip conversion:
 # $readformat -> BSML -> $readformat
 
 my $tempspot = "./bsmltemp";                     # temp folder to hold generated files
 my $readfile = "test.genbank";                     # The name of the file you want to test
 my $readformat = "genbank";                      # The format of the file being tested system "mkdir $tempspot"
                                                                    # unless (-d $tempspot);
 
 # Make Seq object from the $readfile
 my $biostream = Bio::SeqIO->new( -file => "$readfile" );
 my $seq = $biostream->next_seq();              # Write BSML from SeqObject
 my $bsmlout = Bio::SeqIO->new( -format => 'bsml',
                                                      -file => ">$tempspot/out.bsml");
 warn "\nBSML written to $tempspot/out.bsml\n";
 $bsmlout->write_seq($seq);
 
 # Need to kill object for following code to work... Why is this so?
 $bsmlout = "";                                                # Make Seq object from BSML
 my $bsmlin = Bio::SeqIO->new( -file => "$tempspot/out.bsml",
                                                   -format => 'bsml');
 my $seq2 = $bsmlin->next_seq();                   # Write format back from Seq Object
 my $genout = Bio::SeqIO->new( -format => $readformat,
                                                     -file => ">$tempspot/out.$readformat");
 $genout->write_seq($seq2);
 warn "$readformat  written to $tempspot/out.$readformat\n";