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

[Charles Tilford]

Hi Kevin,

I'm unfamilar with Seqfactory, that got added to the module a few
months after I submitted the module. If you check the CVS tree:

http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/Bio/SeqIO/bsml.pm?cvsroot=bioperl

...it looks like there is a bug fix for your problem in revision 1.19.

-Charles

"Clancy, Kevin" wrote:
> 
> 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";

-- 
Charles Tilford, Bioinformatics-Applied Genomics
Bristol-Myers Squibb PRI, Hopewell 3A039
P.O. Box 5400, Princeton, NJ 08543-5400, (609) 818-3213
charles.tilford at bms.com