[BioRuby] trace files (scf/abi) and ruby/bioruby

[Naohisa GOTO]

Thank you.

Please tell us the URL of your git repository.

Which version of Ruby do you use?
% ruby -v 

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org

On Mon, 20 Oct 2008 15:05:35 +0100
Anthony Underwood <email2ants at gmail.com> wrote:

> Work on the chromatogram reading classes in making good progress.  
> Using a fork of the github bioruby repository I have been  
> incorporating the classes into bioruby in the hope that it can be   
> merged into the main bioruby repository.
>
> However I have run into a problem with the to_biosequence method.
> I have a Scf class that is a subclass of Chromatogram
> 
> Chromatogram has a method
>      def to_biosequence
>        Bio::Sequence.adapter(self, Bio::Sequence::Adapter::Chromatogram)
>      end
> 
> I have added a line to autoload the  
> Bio::Sequence::Adapter::Chromatogram module in the  
> Bio::Sequence::Adapter Class.
> 
> The problem is that the to_biosequence method returns nil.
> 
> I have also found that this is the case when I test fasta and genbank  
> sequences using  the existing Bio::FastaFormat and Bio::Genbank  
> Classes when I use a fresh checkout of the main bioruby repository  
> from github, so I don't think it's something I've done.
> 
> I see that the Bio::Sequence adapter method that to_biosequence calls  
> is as follows
> 
>    def self.adapter(source_data, adapter_module)
>      biosequence = self.new(nil)
>      biosequence.instance_eval {
>        remove_instance_variable(:@seq)
>        @source_data = source_data
>      }
>      biosequence.extend(adapter_module)
>      biosequence
>    end
> 
> the last line does not return a biosequence even though if I puts  
> biosequence.class just before the last line the output is Bio::Sequence.
> 
> Strangely if I insert the method call  biosequence.seq just before the  
> last line of the adapter method everything is fine.
> 
> Does anybody know what's occurring here. Any help much appreciated.
> 
> Thanks
> 
> Anthony
> On 3 Oct 2008, at 04:42, Naohisa GOTO wrote:
> 
> > Hi,
> >
> > For ABI traces, as far as I know, some person made previously,
> > but all codes are lost now.
> >
> > http://open-bio.org/pipermail/bioruby/2005-September/000128.html
> > but I cannot access to the URL described in the above archive.
> >
> > I don't remember why it wasn't included in bioruby, but,
> > the thread of ML archive suggests that no one made any efforts
> > to change the code adopting the development guideline.
> >
> > As Jan says, looking at bioperl, biopython, biojava, Staden, etc.
> > and to write your own code seems good.
> >
> > Naohisa Goto
> > ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
> >
> > On Thu, 2 Oct 2008 19:04:45 +0100
> > "Jan Aerts" <jan.aerts at gmail.com> wrote:
> >
> >> If there's nothing there yet, you might have a look at the bioperl  
> >> version
> >> and take that as a guide.
> >>
> >> jan.
> >>
> >> 2008/10/2 Anthony Underwood <email2ants at gmail.com>
> >>
> >>> Hi all,
> >>>
> >>> Does anybody know if there is or someone is working on a ruby  
> >>> module for
> >>> reading abi/scf trace files. I was thinking of perhaps having a go  
> >>> at this
> >>> but thought I would check that there is no work in progress that I  
> >>> should
> >>> know about. I have done a few Google searches but come up with  
> >>> nothing so
> >>> thought I would ask on this list as well.
> >>>
> >>> Many thanks
> >>>
> >>> Anthony
> >>> _______________________________________________
> >>> BioRuby mailing list
> >>> BioRuby at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/bioruby
> >>>
> >> _______________________________________________
> >> BioRuby mailing list
> >> BioRuby at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioruby
> >
> > _______________________________________________
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
>