Bioperl: Bio:Seq->revcom

[Dawei Lin]

Hi Ewan,
 I am using 0.05. Actually I missed the "Returns" part of the doc. I only look
closely to Usage, Function and Example. :-(
 For the question if it should return a string or a reference, I think once doc
is fixed, I agree return a reference is fine.

  thanks,
  Dawei

On Jun 1,  4:42pm, Ewan Birney wrote:
> Subject: Re: Bioperl: Bio:Seq->revcom
>
> On Tue, 1 Jun 1999, Dawei Lin wrote:
>
> > Hi there,
> >   I tried "revcom" method in the Bio::Seq module, it returns an object
> > reference instead of the sequence itself. On the other hand, "complement"
> > method return the sequence string, does the difference is made on purpose
or it
> > is a kind of bug. In the revcom doc, it does not mention the return value
is a
> > reference.
>
> What version of bioperl are you using? I have just looked at the docs for
> the revcom method (0.05) and at the end it says it is a reference but at
> the start it says it is a string, which is possibly worse than it saying
> it is a string everywhere else... ;).
>
> Noone could imagine using a complement DNA that wasn't revcomp as a
> sequence, hence sticking to strings. Complement is a pretty useless
> function: revcomp is generally what is used.
>
> Anyway - many, many thanks for pointing this out and I will try to
> rationalise the documentation so that it is consistent *AND* correct.
>
>
> >   thanks,
> >   Dawei
> >
> >
> > --
> >
> >
> > --------< *** Dr. Dawei LIN *** >---------------
> >
> >              Biology Department
> >         Brookhaven National Laboratory
> >              Upton, NY 11973
> >                   U.S.A
> >         Telepone: 516-344-6359 (office)
> >                   516-345-6533  (home)
> >              Fax: 516-344-5751
> >            Email: lin@bnl.gov
> > ------------------------------------------------
> >
> > =========== Bioperl Project Mailing List Message Footer =======
> > Project URL: http://bio.perl.org/
> > For info about how to (un)subscribe, where messages are archived, etc:
> > http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/vsns-bcd-perl.html
> > ====================================================================
> >
>
> Ewan Birney
> <birney@sanger.ac.uk>
> http://www.sanger.ac.uk/Users/birney/
>-- End of excerpt from Ewan Birney



-- 

 
--------< *** Dr. Dawei LIN *** >---------------

             Biology Department  
        Brookhaven National Laboratory   
             Upton, NY 11973
                  U.S.A
        Telepone: 516-344-6359 (office)
                  516-345-6533  (home)
             Fax: 516-344-5751
           Email: lin@bnl.gov
------------------------------------------------

=========== Bioperl Project Mailing List Message Footer =======
Project URL: http://bio.perl.org/
For info about how to (un)subscribe, where messages are archived, etc:
http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/vsns-bcd-perl.html
====================================================================