Bioperl: Bio:Seq->revcom

[Ewan Birney]

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
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Ewan Birney
<birney@sanger.ac.uk>
http://www.sanger.ac.uk/Users/birney/

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