Bioperl-guts: Reimplementation of Seq.pm

Alessandro Guffanti ag3@sanger.ac.uk
Mon, 23 Aug 1999 12:07:07 +0100


Hi. Some comments to the reimplememntation of Seq.pm. Hope they are
useful.

> Do we specify the case of sequence characters? In which case, is it the 
> same for the DNA and protein types? 

In the output from ABI sequenchers lowercase means lower quality or
otherwise this can be the output from manually edited gel files. I would
stick to case-insensitive for DNA. Forcing to lower- or upper- case will
cause loss of information. 

> $seqtype=$myseq->type(); 

That really should give back the sequence type (Dna or Protein at a
minimum)
*even if this information was not entered when the object was created*,
i.e. no "unknown" answer should be given back. A simple count of
A+C+G+T+N vs. all chars would suffice to say DNA if > 0.8 (as a rule of
thumb). That will be sueful for people working with cgi-based scripts.


BW,

Alessandro.

-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
       Alessandro Guffanti - Informatics      
The Sanger Centre, Wellcome Trust Genome Campus
  Hinxton, Cambridge CB10 1SA, United Kingdom        
    phone: +1223-834244 * fax: +1223-494919
      http://www.sanger.ac.uk/Users/ag3
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