Bioperl-guts: Reimplementation of Seq.pm
Mon, 23 Aug 1999 12:07:07 +0100
Hi. Some comments to the reimplememntation of Seq.pm. Hope they are
> 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.
That really should give back the sequence type (Dna or Protein at a
*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.
Alessandro Guffanti - Informatics
The Sanger Centre, Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SA, United Kingdom
phone: +1223-834244 * fax: +1223-494919
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