[Biopython-dev] [Bug 1689] Seq is broken in CVS

[Michiel Jan Laurens de Hoon]

bugzilla-daemon at portal.open-bio.org wrote:
  > http://bugzilla.open-bio.org/show_bug.cgi?id=1689
  > in Seq.complement() and Seq.reverse_complement() replaced seq.alphabet by
  > self.alphabet.

Oops. That was a typo. Thanks for catching that.

  > Added a method __maketrans in Seq
  >
  > Added support for lower case DNA in Seq.complement() and
  > Seq.reverse_complement. Same thing in MutableSeq.complement()

Looks good to me. I'll add that to CVS. Thanks.


 >> I wonder if returning a Seq from a complement is a good idea as well
 >> if your original sequence is a DNA(going 5'->3') the complement will not be a
 >> DNA (it goes 3'->5').


The complement and reverse_complement were added to Seq.py because previously
several implementations of similar functions existed in different parts of
Biopython. The function forward_complement in Bio.GFF.easy takes a Seq object
and returns a Seq object. The function complement in Bio.SeqUtils takes a string
and returns a string. I have a slight preference for returning a Seq object for
consistency with MutableSeq, and also because a user might expect to receive an
object of the same type. Anybody else have an opinion on this?

  >>> from Bio.Seq import *
  >>> from Bio.GFF.easy import *
  >>> s = Seq('ATCGCT')
  >>> forward_complement(s)
Seq('TAGCGA', Alphabet())
  >>>
  >>> from Bio.SeqUtils import complement
  >>> s = 'ATCGCT'
  >>> complement(s)
'TAGCGA'
  >>>

Thanks, Fred.

--Michiel.
-- 
Michiel de Hoon, Assistant Professor
University of Tokyo, Institute of Medical Science
Human Genome Center
4-6-1 Shirokane-dai, Minato-ku
Tokyo 108-8639
Japan
http://bonsai.ims.u-tokyo.ac.jp/~mdehoon