[Biopython-dev] Restriction analysis package.

[fsms at users.sourceforge.net]

Hi,

The modifications on the packages have been done.
The file is released at http://sourceforge.net/projects/rana.
The name of the release is ranaBiopython-0.2.

I had some problems when trying to use SeqUtils.antiparallel function.

Here is an example. The version I use is pooled out of the CVS

 >>> from Bio.Seq import Seq
 >>> from Bio.Alphabet import IUPAC
 >>> s = Seq('acgt', IUPAC.IUPACAmbiguousDNA)
 >>> from Bio.SeqUtils import antiparallel
 >>> b = antiparallel(s)

Traceback (most recent call last):
  File "<pyshell#4>", line 1, in -toplevel-
    b = antiparallel(s)
  File 
"/home/bssfs/cvsroot/biopython/build/lib.linux-i686-2.3/Bio/SeqUtils/__init__.py", 
line 42, in antiparallel
    s = complement(seq)
  File 
"/home/bssfs/cvsroot/biopython/build/lib.linux-i686-2.3/Bio/SeqUtils/__init__.py", 
line 32, in complement
    return seq.translate(_ttable)
AttributeError: Seq instance has no attribute 'translate'
 >>>

So I replace that by a function of my own. But if somebody can tell
me how it is suppose to be used (there is no doc string either on the 
function)....

I added a new class Analysis. It is messy, but it allow some formating 
of the results
obtained when doing a search() with a RestrictionBatch.

There is also the problem of the documentation. I could write something 
to put in the
cookbook if you explain me how or direct me to the howto.

Bye

Fred