[Biopython-dev] Biopython 1.00a2 release

[Thomas Sicheritz-Ponten]

Jeffrey Chang <jchang at SMI.Stanford.EDU> writes:

> Hey happy developers!
> 
> It smells like time to put together another release to get some bug
> fixes and new functionality out to the public.  I currently have the
> middle of next week in mind, although that's still up for debate.
> 
> Here's my undoubtedly incomplete list of stuff that's been updated
> since the last release (on Mar 3!):
> 
>    deprecated old regression testing frameworks
>    deprecated Sequence.py  (still needs to be done)
>    Swiss-Prot parser bug fixes
>    GenBank parser bug fixes
>    can now download many sequences at a time from GenBank
>    kMeans clustering algorithm

Cool .... Arghhh, I should have spend more time following all development
postings, I spend 2 days implementing kMeans in python ... :-)
- one observation for calculating the euclidean distance, looping over the
  vectors seems to be faster than the vector based operation .... the most
  frequent used function in the kMean algoritm is the euclidean distance
  measure, so we gain significant speed ... (at least on my machine)
 (any thoughts about implementing the bi-secting kmeans algoritm ?)

# this is slow
def EucDist2(v1, v2):
    return sqrt(sum((v1-v2)**2))

# this is faster
def EucDist1(v1, v2):
    sum = 0
    for i in range(0,len(v1)):
        sum += (v1[i] -v2[i])**2
    return sqrt(sum)


>    support for Kabat
>    support for FSSP
>    numerous updates in alignment code
>    fixed memory leak in listfns
>    Martel bundled and part of the install procedure
> 
> Please let me know if:
>    1) you're currently working on something and really want to hold
>    off until it's done.

I have small things I always wanted to include but I never did ...  
Where should we include sequence based calculations like GC-content, GC3
etc. - should we put that in the sequence class (not a good idea IMHO)
or create a new module e.g. seqstat ?

Whats the status of an antiparallel or complementary function - do we still
lack one ?

> Let me know what you think.  Core developers, I will wait until I hear
> from each of you before I move forward.

I think, this month I can spend significantly more time on the biopython
project than the last months - so is anything I mentioned worth to pull in
the next release ?

cheers
-thomas

-- 
Sicheritz-Ponten Thomas, Ph.D  CBS, Department of Biotechnology
thomas at biopython.org           The Technical University of Denmark
CBS:  +45 45 252489            Building 208, DK-2800 Lyngby
Fax   +45 45 931585            http://www.cbs.dtu.dk/thomas

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