[Biopython-dev] Gsoc 2014 aspirant

[Michiel de Hoon]

I would suggest to implement this in C, with a thin wrapper in Python.
Using 3rd-party libraries would increase the compile-time dependencies of Biopython.
Anyway I expect that the tricky part will be the design of the module, rather than the algorithms themselves, so using 3rd-party libraries wouldn't help us so much.
Best,
-Michiel.

--------------------------------------------
On Fri, 2/28/14, Fields, Christopher J <cjfields at illinois.edu> wrote:

 Subject: Re: [Biopython-dev] Gsoc 2014 aspirant
 To: "Michiel de Hoon" <mjldehoon at yahoo.com>
 Cc: "biopython-dev at lists.open-bio.org" <biopython-dev at lists.open-bio.org>, "Harsh Beria" <harsh.beria93 at gmail.com>
 Date: Friday, February 28, 2014, 12:45 PM
 
 I’m wondering, with something that
 is as broadly applicable as pairwise alignment, would it be
 better to implement only in Python (or implement in Python
 wedded to a C backend)?  Or maybe set up something in
 python that taps into an already well-defined C/C++ library
 that does this?  
 
 The reason I mention this: with bioperl we went down this
 route with bioperl-ext a long time ago (these are generally
 C-based backend tools with a perl front-end), that
 bit-rotted simply b/c there were other more maintainable
 options.  IIUC from this post, similar issues re:
 maintainability held for Bio/pairwise2.py (unless I’m
 mistaken, which is entirely possible).  However, tools
 like pysam and Bio::DB::Samtools (on the perl end) seem to
 have been maintained much more readily since they tap into a
 common library.
 
 For instance, my suggestion would be to implement a
 Biopython tool that does pairwise alignment using library X
 (SeqAn, EMBOSS, etc).  Or maybe a generic python
 front-end that allows users to pick the tool/method for the
 alignment, with maybe a library binding as an initial
 implementation.
 
 chris
 
 On Feb 28, 2014, at 4:07 AM, Michiel de Hoon <mjldehoon at yahoo.com>
 wrote:
 
 > Hi Harsh Beria,
 > 
 > One option is to work on pairwise sequence alignments.
 Currently there is some code for that in Biopython (in
 Bio/pairwise2.py), but it is not general and is not being
 maintained. This may need to be rebuilt from the ground up.
 > 
 > Best,
 > -Michiel.
 > 
 > --------------------------------------------
 > On Wed, 2/26/14, Harsh Beria <harsh.beria93 at gmail.com>
 wrote:
 > 
 > Subject: [Biopython-dev] Gsoc 2014 aspirant
 > To: biopython at lists.open-bio.org,
 biopython-dev at lists.open-bio.org,
 gsoc at lists.open-bio.org
 > Date: Wednesday, February 26, 2014, 11:14 AM
 > 
 > Hi,
 > 
 > I am a Harsh Beria, third year UG student at Indian
 > Institute of
 > Technology, Kharagpur. I have started working in
 > Computational Biophysics
 > recently, having written code for pdb to fasta parser,
 > sequence alignment
 > using Needleman Wunch and Smith Waterman, Secondary
 > Structure prediction,
 > Henikoff's weight and am currently working on Monte
 Carlo
 > simulation.
 > Overall, I have started to like this field and want to
 carry
 > my interest
 > forward by pursuing a relevant project for GSOC 2014.
 I
 > mainly code in C
 > and python and would like to start contributing to the
 > Biopython library. I
 > started going through the official contribution wiki
 page (
 > http://biopython.org/wiki/Contributing)
 > 
 > I also went through the wiki page of Bio.SeqlO's. I
 > seriously want to
 > contribute to the Biopython library through GSOC. What
 do I
 > do next ?
 > 
 > Thanks
 > -- 
 > 
 > Harsh Beria,
 > Indian Institute of Technology,Kharagpur
 > <http://www.iitkgp.ac.in/>E-mail: harsh.beria93 at gmail.com
 > _______________________________________________
 > Biopython-dev mailing list
 > Biopython-dev at lists.open-bio.org
 > http://lists.open-bio.org/mailman/listinfo/biopython-dev
 > 
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