[Biopython-dev] Gsoc 2014 aspirant

[Fields, Christopher J]

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
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