[Biopython] Query for GSoc projects on SearchIO and Representation and manipulation of genomic variants

[Peter Cock]

On Mon, Mar 26, 2012 at 5:31 AM, Ankesh Thakur <ankeshth at gmail.com> wrote:
> Dear Sir,
>   I am a student of Biological Sciences and bioengineering at Indian
> Institute of Technology, Kanpur (IIT Kanpur). I am willing to write
> codes for Biopython during this summer. I am not very much clear about
> the goals of this project. I want to know more about the suggested
> projects, like what else I need to do apart from conversion of one file
> format to other and showing the data on the console in human readable
> form.
>
>   I have no prior experience with bio modules of python. I have arround than
> seven months experience with python git hub. And I have done Molecular
> biology, Genetics and Bio-chemistry courses. I would like to learn
> Biopython, BioPerl( if required) and other necessary tools during this
> summer. Eagerly waiting for your reply.
>
> Regards,
> Ankesh Kumar Thakur.

Hello Ankesh,

Both the SearchIO and genomic variant GSoC project ideas are
more than just file format conversion and 'pretty printing' at the
console. An essential part of this is designing a suitable object
representation for efficient use of the data. That probably means
creating objects (Python classes). This will require both a good
understanding of the meaning of the data being represented
(e.g. how are BLAST search results structured) but also how
to design Python objects.

For the SearchIO project, I went into a lot more detail on the
Biopython development mailing list last week:
http://lists.open-bio.org/pipermail/biopython-dev/2012-March/009468.html

Peter