[Biopython] Google Summer of Code (GSoC)

[Brad Chapman]

Zhigang;

> I am, Zhigang Wu, a third year graduate student in UC Riverside with a
> research focus on miRNA evolution. I am interested in implementing the
> Biopython SearchIO module, which is used to parse the blast reports from
> currently popular sequence alignment tools like NCBI BLAST+, FASTA, HMMER3
> and etc.

Welcome. Thanks for the introduction and your interest in the SearchIO
project.

> Right now, I am preparing my proposal that is due by April 6. I am listing
> below the core methods that the Biopythonic SearchIO module is going to
> support. For the sake of consistency, the moethods are very similar to
> existing SeqIO <http://biopython.org/wiki/SeqIO>and
> AlignIO<http://biopython.org/wiki/AlignIO>modules.
> 
>    1. SearchIO.parse(handle, format), is a generator function.
>    2. SearchIO.to_dict(iterator): this function takes in an iterator
>    arguments which is produced by SearchIO.parse(...) function.
>    3. SearchIO.read(handle, format): provide fasta access to blast report
>    have only one record
>    4. SearchIO.write(....) outputs specified blast output
>    5. SearchIO.convert(...) provide format conversion between different
>    formats
>    6. ...
> 
> I'd like to hear back from you any feedback or suggestions on the method or
> any format that in your research field is considered to be popular and you
> want it to be supported in Biopythonic SearchIO module.

This all sounds great. My suggestion would be to make your project
proposal available once you have a first draft, and then folks will have
more detailed comments. The wiki has good information on the project plan:

http://open-bio.org/wiki/Google_Summer_of_Code#When_you_apply

and the NESCent wiki has some examples of well-written proposals from
previous years:

http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2012#Writing_your_application

One of the key aspects is having a detailed week-by-week outline of your
plans for the summer.

Thanks again,
Brad