[GSoC] Feedback of application

[Lluís Revilla]

Dear all,

I would like to have more feedback about my proposal. Mainly because
depending if I get other internships or not I will be able to collaborate.
And I don't know if it was just that there weren't more slots or that the
idea was not well focused or how can I improve my overall proposal.

My proposal was increasing the parsers included in Biopython.

Thanks,

Lluís Revilla

PS: The proposal:

On the Contributing page there is a statement about the parser, they need
to be checked if they still work with each new version of the software
they  parse.

I found the a parser for BLAST and PSI-BLAST, Python Sequence Analysis
Tools consists of modules to parse and iterate through various flat file
databases (EMBL, GENBANK, SWISSPROT, PDBFINDER, ENZYME etc.) and does a few
other things. This should be checked as it is said in the contribution
page<http://biopython.org/wiki/Contributing>
:

"*For example, the GenBank parser needs to be checked to make sure it
handles each new dump of GenBank*."

It seems that it can be improved and better documented according to the SeqIO
dev page. <http://biopython.org/wiki/SeqIO_dev> Where it states that other
parsers could be
integrated<http://biopython.org/wiki/SeqIO_dev#Possible_additional_formats>.


As an active project there is also a parser of GFF under
development<http://biopython.org/wiki/Active_projects#GFF_parser>.
Which I could work on it.

My proposal is to integrate this parsers into SeqIO and add the new
HMMER <http://hmmer.janelia.org> website parser (as suggested in one
contributor's blog <http://bow.web.id/blog/2013/02/state-of-biosearchio/>).