Posts in May 2012

Assembling the Parsers

May2012 | biopython, blast, gsoc, hmmer, python, searchio | comment

Last week was probably my busiest GSoC week so far, but also the most rewarding as well. I worked on three different parsers for SearchIO: two for BLAST+ and one for the HMMER suite. In brief, these are the highlights of my past week: SearchIO now has its own BLAST+ XML parser, powered by the popular cElementTree library. There's also a new blast-tab parser, which handles NCBI tabular output ...

from Bio import SearchIO

May2012 | biopython, gsoc, python, searchio | comment

The coding period has officially started. It's only about one month ago that I was anxiously waiting for the GSoC announcement, not knowing that I would end up coding with the Biopython community. It's been going great and I'm hoping this will remain true for the rest of the summer :). As I've noted last week, I have started the actual coding myself. In the past week I have coded, tested and ...

The Final Preparations

May2012 | biopython, gsoc, python | comment

Another week has passed by and we are getting closer to the official coding start. I spent the past week playing around with XML and SQLite, as mentioned before, among other things. For XML, I find the spec and design easy to grasp. What took me more time than I anticipated was its general parsing mechanism in Python. There are three general XML parsing implementations that comes built in with ...

Warming Up for The Coding Period

May2012 | biopython, gsoc, python, testing | comment

It has been more than two weeks ago since GSoC announced its accepted students list. Officially, we have are given four weeks to bond with the community around our projects and get familiar with any supporting tools we will use (e.g. git and friends). Coding officialy starts after this four-week period. For me specifically, I've spent the past two weeks getting to know the programs I'll use in my ...