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raygun : a simple NCBI BLAST wrapper for Python

Posted by Russell on October 25, 2010 at 11:42 a.m.
Things have been a little quiet on for the last couple of weeks, but a lot of frantic activity has been going on behind the peaceful lack blog updates. When I returned from Kamchatka, Jonathan had a little present for me -- he took the DNA from the 2005 Uzon field season for Arkashin and Zavarzin hotsprings, and ran a whole lane of paired-end sequencing on one of our Illumina machines. Charlie made some really beautiful libraries, and the data is really, really excellent. For the last couple of weeks, I've been trying to do justice to it.

I'm not quite ready to talk about what I've been finding, but I thought I would take a moment to share a little tool I wrote along the way. It's made my life a lot easier, and maybe other people could get some use out of it.

It's called raygun, a very simple Python interface for running local NCBI BLAST queries. You initialize a RayGun object with a FASTA file containing your target sequences, and then you can query it with strings or other FASTA files. It parses the BLAST output into a list of dictionary objects, so that you can get right to work.

It doesn't take a lot of scripting chops to do this without an interface, of course, and there are other Python tools for running BLAST queries. The advantage of raygun over either the DIY approach or the BioPython approach is that raygun is extremely simple to use. I wanted something that would basically be point-and-shoot :

import raygun
import cleverness

rg = raygun.RayGun( 'ZOMG_DNA_OMG_OMG.fa' )

hits = rg.blastfile( 'very_clever_query.fa' )

results = []
for hit in hits :
    results.append( cleverness.good_idea( hit[ 'subject' ] ) )

cleverness.output_phd_thesis( results )
Unfortunately, you must furnish your own implementation of the cleverness module.

I designed raygun is with interactive use in mind, particularly with ipython (by the way, if you do a lot of work in python and you're not using ipython, you're being silly). The code is available on github.

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