How to run local BLAST (Standalone NCBI BLAST+) with Python?

Question

[iggakami]

Hello, I'm new here, but I can't find answer in other topics.

I want to run blast nucelotide, align two sequences using blast (megablast, all options default) amd check their % ident. I have installed locally - Standalone NCBI BLAST+ (2.6). I've got Python 2.7, and installed BioPython, but after reading Biopython Tutorial (http://www.biopython.org/DIST/docs/tutorial/Tutorial.html) I still can't handle with this.

Could anyone show me example of using BioPython with local blast?

Answer 1

[Chen Sun]

My solution is to not use biopython, but directly use python function subprocess:

simply using subprocess.call(command, shell=True), where command is any blast command you want to run locally.

Hope it helps.

[iggakami]

thank you with subprocess.check_output() this is perfect for me

[c_u]

What does the subprocess function do exactly? I looked up the docs, but couldnt figure out. Why wouldnt using BLAST from Biopython be a good idea?

[timothy.kirkwood]

it basically lets you interact with commandline things from within a script (command = what you would type into the commandline, formatted as a list). Biopython BLAST is basically the same except its easier to work with, but your limited to whatever options they put in to their wrapper function