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

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?

blast python biopython
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updated by timothy.kirkwood • timothy.kirkwood • written by iggakami • iggakami

1 answer

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.

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written by Chen Sun Chen Sun

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

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written by iggakami • iggakami

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?

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written by c_u c_u

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

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written by timothy.kirkwood • timothy.kirkwood

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