Question: How to run local BLAST (Standalone NCBI BLAST+) with Python?
0
gravatar for iggakami
2.4 years ago by
iggakami0
iggakami0 wrote:

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 biopython python • 2.2k views
ADD COMMENTlink modified 2.4 years ago by Chen910 • written 2.4 years ago by iggakami0
2
gravatar for Chen
2.4 years ago by
Chen910
Chen910 wrote:

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.

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by Chen910

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

ADD REPLYlink written 2.4 years ago by iggakami0
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