How To Use To Use Standalone Blast In Biopython
I've been trying to get Biopython to use BLAST (the standalone version) and it doesn't seem to work. I'm using blast 2.2.28, python 2.6 and biopython 1.61. I was wondering if anyone could give a short tutorial on how to do this. If there's an easier way of doing this than using Biopython, then that's fine too.
Please DO NOT post the biopython tutorial (http://www.biopython.org/DIST/docs/tutorial/Tutorial.html) because I've already gone through it and everyone seems to refer to it. Thanks.
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" If there's an easier way of doing this than using Biopython" ... how about using a basic command line ?
I'll probably try that out. The documentation seems much better on the Blast website. The only problem is that it will be harder to streamline the program that I'm trying to create, which is written in python.
You can take advantage of the subprocess module to send commands to the system and retrieve their output.
"it doesn't seem to work" is very vague. You'll get better quality answers if you post a detailed error or some code that you're trying.
I wasn't looking for an answer that was directly for my problem, I was hoping for a short walkthrough on how to use standalone BLAST in Biopython that is more clear then the biopython tutorial.
It doesn't get much clearer than the biopython tutorial. With what, exactly, are you having trouble? Understanding the BLAST command line options? Or the python code? "It doesn't seem to work" implies that you have tried and seen some error or failure; as Matt said, more details make it easier to answer.
If you want to keep this question open, please make it more specific. If you're trying something and get an error, tell us the error and the basics about your system (Biopython version, Python version, OS, how you installed things).
It would also help to state if you know how to use standalone BLAST directly at the command line or not.