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Overview

SimpleHMMER is just that, a super simple way to run HMMER3 and parse the output. No biopython, no frills, just parse

Installation

Should be as simple as

pip install SimpleHMMER

Using MetaChecka2000

Running hmmer

from simplehmmer.simplehmmer import HMMERRunner
HR=HMMERRunner(prefix='frode')
HR.search('/path/to/some.hmm', '/path/to/some.fasta', '/path/to/save/to/')

Parsing results

from simplehmmer.simplehmmer import HMMERParser
with open('/path/to/save/to/frode_out.txt', 'r') as fh:
     HP = HMMERParser(fh)
     while True:
         result = HP.next()
         if result:
             print result
         else:
             break

Super simple!

Licence and referencing

Project home page, info on the source tree, documentation, issues and how to contribute, see http://github.com/minillinim/SimpleHMMER

This software is currently unpublished. Please contact me at m_dot_imelfort_at_uq_dot_edu_dot_au for more information about referencing this software.

Copyright © 2012 Michael Imelfort. See LICENSE.txt for further details.