GitHub - minillinim/SimpleHMMER: Super simple wrapper for running hmmer3 and parsing the output

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Super simple wrapper for running hmmer3 and parsing the output

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Name		Name	Last commit message	Last commit date
Latest commit History 30 Commits
simplehmmer		simplehmmer
CHANGES.txt		CHANGES.txt
LICENSE.txt		LICENSE.txt
MANIFEST		MANIFEST
MANIFEST.in		MANIFEST.in
README.txt		README.txt
setup.py		setup.py

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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This software is currently unpublished.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.