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README.txt
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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This software is currently unpublished.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.