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SimpleHMMER

Project Description

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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This software is currently unpublished.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.

Release history Release notifications

This version
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0.2.3

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0.2.2

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0.2.1

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0.1.0

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0.0.2

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0.0.1

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Filename, size & hash SHA256 hash help File type Python version Upload date
SimpleHMMER-0.2.3.tar.gz (18.3 kB) Copy SHA256 hash SHA256 Source None Dec 18, 2012

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