skip to navigation
skip to content

Not Logged In

SimpleHMMER 0.2.3

SimpleHMMER

.
. .d8888b. d8b 888
. d88P Y88b Y8P 888
. Y88b. 888
. "Y888b. 888 88888b.d88b. 88888b. 888 .d88b.
. "Y88b. 888 888 "888 "88b 888 "88b 888 d8P Y8b
. "888 888 888 888 888 888 888 888 88888888
. Y88b d88P 888 888 888 888 888 d88P 888 Y8b.
. "Y8888P" 888 888 888 888 88888P" 888 "Y8888
. 888
. 888
. 888
.
. 888 888 888b d888 888b d888 8888888888 8888888b.
. 888 888 8888b d8888 8888b d8888 888 888 Y88b
. 888 888 88888b.d88888 88888b.d88888 888 888 888
. 8888888888 888Y88888P888 888Y88888P888 8888888 888 d88P
. 888 888 888 Y888P 888 888 Y888P 888 888 8888888P"
. 888 888 888 Y8P 888 888 Y8P 888 888 888 T88b
. 888 888 888 " 888 888 " 888 888 888 T88b
. 888 888 888 888 888 888 8888888888 888 T88b
.

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This software is currently unpublished.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.  
File Type Py Version Uploaded on Size
SimpleHMMER-0.2.3.tar.gz (md5) Source 2012-12-18 17KB
  • Downloads (All Versions):
  • 18 downloads in the last day
  • 105 downloads in the last week
  • 388 downloads in the last month