MOODS-python 1.9.4.1
====================
Motif Occurrence Detection Suite
https://www.cs.helsinki.fi/group/pssmfind/
Installing from PyPi
--------------------
The quickest way to install MOODS is using pip:
(a) Install the module to your local Python library path:
pip install --user MOODS-python
(b) Install the module for all users:
sudo pip install MOODS-python
Installing the MOODS package from PyPi installs the `moods-dna.py` script to
your Python executable directory. Test it by running:
moods-dna.py --help
(Note that this assumes that the appropriate Python executable directory is in
your path. For example, if you install the package with --user, you can do this
with
PATH="$PATH:`python -m site --user-base`/bin"
if it doesn't work otherwise.)
Installing from Source
----------------------
Alternatively, you can install MOODS from the source package, for example if you
don't have your pip configured or you just want a quick throwaway install.
(a) If you don't want to bother installing MOODS, you can compile the extensions
in place and create a symlink under `scripts/`:
python setup.py build_ext --inplace
cd scripts
ln -s ../MOODS/
(b) Install the module to your local Python library path:
python setup.py install --user
(c) Install the module for all users:
sudo python setup.py install
You can test MOODS by running the `moods-dna.py` script with
the example data provided with the package:
cd scripts/
python moods-dna.py -m example-data/matrices/*.{pfm,adm} -s example-data/seq/chr1-5k-55k.fa -p 0.0001
python moods-dna.py --help
Documentation
-------------
Documentation on GitHub wiki: https://github.com/jhkorhonen/MOODS/wiki
Copyright and Licence
---------------------
Copyright (C) 2009 by Petri J Martinmäki, Janne Korhonen, Pasi Rastas
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version, or under the terms of the Biopython
License.
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