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ssHMM/setup.py
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from setuptools import setup | |
from setuptools.extension import Extension | |
long_description = """RNA-binding proteins (RBPs) play a vital role in the post-transcriptional control of RNAs. They are known to recognize RNA molecules by their nucleotide sequence as well as their three-dimensional structure. ssHMM is an RNA motif finder that combines a hidden Markov model (HMM) with Gibbs sampling to learn the joint sequence and structure binding preferences of RBPs from high-throughput RNA-binding experiments, such as CLIP-Seq. The model can be visualized as an intuitive graph illustrating the interplay between RNA sequence and structure.""" | |
setup(name='sshmm', | |
version='1.0.0', | |
description='A sequence-structure hidden Markov model for the analysis of RNA-binding protein data.', | |
long_description=long_description, | |
url='https://github.molgen.mpg.de/heller/ssHMM', | |
author='David Heller, Annalisa Marsico', | |
author_email='heller_d@molgen.mpg.de', | |
license='GPLv3', | |
classifiers=[ | |
'Development Status :: 5 - Production/Stable', | |
'Environment :: Console', | |
'Intended Audience :: Science/Research', | |
'Topic :: Scientific/Engineering :: Bio-Informatics', | |
'License :: OSI Approved :: GNU General Public License v3 (GPLv3)', | |
'Programming Language :: Python :: 2.7' | |
], | |
keywords='sshmm CLIP-Seq RBP RNA RNA-binding protein motif HMM sequence structure', | |
packages=['sshmm'], | |
package_data={'sshmm': ['img/*.png'],}, | |
zip_safe=False, | |
install_requires=['numpy', 'graphviz', 'pygraphviz', 'weblogo', 'forgi'], | |
scripts=['bin/preprocess_dataset', 'bin/train_seqstructhmm', 'bin/batch_seqstructhmm'], | |
ext_modules = [Extension("cEstimate", ["sshmm/cEstimate.c"])]) |