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setup.py
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setup.py
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from distutils.core import setup
from distutils.extension import Extension
from Cython.Build import cythonize
import os
from ast import literal_eval
def get_version(source='vcfnp/__init__.py'):
with open(source) as f:
for line in f:
if line.startswith('__version__'):
return literal_eval(line.partition('=')[2].lstrip())
raise ValueError("__version__ not found")
vcflib_dir = os.path.join(os.getcwd(), 'vcflib')
smithwaterman_dir = os.path.join(vcflib_dir, 'smithwaterman')
tabixpp_dir = os.path.join(vcflib_dir, 'tabixpp')
vcflib_sources = ('Variant.cpp', 'ssw.c', 'ssw_cpp.cpp', 'split.cpp')
smithwaterman_sources = ('BandedSmithWaterman.cpp',
'SmithWatermanGotoh.cpp',
'Repeats.cpp',
'disorder.c',
'LeftAlign.cpp',
'IndelAllele.cpp')
tabixpp_sources = ('bedidx.c', 'bgzf.c', 'index.c', 'knetfile.c', 'kstring.c',
'tabix.cpp')
def get_vcflib_sources():
sources = list()
sources += [os.path.join(vcflib_dir, s) for s in vcflib_sources]
sources += [os.path.join(smithwaterman_dir, s)
for s in smithwaterman_sources]
sources += [os.path.join(tabixpp_dir, s) for s in tabixpp_sources]
return sources
compat_extension = Extension(
'vcfnp.compat',
language='c++',
sources=['vcfnp/compat.pyx']
)
vcflib_extension = Extension(
'vcfnp.vcflib',
sources=['vcfnp/vcflib.pyx'] + get_vcflib_sources(),
language='c++',
include_dirs=[vcflib_dir, smithwaterman_dir, tabixpp_dir, './vcfnp'],
libraries=['m', 'z'],
extra_compile_args=['-O3']
)
iter_extension = Extension(
'vcfnp.iter',
sources=['vcfnp/iter.pyx'] + get_vcflib_sources(),
language='c++',
include_dirs=[vcflib_dir, smithwaterman_dir, tabixpp_dir, './vcfnp'],
libraries=['m', 'z'],
extra_compile_args=['-O3']
)
setup(
name='vcfnp',
version=get_version(),
author='Alistair Miles',
author_email='alimanfoo@googlemail.com',
url='https://github.com/alimanfoo/vcfnp',
license='MIT License',
description='Load numpy arrays from a VCF (variant call file).',
long_description=open('README.rst').read(),
classifiers=['Intended Audience :: Developers',
'License :: OSI Approved :: MIT License',
'Programming Language :: Python',
'Topic :: Software Development :: Libraries :: Python Modules'
],
package_dir={'': '.'},
packages=['vcfnp'],
ext_modules=cythonize([
compat_extension,
vcflib_extension,
iter_extension,
]),
scripts=['scripts/vcf2npy',
'scripts/qsub_vcf2npy',
'scripts/vcfnpy2hdf5',
'scripts/vcf2csv'],
)