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from setuptools import setup
from distutils.core import setup
from distutils.extension import Extension
try:
from Cython.Distutils import build_ext
CYTHON = True
except:
CYTHON = False
requires = []
# python 2.6 does not have argparse
try:
import argparse
except ImportError:
requires.append('argparse')
try:
import collections
collections.OrderedDict
except AttributeError:
requires.append('ordereddict')
# get the version without an import
VERSION = "Undefined"
DOC = ""
inside_doc = False
for line in open('vcf/__init__.py'):
if "'''" in line:
inside_doc = not inside_doc
if inside_doc:
DOC += line.replace("'''", "")
if (line.startswith('VERSION')):
exec(line.strip())
extras = {}
if CYTHON:
extras['cmdclass'] = {'build_ext': build_ext}
extras['ext_modules'] = [Extension("vcf.cparse", ["vcf/cparse.pyx"])]
setup(
name='PyVCF',
packages=['vcf', 'vcf.test'],
scripts=['scripts/vcf_melt', 'scripts/vcf_filter.py'],
author='James Casbon and @jdoughertyii',
author_email='casbon@gmail.com',
description='Variant Call Format (VCF) parser for Python',
long_description=DOC,
test_suite='vcf.test.test_vcf.suite',
install_requires=['distribute'],
requires=requires,
entry_points = {
'vcf.filters': [
'site_quality = vcf.filters:SiteQuality',
'vgq = vcf.filters:VariantGenotypeQuality',
'eb = vcf.filters:ErrorBiasFilter',
'dps = vcf.filters:DepthPerSample',
'avg-dps = vcf.filters:AvgDepthPerSample',
'snp-only = vcf.filters:SnpOnly',
]
},
url='https://github.com/jamescasbon/PyVCF',
version=VERSION,
classifiers = [
'Development Status :: 4 - Beta',
'Intended Audience :: Developers',
'Intended Audience :: Science/Research',
'Operating System :: OS Independent',
'Programming Language :: Python',
'Programming Language :: Python :: 3',
'Topic :: Scientific/Engineering',
],
keywords='bioinformatics',
use_2to3=True,
include_package_data=True,
package_data = {
'': ['*.vcf', '*.gz', '*.tbi'],
},
**extras
)
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