def get_ext_modules():
ext = ".pyx" if HAVE_CYTHON else ".c"
src_files = glob.glob(
os.path.join(os.path.dirname(__file__), "pairtools", "lib", "*" + ext)
)
ext_modules = []
for src_file in src_files:
name = "pairtools.lib." + os.path.splitext(os.path.basename(src_file))[0]
if not "pysam" in name and not "regions" in name:
ext_modules.append(Extension(name, [src_file]))
elif "regions" in name:
ext_modules.append(Extension(
name, [src_file],
language="c++",
))
else:
import pysam
ext_modules.append(
Extension(
name,
[src_file],
extra_link_args=pysam.get_libraries(),
include_dirs=pysam.get_include(),
define_macros=pysam.get_defines(),
)
)
if HAVE_CYTHON:
# .pyx to .c
ext_modules = cythonize(ext_modules) # , annotate=True
return ext_modules
# Nubiscan motif mapping
#Nubiscan = Extension(
# "CGAT.Nubiscan.cnubiscan",
# [ 'CGAT/Nubiscan/cnubiscan.pyx'],
# library_dirs=[],
# libraries=[],
# include_dirs = [numpy.get_include()],
# language="c",
# )
# Automatically build script extensions
pyx_files = glob.glob("scripts/*.pyx")
script_extensions = []
pysam_dirname = os.path.dirname(pysam.__file__)
include_dirs = [numpy.get_include()] + pysam.get_include()
if IS_OSX:
# linking against bundles does no work (and apparently is not needed)
# within OS X
extra_link_args = []
else:
extra_link_args = [os.path.join(pysam_dirname, "csamtools.so")]
for pyx_file in pyx_files:
script_name = os.path.basename(pyx_file)
script_prefix = script_name[:-4]
script_extensions.append(
Extension("CGAT.%s" % (script_prefix),
sources=[pyx_file],
extra_link_args=extra_link_args,
# installs into root dir (not what i want)
#data_files=[('eddlib', ['eddlib/default_parameters.conf'])],
package_data={'': ['*.conf']},
scripts=[
'bin/edd',
#'bin/edd-tools',
],
install_requires=[
'Logbook',
'pybedtools',
'statsmodels',
'patsy', # statsmodels dependency
'pandas',
'python-dateutil', # pandas dependency
'scipy',
'numpy',
],
ext_modules=[
Extension(
'eddlib.read_bam',
sources=['eddlib/read_bam.pyx'],
include_dirs=pysam.get_include() + [np.get_include()],
define_macros=pysam.get_defines(),
),
Extension('eddlib.algorithm.chrom_max_segments',
sources=['eddlib/algorithm/chrom_max_segments.pyx'],
include_dirs=[np.get_include()]),
],
cmdclass={'build_ext': build_ext},
)
import pysam
name = 'genda'
version = '0.1'
try:
from Cython.Distutils import build_ext
except ImportError:
use_cython = False
print("Cython not found")
else:
use_cython = True
cmdclass = {}
ext_modules = []
includes = pysam.get_include()
includes.append(numpy.get_include())
if use_cython:
print('**********using cython*********')
ext_modules += [
Extension("genda.transcripts.exon_utils",
["genda/transcripts/exon_utils.pyx"],
include_dirs=includes),
Extension("genda.pysam_callbacks.allele_counter",
["genda/pysam_callbacks/allele_counter.pyx"],
include_dirs=includes,
define_macros=pysam.get_defines()),
Extension("genda.stats.aei_count_samples",
["genda/stats/aei_count_samples.pyx"],
include_dirs=includes,
from distutils.core import setup
from distutils.extension import Extension
import Cython
from Cython.Build import cythonize
import pysam
from Cython.Compiler.Options import get_directive_defaults
#directive_defaults = get_directive_defaults()
#directive_defaults['linetrace'] = True
#directive_defaults['binding'] = True
setup(
cmdclass={'build_ext': Cython.Build.build_ext},
ext_modules = cythonize([Extension("chileup",
sources=["hile.c", "chileup.pyx"],
depends=["hile.h", "khash.h"],
language='c',
libraries=["z", "hts"],
#define_macros=[('CYTHON_TRACE', '1')],
include_dirs=["."] + pysam.get_include(),
)])
)
import pysam
from Cython.Build import cythonize
if __name__ == '__main__':
cythonize('pysamstats.pyx', include_path=pysam.get_include())
import numpy as np
import sys
from Cython.Compiler.Options import get_directive_defaults
# directive_defaults = get_directive_defaults()
# directive_defaults['linetrace'] = True
# directive_defaults['binding'] = True
setup(
name="chileup",
version="1.0.0",
cmdclass={"build_ext": Cython.Build.build_ext},
install_requires=["pysam", "numpy"],
ext_modules=cythonize(
[
Extension(
"chileup",
sources=["hile.c", "chileup.pyx"],
depends=["hile.h", "khash.h"],
language="c",
libraries=["z", "hts"],
compiler_directives={"language_level", sys.version_info[0]},
# define_macros=[('CYTHON_TRACE', '1')],
# extra_compile_args=['-std=c99'],
include_dirs=["."] + pysam.get_include() + [np.get_include()],
)
]
),
)
import os
import glob
import numpy
from setuptools import setup, Extension
import pysam
src_list = glob.glob("src/*.c")
pyx_list = glob.glob("dnaUtilsPy/*.pyx")
include_dirs = pysam.get_include() + ["src", numpy.get_include()]
extra_link_args = pysam.get_libraries()
extensions = []
for pyx in pyx_list:
assert pyx.endswith(".pyx")
submodule = os.path.basename(pyx)[:-len(".pyx")]
extensions.append(
Extension("dnaUtilsPy." + submodule,
sources=[pyx] + src_list,
include_dirs=include_dirs,
extra_link_args=extra_link_args))
setup(name="dnaUtilsPy",
packages=["dnaUtilsPy"],
ext_modules=extensions,
install_requires=['numpy', 'pysam'],
setup_requires=['numpy', 'pysam', 'cython'])
import pysam
def get_version():
"""Extract version number from source file."""
from ast import literal_eval
with open('pysamstats.pyx') as f:
for line in f:
if line.startswith('__version__'):
return literal_eval(line.partition('=')[2].lstrip())
raise ValueError("__version__ not found")
extensions = [Extension('pysamstats',
sources=['pysamstats.c'],
include_dirs=pysam.get_include(),
define_macros=pysam.get_defines())]
setup(
name='pysamstats',
version=get_version(),
author='Alistair Miles',
author_email='*****@*****.**',
url='https://github.com/alimanfoo/pysamstats',
license='MIT Licenses',
description='A Python utility for calculating statistics against genome '
'position based on sequence alignments from a SAM, '
'BAM or CRAM file.',
scripts=['scripts/pysamstats'],
classifiers=[
name = 'genda'
version = '0.1'
try:
from Cython.Distutils import build_ext
except ImportError:
use_cython = False
print("Cython not found")
else:
use_cython = True
cmdclass = {}
ext_modules = []
includes = pysam.get_include()
includes.append(numpy.get_include())
if use_cython:
print('**********using cython*********')
ext_modules += [
Extension("genda.transcripts.exon_utils",
["genda/transcripts/exon_utils.pyx"],
include_dirs=includes),
Extension("genda.pysam_callbacks.allele_counter",
["genda/pysam_callbacks/allele_counter.pyx"],
include_dirs=includes,
define_macros=pysam.get_defines()),
import numpy as np
import pyximport
import pysam
pyximport.install(setup_args = {'include_dirs':[np.get_include() ]+pysam.get_include()})
from .bam_splitter import *
def __iter__(self):
import pysam
import numpy
return iter(pysam.get_include() + [numpy.get_include()])
#
# if os.getenv("PATH", None):
# for i in os.environ["PATH"].split(":"):
# if "htslib" in os.path.basename(i):
# print(glob.glob(i))
# if any("libhts" in i for i in glob.glob(i + "/*")):
# htslib = i
# break
if htslib is None:
print("Using packaged htslib")
htslib = os.path.join(root, "dysgu/htslib")
libraries = [f"{htslib}/hts"] # Library name for libhts.so
library_dirs = [htslib, numpy.get_include(), f"{htslib}/htslib"] + pysam.get_include()
include_dirs = [numpy.get_include(), root, # htslib,
f"{htslib}/htslib", f"{htslib}/cram"] + pysam.get_include()
runtime_dirs = [htslib] # os.path.join(root, "dysgu/htslib")
# extra_link_args = ["-L ./dysgu/htslib", "-L ./dysgu/htslib/htslib"]
print("Libs", libraries)
print("Library dirs", library_dirs)
print("Include dirs", include_dirs)
print("Runtime dirs", runtime_dirs)
print("Extras compiler args", extras)
for item in ["sv2bam", "io_funcs", "graph", "coverage", "assembler", "call_component",
"map_set_utils", "cluster", "post_call_metrics"]:
def __iter__(self):
import pysam
import numpy
return iter(pysam.get_include()+[numpy.get_include()])
_logger.info("# cython unavailable; using included .c sources")
# ###########################################################################
# extnsion setup
# https://cython.readthedocs.io/en/latest/src/userguide/source_files_and_compilation.html#configuring-the-c-build
# http://docs.cython.org/en/latest/src/userguide/source_files_and_compilation.html#distributing-cython-modules
glob_ext = "pyx" if has_cython else "c"
src_glob = "uta_align/align/*." + glob_ext
if has_cython:
sources = [src_glob]
else:
sources = glob.glob(src_glob)
extensions = [Extension("*", sources, include_dirs=pysam.get_include())]
if has_cython:
compiler_directives = {
'c_string_encoding': 'ascii',
'embedsignature': True,
'language_level': 3
}
extensions = cythonize(extensions, compiler_directives=compiler_directives)
setup(
ext_modules=extensions,
use_scm_version=True,
)
## <LICENSE>
extra_compile_args=compile_options,
extra_link_args=link_options),
Extension("epic2.src.statistics", ["epic2/src/statistics.pyx"],
language="c++",
extra_compile_args=compile_options,
extra_link_args=link_options),
# Extension("epic2.src.differential",
# ["epic2/src/differential.pyx"], language="c++",
# extra_compile_args=compile_options),
Extension("epic2.src.find_islands", ["epic2/src/find_islands.pyx"],
language="c++",
extra_compile_args=compile_options,
extra_link_args=link_options),
Extension("epic2.src.read_bam", ["epic2/src/read_bam.pyx"],
language="c++",
include_dirs=conda_include + pysam.get_include(),
library_dirs=conda_lib,
extra_compile_args=compile_options,
extra_link_args=link_options + pysam.get_libraries(),
define_macros=pysam.get_defines(),
libraries=["z"]),
Extension("epic2.src.genome_info", ["epic2/src/genome_info.pyx"],
language="c++",
extra_compile_args=compile_options,
extra_link_args=link_options)
]
setup(
name="epic2",
packages=find_packages(),
ext_modules=cythonize(extensions, annotate=True, language_level='2'),
"""
from setuptools import setup, find_packages
from Cython.Build import cythonize
import pysam
setup(
name='svtools',
version='0.1',
description='Tools for manipulating structural variant files',
author='Matthew Stone',
author_email='*****@*****.**',
packages=find_packages(),
package_data={'svtools': ['data/standard_template.vcf',
'data/vcfcluster_template.vcf']},
scripts=['scripts/svtools'],
ext_modules=cythonize('svtools/utils/helpers.pyx'),
include_dirs=pysam.get_include(),
install_requires=[
'numpy',
'scipy',
'pysam>=0.11.2.2',
'pybedtools',
'cython',
'natsort',
'boto3',
'pandas',
]
)
raise Exception(
'please upgrade pysam first, e.g.: pip install --upgrade pysam')
from Cython.Distutils import build_ext # Cython should be installed via pysam
except ImportError:
raise Exception(
'please install pysam first, e.g.: pip install --upgrade pysam')
try:
import numpy as np
except ImportError:
raise Exception('please install numpy first')
extensions = [
Extension('SomVarIUS_calling',
sources=['SomVarIUS/SomVarIUS_calling.pyx'],
include_dirs=[np.get_include()] + pysam.get_include(),
define_macros=pysam.get_defines())
]
extensions.append(
Extension('query_muts',
sources=['SomVarIUS/query_muts.pyx'],
include_dirs=[np.get_include()] + pysam.get_include(),
define_macros=pysam.get_defines()))
setup(
name='SomVarIUS',
version='1.2',
author='Kyle S. Smith',
author_email='*****@*****.**',
license="MIT Licenses",
from setuptools import find_packages, setup, Extension
#from distutils.core import setup, Extension
import glob
import numpy as np
import pysam
from Cython.Build import cythonize
from Cython.Distutils import build_ext
include_path = [np.get_include()]
include_path.extend(pysam.get_include())
ext_modules = cythonize(
[Extension('*', ['deep_cfNA/*.pyx'], include_dirs=include_path)])
setup(
name='deep_cfNA',
version='0.1',
description=
'Using deep learning to classify fragments from TGIRT-seq libraries of cell-free genetic materials',
url='',
author='Douglas C. Wu',
author_email='*****@*****.**',
license='MIT',
packages=find_packages(),
scripts=glob.glob('bin/*'),
zip_safe=False,
data_files=[('model', glob.glob('model/deep_cfNA_*'))],
ext_modules=ext_modules,
cmdclass={'build_ext': build_ext})
"Requires cython to "
"be installed before running setup.py (pip install cython)")
try:
import pysam
except ImportError:
raise ImportError(
"Requires pysam to "
"be installed before running setup.py (pip install pysam)")
try:
import numpy as np
except ImportError:
raise ImportError(
"Requires numpy to "
"be installed before running setup.py (pip install numpy)")
include_directory = pysam.get_include()
include_directory.extend([np.get_include()])
setup(name='filterBamClip',
version='0.1',
description=
'Remove clipped alignments from bam file by some fractions threshold',
url='',
author='Douglas Wu',
author_email='*****@*****.**',
license='MIT',
packages=['filterBamClip'],
zip_safe=False,
scripts=['bin/filterSoftClip.py'],
ext_modules=cythonize([
Extension(
name='filterBamClip.bam_splitter',
import pysam
from Cython.Build import cythonize
if __name__ == '__main__':
cythonize('pysamstats.pyx',
include_path=pysam.get_include())
Extension("epic2.src.SICER_stats2", ["epic2/src/SICER_stats2.pyx"],
language="c++",
extra_compile_args=compile_options),
Extension("epic2.src.statistics", ["epic2/src/statistics.pyx"],
language="c++",
extra_compile_args=compile_options),
# Extension("epic2.src.differential",
# ["epic2/src/differential.pyx"], language="c++",
# extra_compile_args=compile_options),
Extension("epic2.src.find_islands", ["epic2/src/find_islands.pyx"],
language="c++",
extra_compile_args=compile_options),
Extension("epic2.src.read_bam", ["epic2/src/read_bam.pyx"],
language="c++",
extra_compile_args=compile_options,
include_dirs=pysam.get_include() + conda_include,
library_dirs=conda_lib,
define_macros=pysam.get_defines(),
libraries=["z"]),
Extension("epic2.src.genome_info", ["epic2/src/genome_info.pyx"],
language="c++",
extra_compile_args=compile_options)
]
setup(
name="epic2",
packages=find_packages(),
ext_modules=cythonize(extensions, annotate=True, language_level='2'),
scripts=["bin/epic2", "bin/epic2-df", "bin/epic2-bw"],
package_data={
'epic2': [
if versiontuple(pysam.__version__) < versiontuple('0.8.1'):
raise Exception('please upgrade pysam first, e.g.: pip install --upgrade pysam')
from Cython.Distutils import build_ext # Cython should be installed via pysam
except ImportError:
raise Exception('please install pysam first, e.g.: pip install --upgrade pysam')
try:
import numpy as np
except ImportError:
raise Exception('please install numpy first')
extensions = [Extension('SomVarIUS_calling',
sources=['SomVarIUS/SomVarIUS_calling.pyx'],
include_dirs=[np.get_include()] + pysam.get_include(),
define_macros=pysam.get_defines())]
extensions.append(Extension('query_muts',
sources=['SomVarIUS/query_muts.pyx'],
include_dirs=[np.get_include()] + pysam.get_include(),
define_macros=pysam.get_defines()))
setup(
name='SomVarIUS',
version='1.2',
author='Kyle S. Smith',
author_email='*****@*****.**',
license="MIT Licenses",
url='https://github.com/kylessmith/SomVarIUS',
# Nubiscan motif mapping
#Nubiscan = Extension(
# "CGAT.Nubiscan.cnubiscan",
# [ 'CGAT/Nubiscan/cnubiscan.pyx'],
# library_dirs=[],
# libraries=[],
# include_dirs = [numpy.get_include()],
# language="c",
# )
# Automatically build script extensions
pyx_files = glob.glob( "scripts/*.pyx" )
script_extensions = []
pysam_dirname = os.path.dirname( pysam.__file__ )
include_dirs = [ numpy.get_include() ] + pysam.get_include()
if IS_OSX:
# linking against bundles does no work (and apparently is not needed)
# within OS X
extra_link_args = []
else:
extra_link_args = [ os.path.join( pysam_dirname, "csamtools.so")]
for pyx_file in pyx_files:
script_name = os.path.basename( pyx_file )
script_prefix = script_name[:-4]
script_extensions.append(
Extension( "CGAT.%s" % (script_prefix),
sources = [pyx_file],
extra_link_args = extra_link_args,
def pysam_incl(cy_ext):
import pysam
cy_ext.extend_includes(pysam.get_include())
cy_ext.extend_macros(pysam.get_defines())
cy_ext.extend_extra_objects([pysam.libchtslib.__file__])
def get_version():
"""Extract version number from source file."""
from ast import literal_eval
with open('fusorsv/fusion_utils.pyx') as f:
for line in f:
if line.startswith('__version__'):
return literal_eval(line.partition('=')[2].lstrip())
raise ValueError("__version__ not found")
cythonize('fusorsv/fusion_utils.pyx')
extensions = [
Extension('fusion_utils',
sources=['fusorsv/fusion_utils.pyx'],
include_dirs=pysam.get_include() + [numpy.get_include()],
define_macros=pysam.get_defines(),
extra_compile_args=['-ffast-math'])
]
setup(name='fusorsv',
version=get_version(),
author='Timothy Becker',
author_email='*****@*****.**',
url='https://github.com/timothyjamesbecker/FusorSV',
license='GPL 3 License',
description='SV calling data fusion framework',
classifiers=[
'Intended Audience :: Developers', 'License :: GPL 3 License',
'Programming Language :: Python :: 2.7',
'Programming Language :: Cython', 'Programming Language :: C',
],
library_dirs=[],
libraries=[],
language="c++",
),
Extension(
"cgat.NCL.cnestedlist",
["cgat/NCL/cnestedlist.pyx", "cgat/NCL/intervaldb.c"],
library_dirs=[],
libraries=[],
language="c",
),
Extension(
"cgat.GeneModelAnalysis",
["cgat/GeneModelAnalysis.pyx"],
include_dirs=conda_includes + pysam.get_include() +
[numpy.get_include()],
library_dirs=[],
libraries=[],
define_macros=pysam.get_defines(),
language="c",
),
Extension(
"cgat.BamTools.bamtools",
["cgat/BamTools/bamtools.pyx"],
include_dirs=conda_includes + pysam.get_include() +
[numpy.get_include()],
library_dirs=pysam_libdirs,
libraries=pysam_libs,
define_macros=pysam.get_defines(),
language="c",
'eddlib.algorithm'],
# installs into root dir (not what i want)
#data_files=[('eddlib', ['eddlib/default_parameters.conf'])],
package_data={'': ['*.conf']},
scripts=[
'bin/edd',
#'bin/edd-tools',
],
install_requires=[
'Logbook',
'pybedtools',
'statsmodels',
'patsy', # statsmodels dependency
'pandas',
'python-dateutil', # pandas dependency
'scipy',
'numpy',
],
ext_modules=[
Extension('eddlib.read_bam',
sources=['eddlib/read_bam.pyx'],
include_dirs=pysam.get_include() + [np.get_include()],
define_macros=pysam.get_defines(),
),
Extension('eddlib.algorithm.chrom_max_segments',
sources=['eddlib/algorithm/chrom_max_segments.pyx'],
include_dirs=[np.get_include()]),
],
cmdclass = {'build_ext': build_ext},
)