示例#1
0
文件: setup.py 项目: open2c/pairtools
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
示例#2
0
# 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,
示例#3
0
文件: setup.py 项目: researchapps/edd
    # 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},
)
示例#4
0
文件: setup.py 项目: jeffhsu3/genda
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,
示例#5
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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(),
                               )])
)
示例#6
0
import pysam
from Cython.Build import cythonize

if __name__ == '__main__':
    cythonize('pysamstats.pyx', include_path=pysam.get_include())
示例#7
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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()],
            )
        ]
    ),
)
示例#8
0
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'])
示例#9
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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=[
示例#10
0
文件: setup.py 项目: jeffhsu3/genda
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()),
示例#11
0
import numpy as np
import pyximport
import pysam
pyximport.install(setup_args = {'include_dirs':[np.get_include() ]+pysam.get_include()})

from .bam_splitter import *
示例#12
0
 def __iter__(self):
     import pysam
     import numpy
     return iter(pysam.get_include() + [numpy.get_include()])
示例#13
0
文件: setup.py 项目: kcleal/dysgu
#
# 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"]:
示例#14
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 def __iter__(self):
     import pysam
     import numpy
     return iter(pysam.get_include()+[numpy.get_include()])
示例#15
0
    _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>
示例#16
0
              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'),
示例#17
0
"""

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',
    ]
)
示例#18
0
        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",
示例#19
0
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})
示例#20
0
        "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',
示例#21
0
import pysam
from Cython.Build import cythonize


if __name__ == '__main__':
    cythonize('pysamstats.pyx',
              include_path=pysam.get_include())
示例#22
0
文件: setup.py 项目: JohnMCMa/epic2
    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': [
示例#23
0
    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',
示例#24
0
文件: setup.py 项目: jmadzo/cgat
# 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,
示例#25
0
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__])
示例#26
0
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',
示例#27
0
     ],
     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",
示例#28
0
                '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},
    )