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
),
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",
extra_link_args=extra_link_args_pysam,
),
Extension(
"cgat.BamTools.geneprofile",
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__])
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',
description='A Python utility for calling somatic mutations from a BAM or SAM file',
'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',
def __iter__(self):
import pysam
return iter(pysam.get_defines())
def __iter__(self):
import pysam
return iter(pysam.get_defines())
