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#! /usr/bin/python
'''pysam - a python module for reading, manipulating and writing
genomic data sets.
pysam is a lightweight wrapper of the htslib C-API and provides
facilities to read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ
files as well as access to the command line functionality of the
samtools and bcftools packages. The module supports compression and
random access through indexing.
This module provides a low-level wrapper around the htslib C-API as
using cython and a high-level API for convenient access to the data
within standard genomic file formats.
The current version wraps htslib-1.3.1, samtools-1.3.1 and bcftools-1.3.1.
See:
http://www.htslib.org
https://github.com/pysam-developers/pysam
http://pysam.readthedocs.org/en/stable
'''
import collections
import glob
import os
import platform
import re
import subprocess
import sys
import sysconfig
from contextlib import contextmanager
from setuptools import Extension, setup
IS_PYTHON3 = sys.version_info.major >= 3
@contextmanager
def changedir(path):
save_dir = os.getcwd()
os.chdir(path)
try:
yield
finally:
os.chdir(save_dir)
def run_configure(option):
try:
retcode = subprocess.call(
" ".join(("./configure", option)),
shell=True)
if retcode != 0:
return False
else:
return True
except OSError as e:
return False
def run_make_print_config():
stdout = subprocess.check_output(["make", "-s", "print-config"])
if IS_PYTHON3:
stdout = stdout.decode("ascii")
make_print_config = {}
for line in stdout.splitlines():
if "=" in line:
row = line.split("=")
if len(row) == 2:
make_print_config.update(
{row[0].strip(): row[1].strip()})
return make_print_config
def configure_library(library_dir, env_options=None, options=[]):
configure_script = os.path.join(library_dir, "configure")
if not os.path.exists(configure_script):
raise ValueError(
"configure script {} does not exist".format(configure_script))
with changedir(library_dir):
if env_options is not None:
if run_configure(env_options):
return env_options
for option in options:
if run_configure(option):
return option
return None
def distutils_dir_name(dname):
"""Returns the name of a distutils build directory
see: http://stackoverflow.com/questions/14320220/
testing-python-c-libraries-get-build-path
"""
f = "{dirname}.{platform}-{version[0]}.{version[1]}"
return f.format(dirname=dname,
platform=sysconfig.get_platform(),
version=sys.version_info)
# How to link against HTSLIB
# separate: use included htslib and include in each extension
# module. No dependencies between modules and works
# with setup.py install, but wasteful in terms of
# memory and compilation time.
# shared: share chtslib across extension modules. This would be
# the ideal method, but currently requires
# LD_LIBRARY_PATH to be set correctly when using
# pysam.
# external: use shared libhts.so compiled outside of
# pysam
HTSLIB_MODE = os.environ.get("HTSLIB_MODE", "shared")
HTSLIB_LIBRARY_DIR = os.environ.get("HTSLIB_LIBRARY_DIR", None)
HTSLIB_INCLUDE_DIR = os.environ.get("HTSLIB_INCLUDE_DIR", None)
HTSLIB_CONFIGURE_OPTIONS = os.environ.get("HTSLIB_CONFIGURE_OPTIONS", None)
HTSLIB_SOURCE = None
package_list = ['pysam',
'pysam.include',
'pysam.include.samtools',
'pysam.include.bcftools',
'pysam.include.samtools.win32']
package_dirs = {'pysam': 'pysam',
'pysam.include.samtools': 'samtools',
'pysam.include.bcftools': 'bcftools'}
config_headers = ["samtools/config.h"]
from cy_build import CyExtension as Extension, cy_build_ext as build_ext
cmdclass = {'build_ext': build_ext}
# Check if cython is available
#
# If cython is available, the pysam will be built using cython from
# the .pyx files. If no cython is available, the C-files included in the
# distribution will be used.
try:
import cython
HAVE_CYTHON = True
print ("# pysam: cython is available - using cythonize if necessary")
source_pattern = "pysam/libc%s.pyx"
except ImportError:
HAVE_CYTHON = False
print ("# pysam: no cython available - using pre-compiled C")
# no Cython available - use existing C code
source_pattern = "pysam/libc%s.c"
# collect pysam version
sys.path.insert(0, "pysam")
import version
version = version.__version__
# exclude sources that contain a main function
EXCLUDE = {
"samtools": (
"razip.c", "bgzip.c", "main.c",
"calDepth.c", "bam2bed.c", "wgsim.c",
"md5fa.c", "md5sum-lite.c", "maq2sam.c",
"bamcheck.c", "chk_indel.c", "vcf-miniview.c",
"htslib-1.3", # do not import twice
"hfile_irods.c", # requires irods library
),
"bcftools": (
"test", "plugins", "peakfit.c",
"peakfit.h",
# needs to renamed, name conflict with samtools reheader
"reheader.c",
"polysomy.c"),
"htslib": (
'htslib/tabix.c', 'htslib/bgzip.c',
'htslib/htsfile.c', 'htslib/hfile_irods.c'),
}
print ("# pysam: htslib mode is {}".format(HTSLIB_MODE))
print ("# pysam: HTSLIB_CONFIGURE_OPTIONS={}".format(
HTSLIB_CONFIGURE_OPTIONS))
htslib_configure_options = None
if HTSLIB_MODE in ['shared', 'separate']:
package_list += ['pysam.include.htslib',
'pysam.include.htslib.htslib']
package_dirs.update({'pysam.include.htslib':'htslib'})
htslib_configure_options = configure_library(
"htslib",
HTSLIB_CONFIGURE_OPTIONS,
["--enable-libcurl",
"--disable-libcurl"])
HTSLIB_SOURCE = "builtin"
print ("# pysam: htslib configure options: {}".format(
str(htslib_configure_options)))
config_headers += ["htslib/config.h"]
if htslib_configure_options is None:
# create empty config.h file
with open("htslib/config.h", "w") as outf:
outf.write(
"/* empty config.h created by pysam */\n")
outf.write(
"/* conservative compilation options */\n")
with changedir("htslib"):
htslib_make_options = run_make_print_config()
for key, value in htslib_make_options.items():
print ("# pysam: htslib_config {}={}".format(key, value))
external_htslib_libraries = ['z']
if "LIBS" in htslib_make_options:
external_htslib_libraries.extend(
[re.sub("^-l", "", x) for x in htslib_make_options["LIBS"].split(" ") if x.strip()])
shared_htslib_sources = [re.sub("\.o", ".c", os.path.join("htslib", x))
for x in
htslib_make_options["LIBHTS_OBJS"].split(" ")]
htslib_sources = []
if HTSLIB_LIBRARY_DIR:
# linking against a shared, externally installed htslib version, no
# sources required for htslib
htslib_sources = []
shared_htslib_sources = []
chtslib_sources = []
htslib_library_dirs = [HTSLIB_LIBRARY_DIR]
htslib_include_dirs = [HTSLIB_INCLUDE_DIR]
external_htslib_libraries = ['z', 'hts']
elif HTSLIB_MODE == 'separate':
# add to each pysam component a separately compiled
# htslib
htslib_sources = shared_htslib_sources
shared_htslib_sources = htslib_sources
htslib_library_dirs = []
htslib_include_dirs = ['htslib']
elif HTSLIB_MODE == 'shared':
# link each pysam component against the same
# htslib built from sources included in the pysam
# package.
htslib_library_dirs = [
'pysam',
".",
os.path.join("build", distutils_dir_name("lib"), "pysam")]
htslib_include_dirs = ['htslib']
else:
raise ValueError("unknown HTSLIB value '%s'" % HTSLIB_MODE)
internal_htslib_libraries = []
# build config.py
with open(os.path.join("pysam", "config.py"), "w") as outf:
outf.write('HTSLIB = "{}"\n'.format(HTSLIB_SOURCE))
config_values = collections.defaultdict(int)
if HTSLIB_SOURCE == "builtin":
with open(os.path.join("htslib", "config.h")) as inf:
for line in inf:
if line.startswith("#define"):
key, value = re.match(
"#define (\S+)\s+(\S+)", line).groups()
config_values[key] = int(value)
for key in ["ENABLE_PLUGINS",
"HAVE_COMMONCRYPTO",
"HAVE_GMTIME_R",
"HAVE_HMAC",
"HAVE_IRODS",
"HAVE_LIBCURL",
"HAVE_MMAP"]:
outf.write("{} = {}\n".format(key, config_values[key]))
print ("# pysam: config_option: {}={}".format(key, config_values[key]))
# create empty config.h files if they have not been created automatically
# or created by the user:
for fn in config_headers:
if not os.path.exists(fn):
with open(fn, "w") as outf:
outf.write(
"/* empty config.h created by pysam */\n")
outf.write(
"/* conservative compilation options */\n")
parts = ["samtools",
"bcftools",
"htslib",
"tabix",
"faidx",
"samfile",
"utils",
"alignmentfile",
"tabixproxies",
"vcf",
"bcf"]
# Exit if there are no pre-compiled files and no cython available
fn = source_pattern % "htslib"
if not os.path.exists(fn):
raise ValueError(
"no cython installed, but can not find {}."
"Make sure that cython is installed when building "
"from the repository"
.format(fn))
#######################################################
classifiers = """
Development Status :: 3 - Beta
Operating System :: MacOS :: MacOS X
Operating System :: POSIX
Operating System :: POSIX :: Linux
Operating System :: Unix
Programming Language :: Python
Topic :: Scientific/Engineering
Topic :: Scientific/Engineering :: Bioinformatics
"""
#######################################################
#######################################################
# Windows compatibility - untested
if platform.system() == 'Windows':
include_os = ['win32']
os_c_files = ['win32/getopt.c']
extra_compile_args = []
else:
include_os = []
os_c_files = []
# for python 3.4, see for example
# http://stackoverflow.com/questions/25587039/
# error-compiling-rpy2-on-python3-4-due-to-werror-
# declaration-after-statement
extra_compile_args = [
"-Wno-unused",
"-Wno-strict-prototypes",
"-Wno-sign-compare",
"-Wno-error=declaration-after-statement"]
define_macros = []
chtslib = Extension(
"pysam.libchtslib",
[source_pattern % "htslib",
"pysam/htslib_util.c"] +
shared_htslib_sources +
os_c_files,
library_dirs=htslib_library_dirs,
include_dirs=["pysam", "."] + include_os + htslib_include_dirs,
libraries=external_htslib_libraries,
language="c",
extra_compile_args=extra_compile_args,
define_macros=define_macros
)
# samfile requires functions defined in bam_md.c
# for __advance_samtools method.
# Selected ones have been copied into samfile_utils.c
# Needs to be devolved somehow.
csamfile = Extension(
"pysam.libcsamfile",
[source_pattern % "samfile",
"pysam/htslib_util.c",
"pysam/samfile_util.c",
"samtools/kprobaln.c"] +
htslib_sources +
os_c_files,
library_dirs=htslib_library_dirs,
include_dirs=["pysam", "samtools", "."] + include_os + htslib_include_dirs,
libraries=external_htslib_libraries + internal_htslib_libraries,
language="c",
extra_compile_args=extra_compile_args,
define_macros=define_macros
)
# alignmentfile requires functions defined in bam_md.c
# for __advance_samtools method.
# Selected ones have been copied into samfile_utils.c
# Needs to be devolved somehow.
calignmentfile = Extension(
"pysam.libcalignmentfile",
[source_pattern % "alignmentfile",
"pysam/htslib_util.c",
"pysam/samfile_util.c",
"samtools/kprobaln.c"] +
htslib_sources +
os_c_files,
library_dirs=htslib_library_dirs,
include_dirs=["pysam", "samtools"] + include_os + htslib_include_dirs,
libraries=external_htslib_libraries + internal_htslib_libraries,
language="c",
extra_compile_args=extra_compile_args,
define_macros=define_macros
)
# alignmentfile requires functions defined in bam_md.c
# for __advance_samtools method.
# Selected ones have been copied into samfile_utils.c
# Needs to be devolved somehow.
calignedsegment = Extension(
"pysam.libcalignedsegment",
[source_pattern % "alignedsegment",
"pysam/htslib_util.c",
"pysam/samfile_util.c",
"samtools/kprobaln.c"] +
htslib_sources +
os_c_files,
library_dirs=htslib_library_dirs,
include_dirs=["pysam", "samtools", "."] + include_os + htslib_include_dirs,
libraries=external_htslib_libraries + internal_htslib_libraries,
language="c",
extra_compile_args=extra_compile_args,
define_macros=define_macros
)
ctabix = Extension(
"pysam.libctabix",
[source_pattern % "tabix",
"pysam/tabix_util.c"] +
htslib_sources +
os_c_files,
library_dirs=["pysam"] + htslib_library_dirs,
include_dirs=["pysam", "."] + include_os + htslib_include_dirs,
libraries=external_htslib_libraries + internal_htslib_libraries,
language="c",
extra_compile_args=extra_compile_args,
define_macros=define_macros
)
cutils = Extension(
"pysam.libcutils",
[source_pattern % "utils", "pysam/pysam_util.c"] +
glob.glob(os.path.join("samtools", "*.pysam.c")) +
# glob.glob(os.path.join("samtools", "*", "*.pysam.c")) +
glob.glob(os.path.join("bcftools", "*.pysam.c")) +
# glob.glob(os.path.join("bcftools", "*", "*.pysam.c")) +
htslib_sources +
os_c_files,
library_dirs=["pysam"] + htslib_library_dirs,
include_dirs=["samtools", "bcftools", "pysam", "."] +
include_os + htslib_include_dirs,
libraries=external_htslib_libraries + internal_htslib_libraries,
language="c",
extra_compile_args=extra_compile_args,
define_macros=define_macros
)
cfaidx = Extension(
"pysam.libcfaidx",
[source_pattern % "faidx"] +
htslib_sources +
os_c_files,
library_dirs=["pysam"] + htslib_library_dirs,
include_dirs=["pysam", "."] + include_os + htslib_include_dirs,
libraries=external_htslib_libraries + internal_htslib_libraries,
language="c",
extra_compile_args=extra_compile_args,
define_macros=define_macros
)
ctabixproxies = Extension(
"pysam.libctabixproxies",
[source_pattern % "tabixproxies"] +
os_c_files,
library_dirs=htslib_library_dirs,
include_dirs=include_os,
libraries=external_htslib_libraries + internal_htslib_libraries,
language="c",
extra_compile_args=extra_compile_args,
define_macros=define_macros
)
cvcf = Extension(
"pysam.libcvcf",
[source_pattern % "vcf"] +
os_c_files,
library_dirs=htslib_library_dirs,
include_dirs=["htslib", "."] + include_os + htslib_include_dirs,
libraries=external_htslib_libraries + internal_htslib_libraries,
language="c",
extra_compile_args=extra_compile_args,
define_macros=define_macros
)
cbcf = Extension(
"pysam.libcbcf",
[source_pattern % "bcf"] +
htslib_sources +
os_c_files,
library_dirs=htslib_library_dirs,
include_dirs=["htslib", "."] + include_os + htslib_include_dirs,
libraries=external_htslib_libraries + internal_htslib_libraries,
language="c",
extra_compile_args=extra_compile_args,
define_macros=define_macros
)
cbgzf = Extension(
"pysam.libcbgzf",
[source_pattern % "bgzf"] +
htslib_sources +
os_c_files,
library_dirs=htslib_library_dirs,
include_dirs=["htslib", "."] + include_os + htslib_include_dirs,
libraries=external_htslib_libraries + internal_htslib_libraries,
language="c",
extra_compile_args=extra_compile_args,
define_macros=define_macros
)
metadata = {
'name': "pysam",
'version': version,
'description': "pysam",
'long_description': __doc__,
'author': "Andreas Heger",
'author_email': "andreas.heger@gmail.com",
'license': "MIT",
'platforms': "ALL",
'url': "https://github.com/pysam-developers/pysam",
'packages': package_list,
'requires': ['cython (>=0.21)'],
'ext_modules': [chtslib,
csamfile,
calignmentfile,
calignedsegment,
ctabix,
ctabixproxies,
cvcf,
cbcf,
cbgzf,
cfaidx,
cutils],
'cmdclass': cmdclass,
'package_dir': package_dirs,
'package_data': {'': ['*.pxd', '*.h'], },
# do not pack in order to permit linking to csamtools.so
'zip_safe': False,
'use_2to3': True,
}
if __name__ == '__main__':
dist = setup(**metadata)
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