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import ctypes
import platform
import os
import re
import sys
import numpy
__version__ = "1.3.3"
__title__ = "parasail"
__description__ = "pairwise sequence alignment library"
__uri__ = "https://github.com/jeffdaily/parasail-python"
__author__ = "Jeff Daily"
__email__ = "jeffrey.daily@gmail.com"
__license__ = "BSD"
__copyright__ = "Copyright (c) 2016 Jeff Daily"
# we need the parasail library loaded so we can query the version
_libname = "libparasail.so"
if platform.system() == 'Darwin':
_libname = "libparasail.dylib"
elif platform.system() == 'Windows':
_libname = "parasail.dll"
_libpath = os.path.join(os.path.dirname(__file__), _libname)
_includepath = os.path.join(os.path.dirname(__file__), "include")
_verbose = os.environ.get("PARASAIL_VERBOSE", False)
# attempt to load library from package location
_lib = None
try:
_lib = ctypes.CDLL(_libpath)
except:
if _verbose: print("failed to open '{}' in package location".format(_libname))
if not _lib:
try:
_lib = ctypes.CDLL(_libname)
except:
if _verbose: print("failed to open '{}' using ctypes.CDLL defaults".format(_libname))
def _lib_search():
global _lib
global _libpath
_libpath = None
for env_var in ["PARASAIL_LIBPATH", "LD_LIBRARY_PATH", "DYLD_LIBRARY_PATH", "PATH"]:
if env_var in os.environ:
if _verbose: print("searching {} for {}".format(env_var,_libname))
for path in re.split("[:;]", os.environ[env_var]):
if _verbose: print("searching {}".format(path))
for attempt in [os.path.join(root,_libname) for root,dirs,files in os.walk(path) if _libname in files]:
try:
_lib = ctypes.CDLL(attempt)
_libpath = attempt
# shortcut the search during bindings import
os.environ["PARASAIL_LIBPATH"] = os.path.dirname(attempt)
if _verbose: print("found '{}'".format(attempt))
return
except:
if _verbose: print("attempted but failed to load '{}'".format(attempt))
else:
if _verbose: print("env var {} not set".format(env_var))
# if library load failed, search for it
if not _lib:
_lib_search()
# library load still failed, hard error
if not _lib:
raise Exception("failed to locate and open '{}'".format(_libname))
c_int_p = ctypes.POINTER(ctypes.c_int)
_lib.parasail_version.argtypes = [c_int_p, c_int_p, c_int_p]
_lib.parasail_version.restype = None
def version():
major = ctypes.c_int()
minor = ctypes.c_int()
patch = ctypes.c_int()
_lib.parasail_version(
ctypes.byref(major),
ctypes.byref(minor),
ctypes.byref(patch))
return major.value, minor.value, patch.value
major,minor,patch = version()
# now that we know the version, import the correct bindings
if major == 1:
from parasail.bindings_v1 import *
else:
from parasail.bindings_v2 import *
def get_include():
""" Returns the path of the Parasail C library include files.
"""
return _includepath
def get_library():
""" Returns the path of the Parasail C library shared object file.
"""
return _libpath
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