def test_find_exe_full_path(self):
"""
find_exe: locates executable file given full path
"""
full_path = os.path.join(self.test_dir,"test.exe")
with open(full_path,'wt') as fp:
fp.write("#!/usr/bin/bash\necho Test")
os.chmod(full_path,0o755)
self.assertEqual(find_exe(full_path),full_path)
def test_find_exe_on_path(self):
"""
find_exe: locates executable file on PATH
"""
full_path = os.path.join(self.test_dir,"test.exe")
with open(full_path,'wt') as fp:
fp.write("#!/usr/bin/bash\necho Test")
os.chmod(full_path,0o755)
os.environ['PATH'] = "%s%s%s" % (os.environ['PATH'],
os.pathsep,
self.test_dir)
self.assertEqual(find_exe(os.path.basename(full_path)),
full_path)
def ensure_bedtools():
# Globals
global BEDTOOLS_INSTALL_DIR
global PATH_NO_BEDTOOLS
global DESTROY_AT_EXIT
# Check if bedtools is already available
if find_exe("bedtools"):
return
# Install bedtools in temp directory
if BEDTOOLS_INSTALL_DIR is None:
bedtools_install_dir = tempfile.mkdtemp()
fetch_bedtools(install_dir=bedtools_install_dir,
create_install_dir=False)
BEDTOOLS_INSTALL_DIR = bedtools_install_dir
print("Installed bedtools in %s" % BEDTOOLS_INSTALL_DIR)
# Append bedtools to the PATH
if PATH_NO_BEDTOOLS is None:
PATH_NO_BEDTOOLS = os.environ['PATH']
os.environ['PATH'] = "%s%s%s" % (os.environ['PATH'], os.pathsep,
BEDTOOLS_INSTALL_DIR)
# Remove temporary bedtools install on exit
if not DESTROY_AT_EXIT:
atexit.register(remove_bedtools)
DESTROY_AT_EXIT = True
def setUp(self):
ensure_bedtools()
if not find_exe("bedtools"):
self.skipTest("bedtools not found")
self.test_dir = tempfile.mkdtemp()
def test_find_exe_for_missing_file(self):
"""
find_exe: returns None if file not found
"""
self.assertEqual(find_exe("doesntexist"),None)
self.assertEqual(find_exe("/no/where/doesntexist"),None)