partition stringclasses 3
values | func_name stringlengths 1 134 | docstring stringlengths 1 46.9k | path stringlengths 4 223 | original_string stringlengths 75 104k | code stringlengths 75 104k | docstring_tokens listlengths 1 1.97k | repo stringlengths 7 55 | language stringclasses 1
value | url stringlengths 87 315 | code_tokens listlengths 19 28.4k | sha stringlengths 40 40 |
|---|---|---|---|---|---|---|---|---|---|---|---|
train | SFTPClone._match_modes | Match mod, utime and uid/gid with locals one. | sftpclone/sftpclone.py | def _match_modes(self, remote_path, l_st):
"""Match mod, utime and uid/gid with locals one."""
self.sftp.chmod(remote_path, S_IMODE(l_st.st_mode))
self.sftp.utime(remote_path, (l_st.st_atime, l_st.st_mtime))
if self.chown:
self.sftp.chown(remote_path, l_st.st_uid, l_st.st_gi... | def _match_modes(self, remote_path, l_st):
"""Match mod, utime and uid/gid with locals one."""
self.sftp.chmod(remote_path, S_IMODE(l_st.st_mode))
self.sftp.utime(remote_path, (l_st.st_atime, l_st.st_mtime))
if self.chown:
self.sftp.chown(remote_path, l_st.st_uid, l_st.st_gi... | [
"Match",
"mod",
"utime",
"and",
"uid",
"/",
"gid",
"with",
"locals",
"one",
"."
] | unbit/sftpclone | python | https://github.com/unbit/sftpclone/blob/1cc89478e680fc4e0d12b1a15b5bafd0390d05da/sftpclone/sftpclone.py#L384-L390 | [
"def",
"_match_modes",
"(",
"self",
",",
"remote_path",
",",
"l_st",
")",
":",
"self",
".",
"sftp",
".",
"chmod",
"(",
"remote_path",
",",
"S_IMODE",
"(",
"l_st",
".",
"st_mode",
")",
")",
"self",
".",
"sftp",
".",
"utime",
"(",
"remote_path",
",",
"... | 1cc89478e680fc4e0d12b1a15b5bafd0390d05da |
train | SFTPClone.file_upload | Upload local_path to remote_path and set permission and mtime. | sftpclone/sftpclone.py | def file_upload(self, local_path, remote_path, l_st):
"""Upload local_path to remote_path and set permission and mtime."""
self.sftp.put(local_path, remote_path)
self._match_modes(remote_path, l_st) | def file_upload(self, local_path, remote_path, l_st):
"""Upload local_path to remote_path and set permission and mtime."""
self.sftp.put(local_path, remote_path)
self._match_modes(remote_path, l_st) | [
"Upload",
"local_path",
"to",
"remote_path",
"and",
"set",
"permission",
"and",
"mtime",
"."
] | unbit/sftpclone | python | https://github.com/unbit/sftpclone/blob/1cc89478e680fc4e0d12b1a15b5bafd0390d05da/sftpclone/sftpclone.py#L392-L395 | [
"def",
"file_upload",
"(",
"self",
",",
"local_path",
",",
"remote_path",
",",
"l_st",
")",
":",
"self",
".",
"sftp",
".",
"put",
"(",
"local_path",
",",
"remote_path",
")",
"self",
".",
"_match_modes",
"(",
"remote_path",
",",
"l_st",
")"
] | 1cc89478e680fc4e0d12b1a15b5bafd0390d05da |
train | SFTPClone.remote_delete | Remove the remote directory node. | sftpclone/sftpclone.py | def remote_delete(self, remote_path, r_st):
"""Remove the remote directory node."""
# If it's a directory, then delete content and directory
if S_ISDIR(r_st.st_mode):
for item in self.sftp.listdir_attr(remote_path):
full_path = path_join(remote_path, item.filename)
... | def remote_delete(self, remote_path, r_st):
"""Remove the remote directory node."""
# If it's a directory, then delete content and directory
if S_ISDIR(r_st.st_mode):
for item in self.sftp.listdir_attr(remote_path):
full_path = path_join(remote_path, item.filename)
... | [
"Remove",
"the",
"remote",
"directory",
"node",
"."
] | unbit/sftpclone | python | https://github.com/unbit/sftpclone/blob/1cc89478e680fc4e0d12b1a15b5bafd0390d05da/sftpclone/sftpclone.py#L397-L413 | [
"def",
"remote_delete",
"(",
"self",
",",
"remote_path",
",",
"r_st",
")",
":",
"# If it's a directory, then delete content and directory",
"if",
"S_ISDIR",
"(",
"r_st",
".",
"st_mode",
")",
":",
"for",
"item",
"in",
"self",
".",
"sftp",
".",
"listdir_attr",
"("... | 1cc89478e680fc4e0d12b1a15b5bafd0390d05da |
train | SFTPClone.check_for_deletion | Traverse the entire remote_path tree.
Find files/directories that need to be deleted,
not being present in the local folder. | sftpclone/sftpclone.py | def check_for_deletion(self, relative_path=None):
"""Traverse the entire remote_path tree.
Find files/directories that need to be deleted,
not being present in the local folder.
"""
if not relative_path:
relative_path = str() # root of shared directory tree
... | def check_for_deletion(self, relative_path=None):
"""Traverse the entire remote_path tree.
Find files/directories that need to be deleted,
not being present in the local folder.
"""
if not relative_path:
relative_path = str() # root of shared directory tree
... | [
"Traverse",
"the",
"entire",
"remote_path",
"tree",
"."
] | unbit/sftpclone | python | https://github.com/unbit/sftpclone/blob/1cc89478e680fc4e0d12b1a15b5bafd0390d05da/sftpclone/sftpclone.py#L415-L445 | [
"def",
"check_for_deletion",
"(",
"self",
",",
"relative_path",
"=",
"None",
")",
":",
"if",
"not",
"relative_path",
":",
"relative_path",
"=",
"str",
"(",
")",
"# root of shared directory tree",
"remote_path",
"=",
"path_join",
"(",
"self",
".",
"remote_path",
... | 1cc89478e680fc4e0d12b1a15b5bafd0390d05da |
train | SFTPClone.create_update_symlink | Create a new link pointing to link_destination in remote_path position. | sftpclone/sftpclone.py | def create_update_symlink(self, link_destination, remote_path):
"""Create a new link pointing to link_destination in remote_path position."""
try: # if there's anything, delete it
self.sftp.remove(remote_path)
except IOError: # that's fine, nothing exists there!
pass
... | def create_update_symlink(self, link_destination, remote_path):
"""Create a new link pointing to link_destination in remote_path position."""
try: # if there's anything, delete it
self.sftp.remove(remote_path)
except IOError: # that's fine, nothing exists there!
pass
... | [
"Create",
"a",
"new",
"link",
"pointing",
"to",
"link_destination",
"in",
"remote_path",
"position",
"."
] | unbit/sftpclone | python | https://github.com/unbit/sftpclone/blob/1cc89478e680fc4e0d12b1a15b5bafd0390d05da/sftpclone/sftpclone.py#L447-L460 | [
"def",
"create_update_symlink",
"(",
"self",
",",
"link_destination",
",",
"remote_path",
")",
":",
"try",
":",
"# if there's anything, delete it",
"self",
".",
"sftp",
".",
"remove",
"(",
"remote_path",
")",
"except",
"IOError",
":",
"# that's fine, nothing exists th... | 1cc89478e680fc4e0d12b1a15b5bafd0390d05da |
train | SFTPClone.node_check_for_upload_create | Check if the given directory tree node has to be uploaded/created on the remote folder. | sftpclone/sftpclone.py | def node_check_for_upload_create(self, relative_path, f):
"""Check if the given directory tree node has to be uploaded/created on the remote folder."""
if not relative_path:
# we're at the root of the shared directory tree
relative_path = str()
# the (absolute) local add... | def node_check_for_upload_create(self, relative_path, f):
"""Check if the given directory tree node has to be uploaded/created on the remote folder."""
if not relative_path:
# we're at the root of the shared directory tree
relative_path = str()
# the (absolute) local add... | [
"Check",
"if",
"the",
"given",
"directory",
"tree",
"node",
"has",
"to",
"be",
"uploaded",
"/",
"created",
"on",
"the",
"remote",
"folder",
"."
] | unbit/sftpclone | python | https://github.com/unbit/sftpclone/blob/1cc89478e680fc4e0d12b1a15b5bafd0390d05da/sftpclone/sftpclone.py#L462-L583 | [
"def",
"node_check_for_upload_create",
"(",
"self",
",",
"relative_path",
",",
"f",
")",
":",
"if",
"not",
"relative_path",
":",
"# we're at the root of the shared directory tree",
"relative_path",
"=",
"str",
"(",
")",
"# the (absolute) local address of f.",
"local_path",
... | 1cc89478e680fc4e0d12b1a15b5bafd0390d05da |
train | SFTPClone.check_for_upload_create | Traverse the relative_path tree and check for files that need to be uploaded/created.
Relativity here refers to the shared directory tree. | sftpclone/sftpclone.py | def check_for_upload_create(self, relative_path=None):
"""Traverse the relative_path tree and check for files that need to be uploaded/created.
Relativity here refers to the shared directory tree."""
for f in os.listdir(
path_join(
self.local_path, relative_path) if ... | def check_for_upload_create(self, relative_path=None):
"""Traverse the relative_path tree and check for files that need to be uploaded/created.
Relativity here refers to the shared directory tree."""
for f in os.listdir(
path_join(
self.local_path, relative_path) if ... | [
"Traverse",
"the",
"relative_path",
"tree",
"and",
"check",
"for",
"files",
"that",
"need",
"to",
"be",
"uploaded",
"/",
"created",
"."
] | unbit/sftpclone | python | https://github.com/unbit/sftpclone/blob/1cc89478e680fc4e0d12b1a15b5bafd0390d05da/sftpclone/sftpclone.py#L585-L593 | [
"def",
"check_for_upload_create",
"(",
"self",
",",
"relative_path",
"=",
"None",
")",
":",
"for",
"f",
"in",
"os",
".",
"listdir",
"(",
"path_join",
"(",
"self",
".",
"local_path",
",",
"relative_path",
")",
"if",
"relative_path",
"else",
"self",
".",
"lo... | 1cc89478e680fc4e0d12b1a15b5bafd0390d05da |
train | SFTPClone.run | Run the sync.
Confront the local and the remote directories and perform the needed changes. | sftpclone/sftpclone.py | def run(self):
"""Run the sync.
Confront the local and the remote directories and perform the needed changes."""
# Check if remote path is present
try:
self.sftp.stat(self.remote_path)
except FileNotFoundError as e:
if self.create_remote_directory:
... | def run(self):
"""Run the sync.
Confront the local and the remote directories and perform the needed changes."""
# Check if remote path is present
try:
self.sftp.stat(self.remote_path)
except FileNotFoundError as e:
if self.create_remote_directory:
... | [
"Run",
"the",
"sync",
"."
] | unbit/sftpclone | python | https://github.com/unbit/sftpclone/blob/1cc89478e680fc4e0d12b1a15b5bafd0390d05da/sftpclone/sftpclone.py#L595-L625 | [
"def",
"run",
"(",
"self",
")",
":",
"# Check if remote path is present",
"try",
":",
"self",
".",
"sftp",
".",
"stat",
"(",
"self",
".",
"remote_path",
")",
"except",
"FileNotFoundError",
"as",
"e",
":",
"if",
"self",
".",
"create_remote_directory",
":",
"s... | 1cc89478e680fc4e0d12b1a15b5bafd0390d05da |
train | list_files | tree unix command replacement. | sftpclone/t/utils.py | def list_files(start_path):
"""tree unix command replacement."""
s = u'\n'
for root, dirs, files in os.walk(start_path):
level = root.replace(start_path, '').count(os.sep)
indent = ' ' * 4 * level
s += u'{}{}/\n'.format(indent, os.path.basename(root))
sub_indent = ' ' * 4 * (... | def list_files(start_path):
"""tree unix command replacement."""
s = u'\n'
for root, dirs, files in os.walk(start_path):
level = root.replace(start_path, '').count(os.sep)
indent = ' ' * 4 * level
s += u'{}{}/\n'.format(indent, os.path.basename(root))
sub_indent = ' ' * 4 * (... | [
"tree",
"unix",
"command",
"replacement",
"."
] | unbit/sftpclone | python | https://github.com/unbit/sftpclone/blob/1cc89478e680fc4e0d12b1a15b5bafd0390d05da/sftpclone/t/utils.py#L26-L36 | [
"def",
"list_files",
"(",
"start_path",
")",
":",
"s",
"=",
"u'\\n'",
"for",
"root",
",",
"dirs",
",",
"files",
"in",
"os",
".",
"walk",
"(",
"start_path",
")",
":",
"level",
"=",
"root",
".",
"replace",
"(",
"start_path",
",",
"''",
")",
".",
"cou... | 1cc89478e680fc4e0d12b1a15b5bafd0390d05da |
train | file_tree | Create a nested dictionary that represents the folder structure of `start_path`.
Liberally adapted from
http://code.activestate.com/recipes/577879-create-a-nested-dictionary-from-oswalk/ | sftpclone/t/utils.py | def file_tree(start_path):
"""
Create a nested dictionary that represents the folder structure of `start_path`.
Liberally adapted from
http://code.activestate.com/recipes/577879-create-a-nested-dictionary-from-oswalk/
"""
nested_dirs = {}
root_dir = start_path.rstrip(os.sep)
start = roo... | def file_tree(start_path):
"""
Create a nested dictionary that represents the folder structure of `start_path`.
Liberally adapted from
http://code.activestate.com/recipes/577879-create-a-nested-dictionary-from-oswalk/
"""
nested_dirs = {}
root_dir = start_path.rstrip(os.sep)
start = roo... | [
"Create",
"a",
"nested",
"dictionary",
"that",
"represents",
"the",
"folder",
"structure",
"of",
"start_path",
"."
] | unbit/sftpclone | python | https://github.com/unbit/sftpclone/blob/1cc89478e680fc4e0d12b1a15b5bafd0390d05da/sftpclone/t/utils.py#L39-L54 | [
"def",
"file_tree",
"(",
"start_path",
")",
":",
"nested_dirs",
"=",
"{",
"}",
"root_dir",
"=",
"start_path",
".",
"rstrip",
"(",
"os",
".",
"sep",
")",
"start",
"=",
"root_dir",
".",
"rfind",
"(",
"os",
".",
"sep",
")",
"+",
"1",
"for",
"path",
",... | 1cc89478e680fc4e0d12b1a15b5bafd0390d05da |
train | capture_sys_output | Capture standard output and error. | sftpclone/t/utils.py | def capture_sys_output():
"""Capture standard output and error."""
capture_out, capture_err = StringIO(), StringIO()
current_out, current_err = sys.stdout, sys.stderr
try:
sys.stdout, sys.stderr = capture_out, capture_err
yield capture_out, capture_err
finally:
sys.stdout, sy... | def capture_sys_output():
"""Capture standard output and error."""
capture_out, capture_err = StringIO(), StringIO()
current_out, current_err = sys.stdout, sys.stderr
try:
sys.stdout, sys.stderr = capture_out, capture_err
yield capture_out, capture_err
finally:
sys.stdout, sy... | [
"Capture",
"standard",
"output",
"and",
"error",
"."
] | unbit/sftpclone | python | https://github.com/unbit/sftpclone/blob/1cc89478e680fc4e0d12b1a15b5bafd0390d05da/sftpclone/t/utils.py#L58-L66 | [
"def",
"capture_sys_output",
"(",
")",
":",
"capture_out",
",",
"capture_err",
"=",
"StringIO",
"(",
")",
",",
"StringIO",
"(",
")",
"current_out",
",",
"current_err",
"=",
"sys",
".",
"stdout",
",",
"sys",
".",
"stderr",
"try",
":",
"sys",
".",
"stdout"... | 1cc89478e680fc4e0d12b1a15b5bafd0390d05da |
train | suppress_logging | Suppress logging. | sftpclone/t/utils.py | def suppress_logging(log_level=logging.CRITICAL):
"""Suppress logging."""
logging.disable(log_level)
yield
logging.disable(logging.NOTSET) | def suppress_logging(log_level=logging.CRITICAL):
"""Suppress logging."""
logging.disable(log_level)
yield
logging.disable(logging.NOTSET) | [
"Suppress",
"logging",
"."
] | unbit/sftpclone | python | https://github.com/unbit/sftpclone/blob/1cc89478e680fc4e0d12b1a15b5bafd0390d05da/sftpclone/t/utils.py#L70-L74 | [
"def",
"suppress_logging",
"(",
"log_level",
"=",
"logging",
".",
"CRITICAL",
")",
":",
"logging",
".",
"disable",
"(",
"log_level",
")",
"yield",
"logging",
".",
"disable",
"(",
"logging",
".",
"NOTSET",
")"
] | 1cc89478e680fc4e0d12b1a15b5bafd0390d05da |
train | override_env_variables | Override user environmental variables with custom one. | sftpclone/t/utils.py | def override_env_variables():
"""Override user environmental variables with custom one."""
env_vars = ("LOGNAME", "USER", "LNAME", "USERNAME")
old = [os.environ[v] if v in os.environ else None for v in env_vars]
for v in env_vars:
os.environ[v] = "test"
yield
for i, v in enumerate(env_... | def override_env_variables():
"""Override user environmental variables with custom one."""
env_vars = ("LOGNAME", "USER", "LNAME", "USERNAME")
old = [os.environ[v] if v in os.environ else None for v in env_vars]
for v in env_vars:
os.environ[v] = "test"
yield
for i, v in enumerate(env_... | [
"Override",
"user",
"environmental",
"variables",
"with",
"custom",
"one",
"."
] | unbit/sftpclone | python | https://github.com/unbit/sftpclone/blob/1cc89478e680fc4e0d12b1a15b5bafd0390d05da/sftpclone/t/utils.py#L78-L89 | [
"def",
"override_env_variables",
"(",
")",
":",
"env_vars",
"=",
"(",
"\"LOGNAME\"",
",",
"\"USER\"",
",",
"\"LNAME\"",
",",
"\"USERNAME\"",
")",
"old",
"=",
"[",
"os",
".",
"environ",
"[",
"v",
"]",
"if",
"v",
"in",
"os",
".",
"environ",
"else",
"None... | 1cc89478e680fc4e0d12b1a15b5bafd0390d05da |
train | override_ssh_auth_env | Override the `$SSH_AUTH_SOCK `env variable to mock the absence of an SSH agent. | sftpclone/t/utils.py | def override_ssh_auth_env():
"""Override the `$SSH_AUTH_SOCK `env variable to mock the absence of an SSH agent."""
ssh_auth_sock = "SSH_AUTH_SOCK"
old_ssh_auth_sock = os.environ.get(ssh_auth_sock)
del os.environ[ssh_auth_sock]
yield
if old_ssh_auth_sock:
os.environ[ssh_auth_sock] = ol... | def override_ssh_auth_env():
"""Override the `$SSH_AUTH_SOCK `env variable to mock the absence of an SSH agent."""
ssh_auth_sock = "SSH_AUTH_SOCK"
old_ssh_auth_sock = os.environ.get(ssh_auth_sock)
del os.environ[ssh_auth_sock]
yield
if old_ssh_auth_sock:
os.environ[ssh_auth_sock] = ol... | [
"Override",
"the",
"$SSH_AUTH_SOCK",
"env",
"variable",
"to",
"mock",
"the",
"absence",
"of",
"an",
"SSH",
"agent",
"."
] | unbit/sftpclone | python | https://github.com/unbit/sftpclone/blob/1cc89478e680fc4e0d12b1a15b5bafd0390d05da/sftpclone/t/utils.py#L93-L103 | [
"def",
"override_ssh_auth_env",
"(",
")",
":",
"ssh_auth_sock",
"=",
"\"SSH_AUTH_SOCK\"",
"old_ssh_auth_sock",
"=",
"os",
".",
"environ",
".",
"get",
"(",
"ssh_auth_sock",
")",
"del",
"os",
".",
"environ",
"[",
"ssh_auth_sock",
"]",
"yield",
"if",
"old_ssh_auth_... | 1cc89478e680fc4e0d12b1a15b5bafd0390d05da |
train | get_config | Get the configurations from .tldrrc and return it as a dict. | tldr/config.py | def get_config():
"""Get the configurations from .tldrrc and return it as a dict."""
config_path = path.join(
(os.environ.get('TLDR_CONFIG_DIR') or path.expanduser('~')),
'.tldrrc')
if not path.exists(config_path):
sys.exit("Can't find config file at: {0}. You may use `tldr init` "
... | def get_config():
"""Get the configurations from .tldrrc and return it as a dict."""
config_path = path.join(
(os.environ.get('TLDR_CONFIG_DIR') or path.expanduser('~')),
'.tldrrc')
if not path.exists(config_path):
sys.exit("Can't find config file at: {0}. You may use `tldr init` "
... | [
"Get",
"the",
"configurations",
"from",
".",
"tldrrc",
"and",
"return",
"it",
"as",
"a",
"dict",
"."
] | lord63/tldr.py | python | https://github.com/lord63/tldr.py/blob/73cf9f86254691b2476910ea6a743b6d8bd04963/tldr/config.py#L14-L38 | [
"def",
"get_config",
"(",
")",
":",
"config_path",
"=",
"path",
".",
"join",
"(",
"(",
"os",
".",
"environ",
".",
"get",
"(",
"'TLDR_CONFIG_DIR'",
")",
"or",
"path",
".",
"expanduser",
"(",
"'~'",
")",
")",
",",
"'.tldrrc'",
")",
"if",
"not",
"path",... | 73cf9f86254691b2476910ea6a743b6d8bd04963 |
train | parse_man_page | Parse the man page and return the parsed lines. | tldr/cli.py | def parse_man_page(command, platform):
"""Parse the man page and return the parsed lines."""
page_path = find_page_location(command, platform)
output_lines = parse_page(page_path)
return output_lines | def parse_man_page(command, platform):
"""Parse the man page and return the parsed lines."""
page_path = find_page_location(command, platform)
output_lines = parse_page(page_path)
return output_lines | [
"Parse",
"the",
"man",
"page",
"and",
"return",
"the",
"parsed",
"lines",
"."
] | lord63/tldr.py | python | https://github.com/lord63/tldr.py/blob/73cf9f86254691b2476910ea6a743b6d8bd04963/tldr/cli.py#L22-L26 | [
"def",
"parse_man_page",
"(",
"command",
",",
"platform",
")",
":",
"page_path",
"=",
"find_page_location",
"(",
"command",
",",
"platform",
")",
"output_lines",
"=",
"parse_page",
"(",
"page_path",
")",
"return",
"output_lines"
] | 73cf9f86254691b2476910ea6a743b6d8bd04963 |
train | find_page_location | Find the command man page in the pages directory. | tldr/cli.py | def find_page_location(command, specified_platform):
"""Find the command man page in the pages directory."""
repo_directory = get_config()['repo_directory']
default_platform = get_config()['platform']
command_platform = (
specified_platform if specified_platform else default_platform)
with ... | def find_page_location(command, specified_platform):
"""Find the command man page in the pages directory."""
repo_directory = get_config()['repo_directory']
default_platform = get_config()['platform']
command_platform = (
specified_platform if specified_platform else default_platform)
with ... | [
"Find",
"the",
"command",
"man",
"page",
"in",
"the",
"pages",
"directory",
"."
] | lord63/tldr.py | python | https://github.com/lord63/tldr.py/blob/73cf9f86254691b2476910ea6a743b6d8bd04963/tldr/cli.py#L29-L62 | [
"def",
"find_page_location",
"(",
"command",
",",
"specified_platform",
")",
":",
"repo_directory",
"=",
"get_config",
"(",
")",
"[",
"'repo_directory'",
"]",
"default_platform",
"=",
"get_config",
"(",
")",
"[",
"'platform'",
"]",
"command_platform",
"=",
"(",
... | 73cf9f86254691b2476910ea6a743b6d8bd04963 |
train | find | Find the command usage. | tldr/cli.py | def find(command, on):
"""Find the command usage."""
output_lines = parse_man_page(command, on)
click.echo(''.join(output_lines)) | def find(command, on):
"""Find the command usage."""
output_lines = parse_man_page(command, on)
click.echo(''.join(output_lines)) | [
"Find",
"the",
"command",
"usage",
"."
] | lord63/tldr.py | python | https://github.com/lord63/tldr.py/blob/73cf9f86254691b2476910ea6a743b6d8bd04963/tldr/cli.py#L101-L104 | [
"def",
"find",
"(",
"command",
",",
"on",
")",
":",
"output_lines",
"=",
"parse_man_page",
"(",
"command",
",",
"on",
")",
"click",
".",
"echo",
"(",
"''",
".",
"join",
"(",
"output_lines",
")",
")"
] | 73cf9f86254691b2476910ea6a743b6d8bd04963 |
train | update | Update to the latest pages. | tldr/cli.py | def update():
"""Update to the latest pages."""
repo_directory = get_config()['repo_directory']
os.chdir(repo_directory)
click.echo("Check for updates...")
local = subprocess.check_output('git rev-parse master'.split()).strip()
remote = subprocess.check_output(
'git ls-remote https://gi... | def update():
"""Update to the latest pages."""
repo_directory = get_config()['repo_directory']
os.chdir(repo_directory)
click.echo("Check for updates...")
local = subprocess.check_output('git rev-parse master'.split()).strip()
remote = subprocess.check_output(
'git ls-remote https://gi... | [
"Update",
"to",
"the",
"latest",
"pages",
"."
] | lord63/tldr.py | python | https://github.com/lord63/tldr.py/blob/73cf9f86254691b2476910ea6a743b6d8bd04963/tldr/cli.py#L108-L125 | [
"def",
"update",
"(",
")",
":",
"repo_directory",
"=",
"get_config",
"(",
")",
"[",
"'repo_directory'",
"]",
"os",
".",
"chdir",
"(",
"repo_directory",
")",
"click",
".",
"echo",
"(",
"\"Check for updates...\"",
")",
"local",
"=",
"subprocess",
".",
"check_o... | 73cf9f86254691b2476910ea6a743b6d8bd04963 |
train | init | Init config file. | tldr/cli.py | def init():
"""Init config file."""
default_config_path = path.join(
(os.environ.get('TLDR_CONFIG_DIR') or path.expanduser('~')),
'.tldrrc')
if path.exists(default_config_path):
click.echo("There is already a config file exists, "
"skip initializing it.")
else:... | def init():
"""Init config file."""
default_config_path = path.join(
(os.environ.get('TLDR_CONFIG_DIR') or path.expanduser('~')),
'.tldrrc')
if path.exists(default_config_path):
click.echo("There is already a config file exists, "
"skip initializing it.")
else:... | [
"Init",
"config",
"file",
"."
] | lord63/tldr.py | python | https://github.com/lord63/tldr.py/blob/73cf9f86254691b2476910ea6a743b6d8bd04963/tldr/cli.py#L129-L161 | [
"def",
"init",
"(",
")",
":",
"default_config_path",
"=",
"path",
".",
"join",
"(",
"(",
"os",
".",
"environ",
".",
"get",
"(",
"'TLDR_CONFIG_DIR'",
")",
"or",
"path",
".",
"expanduser",
"(",
"'~'",
")",
")",
",",
"'.tldrrc'",
")",
"if",
"path",
".",... | 73cf9f86254691b2476910ea6a743b6d8bd04963 |
train | locate | Locate the command's man page. | tldr/cli.py | def locate(command, on):
"""Locate the command's man page."""
location = find_page_location(command, on)
click.echo(location) | def locate(command, on):
"""Locate the command's man page."""
location = find_page_location(command, on)
click.echo(location) | [
"Locate",
"the",
"command",
"s",
"man",
"page",
"."
] | lord63/tldr.py | python | https://github.com/lord63/tldr.py/blob/73cf9f86254691b2476910ea6a743b6d8bd04963/tldr/cli.py#L175-L178 | [
"def",
"locate",
"(",
"command",
",",
"on",
")",
":",
"location",
"=",
"find_page_location",
"(",
"command",
",",
"on",
")",
"click",
".",
"echo",
"(",
"location",
")"
] | 73cf9f86254691b2476910ea6a743b6d8bd04963 |
train | TableClassType.relate | Produce a relationship between this mapped table and another
one.
This makes usage of SQLAlchemy's :func:`sqlalchemy.orm.relationship`
construct. | cruzdb/sqlsoup.py | def relate(cls, propname, *args, **kwargs):
"""Produce a relationship between this mapped table and another
one.
This makes usage of SQLAlchemy's :func:`sqlalchemy.orm.relationship`
construct.
"""
class_mapper(cls)._configure_property(propname, relation... | def relate(cls, propname, *args, **kwargs):
"""Produce a relationship between this mapped table and another
one.
This makes usage of SQLAlchemy's :func:`sqlalchemy.orm.relationship`
construct.
"""
class_mapper(cls)._configure_property(propname, relation... | [
"Produce",
"a",
"relationship",
"between",
"this",
"mapped",
"table",
"and",
"another",
"one",
".",
"This",
"makes",
"usage",
"of",
"SQLAlchemy",
"s",
":",
"func",
":",
"sqlalchemy",
".",
"orm",
".",
"relationship",
"construct",
"."
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/sqlsoup.py#L93-L101 | [
"def",
"relate",
"(",
"cls",
",",
"propname",
",",
"*",
"args",
",",
"*",
"*",
"kwargs",
")",
":",
"class_mapper",
"(",
"cls",
")",
".",
"_configure_property",
"(",
"propname",
",",
"relationship",
"(",
"*",
"args",
",",
"*",
"*",
"kwargs",
")",
")"
... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | SQLSoup.execute | Execute a SQL statement.
The statement may be a string SQL string,
an :func:`sqlalchemy.sql.expression.select` construct, or a
:func:`sqlalchemy.sql.expression.text`
construct. | cruzdb/sqlsoup.py | def execute(self, stmt, **params):
"""Execute a SQL statement.
The statement may be a string SQL string,
an :func:`sqlalchemy.sql.expression.select` construct, or a
:func:`sqlalchemy.sql.expression.text`
construct.
"""
return self.session.execute(sql.text(stmt... | def execute(self, stmt, **params):
"""Execute a SQL statement.
The statement may be a string SQL string,
an :func:`sqlalchemy.sql.expression.select` construct, or a
:func:`sqlalchemy.sql.expression.text`
construct.
"""
return self.session.execute(sql.text(stmt... | [
"Execute",
"a",
"SQL",
"statement",
"."
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/sqlsoup.py#L229-L238 | [
"def",
"execute",
"(",
"self",
",",
"stmt",
",",
"*",
"*",
"params",
")",
":",
"return",
"self",
".",
"session",
".",
"execute",
"(",
"sql",
".",
"text",
"(",
"stmt",
",",
"bind",
"=",
"self",
".",
"bind",
")",
",",
"*",
"*",
"params",
")"
] | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | SQLSoup.map_to | Configure a mapping to the given attrname.
This is the "master" method that can be used to create any
configuration.
:param attrname: String attribute name which will be
established as an attribute on this :class:.`.SQLSoup`
instance.
:param base: a Python class wh... | cruzdb/sqlsoup.py | def map_to(self, attrname, tablename=None, selectable=None,
schema=None, base=None, mapper_args=util.immutabledict()):
"""Configure a mapping to the given attrname.
This is the "master" method that can be used to create any
configuration.
:param attrname: String a... | def map_to(self, attrname, tablename=None, selectable=None,
schema=None, base=None, mapper_args=util.immutabledict()):
"""Configure a mapping to the given attrname.
This is the "master" method that can be used to create any
configuration.
:param attrname: String a... | [
"Configure",
"a",
"mapping",
"to",
"the",
"given",
"attrname",
"."
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/sqlsoup.py#L292-L373 | [
"def",
"map_to",
"(",
"self",
",",
"attrname",
",",
"tablename",
"=",
"None",
",",
"selectable",
"=",
"None",
",",
"schema",
"=",
"None",
",",
"base",
"=",
"None",
",",
"mapper_args",
"=",
"util",
".",
"immutabledict",
"(",
")",
")",
":",
"if",
"attr... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | SQLSoup.map | Map a selectable directly.
The class and its mapping are not cached and will
be discarded once dereferenced (as of 0.6.6).
:param selectable: an :func:`.expression.select` construct.
:param base: a Python class which will be used as the
base for the mapped class. If ``None``,... | cruzdb/sqlsoup.py | def map(self, selectable, base=None, **mapper_args):
"""Map a selectable directly.
The class and its mapping are not cached and will
be discarded once dereferenced (as of 0.6.6).
:param selectable: an :func:`.expression.select` construct.
:param base: a Python class which will ... | def map(self, selectable, base=None, **mapper_args):
"""Map a selectable directly.
The class and its mapping are not cached and will
be discarded once dereferenced (as of 0.6.6).
:param selectable: an :func:`.expression.select` construct.
:param base: a Python class which will ... | [
"Map",
"a",
"selectable",
"directly",
"."
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/sqlsoup.py#L376-L399 | [
"def",
"map",
"(",
"self",
",",
"selectable",
",",
"base",
"=",
"None",
",",
"*",
"*",
"mapper_args",
")",
":",
"return",
"_class_for_table",
"(",
"self",
".",
"session",
",",
"self",
".",
"engine",
",",
"selectable",
",",
"base",
"or",
"self",
".",
... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | SQLSoup.with_labels | Map a selectable directly, wrapping the
selectable in a subquery with labels.
The class and its mapping are not cached and will
be discarded once dereferenced (as of 0.6.6).
:param selectable: an :func:`.expression.select` construct.
:param base: a Python class which will be u... | cruzdb/sqlsoup.py | def with_labels(self, selectable, base=None, **mapper_args):
"""Map a selectable directly, wrapping the
selectable in a subquery with labels.
The class and its mapping are not cached and will
be discarded once dereferenced (as of 0.6.6).
:param selectable: an :func:`.expressio... | def with_labels(self, selectable, base=None, **mapper_args):
"""Map a selectable directly, wrapping the
selectable in a subquery with labels.
The class and its mapping are not cached and will
be discarded once dereferenced (as of 0.6.6).
:param selectable: an :func:`.expressio... | [
"Map",
"a",
"selectable",
"directly",
"wrapping",
"the",
"selectable",
"in",
"a",
"subquery",
"with",
"labels",
"."
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/sqlsoup.py#L401-L423 | [
"def",
"with_labels",
"(",
"self",
",",
"selectable",
",",
"base",
"=",
"None",
",",
"*",
"*",
"mapper_args",
")",
":",
"# TODO give meaningful aliases",
"return",
"self",
".",
"map",
"(",
"expression",
".",
"_clause_element_as_expr",
"(",
"selectable",
")",
"... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | SQLSoup.join | Create an :func:`.expression.join` and map to it.
The class and its mapping are not cached and will
be discarded once dereferenced (as of 0.6.6).
:param left: a mapped class or table object.
:param right: a mapped class or table object.
:param onclause: optional "ON" clause con... | cruzdb/sqlsoup.py | def join(self, left, right, onclause=None, isouter=False,
base=None, **mapper_args):
"""Create an :func:`.expression.join` and map to it.
The class and its mapping are not cached and will
be discarded once dereferenced (as of 0.6.6).
:param left: a mapped class or tabl... | def join(self, left, right, onclause=None, isouter=False,
base=None, **mapper_args):
"""Create an :func:`.expression.join` and map to it.
The class and its mapping are not cached and will
be discarded once dereferenced (as of 0.6.6).
:param left: a mapped class or tabl... | [
"Create",
"an",
":",
"func",
":",
".",
"expression",
".",
"join",
"and",
"map",
"to",
"it",
"."
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/sqlsoup.py#L425-L447 | [
"def",
"join",
"(",
"self",
",",
"left",
",",
"right",
",",
"onclause",
"=",
"None",
",",
"isouter",
"=",
"False",
",",
"base",
"=",
"None",
",",
"*",
"*",
"mapper_args",
")",
":",
"j",
"=",
"join",
"(",
"left",
",",
"right",
",",
"onclause",
"="... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | SQLSoup.entity | Return the named entity from this :class:`.SQLSoup`, or
create if not present.
For more generalized mapping, see :meth:`.map_to`. | cruzdb/sqlsoup.py | def entity(self, attr, schema=None):
"""Return the named entity from this :class:`.SQLSoup`, or
create if not present.
For more generalized mapping, see :meth:`.map_to`.
"""
try:
return self._cache[attr]
except KeyError, ke:
return self.map_to(a... | def entity(self, attr, schema=None):
"""Return the named entity from this :class:`.SQLSoup`, or
create if not present.
For more generalized mapping, see :meth:`.map_to`.
"""
try:
return self._cache[attr]
except KeyError, ke:
return self.map_to(a... | [
"Return",
"the",
"named",
"entity",
"from",
"this",
":",
"class",
":",
".",
"SQLSoup",
"or",
"create",
"if",
"not",
"present",
"."
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/sqlsoup.py#L449-L459 | [
"def",
"entity",
"(",
"self",
",",
"attr",
",",
"schema",
"=",
"None",
")",
":",
"try",
":",
"return",
"self",
".",
"_cache",
"[",
"attr",
"]",
"except",
"KeyError",
",",
"ke",
":",
"return",
"self",
".",
"map_to",
"(",
"attr",
",",
"tablename",
"=... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | distance | \
Distance between 2 features. The integer result is always positive or zero.
If the features overlap or touch, it is zero.
>>> from intersecter import Feature, distance
>>> distance(Feature(1, 2), Feature(12, 13))
10
>>> distance(Feature(1, 2), Feature(2, 3))
0
>>> distance(Feature(1, 1... | cruzdb/intersecter.py | def distance(f1, f2):
"""\
Distance between 2 features. The integer result is always positive or zero.
If the features overlap or touch, it is zero.
>>> from intersecter import Feature, distance
>>> distance(Feature(1, 2), Feature(12, 13))
10
>>> distance(Feature(1, 2), Feature(2, 3))
0
... | def distance(f1, f2):
"""\
Distance between 2 features. The integer result is always positive or zero.
If the features overlap or touch, it is zero.
>>> from intersecter import Feature, distance
>>> distance(Feature(1, 2), Feature(12, 13))
10
>>> distance(Feature(1, 2), Feature(2, 3))
0
... | [
"\\",
"Distance",
"between",
"2",
"features",
".",
"The",
"integer",
"result",
"is",
"always",
"positive",
"or",
"zero",
".",
"If",
"the",
"features",
"overlap",
"or",
"touch",
"it",
"is",
"zero",
".",
">>>",
"from",
"intersecter",
"import",
"Feature",
"di... | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/intersecter.py#L269-L284 | [
"def",
"distance",
"(",
"f1",
",",
"f2",
")",
":",
"if",
"f1",
".",
"end",
"<",
"f2",
".",
"start",
":",
"return",
"f2",
".",
"start",
"-",
"f1",
".",
"end",
"if",
"f2",
".",
"end",
"<",
"f1",
".",
"start",
":",
"return",
"f1",
".",
"start",
... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | Intersecter.find | Return a object of all stored intervals intersecting between (start, end) inclusive. | cruzdb/intersecter.py | def find(self, start, end, chrom=None):
"""Return a object of all stored intervals intersecting between (start, end) inclusive."""
intervals = self.intervals[chrom]
ilen = len(intervals)
# NOTE: we only search for starts, since any feature that starts within max_len of
# the quer... | def find(self, start, end, chrom=None):
"""Return a object of all stored intervals intersecting between (start, end) inclusive."""
intervals = self.intervals[chrom]
ilen = len(intervals)
# NOTE: we only search for starts, since any feature that starts within max_len of
# the quer... | [
"Return",
"a",
"object",
"of",
"all",
"stored",
"intervals",
"intersecting",
"between",
"(",
"start",
"end",
")",
"inclusive",
"."
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/intersecter.py#L147-L161 | [
"def",
"find",
"(",
"self",
",",
"start",
",",
"end",
",",
"chrom",
"=",
"None",
")",
":",
"intervals",
"=",
"self",
".",
"intervals",
"[",
"chrom",
"]",
"ilen",
"=",
"len",
"(",
"intervals",
")",
"# NOTE: we only search for starts, since any feature that star... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | Intersecter.left | return the nearest n features strictly to the left of a Feature f.
Overlapping features are not considered as to the left.
f: a Feature object
n: the number of features to return | cruzdb/intersecter.py | def left(self, f, n=1):
"""return the nearest n features strictly to the left of a Feature f.
Overlapping features are not considered as to the left.
f: a Feature object
n: the number of features to return
"""
intervals = self.intervals[f.chrom]
if intervals == [... | def left(self, f, n=1):
"""return the nearest n features strictly to the left of a Feature f.
Overlapping features are not considered as to the left.
f: a Feature object
n: the number of features to return
"""
intervals = self.intervals[f.chrom]
if intervals == [... | [
"return",
"the",
"nearest",
"n",
"features",
"strictly",
"to",
"the",
"left",
"of",
"a",
"Feature",
"f",
".",
"Overlapping",
"features",
"are",
"not",
"considered",
"as",
"to",
"the",
"left",
"."
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/intersecter.py#L163-L192 | [
"def",
"left",
"(",
"self",
",",
"f",
",",
"n",
"=",
"1",
")",
":",
"intervals",
"=",
"self",
".",
"intervals",
"[",
"f",
".",
"chrom",
"]",
"if",
"intervals",
"==",
"[",
"]",
":",
"return",
"[",
"]",
"iright",
"=",
"binsearch_left_start",
"(",
"... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | Intersecter.right | return the nearest n features strictly to the right of a Feature f.
Overlapping features are not considered as to the right.
f: a Feature object
n: the number of features to return | cruzdb/intersecter.py | def right(self, f, n=1):
"""return the nearest n features strictly to the right of a Feature f.
Overlapping features are not considered as to the right.
f: a Feature object
n: the number of features to return
"""
intervals = self.intervals[f.chrom]
ilen = len(int... | def right(self, f, n=1):
"""return the nearest n features strictly to the right of a Feature f.
Overlapping features are not considered as to the right.
f: a Feature object
n: the number of features to return
"""
intervals = self.intervals[f.chrom]
ilen = len(int... | [
"return",
"the",
"nearest",
"n",
"features",
"strictly",
"to",
"the",
"right",
"of",
"a",
"Feature",
"f",
".",
"Overlapping",
"features",
"are",
"not",
"considered",
"as",
"to",
"the",
"right",
"."
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/intersecter.py#L194-L215 | [
"def",
"right",
"(",
"self",
",",
"f",
",",
"n",
"=",
"1",
")",
":",
"intervals",
"=",
"self",
".",
"intervals",
"[",
"f",
".",
"chrom",
"]",
"ilen",
"=",
"len",
"(",
"intervals",
")",
"iright",
"=",
"binsearch_right_end",
"(",
"intervals",
",",
"f... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | Intersecter.upstream | find n upstream features where upstream is determined by
the strand of the query Feature f
Overlapping features are not considered.
f: a Feature object
n: the number of features to return | cruzdb/intersecter.py | def upstream(self, f, n=1):
"""find n upstream features where upstream is determined by
the strand of the query Feature f
Overlapping features are not considered.
f: a Feature object
n: the number of features to return
"""
if f.strand == -1:
return se... | def upstream(self, f, n=1):
"""find n upstream features where upstream is determined by
the strand of the query Feature f
Overlapping features are not considered.
f: a Feature object
n: the number of features to return
"""
if f.strand == -1:
return se... | [
"find",
"n",
"upstream",
"features",
"where",
"upstream",
"is",
"determined",
"by",
"the",
"strand",
"of",
"the",
"query",
"Feature",
"f",
"Overlapping",
"features",
"are",
"not",
"considered",
"."
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/intersecter.py#L218-L228 | [
"def",
"upstream",
"(",
"self",
",",
"f",
",",
"n",
"=",
"1",
")",
":",
"if",
"f",
".",
"strand",
"==",
"-",
"1",
":",
"return",
"self",
".",
"right",
"(",
"f",
",",
"n",
")",
"return",
"self",
".",
"left",
"(",
"f",
",",
"n",
")"
] | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | Intersecter.downstream | find n downstream features where downstream is determined by
the strand of the query Feature f
Overlapping features are not considered.
f: a Feature object
n: the number of features to return | cruzdb/intersecter.py | def downstream(self, f, n=1):
"""find n downstream features where downstream is determined by
the strand of the query Feature f
Overlapping features are not considered.
f: a Feature object
n: the number of features to return
"""
if f.strand == -1:
ret... | def downstream(self, f, n=1):
"""find n downstream features where downstream is determined by
the strand of the query Feature f
Overlapping features are not considered.
f: a Feature object
n: the number of features to return
"""
if f.strand == -1:
ret... | [
"find",
"n",
"downstream",
"features",
"where",
"downstream",
"is",
"determined",
"by",
"the",
"strand",
"of",
"the",
"query",
"Feature",
"f",
"Overlapping",
"features",
"are",
"not",
"considered",
"."
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/intersecter.py#L231-L241 | [
"def",
"downstream",
"(",
"self",
",",
"f",
",",
"n",
"=",
"1",
")",
":",
"if",
"f",
".",
"strand",
"==",
"-",
"1",
":",
"return",
"self",
".",
"left",
"(",
"f",
",",
"n",
")",
"return",
"self",
".",
"right",
"(",
"f",
",",
"n",
")"
] | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | Intersecter.knearest | return the n nearest neighbors to the given feature
f: a Feature object
k: the number of features to return | cruzdb/intersecter.py | def knearest(self, f_or_start, end=None, chrom=None, k=1):
"""return the n nearest neighbors to the given feature
f: a Feature object
k: the number of features to return
"""
if end is not None:
f = Feature(f_or_start, end, chrom=chrom)
else:
f = ... | def knearest(self, f_or_start, end=None, chrom=None, k=1):
"""return the n nearest neighbors to the given feature
f: a Feature object
k: the number of features to return
"""
if end is not None:
f = Feature(f_or_start, end, chrom=chrom)
else:
f = ... | [
"return",
"the",
"n",
"nearest",
"neighbors",
"to",
"the",
"given",
"feature",
"f",
":",
"a",
"Feature",
"object",
"k",
":",
"the",
"number",
"of",
"features",
"to",
"return"
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/intersecter.py#L243-L266 | [
"def",
"knearest",
"(",
"self",
",",
"f_or_start",
",",
"end",
"=",
"None",
",",
"chrom",
"=",
"None",
",",
"k",
"=",
"1",
")",
":",
"if",
"end",
"is",
"not",
"None",
":",
"f",
"=",
"Feature",
"(",
"f_or_start",
",",
"end",
",",
"chrom",
"=",
"... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | IntervalTree.find | find all elements between (or overlapping) start and end | scripts/interval_tree.py | def find(self, start, end):
"""find all elements between (or overlapping) start and end"""
if self.intervals and not end < self.intervals[0].start:
overlapping = [i for i in self.intervals if i.end >= start
and i.start <= end]
else:... | def find(self, start, end):
"""find all elements between (or overlapping) start and end"""
if self.intervals and not end < self.intervals[0].start:
overlapping = [i for i in self.intervals if i.end >= start
and i.start <= end]
else:... | [
"find",
"all",
"elements",
"between",
"(",
"or",
"overlapping",
")",
"start",
"and",
"end"
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/scripts/interval_tree.py#L77-L91 | [
"def",
"find",
"(",
"self",
",",
"start",
",",
"end",
")",
":",
"if",
"self",
".",
"intervals",
"and",
"not",
"end",
"<",
"self",
".",
"intervals",
"[",
"0",
"]",
".",
"start",
":",
"overlapping",
"=",
"[",
"i",
"for",
"i",
"in",
"self",
".",
"... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | sequence | return the sequence for a region using the UCSC DAS
server. note the start is 1-based
each feature will have it's own .sequence method which sends
the correct start and end to this function.
>>> sequence('hg18', 'chr2', 2223, 2230)
'caacttag' | cruzdb/sequence.py | def sequence(db, chrom, start, end):
"""
return the sequence for a region using the UCSC DAS
server. note the start is 1-based
each feature will have it's own .sequence method which sends
the correct start and end to this function.
>>> sequence('hg18', 'chr2', 2223, 2230)
'caacttag'
"""... | def sequence(db, chrom, start, end):
"""
return the sequence for a region using the UCSC DAS
server. note the start is 1-based
each feature will have it's own .sequence method which sends
the correct start and end to this function.
>>> sequence('hg18', 'chr2', 2223, 2230)
'caacttag'
"""... | [
"return",
"the",
"sequence",
"for",
"a",
"region",
"using",
"the",
"UCSC",
"DAS",
"server",
".",
"note",
"the",
"start",
"is",
"1",
"-",
"based",
"each",
"feature",
"will",
"have",
"it",
"s",
"own",
".",
"sequence",
"method",
"which",
"sends",
"the",
"... | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/sequence.py#L10-L23 | [
"def",
"sequence",
"(",
"db",
",",
"chrom",
",",
"start",
",",
"end",
")",
":",
"url",
"=",
"\"http://genome.ucsc.edu/cgi-bin/das/%s\"",
"%",
"db",
"url",
"+=",
"\"/dna?segment=%s:%i,%i\"",
"xml",
"=",
"U",
".",
"urlopen",
"(",
"url",
"%",
"(",
"chrom",
",... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | set_table | alter the table to work between different
dialects | cruzdb/mirror.py | def set_table(genome, table, table_name, connection_string, metadata):
"""
alter the table to work between different
dialects
"""
table = Table(table_name, genome._metadata, autoload=True,
autoload_with=genome.bind, extend_existing=True)
#print "\t".join([c.name for c in tab... | def set_table(genome, table, table_name, connection_string, metadata):
"""
alter the table to work between different
dialects
"""
table = Table(table_name, genome._metadata, autoload=True,
autoload_with=genome.bind, extend_existing=True)
#print "\t".join([c.name for c in tab... | [
"alter",
"the",
"table",
"to",
"work",
"between",
"different",
"dialects"
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/mirror.py#L39-L80 | [
"def",
"set_table",
"(",
"genome",
",",
"table",
",",
"table_name",
",",
"connection_string",
",",
"metadata",
")",
":",
"table",
"=",
"Table",
"(",
"table_name",
",",
"genome",
".",
"_metadata",
",",
"autoload",
"=",
"True",
",",
"autoload_with",
"=",
"ge... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | Genome.create_url | internal: create a dburl from a set of parameters or the defaults on
this object | cruzdb/__init__.py | def create_url(self, db="", user="genome", host="genome-mysql.cse.ucsc.edu",
password="", dialect="mysqldb"):
"""
internal: create a dburl from a set of parameters or the defaults on
this object
"""
if os.path.exists(db):
db = "sqlite:///" + db
# Is t... | def create_url(self, db="", user="genome", host="genome-mysql.cse.ucsc.edu",
password="", dialect="mysqldb"):
"""
internal: create a dburl from a set of parameters or the defaults on
this object
"""
if os.path.exists(db):
db = "sqlite:///" + db
# Is t... | [
"internal",
":",
"create",
"a",
"dburl",
"from",
"a",
"set",
"of",
"parameters",
"or",
"the",
"defaults",
"on",
"this",
"object"
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/__init__.py#L69-L92 | [
"def",
"create_url",
"(",
"self",
",",
"db",
"=",
"\"\"",
",",
"user",
"=",
"\"genome\"",
",",
"host",
"=",
"\"genome-mysql.cse.ucsc.edu\"",
",",
"password",
"=",
"\"\"",
",",
"dialect",
"=",
"\"mysqldb\"",
")",
":",
"if",
"os",
".",
"path",
".",
"exists... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | Genome.mirror | miror a set of `tables` from `dest_url`
Returns a new Genome object
Parameters
----------
tables : list
an iterable of tables
dest_url: str
a dburl string, e.g. 'sqlite:///local.db' | cruzdb/__init__.py | def mirror(self, tables, dest_url):
"""
miror a set of `tables` from `dest_url`
Returns a new Genome object
Parameters
----------
tables : list
an iterable of tables
dest_url: str
a dburl string, e.g. 'sqlite:///local.db'
"""
... | def mirror(self, tables, dest_url):
"""
miror a set of `tables` from `dest_url`
Returns a new Genome object
Parameters
----------
tables : list
an iterable of tables
dest_url: str
a dburl string, e.g. 'sqlite:///local.db'
"""
... | [
"miror",
"a",
"set",
"of",
"tables",
"from",
"dest_url"
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/__init__.py#L94-L110 | [
"def",
"mirror",
"(",
"self",
",",
"tables",
",",
"dest_url",
")",
":",
"from",
"mirror",
"import",
"mirror",
"return",
"mirror",
"(",
"self",
",",
"tables",
",",
"dest_url",
")"
] | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | Genome.dataframe | create a pandas dataframe from a table or query
Parameters
----------
table : table
a table in this database or a query
limit: integer
an integer limit on the query
offset: integer
an offset for the query | cruzdb/__init__.py | def dataframe(self, table):
"""
create a pandas dataframe from a table or query
Parameters
----------
table : table
a table in this database or a query
limit: integer
an integer limit on the query
offset: integer
an offset f... | def dataframe(self, table):
"""
create a pandas dataframe from a table or query
Parameters
----------
table : table
a table in this database or a query
limit: integer
an integer limit on the query
offset: integer
an offset f... | [
"create",
"a",
"pandas",
"dataframe",
"from",
"a",
"table",
"or",
"query"
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/__init__.py#L112-L140 | [
"def",
"dataframe",
"(",
"self",
",",
"table",
")",
":",
"from",
"pandas",
"import",
"DataFrame",
"if",
"isinstance",
"(",
"table",
",",
"six",
".",
"string_types",
")",
":",
"table",
"=",
"getattr",
"(",
"self",
",",
"table",
")",
"try",
":",
"rec",
... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | Genome.load_file | use some of the machinery in pandas to load a file into a table
Parameters
----------
fname : str
filename or filehandle to load
table : str
table to load the file to
sep : str
CSV separator
bins : bool
add a "bin" colu... | cruzdb/__init__.py | def load_file(self, fname, table=None, sep="\t", bins=False, indexes=None):
"""
use some of the machinery in pandas to load a file into a table
Parameters
----------
fname : str
filename or filehandle to load
table : str
table to load the file t... | def load_file(self, fname, table=None, sep="\t", bins=False, indexes=None):
"""
use some of the machinery in pandas to load a file into a table
Parameters
----------
fname : str
filename or filehandle to load
table : str
table to load the file t... | [
"use",
"some",
"of",
"the",
"machinery",
"in",
"pandas",
"to",
"load",
"a",
"file",
"into",
"a",
"table"
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/__init__.py#L146-L228 | [
"def",
"load_file",
"(",
"self",
",",
"fname",
",",
"table",
"=",
"None",
",",
"sep",
"=",
"\"\\t\"",
",",
"bins",
"=",
"False",
",",
"indexes",
"=",
"None",
")",
":",
"convs",
"=",
"{",
"\"#chr\"",
":",
"\"chrom\"",
",",
"\"start\"",
":",
"\"txStart... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | Genome.david_go | open a web-browser to the DAVID online enrichment tool
Parameters
----------
refseq_list : list
list of refseq names to check for enrichment
annot : list
iterable of DAVID annotations to check for enrichment | cruzdb/__init__.py | def david_go(refseq_list, annot=('SP_PIR_KEYWORDS', 'GOTERM_BP_FAT',
'GOTERM_CC_FAT', 'GOTERM_MF_FAT')):
"""
open a web-browser to the DAVID online enrichment tool
Parameters
----------
refseq_list : list
list of refseq names ... | def david_go(refseq_list, annot=('SP_PIR_KEYWORDS', 'GOTERM_BP_FAT',
'GOTERM_CC_FAT', 'GOTERM_MF_FAT')):
"""
open a web-browser to the DAVID online enrichment tool
Parameters
----------
refseq_list : list
list of refseq names ... | [
"open",
"a",
"web",
"-",
"browser",
"to",
"the",
"DAVID",
"online",
"enrichment",
"tool"
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/__init__.py#L231-L248 | [
"def",
"david_go",
"(",
"refseq_list",
",",
"annot",
"=",
"(",
"'SP_PIR_KEYWORDS'",
",",
"'GOTERM_BP_FAT'",
",",
"'GOTERM_CC_FAT'",
",",
"'GOTERM_MF_FAT'",
")",
")",
":",
"URL",
"=",
"\"http://david.abcc.ncifcrf.gov/api.jsp?type=REFSEQ_MRNA&ids=%s&tool=term2term&annot=\"",
... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | Genome.bin_query | perform an efficient spatial query using the bin column if available.
The possible bins are calculated from the `start` and `end` sent to
this function.
Parameters
----------
table : str or table
table to query
chrom : str
chromosome for the query... | cruzdb/__init__.py | def bin_query(self, table, chrom, start, end):
"""
perform an efficient spatial query using the bin column if available.
The possible bins are calculated from the `start` and `end` sent to
this function.
Parameters
----------
table : str or table
tabl... | def bin_query(self, table, chrom, start, end):
"""
perform an efficient spatial query using the bin column if available.
The possible bins are calculated from the `start` and `end` sent to
this function.
Parameters
----------
table : str or table
tabl... | [
"perform",
"an",
"efficient",
"spatial",
"query",
"using",
"the",
"bin",
"column",
"if",
"available",
".",
"The",
"possible",
"bins",
"are",
"calculated",
"from",
"the",
"start",
"and",
"end",
"sent",
"to",
"this",
"function",
"."
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/__init__.py#L250-L289 | [
"def",
"bin_query",
"(",
"self",
",",
"table",
",",
"chrom",
",",
"start",
",",
"end",
")",
":",
"if",
"isinstance",
"(",
"table",
",",
"six",
".",
"string_types",
")",
":",
"table",
"=",
"getattr",
"(",
"self",
",",
"table",
")",
"try",
":",
"tbl"... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | Genome.upstream | Return k-nearest upstream features
Parameters
----------
table : str or table
table against which to query
chrom_or_feat : str or feat
either a chromosome, e.g. 'chr3' or a feature with .chrom, .start,
.end attributes
start : int
... | cruzdb/__init__.py | def upstream(self, table, chrom_or_feat, start=None, end=None, k=1):
"""
Return k-nearest upstream features
Parameters
----------
table : str or table
table against which to query
chrom_or_feat : str or feat
either a chromosome, e.g. 'chr3' or a... | def upstream(self, table, chrom_or_feat, start=None, end=None, k=1):
"""
Return k-nearest upstream features
Parameters
----------
table : str or table
table against which to query
chrom_or_feat : str or feat
either a chromosome, e.g. 'chr3' or a... | [
"Return",
"k",
"-",
"nearest",
"upstream",
"features"
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/__init__.py#L291-L321 | [
"def",
"upstream",
"(",
"self",
",",
"table",
",",
"chrom_or_feat",
",",
"start",
"=",
"None",
",",
"end",
"=",
"None",
",",
"k",
"=",
"1",
")",
":",
"res",
"=",
"self",
".",
"knearest",
"(",
"table",
",",
"chrom_or_feat",
",",
"start",
",",
"end",... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | Genome.knearest | Return k-nearest features
Parameters
----------
table : str or table
table against which to query
chrom_or_feat : str or feat
either a chromosome, e.g. 'chr3' or a feature with .chrom, .start,
.end attributes
start : int
if `chr... | cruzdb/__init__.py | def knearest(self, table, chrom_or_feat, start=None, end=None, k=1,
_direction=None):
"""
Return k-nearest features
Parameters
----------
table : str or table
table against which to query
chrom_or_feat : str or feat
either a chromoso... | def knearest(self, table, chrom_or_feat, start=None, end=None, k=1,
_direction=None):
"""
Return k-nearest features
Parameters
----------
table : str or table
table against which to query
chrom_or_feat : str or feat
either a chromoso... | [
"Return",
"k",
"-",
"nearest",
"features"
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/__init__.py#L355-L441 | [
"def",
"knearest",
"(",
"self",
",",
"table",
",",
"chrom_or_feat",
",",
"start",
"=",
"None",
",",
"end",
"=",
"None",
",",
"k",
"=",
"1",
",",
"_direction",
"=",
"None",
")",
":",
"assert",
"_direction",
"in",
"(",
"None",
",",
"\"up\"",
",",
"\"... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | Genome.annotate | annotate a file with a number of tables
Parameters
----------
fname : str or file
file name or file-handle
tables : list
list of tables with which to annotate `fname`
feature_strand : bool
if this is True, then the up/downstream designations... | cruzdb/__init__.py | def annotate(self, fname, tables, feature_strand=False, in_memory=False,
header=None, out=sys.stdout, parallel=False):
"""
annotate a file with a number of tables
Parameters
----------
fname : str or file
file name or file-handle
tables : list
... | def annotate(self, fname, tables, feature_strand=False, in_memory=False,
header=None, out=sys.stdout, parallel=False):
"""
annotate a file with a number of tables
Parameters
----------
fname : str or file
file name or file-handle
tables : list
... | [
"annotate",
"a",
"file",
"with",
"a",
"number",
"of",
"tables"
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/__init__.py#L449-L484 | [
"def",
"annotate",
"(",
"self",
",",
"fname",
",",
"tables",
",",
"feature_strand",
"=",
"False",
",",
"in_memory",
"=",
"False",
",",
"header",
"=",
"None",
",",
"out",
"=",
"sys",
".",
"stdout",
",",
"parallel",
"=",
"False",
")",
":",
"from",
".",... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | Genome.bins | Get all the bin numbers for a particular interval defined by
(start, end] | cruzdb/__init__.py | def bins(start, end):
"""
Get all the bin numbers for a particular interval defined by
(start, end]
"""
if end - start < 536870912:
offsets = [585, 73, 9, 1]
else:
raise BigException
offsets = [4681, 585, 73, 9, 1]
binFirstShift... | def bins(start, end):
"""
Get all the bin numbers for a particular interval defined by
(start, end]
"""
if end - start < 536870912:
offsets = [585, 73, 9, 1]
else:
raise BigException
offsets = [4681, 585, 73, 9, 1]
binFirstShift... | [
"Get",
"all",
"the",
"bin",
"numbers",
"for",
"a",
"particular",
"interval",
"defined",
"by",
"(",
"start",
"end",
"]"
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/__init__.py#L487-L508 | [
"def",
"bins",
"(",
"start",
",",
"end",
")",
":",
"if",
"end",
"-",
"start",
"<",
"536870912",
":",
"offsets",
"=",
"[",
"585",
",",
"73",
",",
"9",
",",
"1",
"]",
"else",
":",
"raise",
"BigException",
"offsets",
"=",
"[",
"4681",
",",
"585",
... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | Genome.save_bed | write a bed12 file of the query.
Parameters
----------
query : query
a table or query to save to file
filename : file
string or filehandle to write output | cruzdb/__init__.py | def save_bed(cls, query, filename=sys.stdout):
"""
write a bed12 file of the query.
Parameters
----------
query : query
a table or query to save to file
filename : file
string or filehandle to write output
"""
out = _open(filename... | def save_bed(cls, query, filename=sys.stdout):
"""
write a bed12 file of the query.
Parameters
----------
query : query
a table or query to save to file
filename : file
string or filehandle to write output
"""
out = _open(filename... | [
"write",
"a",
"bed12",
"file",
"of",
"the",
"query",
".",
"Parameters",
"----------"
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/__init__.py#L514-L528 | [
"def",
"save_bed",
"(",
"cls",
",",
"query",
",",
"filename",
"=",
"sys",
".",
"stdout",
")",
":",
"out",
"=",
"_open",
"(",
"filename",
",",
"'w'",
")",
"for",
"o",
"in",
"query",
":",
"out",
".",
"write",
"(",
"o",
".",
"bed",
"(",
")",
"+",
... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | staticfile_node | For example:
{% staticfile "/js/foo.js" %}
or
{% staticfile "/js/foo.js" as variable_name %}
Or for multiples:
{% staticfile "/foo.js; /bar.js" %}
or
{% staticfile "/foo.js; /bar.js" as variable_name %} | django_static/templatetags/django_static.py | def staticfile_node(parser, token, optimize_if_possible=False):
"""For example:
{% staticfile "/js/foo.js" %}
or
{% staticfile "/js/foo.js" as variable_name %}
Or for multiples:
{% staticfile "/foo.js; /bar.js" %}
or
{% staticfile "/foo.js; /bar.js" as varia... | def staticfile_node(parser, token, optimize_if_possible=False):
"""For example:
{% staticfile "/js/foo.js" %}
or
{% staticfile "/js/foo.js" as variable_name %}
Or for multiples:
{% staticfile "/foo.js; /bar.js" %}
or
{% staticfile "/foo.js; /bar.js" as varia... | [
"For",
"example",
":",
"{",
"%",
"staticfile",
"/",
"js",
"/",
"foo",
".",
"js",
"%",
"}",
"or",
"{",
"%",
"staticfile",
"/",
"js",
"/",
"foo",
".",
"js",
"as",
"variable_name",
"%",
"}",
"Or",
"for",
"multiples",
":",
"{",
"%",
"staticfile",
"/"... | peterbe/django-static | python | https://github.com/peterbe/django-static/blob/05c0d2f302274b9d3f7df6ad92bd861889316ebd/django_static/templatetags/django_static.py#L185-L209 | [
"def",
"staticfile_node",
"(",
"parser",
",",
"token",
",",
"optimize_if_possible",
"=",
"False",
")",
":",
"args",
"=",
"token",
".",
"split_contents",
"(",
")",
"tag",
"=",
"args",
"[",
"0",
"]",
"if",
"len",
"(",
"args",
")",
"==",
"4",
"and",
"ar... | 05c0d2f302274b9d3f7df6ad92bd861889316ebd |
train | _mkdir | works the way a good mkdir should :)
- already exists, silently complete
- regular file in the way, raise an exception
- parent directory(ies) does not exist, make them as well | django_static/templatetags/django_static.py | def _mkdir(newdir):
"""works the way a good mkdir should :)
- already exists, silently complete
- regular file in the way, raise an exception
- parent directory(ies) does not exist, make them as well
"""
if os.path.isdir(newdir):
pass
elif os.path.isfile(newdir):
... | def _mkdir(newdir):
"""works the way a good mkdir should :)
- already exists, silently complete
- regular file in the way, raise an exception
- parent directory(ies) does not exist, make them as well
"""
if os.path.isdir(newdir):
pass
elif os.path.isfile(newdir):
... | [
"works",
"the",
"way",
"a",
"good",
"mkdir",
"should",
":",
")",
"-",
"already",
"exists",
"silently",
"complete",
"-",
"regular",
"file",
"in",
"the",
"way",
"raise",
"an",
"exception",
"-",
"parent",
"directory",
"(",
"ies",
")",
"does",
"not",
"exist"... | peterbe/django-static | python | https://github.com/peterbe/django-static/blob/05c0d2f302274b9d3f7df6ad92bd861889316ebd/django_static/templatetags/django_static.py#L641-L657 | [
"def",
"_mkdir",
"(",
"newdir",
")",
":",
"if",
"os",
".",
"path",
".",
"isdir",
"(",
"newdir",
")",
":",
"pass",
"elif",
"os",
".",
"path",
".",
"isfile",
"(",
"newdir",
")",
":",
"raise",
"OSError",
"(",
"\"a file with the same name as the desired \"",
... | 05c0d2f302274b9d3f7df6ad92bd861889316ebd |
train | _find_filepath_in_roots | Look for filename in all MEDIA_ROOTS, and return the first one found. | django_static/templatetags/django_static.py | def _find_filepath_in_roots(filename):
"""Look for filename in all MEDIA_ROOTS, and return the first one found."""
for root in settings.DJANGO_STATIC_MEDIA_ROOTS:
filepath = _filename2filepath(filename, root)
if os.path.isfile(filepath):
return filepath, root
# havent found it in... | def _find_filepath_in_roots(filename):
"""Look for filename in all MEDIA_ROOTS, and return the first one found."""
for root in settings.DJANGO_STATIC_MEDIA_ROOTS:
filepath = _filename2filepath(filename, root)
if os.path.isfile(filepath):
return filepath, root
# havent found it in... | [
"Look",
"for",
"filename",
"in",
"all",
"MEDIA_ROOTS",
"and",
"return",
"the",
"first",
"one",
"found",
"."
] | peterbe/django-static | python | https://github.com/peterbe/django-static/blob/05c0d2f302274b9d3f7df6ad92bd861889316ebd/django_static/templatetags/django_static.py#L660-L677 | [
"def",
"_find_filepath_in_roots",
"(",
"filename",
")",
":",
"for",
"root",
"in",
"settings",
".",
"DJANGO_STATIC_MEDIA_ROOTS",
":",
"filepath",
"=",
"_filename2filepath",
"(",
"filename",
",",
"root",
")",
"if",
"os",
".",
"path",
".",
"isfile",
"(",
"filepat... | 05c0d2f302274b9d3f7df6ad92bd861889316ebd |
train | default_combine_filenames_generator | Return a new filename to use as the combined file name for a
bunch of files.
A precondition is that they all have the same file extension
Given that the list of files can have different paths, we aim to use the
most common path.
Example:
/somewhere/else/foo.js
/somewhere/bar.js
/... | django_static/templatetags/django_static.py | def default_combine_filenames_generator(filenames, max_length=40):
"""Return a new filename to use as the combined file name for a
bunch of files.
A precondition is that they all have the same file extension
Given that the list of files can have different paths, we aim to use the
most common path.
... | def default_combine_filenames_generator(filenames, max_length=40):
"""Return a new filename to use as the combined file name for a
bunch of files.
A precondition is that they all have the same file extension
Given that the list of files can have different paths, we aim to use the
most common path.
... | [
"Return",
"a",
"new",
"filename",
"to",
"use",
"as",
"the",
"combined",
"file",
"name",
"for",
"a",
"bunch",
"of",
"files",
".",
"A",
"precondition",
"is",
"that",
"they",
"all",
"have",
"the",
"same",
"file",
"extension"
] | peterbe/django-static | python | https://github.com/peterbe/django-static/blob/05c0d2f302274b9d3f7df6ad92bd861889316ebd/django_static/templatetags/django_static.py#L695-L745 | [
"def",
"default_combine_filenames_generator",
"(",
"filenames",
",",
"max_length",
"=",
"40",
")",
":",
"path",
"=",
"None",
"names",
"=",
"[",
"]",
"extension",
"=",
"None",
"timestamps",
"=",
"[",
"]",
"for",
"filename",
"in",
"filenames",
":",
"name",
"... | 05c0d2f302274b9d3f7df6ad92bd861889316ebd |
train | StaticFilesNode.render | inspect the code and look for files that can be turned into combos.
Basically, the developer could type this:
{% slimall %}
<link href="/one.css"/>
<link href="/two.css"/>
{% endslimall %}
And it should be reconsidered like this:
<link href="{% slimfile "/on... | django_static/templatetags/django_static.py | def render(self, context):
"""inspect the code and look for files that can be turned into combos.
Basically, the developer could type this:
{% slimall %}
<link href="/one.css"/>
<link href="/two.css"/>
{% endslimall %}
And it should be reconsidered like this:
... | def render(self, context):
"""inspect the code and look for files that can be turned into combos.
Basically, the developer could type this:
{% slimall %}
<link href="/one.css"/>
<link href="/two.css"/>
{% endslimall %}
And it should be reconsidered like this:
... | [
"inspect",
"the",
"code",
"and",
"look",
"for",
"files",
"that",
"can",
"be",
"turned",
"into",
"combos",
".",
"Basically",
"the",
"developer",
"could",
"type",
"this",
":",
"{",
"%",
"slimall",
"%",
"}",
"<link",
"href",
"=",
"/",
"one",
".",
"css",
... | peterbe/django-static | python | https://github.com/peterbe/django-static/blob/05c0d2f302274b9d3f7df6ad92bd861889316ebd/django_static/templatetags/django_static.py#L276-L385 | [
"def",
"render",
"(",
"self",
",",
"context",
")",
":",
"code",
"=",
"self",
".",
"nodelist",
".",
"render",
"(",
"context",
")",
"if",
"not",
"settings",
".",
"DJANGO_STATIC",
":",
"# Append MEDIA_URL if set",
"# quick and dirty",
"if",
"settings",
".",
"DJ... | 05c0d2f302274b9d3f7df6ad92bd861889316ebd |
train | Interval.overlaps | check for overlap with the other interval | cruzdb/models.py | def overlaps(self, other):
"""
check for overlap with the other interval
"""
if self.chrom != other.chrom: return False
if self.start >= other.end: return False
if other.start >= self.end: return False
return True | def overlaps(self, other):
"""
check for overlap with the other interval
"""
if self.chrom != other.chrom: return False
if self.start >= other.end: return False
if other.start >= self.end: return False
return True | [
"check",
"for",
"overlap",
"with",
"the",
"other",
"interval"
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/models.py#L81-L88 | [
"def",
"overlaps",
"(",
"self",
",",
"other",
")",
":",
"if",
"self",
".",
"chrom",
"!=",
"other",
".",
"chrom",
":",
"return",
"False",
"if",
"self",
".",
"start",
">=",
"other",
".",
"end",
":",
"return",
"False",
"if",
"other",
".",
"start",
">=... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | Interval.is_upstream_of | check if this is upstream of the `other` interval taking the strand of
the other interval into account | cruzdb/models.py | def is_upstream_of(self, other):
"""
check if this is upstream of the `other` interval taking the strand of
the other interval into account
"""
if self.chrom != other.chrom: return None
if getattr(other, "strand", None) == "+":
return self.end <= other.start
... | def is_upstream_of(self, other):
"""
check if this is upstream of the `other` interval taking the strand of
the other interval into account
"""
if self.chrom != other.chrom: return None
if getattr(other, "strand", None) == "+":
return self.end <= other.start
... | [
"check",
"if",
"this",
"is",
"upstream",
"of",
"the",
"other",
"interval",
"taking",
"the",
"strand",
"of",
"the",
"other",
"interval",
"into",
"account"
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/models.py#L90-L99 | [
"def",
"is_upstream_of",
"(",
"self",
",",
"other",
")",
":",
"if",
"self",
".",
"chrom",
"!=",
"other",
".",
"chrom",
":",
"return",
"None",
"if",
"getattr",
"(",
"other",
",",
"\"strand\"",
",",
"None",
")",
"==",
"\"+\"",
":",
"return",
"self",
".... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | Interval.distance | check the distance between this an another interval
Parameters
----------
other_or_start : Interval or int
either an integer or an Interval with a start attribute indicating
the start of the interval
end : int
if `other_or_start` is an integer, this ... | cruzdb/models.py | def distance(self, other_or_start=None, end=None, features=False):
"""
check the distance between this an another interval
Parameters
----------
other_or_start : Interval or int
either an integer or an Interval with a start attribute indicating
the start ... | def distance(self, other_or_start=None, end=None, features=False):
"""
check the distance between this an another interval
Parameters
----------
other_or_start : Interval or int
either an integer or an Interval with a start attribute indicating
the start ... | [
"check",
"the",
"distance",
"between",
"this",
"an",
"another",
"interval",
"Parameters",
"----------"
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/models.py#L101-L128 | [
"def",
"distance",
"(",
"self",
",",
"other_or_start",
"=",
"None",
",",
"end",
"=",
"None",
",",
"features",
"=",
"False",
")",
":",
"if",
"end",
"is",
"None",
":",
"assert",
"other_or_start",
".",
"chrom",
"==",
"self",
".",
"chrom",
"other_start",
"... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | ABase.exons | return a list of exons [(start, stop)] for this object if appropriate | cruzdb/models.py | def exons(self):
"""
return a list of exons [(start, stop)] for this object if appropriate
"""
# drop the trailing comma
if not self.is_gene_pred: return []
if hasattr(self, "exonStarts"):
try:
starts = (long(s) for s in self.exonStarts[:-1].sp... | def exons(self):
"""
return a list of exons [(start, stop)] for this object if appropriate
"""
# drop the trailing comma
if not self.is_gene_pred: return []
if hasattr(self, "exonStarts"):
try:
starts = (long(s) for s in self.exonStarts[:-1].sp... | [
"return",
"a",
"list",
"of",
"exons",
"[",
"(",
"start",
"stop",
")",
"]",
"for",
"this",
"object",
"if",
"appropriate"
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/models.py#L160-L180 | [
"def",
"exons",
"(",
"self",
")",
":",
"# drop the trailing comma",
"if",
"not",
"self",
".",
"is_gene_pred",
":",
"return",
"[",
"]",
"if",
"hasattr",
"(",
"self",
",",
"\"exonStarts\"",
")",
":",
"try",
":",
"starts",
"=",
"(",
"long",
"(",
"s",
")",... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | ABase.gene_features | return a list of features for the gene features of this object.
This would include exons, introns, utrs, etc. | cruzdb/models.py | def gene_features(self):
"""
return a list of features for the gene features of this object.
This would include exons, introns, utrs, etc.
"""
nm, strand = self.gene_name, self.strand
feats = [(self.chrom, self.start, self.end, nm, strand, 'gene')]
for feat in ('i... | def gene_features(self):
"""
return a list of features for the gene features of this object.
This would include exons, introns, utrs, etc.
"""
nm, strand = self.gene_name, self.strand
feats = [(self.chrom, self.start, self.end, nm, strand, 'gene')]
for feat in ('i... | [
"return",
"a",
"list",
"of",
"features",
"for",
"the",
"gene",
"features",
"of",
"this",
"object",
".",
"This",
"would",
"include",
"exons",
"introns",
"utrs",
"etc",
"."
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/models.py#L183-L203 | [
"def",
"gene_features",
"(",
"self",
")",
":",
"nm",
",",
"strand",
"=",
"self",
".",
"gene_name",
",",
"self",
".",
"strand",
"feats",
"=",
"[",
"(",
"self",
".",
"chrom",
",",
"self",
".",
"start",
",",
"self",
".",
"end",
",",
"nm",
",",
"stra... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | ABase.tss | Return a start, end tuple of positions around the transcription-start
site
Parameters
----------
up : int
if greature than 0, the strand is used to add this many upstream
bases in the appropriate direction
down : int
if greature than 0, the str... | cruzdb/models.py | def tss(self, up=0, down=0):
"""
Return a start, end tuple of positions around the transcription-start
site
Parameters
----------
up : int
if greature than 0, the strand is used to add this many upstream
bases in the appropriate direction
... | def tss(self, up=0, down=0):
"""
Return a start, end tuple of positions around the transcription-start
site
Parameters
----------
up : int
if greature than 0, the strand is used to add this many upstream
bases in the appropriate direction
... | [
"Return",
"a",
"start",
"end",
"tuple",
"of",
"positions",
"around",
"the",
"transcription",
"-",
"start",
"site"
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/models.py#L205-L231 | [
"def",
"tss",
"(",
"self",
",",
"up",
"=",
"0",
",",
"down",
"=",
"0",
")",
":",
"if",
"not",
"self",
".",
"is_gene_pred",
":",
"return",
"None",
"tss",
"=",
"self",
".",
"txEnd",
"if",
"self",
".",
"strand",
"==",
"'-'",
"else",
"self",
".",
"... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | ABase.promoter | Return a start, end tuple of positions for the promoter region of this
gene
Parameters
----------
up : int
this distance upstream that is considered the promoter
down : int
the strand is used to add this many downstream bases into the gene. | cruzdb/models.py | def promoter(self, up=2000, down=0):
"""
Return a start, end tuple of positions for the promoter region of this
gene
Parameters
----------
up : int
this distance upstream that is considered the promoter
down : int
the strand is used to add... | def promoter(self, up=2000, down=0):
"""
Return a start, end tuple of positions for the promoter region of this
gene
Parameters
----------
up : int
this distance upstream that is considered the promoter
down : int
the strand is used to add... | [
"Return",
"a",
"start",
"end",
"tuple",
"of",
"positions",
"for",
"the",
"promoter",
"region",
"of",
"this",
"gene"
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/models.py#L233-L248 | [
"def",
"promoter",
"(",
"self",
",",
"up",
"=",
"2000",
",",
"down",
"=",
"0",
")",
":",
"if",
"not",
"self",
".",
"is_gene_pred",
":",
"return",
"None",
"return",
"self",
".",
"tss",
"(",
"up",
"=",
"up",
",",
"down",
"=",
"down",
")"
] | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | ABase.coding_exons | includes the entire exon as long as any of it is > cdsStart and <
cdsEnd | cruzdb/models.py | def coding_exons(self):
"""
includes the entire exon as long as any of it is > cdsStart and <
cdsEnd
"""
# drop the trailing comma
starts = (long(s) for s in self.exonStarts[:-1].split(","))
ends = (long(s) for s in self.exonEnds[:-1].split(","))
return [(... | def coding_exons(self):
"""
includes the entire exon as long as any of it is > cdsStart and <
cdsEnd
"""
# drop the trailing comma
starts = (long(s) for s in self.exonStarts[:-1].split(","))
ends = (long(s) for s in self.exonEnds[:-1].split(","))
return [(... | [
"includes",
"the",
"entire",
"exon",
"as",
"long",
"as",
"any",
"of",
"it",
"is",
">",
"cdsStart",
"and",
"<",
"cdsEnd"
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/models.py#L251-L261 | [
"def",
"coding_exons",
"(",
"self",
")",
":",
"# drop the trailing comma",
"starts",
"=",
"(",
"long",
"(",
"s",
")",
"for",
"s",
"in",
"self",
".",
"exonStarts",
"[",
":",
"-",
"1",
"]",
".",
"split",
"(",
"\",\"",
")",
")",
"ends",
"=",
"(",
"lon... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | ABase.cds | just the parts of the exons that are translated | cruzdb/models.py | def cds(self):
"""just the parts of the exons that are translated"""
ces = self.coding_exons
if len(ces) < 1: return ces
ces[0] = (self.cdsStart, ces[0][1])
ces[-1] = (ces[-1][0], self.cdsEnd)
assert all((s < e for s, e in ces))
return ces | def cds(self):
"""just the parts of the exons that are translated"""
ces = self.coding_exons
if len(ces) < 1: return ces
ces[0] = (self.cdsStart, ces[0][1])
ces[-1] = (ces[-1][0], self.cdsEnd)
assert all((s < e for s, e in ces))
return ces | [
"just",
"the",
"parts",
"of",
"the",
"exons",
"that",
"are",
"translated"
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/models.py#L264-L271 | [
"def",
"cds",
"(",
"self",
")",
":",
"ces",
"=",
"self",
".",
"coding_exons",
"if",
"len",
"(",
"ces",
")",
"<",
"1",
":",
"return",
"ces",
"ces",
"[",
"0",
"]",
"=",
"(",
"self",
".",
"cdsStart",
",",
"ces",
"[",
"0",
"]",
"[",
"1",
"]",
"... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | ABase.is_downstream_of | return a boolean indicating whether this feature is downstream of
`other` taking the strand of other into account | cruzdb/models.py | def is_downstream_of(self, other):
"""
return a boolean indicating whether this feature is downstream of
`other` taking the strand of other into account
"""
if self.chrom != other.chrom: return None
if getattr(other, "strand", None) == "-":
# other feature is ... | def is_downstream_of(self, other):
"""
return a boolean indicating whether this feature is downstream of
`other` taking the strand of other into account
"""
if self.chrom != other.chrom: return None
if getattr(other, "strand", None) == "-":
# other feature is ... | [
"return",
"a",
"boolean",
"indicating",
"whether",
"this",
"feature",
"is",
"downstream",
"of",
"other",
"taking",
"the",
"strand",
"of",
"other",
"into",
"account"
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/models.py#L348-L357 | [
"def",
"is_downstream_of",
"(",
"self",
",",
"other",
")",
":",
"if",
"self",
".",
"chrom",
"!=",
"other",
".",
"chrom",
":",
"return",
"None",
"if",
"getattr",
"(",
"other",
",",
"\"strand\"",
",",
"None",
")",
"==",
"\"-\"",
":",
"# other feature is on... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | ABase.features | return e.g. "intron;exon" if the other_start, end overlap introns and
exons | cruzdb/models.py | def features(self, other_start, other_end):
"""
return e.g. "intron;exon" if the other_start, end overlap introns and
exons
"""
# completely encases gene.
if other_start <= self.start and other_end >= self.end:
return ['gene' if self.cdsStart != self.cdsEnd el... | def features(self, other_start, other_end):
"""
return e.g. "intron;exon" if the other_start, end overlap introns and
exons
"""
# completely encases gene.
if other_start <= self.start and other_end >= self.end:
return ['gene' if self.cdsStart != self.cdsEnd el... | [
"return",
"e",
".",
"g",
".",
"intron",
";",
"exon",
"if",
"the",
"other_start",
"end",
"overlap",
"introns",
"and",
"exons"
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/models.py#L359-L382 | [
"def",
"features",
"(",
"self",
",",
"other_start",
",",
"other_end",
")",
":",
"# completely encases gene.",
"if",
"other_start",
"<=",
"self",
".",
"start",
"and",
"other_end",
">=",
"self",
".",
"end",
":",
"return",
"[",
"'gene'",
"if",
"self",
".",
"c... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | ABase.upstream | return the (start, end) of the region before the geneStart | cruzdb/models.py | def upstream(self, distance):
"""
return the (start, end) of the region before the geneStart
"""
if getattr(self, "strand", None) == "+":
e = self.start
s = e - distance
else:
s = self.end
e = s + distance
return self._xstre... | def upstream(self, distance):
"""
return the (start, end) of the region before the geneStart
"""
if getattr(self, "strand", None) == "+":
e = self.start
s = e - distance
else:
s = self.end
e = s + distance
return self._xstre... | [
"return",
"the",
"(",
"start",
"end",
")",
"of",
"the",
"region",
"before",
"the",
"geneStart"
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/models.py#L414-L424 | [
"def",
"upstream",
"(",
"self",
",",
"distance",
")",
":",
"if",
"getattr",
"(",
"self",
",",
"\"strand\"",
",",
"None",
")",
"==",
"\"+\"",
":",
"e",
"=",
"self",
".",
"start",
"s",
"=",
"e",
"-",
"distance",
"else",
":",
"s",
"=",
"self",
".",
... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | ABase.utr5 | return the 5' UTR if appropriate | cruzdb/models.py | def utr5(self):
"""
return the 5' UTR if appropriate
"""
if not self.is_coding or len(self.exons) < 2: return (None, None)
if self.strand == "+":
s, e = (self.txStart, self.cdsStart)
else:
s, e = (self.cdsEnd, self.txEnd)
if s == e: return ... | def utr5(self):
"""
return the 5' UTR if appropriate
"""
if not self.is_coding or len(self.exons) < 2: return (None, None)
if self.strand == "+":
s, e = (self.txStart, self.cdsStart)
else:
s, e = (self.cdsEnd, self.txEnd)
if s == e: return ... | [
"return",
"the",
"5",
"UTR",
"if",
"appropriate"
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/models.py#L439-L449 | [
"def",
"utr5",
"(",
"self",
")",
":",
"if",
"not",
"self",
".",
"is_coding",
"or",
"len",
"(",
"self",
".",
"exons",
")",
"<",
"2",
":",
"return",
"(",
"None",
",",
"None",
")",
"if",
"self",
".",
"strand",
"==",
"\"+\"",
":",
"s",
",",
"e",
... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | ABase.sequence | Return the sequence for this feature.
if per-exon is True, return an array of exon sequences
This sequence is never reverse complemented | cruzdb/models.py | def sequence(self, per_exon=False):
"""
Return the sequence for this feature.
if per-exon is True, return an array of exon sequences
This sequence is never reverse complemented
"""
db = self.db
if not per_exon:
start = self.txStart + 1
retu... | def sequence(self, per_exon=False):
"""
Return the sequence for this feature.
if per-exon is True, return an array of exon sequences
This sequence is never reverse complemented
"""
db = self.db
if not per_exon:
start = self.txStart + 1
retu... | [
"Return",
"the",
"sequence",
"for",
"this",
"feature",
".",
"if",
"per",
"-",
"exon",
"is",
"True",
"return",
"an",
"array",
"of",
"exon",
"sequences",
"This",
"sequence",
"is",
"never",
"reverse",
"complemented"
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/models.py#L527-L542 | [
"def",
"sequence",
"(",
"self",
",",
"per_exon",
"=",
"False",
")",
":",
"db",
"=",
"self",
".",
"db",
"if",
"not",
"per_exon",
":",
"start",
"=",
"self",
".",
"txStart",
"+",
"1",
"return",
"_sequence",
"(",
"db",
",",
"self",
".",
"chrom",
",",
... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | ABase.ncbi_blast | perform an NCBI blast against the sequence of this feature | cruzdb/models.py | def ncbi_blast(self, db="nr", megablast=True, sequence=None):
"""
perform an NCBI blast against the sequence of this feature
"""
import requests
requests.defaults.max_retries = 4
assert sequence in (None, "cds", "mrna")
seq = self.sequence() if sequence is None el... | def ncbi_blast(self, db="nr", megablast=True, sequence=None):
"""
perform an NCBI blast against the sequence of this feature
"""
import requests
requests.defaults.max_retries = 4
assert sequence in (None, "cds", "mrna")
seq = self.sequence() if sequence is None el... | [
"perform",
"an",
"NCBI",
"blast",
"against",
"the",
"sequence",
"of",
"this",
"feature"
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/models.py#L548-L591 | [
"def",
"ncbi_blast",
"(",
"self",
",",
"db",
"=",
"\"nr\"",
",",
"megablast",
"=",
"True",
",",
"sequence",
"=",
"None",
")",
":",
"import",
"requests",
"requests",
".",
"defaults",
".",
"max_retries",
"=",
"4",
"assert",
"sequence",
"in",
"(",
"None",
... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | ABase.blat | make a request to the genome-browsers BLAT interface
sequence is one of None, "mrna", "cds"
returns a list of features that are hits to this sequence. | cruzdb/models.py | def blat(self, db=None, sequence=None, seq_type="DNA"):
"""
make a request to the genome-browsers BLAT interface
sequence is one of None, "mrna", "cds"
returns a list of features that are hits to this sequence.
"""
from . blat_blast import blat, blat_all
assert se... | def blat(self, db=None, sequence=None, seq_type="DNA"):
"""
make a request to the genome-browsers BLAT interface
sequence is one of None, "mrna", "cds"
returns a list of features that are hits to this sequence.
"""
from . blat_blast import blat, blat_all
assert se... | [
"make",
"a",
"request",
"to",
"the",
"genome",
"-",
"browsers",
"BLAT",
"interface",
"sequence",
"is",
"one",
"of",
"None",
"mrna",
"cds",
"returns",
"a",
"list",
"of",
"features",
"that",
"are",
"hits",
"to",
"this",
"sequence",
"."
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/models.py#L593-L605 | [
"def",
"blat",
"(",
"self",
",",
"db",
"=",
"None",
",",
"sequence",
"=",
"None",
",",
"seq_type",
"=",
"\"DNA\"",
")",
":",
"from",
".",
"blat_blast",
"import",
"blat",
",",
"blat_all",
"assert",
"sequence",
"in",
"(",
"None",
",",
"\"cds\"",
",",
"... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | ABase.bed | return a bed formatted string of this feature | cruzdb/models.py | def bed(self, *attrs, **kwargs):
"""
return a bed formatted string of this feature
"""
exclude = ("chrom", "start", "end", "txStart", "txEnd", "chromStart",
"chromEnd")
if self.is_gene_pred:
return self.bed12(**kwargs)
return "\t".join(map(str,... | def bed(self, *attrs, **kwargs):
"""
return a bed formatted string of this feature
"""
exclude = ("chrom", "start", "end", "txStart", "txEnd", "chromStart",
"chromEnd")
if self.is_gene_pred:
return self.bed12(**kwargs)
return "\t".join(map(str,... | [
"return",
"a",
"bed",
"formatted",
"string",
"of",
"this",
"feature"
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/models.py#L614-L625 | [
"def",
"bed",
"(",
"self",
",",
"*",
"attrs",
",",
"*",
"*",
"kwargs",
")",
":",
"exclude",
"=",
"(",
"\"chrom\"",
",",
"\"start\"",
",",
"\"end\"",
",",
"\"txStart\"",
",",
"\"txEnd\"",
",",
"\"chromStart\"",
",",
"\"chromEnd\"",
")",
"if",
"self",
".... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | ABase.bed12 | return a bed12 (http://genome.ucsc.edu/FAQ/FAQformat.html#format1)
representation of this interval | cruzdb/models.py | def bed12(self, score="0", rgb="."):
"""
return a bed12 (http://genome.ucsc.edu/FAQ/FAQformat.html#format1)
representation of this interval
"""
if not self.is_gene_pred:
raise CruzException("can't create bed12 from non genepred feature")
exons = list(self.exon... | def bed12(self, score="0", rgb="."):
"""
return a bed12 (http://genome.ucsc.edu/FAQ/FAQformat.html#format1)
representation of this interval
"""
if not self.is_gene_pred:
raise CruzException("can't create bed12 from non genepred feature")
exons = list(self.exon... | [
"return",
"a",
"bed12",
"(",
"http",
":",
"//",
"genome",
".",
"ucsc",
".",
"edu",
"/",
"FAQ",
"/",
"FAQformat",
".",
"html#format1",
")",
"representation",
"of",
"this",
"interval"
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/models.py#L628-L644 | [
"def",
"bed12",
"(",
"self",
",",
"score",
"=",
"\"0\"",
",",
"rgb",
"=",
"\".\"",
")",
":",
"if",
"not",
"self",
".",
"is_gene_pred",
":",
"raise",
"CruzException",
"(",
"\"can't create bed12 from non genepred feature\"",
")",
"exons",
"=",
"list",
"(",
"se... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | ABase.localize | convert global coordinate(s) to local taking
introns into account and cds/tx-Start depending on cdna=True kwarg | cruzdb/models.py | def localize(self, *positions, **kwargs):
"""
convert global coordinate(s) to local taking
introns into account and cds/tx-Start depending on cdna=True kwarg
"""
cdna = kwargs.get('cdna', False)
# TODO: account for strand ?? add kwarg ??
# if it's to the CDNA, the... | def localize(self, *positions, **kwargs):
"""
convert global coordinate(s) to local taking
introns into account and cds/tx-Start depending on cdna=True kwarg
"""
cdna = kwargs.get('cdna', False)
# TODO: account for strand ?? add kwarg ??
# if it's to the CDNA, the... | [
"convert",
"global",
"coordinate",
"(",
"s",
")",
"to",
"local",
"taking",
"introns",
"into",
"account",
"and",
"cds",
"/",
"tx",
"-",
"Start",
"depending",
"on",
"cdna",
"=",
"True",
"kwarg"
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/models.py#L665-L709 | [
"def",
"localize",
"(",
"self",
",",
"*",
"positions",
",",
"*",
"*",
"kwargs",
")",
":",
"cdna",
"=",
"kwargs",
".",
"get",
"(",
"'cdna'",
",",
"False",
")",
"# TODO: account for strand ?? add kwarg ??",
"# if it's to the CDNA, then it's based on the cdsStart",
"st... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | cpgIslandExt.distance | check the distance between this an another interval
Parameters
----------
other_or_start : Interval or int
either an integer or an Interval with a start attribute indicating
the start of the interval
end : int
if `other_or_start` is an integer, this ... | cruzdb/models.py | def distance(self, other_or_start=None, end=None, features="unused",
shore_dist=3000):
"""
check the distance between this an another interval
Parameters
----------
other_or_start : Interval or int
either an integer or an Interval with a start attribute i... | def distance(self, other_or_start=None, end=None, features="unused",
shore_dist=3000):
"""
check the distance between this an another interval
Parameters
----------
other_or_start : Interval or int
either an integer or an Interval with a start attribute i... | [
"check",
"the",
"distance",
"between",
"this",
"an",
"another",
"interval",
"Parameters",
"----------"
] | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/models.py#L725-L758 | [
"def",
"distance",
"(",
"self",
",",
"other_or_start",
"=",
"None",
",",
"end",
"=",
"None",
",",
"features",
"=",
"\"unused\"",
",",
"shore_dist",
"=",
"3000",
")",
":",
"# leave features kwarg to match signature from Feature.distance",
"if",
"end",
"is",
"None",... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | annotate | annotate bed file in fname with tables.
distances are integers for distance. and intron/exon/utr5 etc for gene-pred
tables. if the annotation features have a strand, the distance reported is
negative if the annotation feature is upstream of the feature in question
if feature_strand is True, then the dis... | cruzdb/annotate.py | def annotate(g, fname, tables, feature_strand=False, in_memory=False,
header=None, out=sys.stdout, _chrom=None, parallel=False):
"""
annotate bed file in fname with tables.
distances are integers for distance. and intron/exon/utr5 etc for gene-pred
tables. if the annotation features have a stran... | def annotate(g, fname, tables, feature_strand=False, in_memory=False,
header=None, out=sys.stdout, _chrom=None, parallel=False):
"""
annotate bed file in fname with tables.
distances are integers for distance. and intron/exon/utr5 etc for gene-pred
tables. if the annotation features have a stran... | [
"annotate",
"bed",
"file",
"in",
"fname",
"with",
"tables",
".",
"distances",
"are",
"integers",
"for",
"distance",
".",
"and",
"intron",
"/",
"exon",
"/",
"utr5",
"etc",
"for",
"gene",
"-",
"pred",
"tables",
".",
"if",
"the",
"annotation",
"features",
"... | brentp/cruzdb | python | https://github.com/brentp/cruzdb/blob/9068d46e25952f4a929dde0242beb31fa4c7e89a/cruzdb/annotate.py#L28-L171 | [
"def",
"annotate",
"(",
"g",
",",
"fname",
",",
"tables",
",",
"feature_strand",
"=",
"False",
",",
"in_memory",
"=",
"False",
",",
"header",
"=",
"None",
",",
"out",
"=",
"sys",
".",
"stdout",
",",
"_chrom",
"=",
"None",
",",
"parallel",
"=",
"False... | 9068d46e25952f4a929dde0242beb31fa4c7e89a |
train | entry_point | External entry point which calls main() and
if Stop is raised, calls sys.exit() | omego/main.py | def entry_point():
"""
External entry point which calls main() and
if Stop is raised, calls sys.exit()
"""
try:
main("omego", items=[
(InstallCommand.NAME, InstallCommand),
(UpgradeCommand.NAME, UpgradeCommand),
(ConvertCommand.NAME, ConvertCommand),
... | def entry_point():
"""
External entry point which calls main() and
if Stop is raised, calls sys.exit()
"""
try:
main("omego", items=[
(InstallCommand.NAME, InstallCommand),
(UpgradeCommand.NAME, UpgradeCommand),
(ConvertCommand.NAME, ConvertCommand),
... | [
"External",
"entry",
"point",
"which",
"calls",
"main",
"()",
"and",
"if",
"Stop",
"is",
"raised",
"calls",
"sys",
".",
"exit",
"()"
] | ome/omego | python | https://github.com/ome/omego/blob/2dadbf3c6342b6c995f9e0dceaf3c0b7fab030fb/omego/main.py#L40-L58 | [
"def",
"entry_point",
"(",
")",
":",
"try",
":",
"main",
"(",
"\"omego\"",
",",
"items",
"=",
"[",
"(",
"InstallCommand",
".",
"NAME",
",",
"InstallCommand",
")",
",",
"(",
"UpgradeCommand",
".",
"NAME",
",",
"UpgradeCommand",
")",
",",
"(",
"ConvertComm... | 2dadbf3c6342b6c995f9e0dceaf3c0b7fab030fb |
train | open_url | Open a URL using an opener that will simulate a browser user-agent
url: The URL
httpuser, httppassword: HTTP authentication credentials (either both or
neither must be provided)
method: The HTTP method
Caller is reponsible for calling close() on the returned object | omego/fileutils.py | def open_url(url, httpuser=None, httppassword=None, method=None):
"""
Open a URL using an opener that will simulate a browser user-agent
url: The URL
httpuser, httppassword: HTTP authentication credentials (either both or
neither must be provided)
method: The HTTP method
Caller is reponsi... | def open_url(url, httpuser=None, httppassword=None, method=None):
"""
Open a URL using an opener that will simulate a browser user-agent
url: The URL
httpuser, httppassword: HTTP authentication credentials (either both or
neither must be provided)
method: The HTTP method
Caller is reponsi... | [
"Open",
"a",
"URL",
"using",
"an",
"opener",
"that",
"will",
"simulate",
"a",
"browser",
"user",
"-",
"agent",
"url",
":",
"The",
"URL",
"httpuser",
"httppassword",
":",
"HTTP",
"authentication",
"credentials",
"(",
"either",
"both",
"or",
"neither",
"must",... | ome/omego | python | https://github.com/ome/omego/blob/2dadbf3c6342b6c995f9e0dceaf3c0b7fab030fb/omego/fileutils.py#L47-L92 | [
"def",
"open_url",
"(",
"url",
",",
"httpuser",
"=",
"None",
",",
"httppassword",
"=",
"None",
",",
"method",
"=",
"None",
")",
":",
"if",
"os",
".",
"getenv",
"(",
"'OMEGO_SSL_NO_VERIFY'",
")",
"==",
"'1'",
":",
"# This needs to come first to override the def... | 2dadbf3c6342b6c995f9e0dceaf3c0b7fab030fb |
train | dereference_url | Makes a HEAD request to find the final destination of a URL after
following any redirects | omego/fileutils.py | def dereference_url(url):
"""
Makes a HEAD request to find the final destination of a URL after
following any redirects
"""
res = open_url(url, method='HEAD')
res.close()
return res.url | def dereference_url(url):
"""
Makes a HEAD request to find the final destination of a URL after
following any redirects
"""
res = open_url(url, method='HEAD')
res.close()
return res.url | [
"Makes",
"a",
"HEAD",
"request",
"to",
"find",
"the",
"final",
"destination",
"of",
"a",
"URL",
"after",
"following",
"any",
"redirects"
] | ome/omego | python | https://github.com/ome/omego/blob/2dadbf3c6342b6c995f9e0dceaf3c0b7fab030fb/omego/fileutils.py#L95-L102 | [
"def",
"dereference_url",
"(",
"url",
")",
":",
"res",
"=",
"open_url",
"(",
"url",
",",
"method",
"=",
"'HEAD'",
")",
"res",
".",
"close",
"(",
")",
"return",
"res",
".",
"url"
] | 2dadbf3c6342b6c995f9e0dceaf3c0b7fab030fb |
train | read | Read the contents of a URL into memory, return | omego/fileutils.py | def read(url, **kwargs):
"""
Read the contents of a URL into memory, return
"""
response = open_url(url, **kwargs)
try:
return response.read()
finally:
response.close() | def read(url, **kwargs):
"""
Read the contents of a URL into memory, return
"""
response = open_url(url, **kwargs)
try:
return response.read()
finally:
response.close() | [
"Read",
"the",
"contents",
"of",
"a",
"URL",
"into",
"memory",
"return"
] | ome/omego | python | https://github.com/ome/omego/blob/2dadbf3c6342b6c995f9e0dceaf3c0b7fab030fb/omego/fileutils.py#L105-L113 | [
"def",
"read",
"(",
"url",
",",
"*",
"*",
"kwargs",
")",
":",
"response",
"=",
"open_url",
"(",
"url",
",",
"*",
"*",
"kwargs",
")",
"try",
":",
"return",
"response",
".",
"read",
"(",
")",
"finally",
":",
"response",
".",
"close",
"(",
")"
] | 2dadbf3c6342b6c995f9e0dceaf3c0b7fab030fb |
train | download | Download a file, optionally printing a simple progress bar
url: The URL to download
filename: The filename to save to, default is to use the URL basename
print_progress: The length of the progress bar, use 0 to disable
delete_fail: If True delete the file if the download was not successful,
defaul... | omego/fileutils.py | def download(url, filename=None, print_progress=0, delete_fail=True,
**kwargs):
"""
Download a file, optionally printing a simple progress bar
url: The URL to download
filename: The filename to save to, default is to use the URL basename
print_progress: The length of the progress bar, u... | def download(url, filename=None, print_progress=0, delete_fail=True,
**kwargs):
"""
Download a file, optionally printing a simple progress bar
url: The URL to download
filename: The filename to save to, default is to use the URL basename
print_progress: The length of the progress bar, u... | [
"Download",
"a",
"file",
"optionally",
"printing",
"a",
"simple",
"progress",
"bar",
"url",
":",
"The",
"URL",
"to",
"download",
"filename",
":",
"The",
"filename",
"to",
"save",
"to",
"default",
"is",
"to",
"use",
"the",
"URL",
"basename",
"print_progress",... | ome/omego | python | https://github.com/ome/omego/blob/2dadbf3c6342b6c995f9e0dceaf3c0b7fab030fb/omego/fileutils.py#L116-L158 | [
"def",
"download",
"(",
"url",
",",
"filename",
"=",
"None",
",",
"print_progress",
"=",
"0",
",",
"delete_fail",
"=",
"True",
",",
"*",
"*",
"kwargs",
")",
":",
"blocksize",
"=",
"1024",
"*",
"1024",
"downloaded",
"=",
"0",
"progress",
"=",
"None",
... | 2dadbf3c6342b6c995f9e0dceaf3c0b7fab030fb |
train | rename_backup | Append a backup prefix to a file or directory, with an increasing numeric
suffix (.N) if a file already exists | omego/fileutils.py | def rename_backup(name, suffix='.bak'):
"""
Append a backup prefix to a file or directory, with an increasing numeric
suffix (.N) if a file already exists
"""
newname = '%s%s' % (name, suffix)
n = 0
while os.path.exists(newname):
n += 1
newname = '%s%s.%d' % (name, suffix, n)... | def rename_backup(name, suffix='.bak'):
"""
Append a backup prefix to a file or directory, with an increasing numeric
suffix (.N) if a file already exists
"""
newname = '%s%s' % (name, suffix)
n = 0
while os.path.exists(newname):
n += 1
newname = '%s%s.%d' % (name, suffix, n)... | [
"Append",
"a",
"backup",
"prefix",
"to",
"a",
"file",
"or",
"directory",
"with",
"an",
"increasing",
"numeric",
"suffix",
"(",
".",
"N",
")",
"if",
"a",
"file",
"already",
"exists"
] | ome/omego | python | https://github.com/ome/omego/blob/2dadbf3c6342b6c995f9e0dceaf3c0b7fab030fb/omego/fileutils.py#L161-L173 | [
"def",
"rename_backup",
"(",
"name",
",",
"suffix",
"=",
"'.bak'",
")",
":",
"newname",
"=",
"'%s%s'",
"%",
"(",
"name",
",",
"suffix",
")",
"n",
"=",
"0",
"while",
"os",
".",
"path",
".",
"exists",
"(",
"newname",
")",
":",
"n",
"+=",
"1",
"newn... | 2dadbf3c6342b6c995f9e0dceaf3c0b7fab030fb |
train | timestamp_filename | Return a string of the form [basename-TIMESTAMP.ext]
where TIMESTAMP is of the form YYYYMMDD-HHMMSS-MILSEC | omego/fileutils.py | def timestamp_filename(basename, ext=None):
"""
Return a string of the form [basename-TIMESTAMP.ext]
where TIMESTAMP is of the form YYYYMMDD-HHMMSS-MILSEC
"""
dt = datetime.now().strftime('%Y%m%d-%H%M%S-%f')
if ext:
return '%s-%s.%s' % (basename, dt, ext)
return '%s-%s' % (basename, ... | def timestamp_filename(basename, ext=None):
"""
Return a string of the form [basename-TIMESTAMP.ext]
where TIMESTAMP is of the form YYYYMMDD-HHMMSS-MILSEC
"""
dt = datetime.now().strftime('%Y%m%d-%H%M%S-%f')
if ext:
return '%s-%s.%s' % (basename, dt, ext)
return '%s-%s' % (basename, ... | [
"Return",
"a",
"string",
"of",
"the",
"form",
"[",
"basename",
"-",
"TIMESTAMP",
".",
"ext",
"]",
"where",
"TIMESTAMP",
"is",
"of",
"the",
"form",
"YYYYMMDD",
"-",
"HHMMSS",
"-",
"MILSEC"
] | ome/omego | python | https://github.com/ome/omego/blob/2dadbf3c6342b6c995f9e0dceaf3c0b7fab030fb/omego/fileutils.py#L176-L184 | [
"def",
"timestamp_filename",
"(",
"basename",
",",
"ext",
"=",
"None",
")",
":",
"dt",
"=",
"datetime",
".",
"now",
"(",
")",
".",
"strftime",
"(",
"'%Y%m%d-%H%M%S-%f'",
")",
"if",
"ext",
":",
"return",
"'%s-%s.%s'",
"%",
"(",
"basename",
",",
"dt",
",... | 2dadbf3c6342b6c995f9e0dceaf3c0b7fab030fb |
train | check_extracted_paths | Check whether zip file paths are all relative, and optionally in a
specified subdirectory, raises an exception if not
namelist: A list of paths from the zip file
subdir: If specified then check whether all paths in the zip file are
under this subdirectory
Python docs are unclear about the securi... | omego/fileutils.py | def check_extracted_paths(namelist, subdir=None):
"""
Check whether zip file paths are all relative, and optionally in a
specified subdirectory, raises an exception if not
namelist: A list of paths from the zip file
subdir: If specified then check whether all paths in the zip file are
under t... | def check_extracted_paths(namelist, subdir=None):
"""
Check whether zip file paths are all relative, and optionally in a
specified subdirectory, raises an exception if not
namelist: A list of paths from the zip file
subdir: If specified then check whether all paths in the zip file are
under t... | [
"Check",
"whether",
"zip",
"file",
"paths",
"are",
"all",
"relative",
"and",
"optionally",
"in",
"a",
"specified",
"subdirectory",
"raises",
"an",
"exception",
"if",
"not"
] | ome/omego | python | https://github.com/ome/omego/blob/2dadbf3c6342b6c995f9e0dceaf3c0b7fab030fb/omego/fileutils.py#L194-L228 | [
"def",
"check_extracted_paths",
"(",
"namelist",
",",
"subdir",
"=",
"None",
")",
":",
"def",
"relpath",
"(",
"p",
")",
":",
"# relpath strips a trailing sep",
"# Windows paths may also use unix sep",
"q",
"=",
"os",
".",
"path",
".",
"relpath",
"(",
"p",
")",
... | 2dadbf3c6342b6c995f9e0dceaf3c0b7fab030fb |
train | unzip | Extract all files from a zip archive
filename: The path to the zip file
match_dir: If True all files in the zip must be contained in a subdirectory
named after the archive file with extension removed
destdir: Extract the zip into this directory, default current directory
return: If match_dir is T... | omego/fileutils.py | def unzip(filename, match_dir=False, destdir=None):
"""
Extract all files from a zip archive
filename: The path to the zip file
match_dir: If True all files in the zip must be contained in a subdirectory
named after the archive file with extension removed
destdir: Extract the zip into this dir... | def unzip(filename, match_dir=False, destdir=None):
"""
Extract all files from a zip archive
filename: The path to the zip file
match_dir: If True all files in the zip must be contained in a subdirectory
named after the archive file with extension removed
destdir: Extract the zip into this dir... | [
"Extract",
"all",
"files",
"from",
"a",
"zip",
"archive",
"filename",
":",
"The",
"path",
"to",
"the",
"zip",
"file",
"match_dir",
":",
"If",
"True",
"all",
"files",
"in",
"the",
"zip",
"must",
"be",
"contained",
"in",
"a",
"subdirectory",
"named",
"afte... | ome/omego | python | https://github.com/ome/omego/blob/2dadbf3c6342b6c995f9e0dceaf3c0b7fab030fb/omego/fileutils.py#L231-L266 | [
"def",
"unzip",
"(",
"filename",
",",
"match_dir",
"=",
"False",
",",
"destdir",
"=",
"None",
")",
":",
"if",
"not",
"destdir",
":",
"destdir",
"=",
"'.'",
"z",
"=",
"zipfile",
".",
"ZipFile",
"(",
"filename",
")",
"unzipped",
"=",
"'.'",
"if",
"matc... | 2dadbf3c6342b6c995f9e0dceaf3c0b7fab030fb |
train | zip | Create a new zip archive containing files
filename: The name of the zip file to be created
paths: A list of files or directories
strip_dir: Remove this prefix from all file-paths before adding to zip | omego/fileutils.py | def zip(filename, paths, strip_prefix=''):
"""
Create a new zip archive containing files
filename: The name of the zip file to be created
paths: A list of files or directories
strip_dir: Remove this prefix from all file-paths before adding to zip
"""
if isinstance(paths, basestring):
... | def zip(filename, paths, strip_prefix=''):
"""
Create a new zip archive containing files
filename: The name of the zip file to be created
paths: A list of files or directories
strip_dir: Remove this prefix from all file-paths before adding to zip
"""
if isinstance(paths, basestring):
... | [
"Create",
"a",
"new",
"zip",
"archive",
"containing",
"files",
"filename",
":",
"The",
"name",
"of",
"the",
"zip",
"file",
"to",
"be",
"created",
"paths",
":",
"A",
"list",
"of",
"files",
"or",
"directories",
"strip_dir",
":",
"Remove",
"this",
"prefix",
... | ome/omego | python | https://github.com/ome/omego/blob/2dadbf3c6342b6c995f9e0dceaf3c0b7fab030fb/omego/fileutils.py#L269-L298 | [
"def",
"zip",
"(",
"filename",
",",
"paths",
",",
"strip_prefix",
"=",
"''",
")",
":",
"if",
"isinstance",
"(",
"paths",
",",
"basestring",
")",
":",
"paths",
"=",
"[",
"paths",
"]",
"filelist",
"=",
"set",
"(",
")",
"for",
"p",
"in",
"paths",
":",... | 2dadbf3c6342b6c995f9e0dceaf3c0b7fab030fb |
train | get_as_local_path | Automatically handle local and remote URLs, files and directories
path: Either a local directory, file or remote URL. If a URL is given
it will be fetched. If this is a zip it will be automatically
expanded by default.
overwrite: Whether to overwrite an existing file:
'error': Raise an except... | omego/fileutils.py | def get_as_local_path(path, overwrite, progress=0,
httpuser=None, httppassword=None):
"""
Automatically handle local and remote URLs, files and directories
path: Either a local directory, file or remote URL. If a URL is given
it will be fetched. If this is a zip it will be autom... | def get_as_local_path(path, overwrite, progress=0,
httpuser=None, httppassword=None):
"""
Automatically handle local and remote URLs, files and directories
path: Either a local directory, file or remote URL. If a URL is given
it will be fetched. If this is a zip it will be autom... | [
"Automatically",
"handle",
"local",
"and",
"remote",
"URLs",
"files",
"and",
"directories"
] | ome/omego | python | https://github.com/ome/omego/blob/2dadbf3c6342b6c995f9e0dceaf3c0b7fab030fb/omego/fileutils.py#L301-L356 | [
"def",
"get_as_local_path",
"(",
"path",
",",
"overwrite",
",",
"progress",
"=",
"0",
",",
"httpuser",
"=",
"None",
",",
"httppassword",
"=",
"None",
")",
":",
"m",
"=",
"re",
".",
"match",
"(",
"'([A-Za-z]+)://'",
",",
"path",
")",
"if",
"m",
":",
"... | 2dadbf3c6342b6c995f9e0dceaf3c0b7fab030fb |
train | create | Allocates and initializes an encoder state. | opus/api/encoder.py | def create(fs, channels, application):
"""Allocates and initializes an encoder state."""
result_code = ctypes.c_int()
result = _create(fs, channels, application, ctypes.byref(result_code))
if result_code.value is not constants.OK:
raise OpusError(result_code.value)
return result | def create(fs, channels, application):
"""Allocates and initializes an encoder state."""
result_code = ctypes.c_int()
result = _create(fs, channels, application, ctypes.byref(result_code))
if result_code.value is not constants.OK:
raise OpusError(result_code.value)
return result | [
"Allocates",
"and",
"initializes",
"an",
"encoder",
"state",
"."
] | svartalf/python-opus | python | https://github.com/svartalf/python-opus/blob/a3c1d556d2772b5be659ddd08c033ddd4d566b3a/opus/api/encoder.py#L40-L49 | [
"def",
"create",
"(",
"fs",
",",
"channels",
",",
"application",
")",
":",
"result_code",
"=",
"ctypes",
".",
"c_int",
"(",
")",
"result",
"=",
"_create",
"(",
"fs",
",",
"channels",
",",
"application",
",",
"ctypes",
".",
"byref",
"(",
"result_code",
... | a3c1d556d2772b5be659ddd08c033ddd4d566b3a |
train | encode | Encodes an Opus frame
Returns string output payload | opus/api/encoder.py | def encode(encoder, pcm, frame_size, max_data_bytes):
"""Encodes an Opus frame
Returns string output payload
"""
pcm = ctypes.cast(pcm, c_int16_pointer)
data = (ctypes.c_char * max_data_bytes)()
result = _encode(encoder, pcm, frame_size, data, max_data_bytes)
if result < 0:
raise ... | def encode(encoder, pcm, frame_size, max_data_bytes):
"""Encodes an Opus frame
Returns string output payload
"""
pcm = ctypes.cast(pcm, c_int16_pointer)
data = (ctypes.c_char * max_data_bytes)()
result = _encode(encoder, pcm, frame_size, data, max_data_bytes)
if result < 0:
raise ... | [
"Encodes",
"an",
"Opus",
"frame"
] | svartalf/python-opus | python | https://github.com/svartalf/python-opus/blob/a3c1d556d2772b5be659ddd08c033ddd4d566b3a/opus/api/encoder.py#L68-L81 | [
"def",
"encode",
"(",
"encoder",
",",
"pcm",
",",
"frame_size",
",",
"max_data_bytes",
")",
":",
"pcm",
"=",
"ctypes",
".",
"cast",
"(",
"pcm",
",",
"c_int16_pointer",
")",
"data",
"=",
"(",
"ctypes",
".",
"c_char",
"*",
"max_data_bytes",
")",
"(",
")"... | a3c1d556d2772b5be659ddd08c033ddd4d566b3a |
train | encode_float | Encodes an Opus frame from floating point input | opus/api/encoder.py | def encode_float(encoder, pcm, frame_size, max_data_bytes):
"""Encodes an Opus frame from floating point input"""
pcm = ctypes.cast(pcm, c_float_pointer)
data = (ctypes.c_char * max_data_bytes)()
result = _encode_float(encoder, pcm, frame_size, data, max_data_bytes)
if result < 0:
raise Op... | def encode_float(encoder, pcm, frame_size, max_data_bytes):
"""Encodes an Opus frame from floating point input"""
pcm = ctypes.cast(pcm, c_float_pointer)
data = (ctypes.c_char * max_data_bytes)()
result = _encode_float(encoder, pcm, frame_size, data, max_data_bytes)
if result < 0:
raise Op... | [
"Encodes",
"an",
"Opus",
"frame",
"from",
"floating",
"point",
"input"
] | svartalf/python-opus | python | https://github.com/svartalf/python-opus/blob/a3c1d556d2772b5be659ddd08c033ddd4d566b3a/opus/api/encoder.py#L89-L99 | [
"def",
"encode_float",
"(",
"encoder",
",",
"pcm",
",",
"frame_size",
",",
"max_data_bytes",
")",
":",
"pcm",
"=",
"ctypes",
".",
"cast",
"(",
"pcm",
",",
"c_float_pointer",
")",
"data",
"=",
"(",
"ctypes",
".",
"c_char",
"*",
"max_data_bytes",
")",
"(",... | a3c1d556d2772b5be659ddd08c033ddd4d566b3a |
train | MeCab.__parse_tostr | Builds and returns the MeCab function for parsing Unicode text.
Args:
fn_name: MeCab function name that determines the function
behavior, either 'mecab_sparse_tostr' or
'mecab_nbest_sparse_tostr'.
Returns:
A function definition, tailored to parsi... | natto/mecab.py | def __parse_tostr(self, text, **kwargs):
'''Builds and returns the MeCab function for parsing Unicode text.
Args:
fn_name: MeCab function name that determines the function
behavior, either 'mecab_sparse_tostr' or
'mecab_nbest_sparse_tostr'.
Returns:
... | def __parse_tostr(self, text, **kwargs):
'''Builds and returns the MeCab function for parsing Unicode text.
Args:
fn_name: MeCab function name that determines the function
behavior, either 'mecab_sparse_tostr' or
'mecab_nbest_sparse_tostr'.
Returns:
... | [
"Builds",
"and",
"returns",
"the",
"MeCab",
"function",
"for",
"parsing",
"Unicode",
"text",
"."
] | buruzaemon/natto-py | python | https://github.com/buruzaemon/natto-py/blob/018fe004c47c45c66bdf2e03fe24e981ae089b76/natto/mecab.py#L248-L322 | [
"def",
"__parse_tostr",
"(",
"self",
",",
"text",
",",
"*",
"*",
"kwargs",
")",
":",
"n",
"=",
"self",
".",
"options",
".",
"get",
"(",
"'nbest'",
",",
"1",
")",
"if",
"self",
".",
"_KW_BOUNDARY",
"in",
"kwargs",
":",
"patt",
"=",
"kwargs",
".",
... | 018fe004c47c45c66bdf2e03fe24e981ae089b76 |
train | MeCab.__parse_tonodes | Builds and returns the MeCab function for parsing to nodes using
morpheme boundary constraints.
Args:
format_feature: flag indicating whether or not to format the feature
value for each node yielded.
Returns:
A function which returns a Generator, tailore... | natto/mecab.py | def __parse_tonodes(self, text, **kwargs):
'''Builds and returns the MeCab function for parsing to nodes using
morpheme boundary constraints.
Args:
format_feature: flag indicating whether or not to format the feature
value for each node yielded.
Returns:
... | def __parse_tonodes(self, text, **kwargs):
'''Builds and returns the MeCab function for parsing to nodes using
morpheme boundary constraints.
Args:
format_feature: flag indicating whether or not to format the feature
value for each node yielded.
Returns:
... | [
"Builds",
"and",
"returns",
"the",
"MeCab",
"function",
"for",
"parsing",
"to",
"nodes",
"using",
"morpheme",
"boundary",
"constraints",
"."
] | buruzaemon/natto-py | python | https://github.com/buruzaemon/natto-py/blob/018fe004c47c45c66bdf2e03fe24e981ae089b76/natto/mecab.py#L324-L427 | [
"def",
"__parse_tonodes",
"(",
"self",
",",
"text",
",",
"*",
"*",
"kwargs",
")",
":",
"n",
"=",
"self",
".",
"options",
".",
"get",
"(",
"'nbest'",
",",
"1",
")",
"try",
":",
"if",
"self",
".",
"_KW_BOUNDARY",
"in",
"kwargs",
":",
"patt",
"=",
"... | 018fe004c47c45c66bdf2e03fe24e981ae089b76 |
train | MeCab.parse | Parse the given text and return result from MeCab.
:param text: the text to parse.
:type text: str
:param as_nodes: return generator of MeCabNodes if True;
or string if False.
:type as_nodes: bool, defaults to False
:param boundary_constraints: regular expression for... | natto/mecab.py | def parse(self, text, **kwargs):
'''Parse the given text and return result from MeCab.
:param text: the text to parse.
:type text: str
:param as_nodes: return generator of MeCabNodes if True;
or string if False.
:type as_nodes: bool, defaults to False
:param ... | def parse(self, text, **kwargs):
'''Parse the given text and return result from MeCab.
:param text: the text to parse.
:type text: str
:param as_nodes: return generator of MeCabNodes if True;
or string if False.
:type as_nodes: bool, defaults to False
:param ... | [
"Parse",
"the",
"given",
"text",
"and",
"return",
"result",
"from",
"MeCab",
"."
] | buruzaemon/natto-py | python | https://github.com/buruzaemon/natto-py/blob/018fe004c47c45c66bdf2e03fe24e981ae089b76/natto/mecab.py#L441-L488 | [
"def",
"parse",
"(",
"self",
",",
"text",
",",
"*",
"*",
"kwargs",
")",
":",
"if",
"text",
"is",
"None",
":",
"logger",
".",
"error",
"(",
"self",
".",
"_ERROR_EMPTY_STR",
")",
"raise",
"MeCabError",
"(",
"self",
".",
"_ERROR_EMPTY_STR",
")",
"elif",
... | 018fe004c47c45c66bdf2e03fe24e981ae089b76 |
train | parse | MAX_TERM_COUNT = 10000 # There are 39,000 terms in the GO! | omego/convert.py | def parse(filename, MAX_TERM_COUNT=1000):
"""
MAX_TERM_COUNT = 10000 # There are 39,000 terms in the GO!
"""
with open(filename, "r") as f:
termId = None
name = None
desc = None
parents = []
termCount = 0
for l in f.readlines():
if l.st... | def parse(filename, MAX_TERM_COUNT=1000):
"""
MAX_TERM_COUNT = 10000 # There are 39,000 terms in the GO!
"""
with open(filename, "r") as f:
termId = None
name = None
desc = None
parents = []
termCount = 0
for l in f.readlines():
if l.st... | [
"MAX_TERM_COUNT",
"=",
"10000",
"#",
"There",
"are",
"39",
"000",
"terms",
"in",
"the",
"GO!"
] | ome/omego | python | https://github.com/ome/omego/blob/2dadbf3c6342b6c995f9e0dceaf3c0b7fab030fb/omego/convert.py#L59-L109 | [
"def",
"parse",
"(",
"filename",
",",
"MAX_TERM_COUNT",
"=",
"1000",
")",
":",
"with",
"open",
"(",
"filename",
",",
"\"r\"",
")",
"as",
"f",
":",
"termId",
"=",
"None",
"name",
"=",
"None",
"desc",
"=",
"None",
"parents",
"=",
"[",
"]",
"termCount",... | 2dadbf3c6342b6c995f9e0dceaf3c0b7fab030fb |
train | generate | create Tag Groups and Child Tags using data from terms dict | omego/convert.py | def generate(tagGroups, terms):
"""
create Tag Groups and Child Tags using data from terms dict
"""
rv = []
for pid in tagGroups:
# In testing we may not have complete set
if pid not in terms.keys():
continue
groupData = terms[pid]
groupName = "[%s] %s" ... | def generate(tagGroups, terms):
"""
create Tag Groups and Child Tags using data from terms dict
"""
rv = []
for pid in tagGroups:
# In testing we may not have complete set
if pid not in terms.keys():
continue
groupData = terms[pid]
groupName = "[%s] %s" ... | [
"create",
"Tag",
"Groups",
"and",
"Child",
"Tags",
"using",
"data",
"from",
"terms",
"dict"
] | ome/omego | python | https://github.com/ome/omego/blob/2dadbf3c6342b6c995f9e0dceaf3c0b7fab030fb/omego/convert.py#L112-L137 | [
"def",
"generate",
"(",
"tagGroups",
",",
"terms",
")",
":",
"rv",
"=",
"[",
"]",
"for",
"pid",
"in",
"tagGroups",
":",
"# In testing we may not have complete set",
"if",
"pid",
"not",
"in",
"terms",
".",
"keys",
"(",
")",
":",
"continue",
"groupData",
"="... | 2dadbf3c6342b6c995f9e0dceaf3c0b7fab030fb |
train | Install._handle_args | We need to support deprecated behaviour for now which makes this
quite complicated
Current behaviour:
- install: Installs a new server, existing server causes an error
- install --upgrade: Installs or upgrades a server
- install --managedb: Automatically initialise or upgrade th... | omego/upgrade.py | def _handle_args(self, cmd, args):
"""
We need to support deprecated behaviour for now which makes this
quite complicated
Current behaviour:
- install: Installs a new server, existing server causes an error
- install --upgrade: Installs or upgrades a server
- ins... | def _handle_args(self, cmd, args):
"""
We need to support deprecated behaviour for now which makes this
quite complicated
Current behaviour:
- install: Installs a new server, existing server causes an error
- install --upgrade: Installs or upgrades a server
- ins... | [
"We",
"need",
"to",
"support",
"deprecated",
"behaviour",
"for",
"now",
"which",
"makes",
"this",
"quite",
"complicated"
] | ome/omego | python | https://github.com/ome/omego/blob/2dadbf3c6342b6c995f9e0dceaf3c0b7fab030fb/omego/upgrade.py#L75-L132 | [
"def",
"_handle_args",
"(",
"self",
",",
"cmd",
",",
"args",
")",
":",
"if",
"cmd",
"==",
"'install'",
":",
"if",
"args",
".",
"upgrade",
":",
"# Current behaviour: install or upgrade",
"if",
"args",
".",
"initdb",
"or",
"args",
".",
"upgradedb",
":",
"rai... | 2dadbf3c6342b6c995f9e0dceaf3c0b7fab030fb |
train | Install.get_server_dir | Either downloads and/or unzips the server if necessary
return: the directory of the unzipped server | omego/upgrade.py | def get_server_dir(self):
"""
Either downloads and/or unzips the server if necessary
return: the directory of the unzipped server
"""
if not self.args.server:
if self.args.skipunzip:
raise Stop(0, 'Unzip disabled, exiting')
log.info('Downl... | def get_server_dir(self):
"""
Either downloads and/or unzips the server if necessary
return: the directory of the unzipped server
"""
if not self.args.server:
if self.args.skipunzip:
raise Stop(0, 'Unzip disabled, exiting')
log.info('Downl... | [
"Either",
"downloads",
"and",
"/",
"or",
"unzips",
"the",
"server",
"if",
"necessary",
"return",
":",
"the",
"directory",
"of",
"the",
"unzipped",
"server"
] | ome/omego | python | https://github.com/ome/omego/blob/2dadbf3c6342b6c995f9e0dceaf3c0b7fab030fb/omego/upgrade.py#L134-L169 | [
"def",
"get_server_dir",
"(",
"self",
")",
":",
"if",
"not",
"self",
".",
"args",
".",
"server",
":",
"if",
"self",
".",
"args",
".",
"skipunzip",
":",
"raise",
"Stop",
"(",
"0",
",",
"'Unzip disabled, exiting'",
")",
"log",
".",
"info",
"(",
"'Downloa... | 2dadbf3c6342b6c995f9e0dceaf3c0b7fab030fb |
train | Install.handle_database | Handle database initialisation and upgrade, taking into account
command line arguments | omego/upgrade.py | def handle_database(self):
"""
Handle database initialisation and upgrade, taking into account
command line arguments
"""
# TODO: When initdb and upgradedb are dropped we can just test
# managedb, but for backwards compatibility we need to support
# initdb without... | def handle_database(self):
"""
Handle database initialisation and upgrade, taking into account
command line arguments
"""
# TODO: When initdb and upgradedb are dropped we can just test
# managedb, but for backwards compatibility we need to support
# initdb without... | [
"Handle",
"database",
"initialisation",
"and",
"upgrade",
"taking",
"into",
"account",
"command",
"line",
"arguments"
] | ome/omego | python | https://github.com/ome/omego/blob/2dadbf3c6342b6c995f9e0dceaf3c0b7fab030fb/omego/upgrade.py#L263-L302 | [
"def",
"handle_database",
"(",
"self",
")",
":",
"# TODO: When initdb and upgradedb are dropped we can just test",
"# managedb, but for backwards compatibility we need to support",
"# initdb without upgradedb and vice-versa",
"if",
"self",
".",
"args",
".",
"initdb",
"or",
"self",
... | 2dadbf3c6342b6c995f9e0dceaf3c0b7fab030fb |
train | Install.run | Runs a command as if from the command-line
without the need for using popen or subprocess | omego/upgrade.py | def run(self, command):
"""
Runs a command as if from the command-line
without the need for using popen or subprocess
"""
if isinstance(command, basestring):
command = command.split()
else:
command = list(command)
self.external.omero_cli(co... | def run(self, command):
"""
Runs a command as if from the command-line
without the need for using popen or subprocess
"""
if isinstance(command, basestring):
command = command.split()
else:
command = list(command)
self.external.omero_cli(co... | [
"Runs",
"a",
"command",
"as",
"if",
"from",
"the",
"command",
"-",
"line",
"without",
"the",
"need",
"for",
"using",
"popen",
"or",
"subprocess"
] | ome/omego | python | https://github.com/ome/omego/blob/2dadbf3c6342b6c995f9e0dceaf3c0b7fab030fb/omego/upgrade.py#L314-L323 | [
"def",
"run",
"(",
"self",
",",
"command",
")",
":",
"if",
"isinstance",
"(",
"command",
",",
"basestring",
")",
":",
"command",
"=",
"command",
".",
"split",
"(",
")",
"else",
":",
"command",
"=",
"list",
"(",
"command",
")",
"self",
".",
"external"... | 2dadbf3c6342b6c995f9e0dceaf3c0b7fab030fb |
train | Install.bin | Runs the omero command-line client with an array of arguments using the
old environment | omego/upgrade.py | def bin(self, command):
"""
Runs the omero command-line client with an array of arguments using the
old environment
"""
if isinstance(command, basestring):
command = command.split()
self.external.omero_bin(command) | def bin(self, command):
"""
Runs the omero command-line client with an array of arguments using the
old environment
"""
if isinstance(command, basestring):
command = command.split()
self.external.omero_bin(command) | [
"Runs",
"the",
"omero",
"command",
"-",
"line",
"client",
"with",
"an",
"array",
"of",
"arguments",
"using",
"the",
"old",
"environment"
] | ome/omego | python | https://github.com/ome/omego/blob/2dadbf3c6342b6c995f9e0dceaf3c0b7fab030fb/omego/upgrade.py#L325-L332 | [
"def",
"bin",
"(",
"self",
",",
"command",
")",
":",
"if",
"isinstance",
"(",
"command",
",",
"basestring",
")",
":",
"command",
"=",
"command",
".",
"split",
"(",
")",
"self",
".",
"external",
".",
"omero_bin",
"(",
"command",
")"
] | 2dadbf3c6342b6c995f9e0dceaf3c0b7fab030fb |
train | Install.symlink_check_and_set | The default symlink was changed from OMERO-CURRENT to OMERO.server.
If `--sym` was not specified and OMERO-CURRENT exists in the current
directory stop and warn. | omego/upgrade.py | def symlink_check_and_set(self):
"""
The default symlink was changed from OMERO-CURRENT to OMERO.server.
If `--sym` was not specified and OMERO-CURRENT exists in the current
directory stop and warn.
"""
if self.args.sym == '':
if os.path.exists('OMERO-CURRENT'... | def symlink_check_and_set(self):
"""
The default symlink was changed from OMERO-CURRENT to OMERO.server.
If `--sym` was not specified and OMERO-CURRENT exists in the current
directory stop and warn.
"""
if self.args.sym == '':
if os.path.exists('OMERO-CURRENT'... | [
"The",
"default",
"symlink",
"was",
"changed",
"from",
"OMERO",
"-",
"CURRENT",
"to",
"OMERO",
".",
"server",
".",
"If",
"--",
"sym",
"was",
"not",
"specified",
"and",
"OMERO",
"-",
"CURRENT",
"exists",
"in",
"the",
"current",
"directory",
"stop",
"and",
... | ome/omego | python | https://github.com/ome/omego/blob/2dadbf3c6342b6c995f9e0dceaf3c0b7fab030fb/omego/upgrade.py#L334-L348 | [
"def",
"symlink_check_and_set",
"(",
"self",
")",
":",
"if",
"self",
".",
"args",
".",
"sym",
"==",
"''",
":",
"if",
"os",
".",
"path",
".",
"exists",
"(",
"'OMERO-CURRENT'",
")",
":",
"log",
".",
"error",
"(",
"'Deprecated OMERO-CURRENT found but --sym not ... | 2dadbf3c6342b6c995f9e0dceaf3c0b7fab030fb |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.