text_prompt stringlengths 157 13.1k | code_prompt stringlengths 7 19.8k ⌀ |
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| def full_width_svg(url, width, height, alt_text=None):
''' Helper to render an SVG that will size to fill
its element while keeping its dimentions.
'''
return {
'ratio': str((float(height)/float(width))*100)[:2],
'url': url,
'alt_text': alt_text
} |
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def open(self):
"""Opens a SSH connection with a Pluribus machine.""" |
self._connection = paramiko.SSHClient()
self._connection.set_missing_host_key_policy(paramiko.AutoAddPolicy())
try:
self._connection.connect(hostname=self._hostname,
username=self._username,
password=self._pas... |
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def close(self):
"""Closes the SSH connection if the connection is UP.""" |
if not self.connected:
return None
if self.config is not None:
if self.config.changed() and not self.config.committed():
try:
self.config.discard() # if configuration changed and not committed, will rollback
except pyPluribus.... |
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def cli(self, command):
""" Executes a command and returns raw output from the CLI. :param command: Command to be executed on the CLI. :raise pyPluribus.exceptio... |
if not self.connected:
raise pyPluribus.exceptions.ConnectionError("Not connected to the deivce.")
cli_output = ''
ssh_session = self._connection.get_transport().open_session() # opens a new SSH session
ssh_session.settimeout(self._timeout)
ssh_session.exec_comma... |
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Description:
| def get_data_xlsx(file_name, file_contents=None, on_demand=False):
'''
Loads the new excel format files. Old format files will automatically get loaded as well.
Args:
file_name: The name of the local file, or the holder for the
extension type when the file_contents are supplied.
... |
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| def get_data_xls(file_name, file_contents=None, on_demand=False):
'''
Loads the old excel format files. New format files will automatically
get loaded as well.
Args:
file_name: The name of the local file, or the holder for the
extension type when the file_contents are supplied.
... |
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| def get_data_excel_xml(file_name, file_contents=None, on_demand=False):
'''
Loads xml excel format files.
Args:
file_name: The name of the local file, or the holder for the
extension type when the file_contents are supplied.
file_contents: The file-like object holding contents o... |
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| def get_data_csv(file_name, encoding='utf-8', file_contents=None, on_demand=False):
'''
Gets good old csv data from a file.
Args:
file_name: The name of the local file, or the holder for the
extension type when the file_contents are supplied.
encoding: Loads the file with the sp... |
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Description:
| def write(data, file_name, worksheet_names=None):
'''
Writes 2D tables to file.
Args:
data: 2D list of tables/worksheets.
file_name: Name of the output file (determines type).
worksheet_names: A list of worksheet names (optional).
'''
if re.search(XML_EXT_REGEX, file_name):
... |
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| def write_xls(data, file_name, worksheet_names=None):
'''
Writes out to old excel format.
Args:
data: 2D list of tables/worksheets.
file_name: Name of the output file.
worksheet_names: A list of worksheet names (optional).
'''
workbook = xlwt.Workbook()
for sheet_index, ... |
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| def write_csv(data, file_name, encoding='utf-8'):
'''
Writes out to csv format.
Args:
data: 2D list of tables/worksheets.
file_name: Name of the output file.
'''
name_extension = len(data) > 1
root, ext = os.path.splitext(file_name)
for i, sheet in enumerate(data):
... |
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def get_group(name):
""" Return group with given name, if it exists. Check cache first. """ |
group = cache.get('bits.general.group_%s' % name)
if not group:
group = Group.objects.get(name=name)
cache.set('bits.general.group_%s' % name, group, 365 * 24 * 60 * 60)
return group |
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| def uniqify(list_):
"inefficient on long lists; short lists only. preserves order."
a=[]
for x in list_:
if x not in a: a.append(x)
return a |
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| def eliminate_sequential_children(paths):
"helper for infer_columns. removes paths that are direct children of the n-1 or n-2 path"
return [p for i,p in enumerate(paths) if not ((i>0 and paths[i-1]==p[:-1]) or (i>1 and paths[i-2]==p[:-1]))] |
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| def collapse_group_expr(groupx,cols,ret_row):
"collapses columns matching the group expression. I'm sure this is buggy; look at a real DB's imp of this."
for i,col in enumerate(cols.children):
if col==groupx: ret_row[i]=ret_row[i][0]
return ret_row |
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| def update_aliases(aliases,aonly,x):
"helper for ctor. takes AliasX or string as second arg"
if isinstance(x,basestring): aliases[x]=x
elif isinstance(x,sqparse2.AliasX):
if not isinstance(x.alias,basestring): raise TypeError('alias not string',type(x.alias))
if isinstance(x.name,sqparse2.NameX)... |
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| def resolve_aonly(self,tables_dict,table_ctor):
"circular depends on pgmock.Table. refactor."
for alias,selectx in self.aonly.items():
table = table_ctor(alias,infer_columns(selectx,tables_dict),None)
table.rows = run_select(selectx,tables_dict,table_ctor)
self.aonly[alias] = table
self.ao... |
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| def rowget(self,tables_dict,row_list,index):
"row_list in self.row_order"
tmp=row_list
for i in self.index_tuple(tables_dict,index,False): tmp=tmp[i]
return tmp |
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| def eval_agg_call(self, exp):
"helper for eval_callx; evaluator for CallX that consume multiple rows"
if not isinstance(self.c_row,list): raise TypeError('aggregate function expected a list of rows')
if len(exp.args.children)!=1: raise ValueError('aggregate function expected a single value',exp.args)
ar... |
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| def eval_nonagg_call(self, exp):
"helper for eval_callx; evaluator for CallX that consume a single value"
# todo: get more concrete about argument counts
args=self.eval(exp.args)
if exp.f=='coalesce':
a,b=args # todo: does coalesce take more than 2 args?
return b if a is None else a
elif... |
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| def eval_callx(self, exp):
"dispatch for CallX"
# below: this isn't contains(exp,consumes_row) -- it's just checking the current expression
return (self.eval_agg_call if consumes_rows(exp) else self.eval_nonagg_call)(exp) |
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def redirect_to_handler(error, location):
""" Cause a requset with an error to internally redirect to a URI path. This is generally for internal use, but can be ... |
if callable(location):
location = location()
request.environ['REQUEST_METHOD'] = 'GET'
redirect(location, internal=True) |
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| def _transfer_str(self, conn, tmp, name, data):
''' transfer string to remote file '''
if type(data) == dict:
data = utils.jsonify(data)
afd, afile = tempfile.mkstemp()
afo = os.fdopen(afd, 'w')
try:
afo.write(data.encode('utf8'))
except:
... |
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| def _execute_module(self, conn, tmp, module_name, args,
async_jid=None, async_module=None, async_limit=None, inject=None):
''' runs a module that has already been transferred '''
# hack to support fireball mode
if module_name == 'fireball':
args = "%s password=%s" % (args, ... |
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| def _executor(self, host):
''' handler for multiprocessing library '''
try:
exec_rc = self._executor_internal(host)
#if type(exec_rc) != ReturnData and type(exec_rc) != ansible.runner.return_data.ReturnData:
# raise Exception("unexpected return type: %s" % type(ex... |
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| def _executor_internal(self, host):
''' executes any module one or more times '''
host_variables = self.inventory.get_variables(host)
if self.transport in [ 'paramiko', 'ssh' ]:
port = host_variables.get('ansible_ssh_port', self.remote_port)
if port is None:
... |
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| def _low_level_exec_command(self, conn, cmd, tmp, sudoable=False, executable=None):
''' execute a command string over SSH, return the output '''
if executable is None:
executable = '/bin/sh'
sudo_user = self.sudo_user
rc, stdin, stdout, stderr = conn.exec_command(cmd, tmp, ... |
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| def _remote_md5(self, conn, tmp, path):
''' takes a remote md5sum without requiring python, and returns 0 if no file '''
test = "rc=0; [ -r \"%s\" ] || rc=2; [ -f \"%s\" ] || rc=1" % (path,path)
md5s = [
"(/usr/bin/md5sum %s 2>/dev/null)" % path, # Linux
"(/sbin/md5sum ... |
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| def _make_tmp_path(self, conn):
''' make and return a temporary path on a remote box '''
basefile = 'ansible-%s-%s' % (time.time(), random.randint(0, 2**48))
basetmp = os.path.join(C.DEFAULT_REMOTE_TMP, basefile)
if self.sudo and self.sudo_user != 'root':
basetmp = os.path.j... |
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| def _copy_module(self, conn, tmp, module_name, module_args, inject):
''' transfer a module over SFTP, does not run it '''
if module_name.startswith("/"):
raise errors.AnsibleFileNotFound("%s is not a module" % module_name)
# Search module path(s) for named module.
in_path =... |
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| def _parallel_exec(self, hosts):
''' handles mulitprocessing when more than 1 fork is required '''
if not hosts:
return
p = multiprocessing.Pool(self.forks)
results = []
#results = p.map(multiprocessing_runner, hosts) # can't handle keyboard interrupt
results ... |
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| def _partition_results(self, results):
''' seperate results by ones we contacted & ones we didn't '''
if results is None:
return None
results2 = dict(contacted={}, dark={})
for result in results:
host = result.host
if host is None:
ra... |
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| def run(self):
''' xfer & run module on all matched hosts '''
# find hosts that match the pattern
hosts = self.inventory.list_hosts(self.pattern)
if len(hosts) == 0:
self.callbacks.on_no_hosts()
return dict(contacted={}, dark={})
global multiprocessing_r... |
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| def run_async(self, time_limit):
''' Run this module asynchronously and return a poller. '''
self.background = time_limit
results = self.run()
return results, poller.AsyncPoller(results, self) |
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def image_by_id(self, id):
""" Return image with given Id """ |
if not id:
return None
return next((image for image in self.images() if image['Id'] == id),
None) |
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def image_by_tag(self, tag):
""" Return image with given tag """ |
if not tag:
return None
return next((image for image in self.images() if tag
in image['RepoTags']), None) |
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def image_exists(self, id=None, tag=None):
""" Check if specified image exists """ |
exists = False
if id and self.image_by_id(id):
exists = True
elif tag and self.image_by_tag(tag):
exists = True
return exists |
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def container_by_id(self, id):
""" Returns container with given id """ |
if not id:
return None
return next((container for container in self.containers(all=True)
if container['Id'] == id), None) |
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def container_by_name(self, name):
""" Returns container with given name """ |
if not name:
return None
# docker prepends a '/' to container names in the container dict
name = '/'+name
return next((container for container in self.containers(all=True)
if name in container['Names']), None) |
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def container_exists(self, id=None, name=None):
""" Checks if container exists already """ |
exists = False
if id and self.container_by_id(id):
exists = True
elif name and self.container_by_name(name):
exists = True
return exists |
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def container_running(self, id=None, name=None):
""" Checks if container is running """ |
running = False
if id:
running = self.inspect_container(id)['State']['Running']
elif name:
running = self.inspect_container(name)['State']['Running']
return running |
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def get_container_ip(self, container):
""" Returns the internal ip of the container if available """ |
info = self.inspect_container(container)
if not info:
return None
netInfo = info['NetworkSettings']
if not netInfo:
return None
ip = netInfo['IPAddress']
if not ip:
return None
return ip |
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def _parse(fileobj):
"""Parse fileobj for a shebang.""" |
fileobj.seek(0)
try:
part = fileobj.read(2)
except UnicodeDecodeError:
part = ""
if part == "#!":
shebang = shlex.split(fileobj.readline().strip())
if (platform.system() == "Windows" and
len(shebang) and
os.path.basename(shebang[0]) == "e... |
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def run(self, port=5000, background=False):
""" Runs this application with builtin server for testing. This is only for test usage, do not use in production stag... |
target = os.path.dirname(os.path.abspath(sys.argv[0]))
driver = Driver(self, port, target, 1)
if background:
driver.run_background()
else:
driver.run() |
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def unbind(self, handler, argspec):
""" handler will no longer be called if args match argspec :param argspec: instance of ArgSpec - args to be matched """ |
self.handlers[argspec.key].remove((handler, argspec))
if not len(self.handlers[argspec.key]):
del self.handlers[argspec.key] |
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def dispatch(self, *args, **kwargs):
""" Call handlers that match args or kwargs :return: set of handlers called """ |
called_handlers = set()
for handler_list in self.handlers.values():
for handler, argspec in handler_list:
accept_args, accept_kwargs = argspec.accepts
if handler in called_handlers and False:
continue
else:
... |
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def iterencode(self, o, _one_shot=False):
"""Encode the given object and yield each string representation as available. For example:: for chunk in JSONEncoder().... |
if self.check_circular:
markers = {}
else:
markers = None
if self.ensure_ascii:
_encoder = encode_basestring_ascii
else:
_encoder = encode_basestring
if self.encoding != 'utf-8':
def _encoder(o, _orig_encoder=_encoder, ... |
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def update(self):
""" Updates intension and then adds or includes extension """ |
# updates intension
self.update_intension()
self._size_known_intension = len(self.members)
self._update_members = False |
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def is_entailed_by(self, other):
""" Means merging other with self does not produce any new information. """ |
if not set(self.include.keys()).issubset(set(other.include.keys())):
return False
if not self.exclude.isuperset(other.exclude):
return False
if not self.prototype.is_entailed_by(other.prototype):
return False
return True |
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def get_instances(self):
""" Returns the members of the LazyDict """ |
if self._update_members: self.update()
return iter(sorted(self.members.iteritems())) |
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def bots_list(self):
""" List all user's bots :rtype: list of Bot :return: user's bots """ |
data = self.client.bots()
return [Bot(item) for item in data] |
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def bots_create(self, bot):
""" Save new bot :param bot: bot object to save :type bot: Bot """ |
self.client.bots(_method="POST", _json=bot.to_json(), _params=dict(userToken=self.token)) |
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def bots_get(self, bot):
""" Fetch and fill Bot object :param bot: empty bot object with name to search :type bot: Bot :rtype: Bot :return: filled bot object """ |
data = self.client.bots.__getattr__(bot.name).__call__()
return Bot(data) |
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def bots_delete(self, bot):
""" Delete existing bot :param bot: bot to delete :type bot: Bot """ |
self.client.bots.__getattr__(bot.name).__call__(_method="DELETE", _params=dict(botName=bot.name)) |
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def talk(self, bot, message):
""" Talk to bot and get response based You can use this method to integrate the platform with your own channels :param bot: bot to ... |
data = self.client.talk(_method="POST", _params=dict(botName=bot.name), _json=message.to_json())
return ActionResponse(data) |
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def push(self, bot, channel_type, ar, user_id):
""" Use this method to push message to user of bot. The message should be packed into ActionResponse object. This... |
self.client.push.__getattr__(bot.name).__call__(_method="POST",
_params=dict(id=user_id, channel=channel_type),
_json=ar.to_json()) |
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def broadcast(self, bot, channel_type, text):
""" Use this method to broadcast text message to all users of bot. :param bot: bot that will push user :type bot: B... |
self.client.broadcast.__getattr__(bot.name).__call__(_method="POST",
_params=dict(channel=channel_type),
_json=dict(message=text)) |
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def __parse(self, lines):
""" Parse a list of lines and create an internal property dictionary """ |
# Every line in the file must consist of either a comment
# or a key-value pair. A key-value pair is a line consisting
# of a key which is a combination of non-white space characters
# The separator character between key-value pairs is a '=',
# ':' or a whitespace character not... |
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def load(self, stream):
""" Load properties from an open file stream """ |
# For the time being only accept file input streams
if not _is_file(stream):
raise TypeError('Argument should be a file object!')
# Check for the opened mode
if stream.mode != 'r':
raise ValueError('Stream should be opened in read-only mode!')
try:
... |
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def set_property(self, key, value):
""" Set the property for the given key """ |
if type(key) is str and type(value) is str:
self.process_pair(key, value)
else:
raise TypeError('Both key and value should be strings!') |
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def list(self, out=sys.stdout):
""" Prints a listing of the properties to the stream 'out' which defaults to the standard output """ |
out.write('-- listing properties --\n')
for key,value in self._properties.items():
out.write(''.join((key,'=',value,'\n'))) |
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def store(self, out, header=""):
""" Write the properties list to the stream 'out' along with the optional 'header' """ |
if out.mode[0] != 'w':
raise ValueError('Steam should be opened in write mode!')
try:
out.write(''.join(('#',header,'\n')))
# Write timestamp
tstamp = time.strftime('%a %b %d %H:%M:%S %Z %Y', time.localtime())
out.write(''.join(('#',tstamp,'... |
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Description:
def get_random(self):
"""Get a kitten, either from the db, or a new one. """ |
num_kittens = self.count()
new_cutoff = (num_kittens / (num_kittens + constants.KITTEN_FRESHNESS))
if random.random() < new_cutoff:
return self._rand_inst()
else:
return self.create_new() |
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Description:
def boot():
"""Read configuration files, initialize glin and run main loop""" |
argparser = argparse.ArgumentParser(
description="Controller for LED stripes (WS2801, WS2811 an similar)")
argparser.add_argument("-c", "--config", metavar="CONFIGFILE", dest="configfiles", action='append',
help='Configuration File. May be repeated multiple times. Later confi... |
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def _play_sound(self, filename):
""" Shells player with the provided filename. `filename` Filename for sound file. """ |
command = self._get_external_player()
if not command:
return # no player found
if common.IS_MACOSX:
command += ' "{0}"'.format(filename)
else:
# append quiet flag and filename
is_play = (command == 'play')
command += ' -q "{... |
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def parse_option(self, option, block_name, *values):
""" Parse options for play, end_play, and timer_play. """ |
if len(values) != 1:
raise TypeError
value = os.path.realpath(os.path.expanduser(values[0]))
if not os.path.isfile(value) and not os.path.islink(value):
raise ValueError(u'Sound file "{0}" does not exist'
.format(value))
# special ... |
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def on_taskend(self, task):
""" Play sounds at task end. """ |
key = 'timer' if task.elapsed else 'end'
filename = self.files.get(key)
if filename:
self._play_sound(filename) |
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def _fixpath(root, base):
"""Return absolute, normalized, joined paths""" |
return os.path.abspath(os.path.normpath(os.path.join(root, base))) |
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def _sorter(generated):
"""Return a list of paths sorted by dirname & basename.""" |
pairs = [(os.path.dirname(f), os.path.basename(f))
for f in set(list(generated))]
pairs.sort()
return [os.path.join(pair[0], pair[1]) for pair in pairs] |
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def _walk(recursion):
"""Returns a recursive or non-recursive directory walker""" |
try:
from scandir import walk as walk_function
except ImportError:
from os import walk as walk_function
if recursion:
walk = partial(walk_function)
else:
def walk(path): # pylint: disable=C0111
try:
yield next(walk_function(path))
... |
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def isvalid(path, access=None, extensions=None, filetype=None, minsize=None):
"""Check whether file meets access, extension, size, and type criteria.""" |
return ((access is None or os.access(path, access)) and
(extensions is None or checkext(path, extensions)) and
(((filetype == 'all' and os.path.exists(path)) or
(filetype == 'dir' and os.path.isdir(path)) or
(filetype == 'file' and os.path.isfile(path))) or
... |
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def _generator_file(self):
"""Generator for `self.filetype` of 'file'""" |
for path in self.paths:
if os.path.isfile(path):
if isvalid(path, self.access, self.extensions,
minsize=self.minsize):
yield os.path.abspath(path)
elif os.path.isdir(path):
for root, _, fnames in self._walker... |
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def _generator_other(self):
"""Generator for `self.filetype` other than file""" |
for path in self.paths:
for root, dnames, fnames in self._walker(path):
yield from self._generator_rebase(dnames, root)
yield from self._generator_rebase(fnames, root) |
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def all(self, paths, access=None):
"""Verify list of paths""" |
self.failures = [path for path in paths if not
isvalid(path, access, filetype='all')]
return not self.failures |
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def dirs(self, paths, access=None):
"""Verify list of directories""" |
self.failures = [path for path in paths if not
isvalid(path, access, filetype='dir')]
return not self.failures |
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def files(self, paths, access=None, extensions=None, minsize=None):
"""Verify list of files""" |
self.failures = [path for path in paths if not
isvalid(path, access, extensions, 'file', minsize)]
return not self.failures |
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Description:
def get_manhole_factory(namespace, **passwords):
"""Get a Manhole Factory """ |
realm = manhole_ssh.TerminalRealm()
realm.chainedProtocolFactory.protocolFactory = (
lambda _: EnhancedColoredManhole(namespace)
)
p = portal.Portal(realm)
p.registerChecker(
checkers.InMemoryUsernamePasswordDatabaseDontUse(**passwords)
)
return manhole_ssh.ConchFactory(p) |
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def create_entity(self):
"""Create a new entity. The entity will have a higher UID than any previously associated with this world. :return: the new entity :rtype... |
self._highest_id_seen += 1
entity = Entity(self._highest_id_seen, self)
self._entities.append(entity)
return entity |
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def destroy_entitiy(self, entity):
"""Remove the entity and all connected components from the world. Long-hand for :func:`essence.Entity.destroy`. """ |
for relation in self._database.values():
relation.pop(entity, None)
for l in self._entities_by_component.values():
l.discard(entity)
self._entities.remove(entity) |
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def add_component(self, entity, component):
"""Add component to entity. Long-hand for :func:`essence.Entity.add`. :param entity: entity to associate :type entity... |
component_type = type(component)
relation = self._get_relation(component_type)
if entity in relation:
# PYTHON2.6: Numbers required in format string.
msg = "Component {0} can't be added to entity {1} since it already has a component of type {2}.".format(component, entity... |
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def get_component(self, entity, component_type, missing=MISSING):
"""Get the component of type component_type associated with entity. Long-hand for :func:`essenc... |
relation = self._get_relation(component_type)
if entity not in relation:
if missing is MISSING:
raise NoSuchComponentError()
else:
return missing
return relation[entity] |
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def remove_component(self, entity, component_type):
"""Remove the component of component_type from entity. Long-hand for :func:`essence.Entity.remove`. :param en... |
relation = self._get_relation(component_type)
del relation[entity]
self._entities_with(component_type).remove(entity) |
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def update(self, *args, **kwargs):
"""Calls update on each of the systems self.systems.""" |
for system in self.systems:
system.update(self, *args, **kwargs) |
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def auto_discover():
""" Auto-map urls from controllers directory. Ignored only files and classes that start from underscore. """ |
urls = [
url(r'^admin/', admin.site.urls),
]
# TODO: we can create python package to have a lot of controllers
# in separate files
def get_controllers(module_name):
"""Return list of controllers in a module."""
module = import_module('app.controllers.{}'.format(module_name)... |
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def download_file(url, suffix=''):
"""Download attached file as temporary file. Parameters url : string SCO-API download Url suffix : string, optional If suffix ... |
r = urllib2.urlopen(url)
# Save attached file in temp file and return path to temp file
fd, f_path = tempfile.mkstemp(suffix=suffix)
os.write(fd, r.read())
os.close(fd)
return f_path, suffix |
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def get_resource_listing(url, offset, limit, properties):
"""Gneric method to retrieve a resource listing from a SCO-API. Takes the resource-specific API listing... |
# Create listing query based on given arguments
query = [
QPARA_OFFSET + '=' + str(offset),
QPARA_LIMIT + '=' + str(limit)
]
# Add properties argument if property list is not None and not empty
if not properties is None:
if len(properties) > 0:
query.append(QPARA... |
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def to_local_time(timestamp):
"""Convert a datatime object from UTC time to local time. Adopted from: http://stackoverflow.com/questions/4770297/python-convert-u... |
utc = dt.datetime.strptime(timestamp, '%Y-%m-%dT%H:%M:%S.%f')
# Get UTC and local time zone
from_zone = tz.gettz('UTC')
to_zone = tz.tzlocal()
# Tell the utc object that it is in UTC time zone
utc = utc.replace(tzinfo=from_zone)
# Convert time zone
return utc.astimezone(to_zone) |
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def _load_secret(self, creds_file):
'''read the oauth secrets and account ID from a credentials configuration file''' try: with open(creds_file) as fp: creds = j... | )
sys.stderr.write("\n")
raise e |
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| def get_video_count(self, search_q=None):
'''Return the number of videos in the account'''
if search_q is not None:
params = {'q': search_q}
else:
params = None
url = "/counts/videos"
result = self._make_request(self.CMS_Server, 'GET', url, params=params)... |
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| def post_video(self, videoUrl, name=None, ingestMedia=True):
'''Post and optionally ingest media from the specified URL'''
if name is None:
name = os.path.basename(videoUrl)
url = '/videos'
data = {'name': name}
new_video = self._make_request(self.CMS_Server, 'POST',... |
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Description:
def connect(self):
""" Connects the client to the server and returns it. """ |
key = paramiko.RSAKey(data=base64.b64decode(
app.config['SSH_HOST_KEY']
))
client = paramiko.SSHClient()
client.get_host_keys().add(
app.config['SSH_HOST'],
'ssh-rsa',
key
)
client.connect(
app.config['SSH_HOST'... |
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Description:
def server_rules(self):
""" Reads the server rules from the client and returns it. """ |
sftp = self.client.open_sftp()
try:
rule_path = self.rule_location
try:
stat_entry = sftp.stat(rule_path)
if stat.S_ISDIR(stat_entry.st_mode):
sftp.rmdir(rule_path)
return []
except IOError:
... |
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def _parse(data: str) -> list: """ Parses the given data string and returns a list of rule objects. """ |
if isinstance(data, bytes):
data = data.decode('utf-8')
lines = (
item for item in
(item.strip() for item in data.split('\n'))
if len(item) and not item.startswith('#')
)
rules = []
for line in lines:
rules.append(
... |
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Description:
def jaccardIndex(s1, s2, stranded=False):
""" Compute the Jaccard index for two collections of genomic intervals :param s1: the first set of genomic intervals :p... |
def count(s):
""" sum the size of regions in s. """
tot = 0
for r in s:
tot += len(r)
return tot
if stranded:
raise GenomicIntervalError("Sorry, stranded mode for computing Jaccard " +
"index hasn't been implemented yet.")
s1 = collapseRegions(s1)
s2 ... |
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def intervalTreesFromList(inElements, verbose=False, openEnded=False):
""" build a dictionary, indexed by chrom name, of interval trees for each chrom. :param in... |
elements = {}
if verbose:
totalLines = len(inElements)
pind = ProgressIndicator(totalToDo=totalLines,
messagePrefix="completed",
messageSuffix="of parsing")
for element in inElements:
if element.chrom not in elements:
elements[element.c... |
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Description:
def regionsIntersection(s1, s2, collapse=True):
""" given two lists of genomic regions with chromosome, start and end coordinates, return a new list of regions w... |
debug = False
# we don't need to explicitly check for sorting because sorted order is
# a post-condition of the collapsing function
s1_c = collapseRegions(s1)
s2_c = collapseRegions(s2)
if len(s1_c) == 0 or len(s2_c) == 0:
return []
res = []
j = 0
for i in range(0, len(s1_c)):
if debug:
... |
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Description:
def bucketIterator(elements, buckets):
""" For each bucket in buckets, yield it and any elements that overlap it. :param elements: the genomic intervals to place... |
def check_sorted(current, previous):
if (previous is not None) and \
((previous.chrom > current.chrom) or
((previous.chrom == current.chrom) and
(previous.start > current.start))):
raise GenomicIntervalError("elements not sorted. Saw " +
str(previous... |
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Description:
def parseWigString(line, scoreType=int):
""" Parse a string in simple Wig format and return a GenomicInterval. :param line: the string to be parsed :param scoreT... |
parts = line.split("\t")
if (len(parts) < 4):
raise GenomicIntervalError("failed to parse " + line +
" as wig format, too few fields")
return GenomicInterval(parts[0].strip(), int(parts[1]), int(parts[2]), None,
scoreType(parts[3])) |
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Description:
def parseBEDString(line, scoreType=int, dropAfter=None):
""" Parse a string in BED format and return a GenomicInterval object. :param line: the string to be pars... |
peices = line.split("\t")
if dropAfter is not None:
peices = peices[0:dropAfter]
if len(peices) < 3:
raise GenomicIntervalError("BED elements must have at least chrom, " +
"start and end; found only " +
str(len(peices)) + " in " + line)
chro... |
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Description:
def sameRegion(self, e):
""" Check whether self represents the same DNA region as e. :param e: genomic region to compare against :return: True if self and e are ... |
if e is None:
return False
return (self.chrom == e.chrom and self.start == e.start and
self.end == e.end and self.name == e.name and
self.strand == e.strand) |
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