text stringlengths 78 104k | score float64 0 0.18 |
|---|---|
def __get_keys(self):
""" Return the keys associated with this node by adding its key and then adding parent keys recursively. """
keys = list()
tree_node = self
while tree_node is not None and tree_node.key is not None:
keys.insert(0, tree_node.key)
tree_node = t... | 0.008451 |
def _get_field_values(item, fldnames, rpt_fmt=None, itemid2name=None):
"""Return fieldnames and values of either a namedtuple or GOEnrichmentRecord."""
if hasattr(item, "_fldsdefprt"): # Is a GOEnrichmentRecord
return item.get_field_values(fldnames, rpt_fmt, itemid2name)
if hasattr(i... | 0.012195 |
def get_policy_config(platform,
filters=None,
prepend=True,
pillar_key='acl',
pillarenv=None,
saltenv=None,
merge_pillar=True,
only_lower_merge=False,
... | 0.002194 |
def cond_pop(ol,index,**kwargs):
'''
from elist.jprint import pobj
from elist.elist import *
ol = [{'data':0;'type':'number'},{'data':'x';'type':'str'},{'data':'y';'type':'str'},4]
#cond_func_args is a array
def cond_func(index,value,cond_func_args):
'''
... | 0.01197 |
def device_add(self, mountpoint, *device):
"""
Add one or more devices to btrfs filesystem mounted under `mountpoint`
:param mountpoint: mount point of the btrfs system
:param devices: one ore more devices to add
:return:
"""
if len(device) == 0:
retu... | 0.003922 |
def get_box_files(self, box_key):
'''Gets to file infos in a single box.
Args:
box_key key for the file
return (status code, list of file info dicts)
'''
uri = '/'.join([self.api_uri,
self.boxes_suffix,
box_key,
self.files_suffix
])
return self._req('get', uri) | 0.059016 |
def get_by_index(self, i):
"""Look up a gene set by its index.
Parameters
----------
i: int
The index of the gene set.
Returns
-------
GeneSet
The gene set.
Raises
------
ValueError
If the given index ... | 0.003565 |
def set_contents_from_file(self, fp, headers=None, replace=True,
cb=None, num_cb=10, policy=None, md5=None,
reduced_redundancy=False, query_args=None,
encrypt_key=False, size=None):
"""
Store an object in S3 usi... | 0.001349 |
def bedpe(args):
"""
%prog bedpe bedfile
Convert to bedpe format. Use --span to write another bed file that contain
the span of the read pairs.
"""
from jcvi.assembly.coverage import bed_to_bedpe
p = OptionParser(bedpe.__doc__)
p.add_option("--span", default=False, action="store_true",... | 0.003956 |
def get_area_def(self, dsid):
"""Get area definition for message.
If latlong grid then convert to valid eqc grid.
"""
msg = self._get_message(self._msg_datasets[dsid])
try:
return self._area_def_from_msg(msg)
except (RuntimeError, KeyError):
rais... | 0.005362 |
def jco_from_pestpp_runstorage(rnj_filename,pst_filename):
""" read pars and obs from a pest++ serialized run storage file (e.g., .rnj) and return
pyemu.Jco. This can then be passed to Jco.to_binary or Jco.to_coo, etc., to write jco file
in a subsequent step to avoid memory resource issues associated with... | 0.013523 |
def com_google_fonts_check_metadata_valid_copyright(font_metadata):
"""Copyright notices match canonical pattern in METADATA.pb"""
import re
string = font_metadata.copyright
does_match = re.search(r'Copyright [0-9]{4} The .* Project Authors \([^\@]*\)',
string)
if does_match:
yi... | 0.013514 |
def findHTMLMeta(stream):
"""Look for a meta http-equiv tag with the YADIS header name.
@param stream: Source of the html text
@type stream: Object that implements a read() method that works
like file.read
@return: The URI from which to fetch the XRDS document
@rtype: str
@raises Meta... | 0.000895 |
def paste(self, *args):
""" Usage: paste([PSMRL], text)
If a pattern is specified, the pattern is clicked first. Doesn't support text paths.
``text`` is pasted as is using the OS paste shortcut (Ctrl+V for Windows/Linux, Cmd+V
for OS X). Note that `paste()` does NOT use special formatti... | 0.00609 |
def extend_distribution_substation_overvoltage(network, critical_stations):
"""
Reinforce MV/LV substations due to voltage issues.
A parallel standard transformer is installed.
Parameters
----------
network : :class:`~.grid.network.Network`
critical_stations : :obj:`dict`
Dictionar... | 0.000434 |
def unique_deps(deps):
"""Remove duplicities from deps list of the lists"""
deps.sort()
return list(k for k, _ in itertools.groupby(deps)) | 0.006667 |
def sim(adata, tmax_realization=None, as_heatmap=False, shuffle=False,
show=None, save=None):
"""Plot results of simulation.
Parameters
----------
as_heatmap : bool (default: False)
Plot the timeseries as heatmap.
tmax_realization : int or None (default: False)
Number of obs... | 0.003568 |
def add_server(self,address,port=default_port,password=None,speed=None,valid_times=None,invalid_times=None):
'''
:address: remote address of server, or special string ``local`` to
run the command locally
:valid_times: times when this server is availabl... | 0.014247 |
def _init_metadata(self):
"""stub"""
self._learning_objective_id_metadata = {
'element_id': Id(self.my_osid_object_form._authority,
self.my_osid_object_form._namespace,
'learning_objective_id'),
'element_label': 'Learning ... | 0.002461 |
def gvd(self, wavelength):
'''
The group velocity dispersion (GVD) with respect to wavelength.
Args:
wavelength (float, list, None): The wavelength(s) the GVD will
be evaluated at.
Returns:
float, list: The GVD at the target wavelength(s).
... | 0.007075 |
def list_users(root=None):
'''
.. versionadded:: 2018.3.0
Return a list of all shadow users
root
Directory to chroot into
CLI Example:
.. code-block:: bash
salt '*' shadow.list_users
'''
if root is not None:
getspall = functools.partial(_getspall, root=root)
... | 0.001988 |
def add_command_hooks(commands, srcdir='.'):
"""
Look through setup_package.py modules for functions with names like
``pre_<command_name>_hook`` and ``post_<command_name>_hook`` where
``<command_name>`` is the name of a ``setup.py`` command (e.g. build_ext).
If either hook is present this adds a wr... | 0.000596 |
def do_alarm_update(mc, args):
'''Update the alarm state.'''
fields = {}
fields['alarm_id'] = args.id
if args.state.upper() not in state_types:
errmsg = ('Invalid state, not one of [' +
', '.join(state_types) + ']')
print(errmsg)
return
field... | 0.002985 |
def get_queues(self, service_desk_id, include_count=False, start=0, limit=50):
"""
Returns a page of queues defined inside a service desk, for a given service desk ID.
The returned queues will include an issue count for each queue (represented in issueCount field)
if the query param incl... | 0.005792 |
def toxml(self):
"""
Exports this object into a LEMS XML object
"""
xmlstr = '<ConditionalDerivedVariable name="{0}"'.format(self.name) +\
(' dimension="{0}"'.format(self.dimension) if self.dimension else '') +\
(' exposure="{0}"'.format(self.exposure) if self.exposu... | 0.011589 |
def __get_language_data(self, bundleId, languageId, fallback=False):
"""``GET /{serviceInstanceId}/v2/bundles/{bundleId}/{languageId}``
Gets the resource strings (key/value pairs) for the language. If
``fallback`` is ``True``, source language value is used if translated
value is no... | 0.002766 |
def soft_define_alias(self, name, cmd):
"""Define an alias, but don't raise on an AliasError."""
try:
self.define_alias(name, cmd)
except AliasError, e:
error("Invalid alias: %s" % e) | 0.008658 |
def rerun(client, run, job):
"""Re-run existing workflow or tool using CWL runner."""
from renku.models.provenance import ProcessRun
activity = client.process_commmit()
if not isinstance(activity, ProcessRun):
click.secho('No tool was found.', fg='red', file=sys.stderr)
return
try:... | 0.001271 |
def get_next_sibling(self):
"""
:returns:
The next node's sibling, or None if it was the rightmost
sibling.
"""
siblings = self.get_siblings()
ids = [obj.pk for obj in siblings]
if self.pk in ids:
idx = ids.index(self.pk)
i... | 0.005168 |
def repo_exists(self, auth, username, repo_name):
"""
Returns whether a repository with name ``repo_name`` owned by the user with username ``username`` exists.
:param auth.Authentication auth: authentication object
:param str username: username of owner of repository
:param str ... | 0.005857 |
def get_html_tag_lang_params(index_page):
"""
Parse lang and xml:lang parameters in the ``<html>`` tag.
See
https://www.w3.org/International/questions/qa-html-language-declarations
for details.
Args:
index_page (str): HTML content of the page you wisht to analyze.
Returns:
... | 0.001083 |
def _outputMessages(self, warnings, node):
"""
Map pycodestyle results to messages in pylint, then output them.
@param warnings: it should be a list of tuple including
line number and message id
"""
if not warnings:
# No warnings were found
return... | 0.004902 |
def expand(self, model=None, ignoreFilter=False):
"""
Expands any shortcuts that were created for this query. Shortcuts
provide the user access to joined methods using the '.' accessor to
access individual columns for referenced tables.
:param model | <orb.Model> |... | 0.003809 |
def reset_title(self, title, notebook_identifier):
"""Triggered whenever a notebook tab is switched in the left bar.
Resets the title of the un-docked window to the format 'upper_open_tab / lower_open_tab'
:param title: The name of the newly selected tab
:param notebook: string taking ... | 0.005057 |
def backup_database(args):
'''
Backup one database from CLI
'''
username = args.get('<user>')
password = args.get('<password>')
database = args['<database>']
host = args.get('<host>') or '127.0.0.1'
path = args.get('--path') or os.getcwd()
s3 = args.get('--upload_s3')
glacier = a... | 0.000751 |
def check_length(value, length):
"""
Checks length of value
@param value: value to check
@type value: C{str}
@param length: length checking for
@type length: C{int}
@return: None when check successful
@raise ValueError: check failed
"""
_length = len(value)
if _length != ... | 0.004673 |
def submit(self, job):
""" Submit job to the engine
Args:
job (pyccc.job.Job): Job to submit
"""
self._check_job(job)
if job.workingdir is None:
job.workingdir = self.default_wdir
job.imageid = du.create_provisioned_image(self.client, job.image,
... | 0.004249 |
def check_exclamations_ppm(text):
"""Make sure that the exclamation ppm is under 30."""
err = "leonard.exclamation.30ppm"
msg = u"More than 30 ppm of exclamations. Keep them under control."
regex = r"\w!"
count = len(re.findall(regex, text))
num_words = len(text.split(" "))
ppm = (count*1... | 0.00202 |
def replace(self, pattern, replacement_pattern, **kwargs):
"""
Replaces current given pattern occurence in the document with the replacement pattern.
Usage::
>>> script_editor = Umbra.components_manager.get_interface("factory.script_editor")
True
>>> codeEdi... | 0.006963 |
def unique_iterator(seq):
"""
Returns an iterator containing all non-duplicate elements
in the input sequence.
"""
seen = set()
for item in seq:
if item not in seen:
seen.add(item)
yield item | 0.004049 |
def pitch(times, frequencies, midi=False, unvoiced=False, ax=None, **kwargs):
'''Visualize pitch contours
Parameters
----------
times : np.ndarray, shape=(n,)
Sample times of frequencies
frequencies : np.ndarray, shape=(n,)
frequencies (in Hz) of the pitch contours.
Voicing... | 0.00038 |
def convexhull(data, col, fill=True, point_size=4):
"""
Convex hull for a set of points
:param data: points
:param col: color
:param fill: whether to fill the convexhull polygon or not
:param point_size: size of the points on the convexhull. Points are not rendered if None
"""
from geop... | 0.004598 |
def getDraftThingType(self, thingTypeId, parameters = None):
"""
Retrieves all existing draft thing types.
It accepts accepts an optional query parameters (Dictionary)
In case of failure it throws APIException
"""
draftThingTypeUrl = ApiClient.draftThingTypeUrl % (self.ho... | 0.008463 |
def contains_duplicates(values: Iterable[Any]) -> bool:
"""
Does the iterable contain any duplicate values?
"""
for v in Counter(values).values():
if v > 1:
return True
return False | 0.004525 |
def _serial_send(self, port, payload):
'''
Send data to connected device.
Parameters
----------
port : str
Device name/port.
payload : bytes
Payload to send to device.
'''
if port not in self.open_devices:
# Not connect... | 0.002695 |
def handleProfileChange(self):
"""
Emits that the current profile has changed.
"""
# restore the profile settings
prof = self.currentProfile()
vwidget = self.viewWidget()
if vwidget:
prof.restore(vwidget)
if not self.signalsBlocked(... | 0.010283 |
def send_calibrate_barometer(self):
"""Request barometer calibration."""
calibration_command = self.message_factory.command_long_encode(
self._handler.target_system, 0, # target_system, target_component
mavutil.mavlink.MAV_CMD_PREFLIGHT_CALIBRATION, # command
0, #... | 0.004184 |
def events(network, previous_state, current_state, next_state, nodes,
mechanisms=False):
"""Find all events (mechanisms with actual causes and actual effects)."""
actual_causes = _actual_causes(network, previous_state, current_state,
nodes, mechanisms)
actual_ef... | 0.000896 |
def make_local_settings(argv=None):
"""Generate a local settings file.
The most common usage is:
make-local-settings <env>
where env is replaced with and environment name such as stage or
prod. For example:
make-local-settings prod
This will create a local settings file named lo... | 0.002027 |
def parse_bookmark_node (node):
"""Parse one JSON node of Chromium Bookmarks."""
if node["type"] == "url":
yield node["url"], node["name"]
elif node["type"] == "folder":
for child in node["children"]:
for entry in parse_bookmark_node(child):
yield entry | 0.006472 |
def register_minter(self, name, minter):
"""Register a minter.
:param name: Minter name.
:param minter: The new minter.
"""
assert name not in self.minters
self.minters[name] = minter | 0.008621 |
def get_jids():
'''
Return all job data from all returners
'''
ret = {}
for returner_ in __opts__[CONFIG_KEY]:
ret.update(_mminion().returners['{0}.get_jids'.format(returner_)]())
return ret | 0.004484 |
def frequency_app(parser, cmd, args): # pragma: no cover
"""
perform frequency analysis on a value.
"""
parser.add_argument('value', help='the value to analyse, read from stdin if omitted', nargs='?')
args = parser.parse_args(args)
data = frequency(six.iterbytes(pwnypack.main.binary_value_or_s... | 0.005405 |
def conflicting_pairs(left, right):
"""Yield all ``(object, property)`` pairs where the two definitions disagree."""
objects = left._objects & right._objects
properties = left._properties & right._properties
difference = left._pairs ^ right._pairs
for o in objects:
for p in properties:
... | 0.005263 |
def _unwrap_one_layer(r, L, n):
"""For a set of points in a 2 dimensional periodic system, extend the set of
points to tile the points at a given period.
Parameters
----------
r: float array, shape (:, 2).
Set of points.
L: float array, shape (2,)
System lengths.
n: integer.... | 0.00226 |
def verify_response_time(self, expected_below):
"""
Verify that response time (time span between request-response) is reasonable.
:param expected_below: integer
:return: Nothing
:raises: ValueError if timedelta > expected time
"""
if self.timedelta > expected_bel... | 0.006438 |
def parse_hpo_diseases(hpo_lines):
"""Parse hpo disease phenotypes
Args:
hpo_lines(iterable(str))
Returns:
diseases(dict): A dictionary with mim numbers as keys
"""
diseases = {}
LOG.info("Parsing hpo diseases...")
for index, line in enumerate(hp... | 0.002928 |
def get_doc(self, tag_name):
"Get documentation for the first tag matching the given name"
for tag,func in self.tags:
if tag.startswith(tag_name) and func.__doc__:
return func.__doc__ | 0.013216 |
def put_http_connection(self, host, is_secure, conn):
"""
Adds a connection to the pool of connections that can be
reused for the named host.
"""
with self.mutex:
key = (host, is_secure)
if key not in self.host_to_pool:
self.host_to_pool[ke... | 0.005128 |
async def restart_walk(self):
"""
Force a re-walk
"""
if not self._restartwalk:
self._restartwalk = True
await self.wait_for_send(FlowUpdaterNotification(self, FlowUpdaterNotification.STARTWALK)) | 0.011952 |
def get_html_values(self, pydict, recovery_name=True):
"""Convert naive get response data to human readable field name format.
using html data format.
"""
new_dict = {"id": pydict["id"]}
for field in self:
if field.key in pydict:
if recovery_n... | 0.00611 |
def clean_security_hash(self):
"""Check the security hash."""
security_hash_dict = {
'content_type': self.data.get("content_type", ""),
'object_pk': self.data.get("object_pk", ""),
'timestamp': self.data.get("timestamp", ""),
}
expected_hash = self.gen... | 0.003436 |
def insert_df(self, table_name, df):
"""Create a table and populate it with data from a dataframe."""
df.to_sql(table_name, con=self.own_connection) | 0.012195 |
def register_predictor(cls, name):
"""Register method to keep list of predictors."""
def decorator(subclass):
"""Register as decorator function."""
cls._predictors[name.lower()] = subclass
subclass.name = name.lower()
return subclass
return decorat... | 0.006211 |
def join(self, glue=" "):
""" Javascript's join implementation
"""
j = glue.join([str(x) for x in self.obj])
return self._wrap(j) | 0.012422 |
def mac_set_relative_dylib_deps(libname):
"""
On Mac OS X set relative paths to dynamic library dependencies of `libname`.
Relative paths allow to avoid using environment variable DYLD_LIBRARY_PATH.
There are known some issues with DYLD_LIBRARY_PATH. Relative paths is
more flexible mechanism.
... | 0.00176 |
def get_logged_in_account(token_manager=None,
app_url=defaults.APP_URL):
"""
get the account details for logged in account of the auth token_manager
"""
return get_logged_in_account(token_manager=token_manager,
app_url=app_url)['id'] | 0.003236 |
def inspect_to_container_metadata(c_metadata_object, inspect_data, image_instance):
"""
process data from `docker container inspect` and update provided container metadata object
:param c_metadata_object: instance of ContainerMetadata
:param inspect_data: dict, metadata from `docker inspect` or `docker... | 0.002846 |
def soft_kill(jid, state_id=None):
'''
Set up a state run to die before executing the given state id,
this instructs a running state to safely exit at a given
state id. This needs to pass in the jid of the running state.
If a state_id is not passed then the jid referenced will be safely exited
a... | 0.000978 |
def update_member_data(self, member, member_data):
'''
Update the optional member data for a given member in the leaderboard.
@param member [String] Member name.
@param member_data [String] Optional member data.
'''
self.update_member_data_in(self.leaderboard_name, membe... | 0.00597 |
def set_in(self, que_in, num_senders):
"""Set the queue in input and the number of parallel tasks that send inputs"""
for p in self.processes:
p.set_in(que_in, num_senders) | 0.015 |
def p12d_local(vertices, lame, mu):
"""Local stiffness matrix for P1 elements in 2d."""
assert(vertices.shape == (3, 2))
A = np.vstack((np.ones((1, 3)), vertices.T))
PhiGrad = inv(A)[:, 1:] # gradients of basis functions
R = np.zeros((3, 6))
R[[[0], [2]], [0, 2, 4]] = PhiGrad.T
R[[[2], [1]... | 0.001931 |
def remove_terms(self, terms, ignore_absences=False):
'''Non destructive term removal.
Parameters
----------
terms : list
list of terms to remove
ignore_absences : bool, False by default
if term does not appear, don't raise an error, just move on.
... | 0.005396 |
def loggerLevel(self, logger='root'):
"""
Returns the logging level for the inputed logger.
:param logger | <str> || <logging.Logger>
"""
if isinstance(logger, logging.Logger):
logger = logger.name
return self.handler().loggerLe... | 0.012085 |
def getTypeWidth(self, dtype: "HdlType", do_eval=False) -> Tuple[int, str, bool]:
"""
:return: tuple (current value of width,
string of value (can be ID or int),
Flag which specifies if width of signal is locked
or can be changed by parameter)
"""
rais... | 0.007444 |
def getElementsByClassName(self, className, root='root', useIndex=True):
'''
getElementsByClassName - Searches and returns all elements containing a given class name.
@param className <str> - A one-word class name
@param root <AdvancedTag/'root'> - Sea... | 0.006393 |
def run(self, steps=1000):
"Run the Environment for given number of time steps."
for step in range(steps):
if self.is_done(): return
self.step() | 0.016304 |
def dt_to_struct_time(dt):
"""
Convert a `datetime.date` or `datetime.datetime` to a `struct_time`
representation *with zero values* for data fields that we cannot always
rely on for ancient or far-future dates: tm_wday, tm_yday, tm_isdst
NOTE: If it wasn't for the requirement that the extra fields... | 0.0012 |
def reset(self, *args):
"""Resets any of the tokens for this Application.
Note that you may have to reauthenticate afterwards.
Usage:
application.reset('api_token')
application.reset('api_token', 'totp_secret')
Args:
*args (list of str): one or more of
... | 0.003906 |
def recalculate_stock_values_into_base(self):
""" Loads the exchange rates and recalculates stock holding values into
base currency """
from .currency import CurrencyConverter
conv = CurrencyConverter()
cash = self.model.get_cash_asset_class()
for stock in self.model.s... | 0.004021 |
def wrap_spark_sql_udf(self, name, package_name=None, object_name=None, java_class_instance=None, doc=""):
"""Wraps a scala/java spark user defined function """
def _(*cols):
jcontainer = self.get_java_container(package_name=package_name, object_name=object_name, java_class_instance=java_cla... | 0.007776 |
def plot(*args, legend=None, title=None, x_axis_label="Time (s)", y_axis_label=None,
grid_plot=False, grid_lines=None, grid_columns=None, hor_lines=None, hor_lines_leg=None,
vert_lines=None, vert_lines_leg=None, apply_opensignals_style=True, show_plot=True,
warn_print=False, get_fig_list=Fals... | 0.005218 |
def interpolate_na(self, dim=None, method='linear', limit=None,
use_coordinate=True,
**kwargs):
"""Interpolate values according to different methods.
Parameters
----------
dim : str
Specifies the dimension along which to interpol... | 0.001888 |
def stream(self):
"""The workhorse of cinje: transform input lines and emit output lines.
After constructing an instance with a set of input lines iterate this property to generate the template.
"""
if 'init' not in self.flag:
root = True
self.prepare()
else:
root = False
# Track which lin... | 0.039242 |
def read(cls, source, *args, **kwargs):
"""Read data from a source into a `gwpy.timeseries` object.
This method is just the internal worker for `TimeSeries.read`, and
`TimeSeriesDict.read`, and isn't meant to be called directly.
"""
# if reading a cache, read it now and sieve
if io_cache.is_cac... | 0.001279 |
def set_locale(locale):
'''
Sets the current system locale
CLI Example:
.. code-block:: bash
salt '*' locale.set_locale 'en_US.UTF-8'
'''
lc_ctl = salt.utils.systemd.booted(__context__)
# localectl on SLE12 is installed but the integration is broken -- config is rewritten by YaST2... | 0.001248 |
def create_group(self, data):
"""Create a Group."""
# http://teampasswordmanager.com/docs/api-groups/#create_group
log.info('Create group with %s' % data)
NewID = self.post('groups.json', data).get('id')
log.info('Group has been created with ID %s' % NewID)
return NewID | 0.006289 |
def get_parameters(self):
"""returns a dictionary with the processor's stored parameters"""
parameter_names = self.PARAMETERS.keys()
# TODO: Unresolved reference for processor
parameter_values = [getattr(processor, n) for n in parameter_names]
return dict(zip(parameter_names, par... | 0.00597 |
def sign(payload, key, headers=None, algorithm=ALGORITHMS.HS256):
"""Signs a claims set and returns a JWS string.
Args:
payload (str): A string to sign
key (str or dict): The key to use for signing the claim set. Can be
individual JWK or JWK set.
headers (dict, optional): A ... | 0.001527 |
def draw(self, ar, can, x_tick, x_label, y):
"""Draw a legend entry. X_TICK and X_LABEL are the X location \
(in points) of where the sample and label are drawn."""
rect_size = self.get_rect_size()
line_len = self.get_line_len()
nr_lines = len(self.label.split("\n"))
te... | 0.005348 |
def simulate(self, steps, time, collect_dynamic = False):
"""!
@brief Performs static simulation of oscillatory network.
@param[in] steps (uint): Number simulation steps.
@param[in] time (double): Time of simulation.
@param[in] collect_dynamic (bool): If True - ret... | 0.020651 |
def _process_genes_kegg2ncbi(self, limit=None):
"""
This method maps the KEGG human gene IDs
to the corresponding NCBI Gene IDs.
Triples created:
<kegg_gene_id> is a class
<ncbi_gene_id> is a class
<kegg_gene_id> equivalentClass <ncbi_gene_id>
:param ... | 0.001647 |
def merge_by_adding_new_alts(self, other, ref_seq):
'''Adds other VcfRecord to this one, by adding new field(s) in the ALT
column. Also adds REF nucleotides if they are needed. eg:
ref: ACGT
this var: pos=3, REF=T, ALT=A
other var: pos=1, REF=C, ALT=T
will change this var... | 0.003043 |
def encode(cls, document, check_keys=False,
codec_options=DEFAULT_CODEC_OPTIONS):
"""Encode a document to a new :class:`BSON` instance.
A document can be any mapping type (like :class:`dict`).
Raises :class:`TypeError` if `document` is not a mapping type,
or contains key... | 0.002593 |
def run(pcap):
"""
Runs all configured IDS instances against the supplied pcap.
:param pcap: File path to pcap file to analyse
:returns: Dict with details and results of run/s
"""
start = datetime.now()
errors = []
status = STATUS_FAILED
analyses = []
pool = ThreadPool(MAX_THREA... | 0.007373 |
def fit(self, X, R):
"""Compute Hierarchical Topographical Factor Analysis Model
[Manning2014-1][Manning2014-2]
Parameters
----------
X : list of 2D arrays, element i has shape=[voxels_i, samples]
Each element in the list contains the fMRI data of one subject.
... | 0.001832 |
def process_post_form(self, success_message=None):
"""
As long as the form is set on the view this method will validate the form
and save the submitted data. Only call this if you are posting data.
The given success_message will be used with the djanog messages framework
if the ... | 0.003872 |
def date_map(doc, datemap_list, time_format=None):
'''
For all the datetime fields in "datemap" find that key in doc and map the datetime object to
a strftime string. This pprint and others will print out readable datetimes.
'''
if datemap_list:
for i in datemap_list:... | 0.012739 |
def terms_updated(sender, **kwargs):
"""Called when terms and conditions is changed - to force cache clearing"""
LOGGER.debug("T&C Updated Signal Handler")
cache.delete('tandc.active_terms_ids')
cache.delete('tandc.active_terms_list')
if kwargs.get('instance').slug:
cache.delete('tandc.activ... | 0.002028 |
def _allocate_address(self, instance, network_ids):
"""
Allocates a floating/public ip address to the given instance.
:param instance: instance to assign address to
:param list network_id: List of IDs (as strings) of networks where to
request allocation the floating IP.
... | 0.002911 |
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