_id stringlengths 2 7 | title stringlengths 1 88 | partition stringclasses 3
values | text stringlengths 75 19.8k | language stringclasses 1
value | meta_information dict |
|---|---|---|---|---|---|
q47700 | ObjectiveRequisiteSession.is_objective_required | train | def is_objective_required(self, objective_id=None, required_objective_id=None):
"""Tests if an objective is required before proceeding with an
objective.
arg: objective_id (osid.id.Id): Id of the dependent Objective
arg: required_objective_id (osid.id.Id): Id of the required
... | python | {
"resource": ""
} |
q47701 | ObjectiveRequisiteAssignmentSession.can_assign_requisites | train | def can_assign_requisites(self):
"""Tests if this user can manage objective requisites.
A return of true does not guarantee successful authorization. A
return of false indicates that it is known mapping methods in
this session will result in a PermissionDenied. This is intended
... | python | {
"resource": ""
} |
q47702 | ObjectiveRequisiteAssignmentSession.assign_objective_requisites | train | def assign_objective_requisites(self, objective_id=None, requisite_objective_ids=None):
"""Creates a requirement dependency between Objective + a list of objectives.
NON-standard method impl by cjshaw
arg: objective_id (osid.id.Id): the Id of the dependent
Objective
a... | python | {
"resource": ""
} |
q47703 | ObjectiveBankAdminSession.create_objective_bank | train | def create_objective_bank(self, objective_bank_form=None):
"""Creates a new ObjectiveBank.
arg: objectiveBankForm (osid.learning.ObjectiveBankForm): the
form for this ObjectiveBank
return: (osid.learning.ObjectiveBankForm) - the new
ObjectiveBank
raise... | python | {
"resource": ""
} |
q47704 | ObjectiveBankAdminSession.delete_objective_bank | train | def delete_objective_bank(self, objective_bank_id=None):
"""Deletes an ObjectiveBank.
arg: objectiveBankId (osid.id.Id): the Id of the
ObjectiveBank to remove
raise: NotFound - objectiveBankId not found
raise: NullArgument - objectiveBankId is null
raise: O... | python | {
"resource": ""
} |
q47705 | ObjectiveBankHierarchySession.get_root_objective_bank_ids | train | def get_root_objective_bank_ids(self, alias):
"""Gets the root objective bank Ids in this hierarchy.
return: (osid.id.IdList) - the root objective bank Ids
raise: OperationFailed - unable to complete request
raise: PermissionDenied - authorization failure
compliance: mandatory... | python | {
"resource": ""
} |
q47706 | _jsTypeof | train | def _jsTypeof(o):
'''Return a string similar to JS's typeof.'''
if o == None:
return 'object'
elif o == Undefined:
return 'undefined'
elif isinstance(o, bool):
return 'boolean'
if isinstance(o, int) or isinstance(o, float):
return 'number'
elif isinstance(o, list)... | python | {
"resource": ""
} |
q47707 | match | train | def match(sel, obj, arr=None, bailout_fn=None):
'''Match a selector to an object, yielding the matched values.
Args:
sel: The JSONSelect selector to apply (a string)
obj: The object against which to apply the selector
arr: If sel contains ? characters, then the values in this array will... | python | {
"resource": ""
} |
q47708 | AgentSearchSession.get_agents_by_search | train | def get_agents_by_search(self, agent_query, agent_search):
"""Pass through to provider AgentSearchSession.get_agents_by_search"""
# Implemented from azosid template for -
# osid.resource.ResourceSearchSession.get_resources_by_search_template
if not self._can('search'):
raise ... | python | {
"resource": ""
} |
q47709 | ffmpeg | train | def ffmpeg(*args, **kwargs):
"""Universal ffmpeg wrapper with progress and error handling"""
ff = FFMPEG(*args, **kwargs)
ff.start(
stdin=kwargs.get("stdin", None),
stdout=kwargs.get("stdout", None),
stderr=kwargs.get("stderr", subprocess.PIPE)
)
ff.wait(kwa... | python | {
"resource": ""
} |
q47710 | Response._get_xml | train | def _get_xml(self, metric):
"""Returns the channel element of the RSS feed"""
self._opener = urllib2.build_opener()
self._opener.addheaders = [('User-agent', self.user_agent)]
if metric:
url = self.base_url + '?w={0}&u=c'.format(self.woeid)
else:
url = se... | python | {
"resource": ""
} |
q47711 | Response._parse_text | train | def _parse_text(self, element_name, namespace=''):
"""
Returns the text, as a string, of the specified element in the specified
namespace of the RSS feed.
Takes element_name and namespace as strings.
"""
try:
text = self._channel.find('.//' + namespace + elem... | python | {
"resource": ""
} |
q47712 | Response._parse_attributes | train | def _parse_attributes(self, element_name, package_class, namespace=''):
"""
Returns an instance of the package_class instantiated with a
dictionary of the attributes from element_name in the specified
namespace of the RSS feed.
"""
return package_class(
self._... | python | {
"resource": ""
} |
q47713 | Response._parse_forecasts | train | def _parse_forecasts(self):
"""
Returns a list of instances of the forecast.Forecast class. Each
instance of the class is instantiated with the attributes of the
forecast elements in the RSS feed.
"""
forecasts = self._channel.findall(
'.//{0}{1}'.format(self.... | python | {
"resource": ""
} |
q47714 | Response._parse_image | train | def _parse_image(self):
"""
Returns an instance of the image.Image class for the RSS feed.
"""
image = {
'title': self._channel.find('./image/title').text,
'width': int(self._channel.find('./image/width').text),
'height': int(self._channel.find('./imag... | python | {
"resource": ""
} |
q47715 | Response._parse_last_build_date | train | def _parse_last_build_date(self):
"""
Returns the last build date of the RSS feed as datetime.datetime
object. Returned datetime is not time-zone aware
"""
date = self._channel.find('lastBuildDate').text
date = parser.parse(date, ignoretz=True)
return date | python | {
"resource": ""
} |
q47716 | Client._get_proxy_info | train | def _get_proxy_info(self, _=None):
"""Generate a ProxyInfo class from a connected SSH transport
Args:
_ (None): Ignored. This is just here as the ProxyInfo spec requires it.
Returns:
SSHTunnelProxyInfo: A ProxyInfo with an active socket tunneled through SSH
"... | python | {
"resource": ""
} |
q47717 | Client._single_request | train | def _single_request(self, method, *args, **kwargs):
"""Make a single request to the fleet API endpoint
Args:
method (str): A dot delimited string indicating the method to call. Example: 'Machines.List'
*args: Passed directly to the method being called.
**kwargs: Pas... | python | {
"resource": ""
} |
q47718 | Client._request | train | def _request(self, method, *args, **kwargs):
"""Make a request with automatic pagination handling
Args:
method (str): A dot delimited string indicating the method to call. Example: 'Machines.List'
*args: Passed directly to the method being called.
**kwargs: Passed d... | python | {
"resource": ""
} |
q47719 | Client.create_unit | train | def create_unit(self, name, unit):
"""Create a new Unit in the cluster
Create and modify Unit entities to communicate to fleet the desired state of the cluster.
This simply declares what should be happening; the backend system still has to react to
the changes in this desired state. The... | python | {
"resource": ""
} |
q47720 | Client.set_unit_desired_state | train | def set_unit_desired_state(self, unit, desired_state):
"""Update the desired state of a unit running in the cluster
Args:
unit (str, Unit): The Unit, or name of the unit to update
desired_state: State the user wishes the Unit to be in
("inactive", "loa... | python | {
"resource": ""
} |
q47721 | Client.destroy_unit | train | def destroy_unit(self, unit):
"""Delete a unit from the cluster
Args:
unit (str, Unit): The Unit, or name of the unit to delete
Returns:
True: The unit was deleted
Raises:
fleet.v1.errors.APIError: Fleet returned a response code >= 400
"""
... | python | {
"resource": ""
} |
q47722 | Client.list_units | train | def list_units(self):
"""Return the current list of the Units in the fleet cluster
Yields:
Unit: The next Unit in the cluster
Raises:
fleet.v1.errors.APIError: Fleet returned a response code >= 400
"""
for page in self._request('Units.List'):
... | python | {
"resource": ""
} |
q47723 | Client.get_unit | train | def get_unit(self, name):
"""Retreive a specifi unit from the fleet cluster by name
Args:
name (str): If specified, only this unit name is returned
Returns:
Unit: The unit identified by ``name`` in the fleet cluster
Raises:
fleet.v1.errors.APIError:... | python | {
"resource": ""
} |
q47724 | Client.list_unit_states | train | def list_unit_states(self, machine_id=None, unit_name=None):
"""Return the current UnitState for the fleet cluster
Args:
machine_id (str): filter all UnitState objects to those
originating from a specific machine
unit_name (str): filter all UnitSt... | python | {
"resource": ""
} |
q47725 | Client.list_machines | train | def list_machines(self):
"""Retrieve a list of machines in the fleet cluster
Yields:
Machine: The next machine in the cluster
Raises:
fleet.v1.errors.APIError: Fleet returned a response code >= 400
"""
# loop through each page of results
for pag... | python | {
"resource": ""
} |
q47726 | Nats.convert | train | def convert(cls, value, from_base, to_base):
"""
Convert value from a base to a base.
:param value: the value to convert
:type value: sequence of int
:param int from_base: base of value
:param int to_base: base of result
:returns: the conversion result
:r... | python | {
"resource": ""
} |
q47727 | Nats.convert_to_int | train | def convert_to_int(value, from_base):
"""
Convert value to an int.
:param value: the value to convert
:type value: sequence of int
:param int from_base: base of value
:returns: the conversion result
:rtype: int
:raises ConvertError: if from_base is less t... | python | {
"resource": ""
} |
q47728 | Nats.convert_from_int | train | def convert_from_int(value, to_base):
"""
Convert int value to a base.
:param int value: the value to convert, must be at least 0
:param int to_base: base of result, must be at least 2
:returns: the conversion result
:rtype: list of int
:raises BasesValueError: i... | python | {
"resource": ""
} |
q47729 | Nats.carry_in | train | def carry_in(value, carry, base):
"""
Add a carry digit to a number represented by ``value``.
:param value: the value
:type value: list of int
:param int carry: the carry digit (>= 0)
:param int base: the base (>= 2)
:returns: carry-out and result
:rtype... | python | {
"resource": ""
} |
q47730 | BitMEX.create_key | train | def create_key(self):
"""Create an API key."""
print("Creating key. Please input the following options:")
name = input("Key name (optional): ")
print("To make this key more secure, you should restrict the IP addresses that can use it. ")
print("To use with all IPs, leave blank or... | python | {
"resource": ""
} |
q47731 | BitMEX.list_keys | train | def list_keys(self):
"""List your API Keys."""
keys = self._curl_bitmex("/apiKey/")
print(json.dumps(keys, sort_keys=True, indent=4)) | python | {
"resource": ""
} |
q47732 | BitMEX.enable_key | train | def enable_key(self):
"""Enable an existing API Key."""
print("This command will enable a disabled key.")
apiKeyID = input("API Key ID: ")
try:
key = self._curl_bitmex("/apiKey/enable",
postdict={"apiKeyID": apiKeyID})
print("Ke... | python | {
"resource": ""
} |
q47733 | BitMEX.disable_key | train | def disable_key(self):
"""Disable an existing API Key."""
print("This command will disable a enabled key.")
apiKeyID = input("API Key ID: ")
try:
key = self._curl_bitmex("/apiKey/disable",
postdict={"apiKeyID": apiKeyID})
print(... | python | {
"resource": ""
} |
q47734 | BitMEX.delete_key | train | def delete_key(self):
"""Delete an existing API Key."""
print("This command will delete an API key.")
apiKeyID = input("API Key ID: ")
try:
self._curl_bitmex("/apiKey/",
postdict={"apiKeyID": apiKeyID}, verb='DELETE')
print("Key with ... | python | {
"resource": ""
} |
q47735 | ColorSystem.load | train | def load(self, filename=None, refresh=False):
"""
Try to load the data from a pre existing data file if it exists.
If the data file does not exist, refresh the data and save it in
the data file for future use.
The data file is a json file.
:param filename: The filename t... | python | {
"resource": ""
} |
q47736 | ColorSystem.request | train | def request(self, *args, **kwargs):
"""
Gets the request using the `_url` and converts it into a
beautiful soup object.
:param args: The args to pass on to `requests`.
:param kwargs: The kwargs to pass on to `requests`.
"""
response = requests... | python | {
"resource": ""
} |
q47737 | ColorSystem.find_closest | train | def find_closest(self, color):
"""
Find the closest color in the system to the given rgb values.
:param color: Tuple of r, g, b values (scaled to 255).
:returns: Tuple of name and rgb closest to the given color.
"""
# Find distance between colors and find name based ... | python | {
"resource": ""
} |
q47738 | Objective.get_assessment_id | train | def get_assessment_id(self):
"""Gets the assessment ``Id`` associated with this learning objective.
return: (osid.id.Id) - the assessment ``Id``
raise: IllegalState - ``has_assessment()`` is ``false``
*compliance: mandatory -- This method must be implemented.*
"""
# Im... | python | {
"resource": ""
} |
q47739 | Objective.get_knowledge_category_id | train | def get_knowledge_category_id(self):
"""Gets the grade ``Id`` associated with the knowledge dimension.
return: (osid.id.Id) - the grade ``Id``
raise: IllegalState - ``has_knowledge_category()`` is ``false``
*compliance: mandatory -- This method must be implemented.*
"""
... | python | {
"resource": ""
} |
q47740 | Objective.get_cognitive_process_id | train | def get_cognitive_process_id(self):
"""Gets the grade ``Id`` associated with the cognitive process.
return: (osid.id.Id) - the grade ``Id``
raise: IllegalState - ``has_cognitive_process()`` is ``false``
*compliance: mandatory -- This method must be implemented.*
"""
# ... | python | {
"resource": ""
} |
q47741 | ObjectiveForm.get_assessment_metadata | train | def get_assessment_metadata(self):
"""Gets the metadata for an assessment.
return: (osid.Metadata) - metadata for the assessment
*compliance: mandatory -- This method must be implemented.*
"""
# Implemented from template for osid.resource.ResourceForm.get_group_metadata_templat... | python | {
"resource": ""
} |
q47742 | ObjectiveForm.clear_assessment | train | def clear_assessment(self):
"""Clears the assessment.
raise: NoAccess - ``Metadata.isRequired()`` or
``Metadata.isReadOnly()`` is ``true``
*compliance: mandatory -- This method must be implemented.*
"""
# Implemented from template for osid.resource.ResourceForm... | python | {
"resource": ""
} |
q47743 | ObjectiveForm.get_knowledge_category_metadata | train | def get_knowledge_category_metadata(self):
"""Gets the metadata for a knowledge category.
return: (osid.Metadata) - metadata for the knowledge category
*compliance: mandatory -- This method must be implemented.*
"""
# Implemented from template for osid.resource.ResourceForm.get... | python | {
"resource": ""
} |
q47744 | ObjectiveForm.set_knowledge_category | train | def set_knowledge_category(self, grade_id):
"""Sets the knowledge category.
arg: grade_id (osid.id.Id): the new knowledge category
raise: InvalidArgument - ``grade_id`` is invalid
raise: NoAccess - ``grade_id`` cannot be modified
raise: NullArgument - ``grade_id`` is ``nul... | python | {
"resource": ""
} |
q47745 | ObjectiveForm.clear_knowledge_category | train | def clear_knowledge_category(self):
"""Clears the knowledge category.
raise: NoAccess - ``Metadata.isRequired()`` or
``Metadata.isReadOnly()`` is ``true``
*compliance: mandatory -- This method must be implemented.*
"""
# Implemented from template for osid.resou... | python | {
"resource": ""
} |
q47746 | ObjectiveForm.get_cognitive_process_metadata | train | def get_cognitive_process_metadata(self):
"""Gets the metadata for a cognitive process.
return: (osid.Metadata) - metadata for the cognitive process
*compliance: mandatory -- This method must be implemented.*
"""
# Implemented from template for osid.resource.ResourceForm.get_gr... | python | {
"resource": ""
} |
q47747 | ObjectiveForm.clear_cognitive_process | train | def clear_cognitive_process(self):
"""Clears the cognitive process.
raise: NoAccess - ``Metadata.isRequired()`` or
``Metadata.isReadOnly()`` is ``true``
*compliance: mandatory -- This method must be implemented.*
"""
# Implemented from template for osid.resourc... | python | {
"resource": ""
} |
q47748 | Activity.get_objective_id | train | def get_objective_id(self):
"""Gets the ``Id`` of the related objective.
return: (osid.id.Id) - the objective ``Id``
*compliance: mandatory -- This method must be implemented.*
"""
# Implemented from template for osid.learning.Activity.get_objective_id
if not bool(self.... | python | {
"resource": ""
} |
q47749 | Activity.get_courses | train | def get_courses(self):
"""Gets any courses associated with this activity.
return: (osid.course.CourseList) - list of courses
raise: IllegalState - ``is_course_based_activity()`` is
``false``
raise: OperationFailed - unable to complete request
*compliance: manda... | python | {
"resource": ""
} |
q47750 | Activity.get_assessments | train | def get_assessments(self):
"""Gets any assessments associated with this activity.
return: (osid.assessment.AssessmentList) - list of assessments
raise: IllegalState - ``is_assessment_based_activity()`` is
``false``
raise: OperationFailed - unable to complete request
... | python | {
"resource": ""
} |
q47751 | ActivityForm.get_assets_metadata | train | def get_assets_metadata(self):
"""Gets the metadata for the assets.
return: (osid.Metadata) - metadata for the assets
*compliance: mandatory -- This method must be implemented.*
"""
# Implemented from template for osid.learning.ActivityForm.get_assets_metadata_template
... | python | {
"resource": ""
} |
q47752 | ActivityForm.clear_assets | train | def clear_assets(self):
"""Clears the assets.
raise: NoAccess - ``Metadata.isRequired()`` or
``Metadata.isReadOnly()`` is ``true``
*compliance: mandatory -- This method must be implemented.*
"""
# Implemented from template for osid.learning.ActivityForm.clear_a... | python | {
"resource": ""
} |
q47753 | ActivityForm.get_courses_metadata | train | def get_courses_metadata(self):
"""Gets the metadata for the courses.
return: (osid.Metadata) - metadata for the courses
*compliance: mandatory -- This method must be implemented.*
"""
# Implemented from template for osid.learning.ActivityForm.get_assets_metadata_template
... | python | {
"resource": ""
} |
q47754 | ActivityForm.clear_courses | train | def clear_courses(self):
"""Clears the courses.
raise: NoAccess - ``Metadata.isRequired()`` or
``Metadata.isReadOnly()`` is ``true``
*compliance: mandatory -- This method must be implemented.*
"""
# Implemented from template for osid.learning.ActivityForm.clear... | python | {
"resource": ""
} |
q47755 | ActivityForm.get_assessments_metadata | train | def get_assessments_metadata(self):
"""Gets the metadata for the assessments.
return: (osid.Metadata) - metadata for the assessments
*compliance: mandatory -- This method must be implemented.*
"""
# Implemented from template for osid.learning.ActivityForm.get_assets_metadata_te... | python | {
"resource": ""
} |
q47756 | ActivityForm.clear_assessments | train | def clear_assessments(self):
"""Clears the assessments.
raise: NoAccess - ``Metadata.isRequired()`` or
``Metadata.isReadOnly()`` is ``true``
*compliance: mandatory -- This method must be implemented.*
"""
# Implemented from template for osid.learning.ActivityFo... | python | {
"resource": ""
} |
q47757 | ProficiencyForm.get_completion_metadata | train | def get_completion_metadata(self):
"""Gets the metadata for completion percentage.
return: (osid.Metadata) - metadata for the completion percentage
*compliance: mandatory -- This method must be implemented.*
"""
# Implemented from template for osid.resource.ResourceForm.get_gro... | python | {
"resource": ""
} |
q47758 | ProficiencyForm.set_completion | train | def set_completion(self, completion):
"""Sets the completion percentage.
arg: completion (decimal): the completion percentage
raise: InvalidArgument - ``completion`` is invalid
raise: NoAccess - ``Metadata.isReadOnly()`` is ``true``
*compliance: mandatory -- This method mus... | python | {
"resource": ""
} |
q47759 | ProficiencyForm.clear_completion | train | def clear_completion(self):
"""Clears the completion.
raise: NoAccess - ``Metadata.isRequired()`` or
``Metadata.isReadOnly()`` is ``true``
*compliance: mandatory -- This method must be implemented.*
"""
# Implemented from template for osid.grading.GradeSystemFo... | python | {
"resource": ""
} |
q47760 | ProficiencyForm.clear_level | train | def clear_level(self):
"""Clears the level.
raise: NoAccess - ``Metadata.isRequired()`` or
``Metadata.isReadOnly()`` is ``true``
*compliance: mandatory -- This method must be implemented.*
"""
if (self.get_level_metadata().is_read_only() or
self... | python | {
"resource": ""
} |
q47761 | ObjectiveBankNode.get_objective_bank | train | def get_objective_bank(self):
"""Gets the ``ObjectiveBank`` at this node.
return: (osid.learning.ObjectiveBank) - the objective bank
represented by this node
*compliance: mandatory -- This method must be implemented.*
"""
if self._lookup_session is None:
... | python | {
"resource": ""
} |
q47762 | ObjectiveBankNode.get_parent_objective_bank_nodes | train | def get_parent_objective_bank_nodes(self):
"""Gets the parents of this objective bank.
return: (osid.learning.ObjectiveBankNodeList) - the parents of
the ``id``
*compliance: mandatory -- This method must be implemented.*
"""
parent_objective_bank_nodes = []
... | python | {
"resource": ""
} |
q47763 | ObjectiveSearchSession.get_objectives_by_search | train | def get_objectives_by_search(self, objective_query, objective_search):
"""Pass through to provider ObjectiveSearchSession.get_objectives_by_search"""
# Implemented from azosid template for -
# osid.resource.ResourceSearchSession.get_resources_by_search_template
if not self._can('search')... | python | {
"resource": ""
} |
q47764 | ActivitySearchSession.get_activities_by_search | train | def get_activities_by_search(self, activity_query, activitiesearch):
"""Pass through to provider ActivitySearchSession.get_activities_by_search"""
# Implemented from azosid template for -
# osid.resource.ResourceSearchSession.get_resources_by_search_template
if not self._can('search'):
... | python | {
"resource": ""
} |
q47765 | ProficiencyLookupSession.get_proficiencies_for_resource_on_date | train | def get_proficiencies_for_resource_on_date(self, resource_id, from_, to):
"""Pass through to provider ProficiencyLookupSession.get_proficiencies_for_resource_on_date"""
# Implemented from azosid template for -
# osid.relationship.RelationshipLookupSession.get_relationships_for_source_on_date_tem... | python | {
"resource": ""
} |
q47766 | ProficiencySearchSession.get_proficiencies_by_search | train | def get_proficiencies_by_search(self, proficiency_query, proficiency_search):
"""Pass through to provider ProficiencySearchSession.get_proficiencies_by_search"""
# Implemented from azosid template for -
# osid.resource.ResourceSearchSession.get_resources_by_search_template
if not self._c... | python | {
"resource": ""
} |
q47767 | compute_bin_edges | train | def compute_bin_edges(features, num_bins, edge_range, trim_outliers, trim_percentile, use_orig_distr=False):
"Compute the edges for the histogram bins to keep it the same for all nodes."
if use_orig_distr:
print('Using original distribution (without histogram) to compute edge weights!')
edges=N... | python | {
"resource": ""
} |
q47768 | extract | train | def extract(features, groups,
weight_method=default_weight_method,
num_bins=default_num_bins,
edge_range=default_edge_range,
trim_outliers=default_trim_behaviour,
trim_percentile=default_trim_percentile,
use_original_distribution=False,
... | python | {
"resource": ""
} |
q47769 | pairwise_extract | train | def pairwise_extract(features, groups, edges, weight_func, use_orig_distr,
group_ids, num_groups, num_links,
non_symmetric, return_networkx_graph, out_weights_path):
"""
Core function to compute the pair-wise histogram distance between all ROIs.
Parameters
----... | python | {
"resource": ""
} |
q47770 | identify_groups | train | def identify_groups(groups):
"""
To compute number of unique elements in a given membership specification.
Parameters
----------
groups : numpy 1d array of length p, each value specifying which group that particular node belongs to.
For examlpe, if you have a cortical thickness values for 1... | python | {
"resource": ""
} |
q47771 | check_param_ranges | train | def check_param_ranges(num_bins, num_groups, num_values, trim_outliers, trim_percentile):
"""Ensuring the parameters are in valid ranges."""
if num_bins < minimum_num_bins:
raise ValueError('Too few bins! The number of bins must be >= 5')
if num_values < num_groups:
raise ValueError('Insuf... | python | {
"resource": ""
} |
q47772 | type_cast_params | train | def type_cast_params(num_bins, edge_range_spec, features, groups):
"""Casting inputs to required types."""
if isinstance(num_bins, str):
# possible when called from CLI
num_bins = np.float(num_bins)
# rounding it to ensure it is int
num_bins = np.rint(num_bins)
if np.isnan(num_bin... | python | {
"resource": ""
} |
q47773 | check_weight_method | train | def check_weight_method(weight_method_spec,
use_orig_distr=False,
allow_non_symmetric=False):
"Check if weight_method is recognized and implemented, or ensure it is callable."
if not isinstance(use_orig_distr, bool):
raise TypeError('use_original_distribu... | python | {
"resource": ""
} |
q47774 | check_params | train | def check_params(features_spec, groups_spec, num_bins, edge_range_spec, trim_outliers, trim_percentile):
"""Necessary check on values, ranges, and types."""
if isinstance(features_spec, str) and isinstance(groups_spec, str):
features, groups = read_features_and_groups(features_spec, groups_spec)
el... | python | {
"resource": ""
} |
q47775 | run_cli | train | def run_cli():
"Command line interface to hiwenet."
features_path, groups_path, weight_method, num_bins, edge_range, \
trim_outliers, trim_percentile, return_networkx_graph, out_weights_path = parse_args()
# TODO add the possibility to process multiple combinations of parameters: diff subjects, diff m... | python | {
"resource": ""
} |
q47776 | read_features_and_groups | train | def read_features_and_groups(features_path, groups_path):
"Reader for data and groups"
try:
if not pexists(features_path):
raise ValueError('non-existent features file')
if not pexists(groups_path):
raise ValueError('non-existent groups file')
if isinstance(fea... | python | {
"resource": ""
} |
q47777 | get_parser | train | def get_parser():
"Specifies the arguments and defaults, and returns the parser."
parser = argparse.ArgumentParser(prog="hiwenet")
parser.add_argument("-f", "--in_features_path", action="store", dest="in_features_path",
required=True,
help="Abs. path to file... | python | {
"resource": ""
} |
q47778 | _init | train | def _init(board, project_dir):
"""
Initialize an OpenAg-based project.
Internal function we use for both init and flash commands.
"""
project_dir = os.path.abspath(project_dir)
# Initialize the platformio project
pio_config_path = os.path.join(project_dir, "platformio.ini")
if not os.pa... | python | {
"resource": ""
} |
q47779 | run | train | def run(
categories, param_file, project_dir, plugin, target,
status_update_interval
):
""" Generate code for this project and run it """
return _run(
categories, param_file, project_dir, plugin, target,
status_update_interval
) | python | {
"resource": ""
} |
q47780 | prune_unspecified_categories | train | def prune_unspecified_categories(modules, categories):
"""
Removes unspecified module categories.
Mutates dictionary and returns it.
"""
res = {}
for mod_name, mod_info in modules.items():
mod_categories = mod_info.get("categories", all_categories)
for category in categories:
... | python | {
"resource": ""
} |
q47781 | load_plugin | train | def load_plugin(plugin_name):
"""
Given a plugin name, load plugin cls from plugin directory.
Will throw an exception if no plugin can be found.
"""
plugin_cls = plugin_map.get(plugin_name, None)
if not plugin_cls:
try:
plugin_module_name, plugin_cls_name = plugin_name.split(... | python | {
"resource": ""
} |
q47782 | lengths_offsets | train | def lengths_offsets(value):
"""Split the given comma separated value to multiple integer values. """
values = []
for item in value.split(','):
item = int(item)
values.append(item)
return values | python | {
"resource": ""
} |
q47783 | is_bam_valid | train | def is_bam_valid(bam_file):
"""Check if bam file is valid. Raises a ValueError if pysam cannot read the file.
#TODO: pysam does not differentiate between BAM and SAM
"""
try:
f = pysam.AlignmentFile(bam_file)
except ValueError:
raise
except:
raise
else:
f.cl... | python | {
"resource": ""
} |
q47784 | is_fasta_valid | train | def is_fasta_valid(fasta_file):
"""Check if fasta file is valid. Raises a ValueError if pysam cannot read the file.
#TODO: pysam does not differentiate between BAM and SAM
"""
try:
f = pysam.FastaFile(fasta_file)
except IOError:
raise
else:
f.close()
return True | python | {
"resource": ""
} |
q47785 | get_first_transcript_name | train | def get_first_transcript_name(fasta_file):
"""Return the first FASTA sequence from the given FASTA file.
Keyword arguments:
fasta_file -- FASTA format file of the transcriptome
"""
with open_pysam_file(fname=fasta_file, ftype='fasta') as f:
transcript_name = f.references[0]
return tran... | python | {
"resource": ""
} |
q47786 | get_fasta_record | train | def get_fasta_record(fasta_file, transcript_name):
"""Return a single transcript from a valid fasta file as a record.
record[transcript_name] = sequence
Keyword arguments:
fasta_file -- FASTA format file of the transcriptome
transcript_name -- Name of the transcript as in the FASTA header
"""... | python | {
"resource": ""
} |
q47787 | get_three_frame_orfs | train | def get_three_frame_orfs(sequence, starts=None, stops=None):
"""Find ORF's in frames 1, 2 and 3 for the given sequence.
Positions returned are 1-based (not 0)
Return format [{'start': start_position, 'stop': stop_position, 'sequence': sequence}, ]
Keyword arguments:
sequence -- sequence for the t... | python | {
"resource": ""
} |
q47788 | get_longest_orf | train | def get_longest_orf(orfs):
"""Find longest ORF from the given list of ORFs."""
sorted_orf = sorted(orfs, key=lambda x: len(x['sequence']), reverse=True)[0]
return sorted_orf | python | {
"resource": ""
} |
q47789 | filter_ribo_counts | train | def filter_ribo_counts(counts, orf_start=None, orf_stop=None):
"""Filter read counts and return only upstream of orf_start or downstream
of orf_stop.
Keyword arguments:
counts -- Ribo-Seq read counts obtained from get_ribo_counts.
orf_start -- Start position of the longest ORF.
orf_stop -- Sto... | python | {
"resource": ""
} |
q47790 | check_required_arguments | train | def check_required_arguments(ribo_file, transcriptome_fasta, transcript_name=None):
"""Check required arguments of both riboplot and ribocount."""
# Is this a valid BAM file? i.e., can pysam read it?
try:
is_bam_valid(ribo_file)
except ValueError:
log.error('The given RiboSeq BAM file is... | python | {
"resource": ""
} |
q47791 | check_rna_file | train | def check_rna_file(rna_file):
"""Check if bedtools is available and if the given RNA-Seq bam file is valid. """
try:
subprocess.check_output(['bedtools', '--version'])
except OSError:
log.error('Could not find bedtools in PATH. bedtools is required '
'for generating RNA cov... | python | {
"resource": ""
} |
q47792 | is_header | train | def is_header(line):
"""true if we are in a header"""
if re.match('^@',line):
f = line.rstrip().split("\t")
if(len(f) > 9):
return False
return True
return False | python | {
"resource": ""
} |
q47793 | sort_header | train | def sort_header(header_text):
"""sort the chromosomes in a header text"""
lines = header_text.rstrip().split("\n")
rlens = {}
for ln in lines:
m = re.match('@SQ\tSN:(\S+)\tLN:(\S+)',ln)
if m:
rlens[m.group(1)] = m.group(2)
output = ''
done_lens = False
for ln in lines:
if re.match('@SQ\t... | python | {
"resource": ""
} |
q47794 | SAM.alignment_ranges | train | def alignment_ranges(self):
"""Put the heavy alignment ranges calculation called on demand and then cached"""
if not self.is_aligned(): raise ValueError("you can't get alignment ranges from something that didn't align")
if self._alignment_ranges: return self._alignment_ranges
self._alignment_ranges ... | python | {
"resource": ""
} |
q47795 | SAM.target_sequence_length | train | def target_sequence_length(self):
""" Get the length of the target sequence. length of the entire chromosome
throws an error if there is no information available
:return: length
:rtype: int
"""
if not self.is_aligned():
raise ValueError("no length for reference when read is not not alig... | python | {
"resource": ""
} |
q47796 | SAM.query_sequence | train | def query_sequence(self):
""" Overrides align. corrects orientation with reverse complement if on negative strand
.. warning:: this returns the full query sequence, not just the aligned portion, but i also does not include hard clipped portions (only soft clipped)
"""
if not self.entries.seq: return No... | python | {
"resource": ""
} |
q47797 | SAM.query_sequence_length | train | def query_sequence_length(self):
""" does not include hard clipped"""
if self.entries.seq: return len(self.entries.seq)
if not self.entries.cigar:
raise ValueError('Cannot give a query length if no cigar and no query sequence are present')
return sum([x[0] for x in self.cigar_array if re.match('[... | python | {
"resource": ""
} |
q47798 | SAM.original_query_sequence_length | train | def original_query_sequence_length(self):
"""Similar to get_get_query_sequence_length, but it also includes
hard clipped bases
if there is no cigar, then default to trying the sequence
:return: the length of the query before any clipping
:rtype: int
"""
if not self.is_aligned() or not self.... | python | {
"resource": ""
} |
q47799 | SAM.actual_original_query_range | train | def actual_original_query_range(self):
""" This accounts for hard clipped bases
and a query sequence that hasnt been reverse complemented
:return: the range covered on the original query sequence
:rtype: GenomicRange
"""
l = self.original_query_sequence_length
a = self.alignment_ranges
... | python | {
"resource": ""
} |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.