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sanoma/django-arctic | arctic/templatetags/arctic_pagination_tags.py | str_to_bool | def str_to_bool(val):
"""
Helper function to turn a string representation of "true" into
boolean True.
"""
if isinstance(val, str):
val = val.lower()
return val in ["true", "on", "yes", True] | python | def str_to_bool(val):
"""
Helper function to turn a string representation of "true" into
boolean True.
"""
if isinstance(val, str):
val = val.lower()
return val in ["true", "on", "yes", True] | [
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sanoma/django-arctic | arctic/templatetags/arctic_pagination_tags.py | arctic_paginate | def arctic_paginate(parser, token):
"""
Renders a Page object with pagination bar.
Example::
{% arctic_paginate page_obj paginator=page_obj.paginator range=10 %}
Named Parameters::
range - The size of the pagination bar (ie, if set to 10 then, at most,
10 page numbers wil... | python | def arctic_paginate(parser, token):
"""
Renders a Page object with pagination bar.
Example::
{% arctic_paginate page_obj paginator=page_obj.paginator range=10 %}
Named Parameters::
range - The size of the pagination bar (ie, if set to 10 then, at most,
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sanoma/django-arctic | arctic/utils.py | menu | def menu(menu_config=None, **kwargs):
"""
Tranforms a menu definition into a dictionary which is a frendlier format
to parse in a template.
"""
request = kwargs.pop("request", None)
user = kwargs.pop("user", None)
url_full_name = ":".join(
[request.resolver_match.namespace, request.r... | python | def menu(menu_config=None, **kwargs):
"""
Tranforms a menu definition into a dictionary which is a frendlier format
to parse in a template.
"""
request = kwargs.pop("request", None)
user = kwargs.pop("user", None)
url_full_name = ":".join(
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sanoma/django-arctic | arctic/utils.py | menu_clean | def menu_clean(menu_config):
"""
Make sure that only the menu item with the largest weight is active.
If a child of a menu item is active, the parent should be active too.
:param menu:
:return:
"""
max_weight = -1
for _, value in list(menu_config.items()):
if value["submenu"]:
... | python | def menu_clean(menu_config):
"""
Make sure that only the menu item with the largest weight is active.
If a child of a menu item is active, the parent should be active too.
:param menu:
:return:
"""
max_weight = -1
for _, value in list(menu_config.items()):
if value["submenu"]:
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sanoma/django-arctic | arctic/utils.py | view_from_url | def view_from_url(named_url): # noqa
"""
Finds and returns the view class from a named url
"""
# code below is `stolen` from django's reverse method.
resolver = get_resolver(get_urlconf())
if type(named_url) in (list, tuple):
named_url = named_url[0]
parts = named_url.split(":")
... | python | def view_from_url(named_url): # noqa
"""
Finds and returns the view class from a named url
"""
# code below is `stolen` from django's reverse method.
resolver = get_resolver(get_urlconf())
if type(named_url) in (list, tuple):
named_url = named_url[0]
parts = named_url.split(":")
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sanoma/django-arctic | arctic/utils.py | find_attribute | def find_attribute(obj, value):
"""
Finds the attribute connected to the last object when a chain of
connected objects is given in a string separated with double underscores.
For example when a model x has a foreign key to model y and model y has
attribute a, findattr(x, 'y__a') will return the a at... | python | def find_attribute(obj, value):
"""
Finds the attribute connected to the last object when a chain of
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sanoma/django-arctic | arctic/utils.py | get_attribute | def get_attribute(obj, value):
"""
Normally the result of list_items for listviews are a set of model objects.
But when you want a GROUP_BY query (with 'values' method), than
the result will be a dict. This method will help you find an item for
either objects or dictionaries.
"""
if type(obj... | python | def get_attribute(obj, value):
"""
Normally the result of list_items for listviews are a set of model objects.
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the result will be a dict. This method will help you find an item for
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sanoma/django-arctic | arctic/utils.py | find_field_meta | def find_field_meta(obj, value):
"""
In a model, finds the attribute meta connected to the last object when
a chain of connected objects is given in a string separated with double
underscores.
"""
if "__" in value:
value_list = value.split("__")
child_obj = obj._meta.get_field(v... | python | def find_field_meta(obj, value):
"""
In a model, finds the attribute meta connected to the last object when
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underscores.
"""
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value_list = value.split("__")
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sanoma/django-arctic | arctic/utils.py | get_field_class | def get_field_class(qs, field_name):
"""
Given a queryset and a field name, it will return the field's class
"""
try:
return qs.model._meta.get_field(field_name).__class__.__name__
# while annotating, it's possible that field does not exists.
except FieldDoesNotExist:
return None | python | def get_field_class(qs, field_name):
"""
Given a queryset and a field name, it will return the field's class
"""
try:
return qs.model._meta.get_field(field_name).__class__.__name__
# while annotating, it's possible that field does not exists.
except FieldDoesNotExist:
return None | [
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sanoma/django-arctic | arctic/utils.py | reverse_url | def reverse_url(url, obj, fallback_field=None):
"""
Reverses a named url, in addition to the standard django reverse, it also
accepts a list of ('named url', 'field1', 'field2', ...) and will use the
value of the supplied fields as arguments.
When a fallback field is given it will use it as an argum... | python | def reverse_url(url, obj, fallback_field=None):
"""
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sanoma/django-arctic | arctic/utils.py | arctic_setting | def arctic_setting(setting_name, valid_options=None):
"""
Tries to get a setting from the django settings, if not available defaults
to the one defined in defaults.py
"""
try:
value = getattr(settings, setting_name)
if valid_options and value not in valid_options:
error_m... | python | def arctic_setting(setting_name, valid_options=None):
"""
Tries to get a setting from the django settings, if not available defaults
to the one defined in defaults.py
"""
try:
value = getattr(settings, setting_name)
if valid_options and value not in valid_options:
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sanoma/django-arctic | arctic/utils.py | offset_limit | def offset_limit(func):
"""
Decorator that converts python slicing to offset and limit
"""
def func_wrapper(self, start, stop):
offset = start
limit = stop - start
return func(self, offset, limit)
return func_wrapper | python | def offset_limit(func):
"""
Decorator that converts python slicing to offset and limit
"""
def func_wrapper(self, start, stop):
offset = start
limit = stop - start
return func(self, offset, limit)
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sanoma/django-arctic | arctic/utils.py | is_list_of_list | def is_list_of_list(item):
"""
check whether the item is list (tuple)
and consist of list (tuple) elements
"""
if (
type(item) in (list, tuple)
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):
return True
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"""
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"""
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sanoma/django-arctic | arctic/utils.py | generate_id | def generate_id(*s):
"""
generates an id from one or more given strings
it uses english as the base language in case some strings
are translated, this ensures consistent ids
"""
with translation.override("en"):
generated_id = slugify("-".join([str(i) for i in s]))
return generated_id | python | def generate_id(*s):
"""
generates an id from one or more given strings
it uses english as the base language in case some strings
are translated, this ensures consistent ids
"""
with translation.override("en"):
generated_id = slugify("-".join([str(i) for i in s]))
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sanoma/django-arctic | arctic/utils.py | append_query_parameter | def append_query_parameter(url, parameters, ignore_if_exists=True):
""" quick and dirty appending of query parameters to a url """
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if key + "=" in url:
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""" quick and dirty appending of query parameters to a url """
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ncrocfer/whatportis | whatportis/__main__.py | get_table | def get_table(ports):
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:param ports: list of found ports
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ncrocfer/whatportis | whatportis/core.py | get_ports | def get_ports(port, like=False):
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CityOfZion/neo-python-rpc | neorpc/Client.py | RPCClient.get_account | def get_account(self, address, id=None, endpoint=None):
"""
Look up an account on the blockchain. Sample output:
Args:
address: (str) address to lookup ( in format 'AXjaFSP23Jkbe6Pk9pPGT6NBDs1HVdqaXK')
id: (int, optional) id to use for response tracking
endp... | python | def get_account(self, address, id=None, endpoint=None):
"""
Look up an account on the blockchain. Sample output:
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address: (str) address to lookup ( in format 'AXjaFSP23Jkbe6Pk9pPGT6NBDs1HVdqaXK')
id: (int, optional) id to use for response tracking
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CityOfZion/neo-python-rpc | neorpc/Client.py | RPCClient.get_height | def get_height(self, id=None, endpoint=None):
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endpoint: (RPCEndpoint, optional) endpoint to specify to use
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json object of the result or the... | python | def get_height(self, id=None, endpoint=None):
"""
Get the current height of the blockchain
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CityOfZion/neo-python-rpc | neorpc/Client.py | RPCClient.get_asset | def get_asset(self, asset_hash, id=None, endpoint=None):
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Get an asset by its hash
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id: (int, optional) id to use for response tracking
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Get an asset by its hash
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CityOfZion/neo-python-rpc | neorpc/Client.py | RPCClient.get_balance | def get_balance(self, asset_hash, id=None, endpoint=None):
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id: (int, optional) id to use for response tracking
... | python | def get_balance(self, asset_hash, id=None, endpoint=None):
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CityOfZion/neo-python-rpc | neorpc/Client.py | RPCClient.get_best_blockhash | def get_best_blockhash(self, id=None, endpoint=None):
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endpoint: (RPCEndpoint, optional) endpoint to specify to use
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json object of the result or the... | python | def get_best_blockhash(self, id=None, endpoint=None):
"""
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endpoint: (RPCEndpoint, optional) endpoint to specify to use
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CityOfZion/neo-python-rpc | neorpc/Client.py | RPCClient.get_block | def get_block(self, height_or_hash, id=None, endpoint=None):
"""
Look up a block by the height or hash of the block.
Args:
height_or_hash: (int or str) either the height of the desired block or its hash in the form '1e67372c158a4cfbb17b9ad3aaae77001a4247a00318e354c62e53b56af4006f'
... | python | def get_block(self, height_or_hash, id=None, endpoint=None):
"""
Look up a block by the height or hash of the block.
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height_or_hash: (int or str) either the height of the desired block or its hash in the form '1e67372c158a4cfbb17b9ad3aaae77001a4247a00318e354c62e53b56af4006f'
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CityOfZion/neo-python-rpc | neorpc/Client.py | RPCClient.get_block_hash | def get_block_hash(self, height, id=None, endpoint=None):
"""
Get hash of a block by its height
Args:
height: (int) height of the block to lookup
id: (int, optional) id to use for response tracking
endpoint: (RPCEndpoint, optional) endpoint to specify to use
... | python | def get_block_hash(self, height, id=None, endpoint=None):
"""
Get hash of a block by its height
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height: (int) height of the block to lookup
id: (int, optional) id to use for response tracking
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CityOfZion/neo-python-rpc | neorpc/Client.py | RPCClient.get_block_header | def get_block_header(self, block_hash, id=None, endpoint=None):
"""
Get the corresponding block header information according to the specified script hash.
Args:
block_hash: (str) the block scripthash (e.g. 'a5508c9b6ed0fc09a531a62bc0b3efcb6b8a9250abaf72ab8e9591294c1f6957')
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Get the corresponding block header information according to the specified script hash.
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block_hash: (str) the block scripthash (e.g. 'a5508c9b6ed0fc09a531a62bc0b3efcb6b8a9250abaf72ab8e9591294c1f6957')
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CityOfZion/neo-python-rpc | neorpc/Client.py | RPCClient.get_block_sysfee | def get_block_sysfee(self, height, id=None, endpoint=None):
"""
Get the system fee of a block by height. This is used in calculating gas claims
Args:
height: (int) height of the block to lookup
id: (int, optional) id to use for response tracking
endpoint: (RP... | python | def get_block_sysfee(self, height, id=None, endpoint=None):
"""
Get the system fee of a block by height. This is used in calculating gas claims
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height: (int) height of the block to lookup
id: (int, optional) id to use for response tracking
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CityOfZion/neo-python-rpc | neorpc/Client.py | RPCClient.get_connection_count | def get_connection_count(self, id=None, endpoint=None):
"""
Gets the number of nodes connected to the endpoint
Args:
id: (int, optional) id to use for response tracking
endpoint: (RPCEndpoint, optional) endpoint to specify to use
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id: (int, optional) id to use for response tracking
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CityOfZion/neo-python-rpc | neorpc/Client.py | RPCClient.get_contract_state | def get_contract_state(self, contract_hash, id=None, endpoint=None):
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Get a contract state object by its hash
Args:
contract_hash: (str) the hash of the contract to lookup, for example 'd7678dd97c000be3f33e9362e673101bac4ca654'
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"""
Get a contract state object by its hash
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CityOfZion/neo-python-rpc | neorpc/Client.py | RPCClient.get_raw_mempool | def get_raw_mempool(self, id=None, endpoint=None):
"""
Returns the tx that are in the memorypool of the endpoint
Args:
id: (int, optional) id to use for response tracking
endpoint: (RPCEndpoint, optional) endpoint to specify to use
Returns:
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"""
Returns the tx that are in the memorypool of the endpoint
Args:
id: (int, optional) id to use for response tracking
endpoint: (RPCEndpoint, optional) endpoint to specify to use
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CityOfZion/neo-python-rpc | neorpc/Client.py | RPCClient.get_transaction | def get_transaction(self, tx_hash, id=None, endpoint=None):
"""
Look up a transaction by hash.
Args:
tx_hash: (str) hash in the form '58c634f81fbd4ae2733d7e3930a9849021840fc19dc6af064d6f2812a333f91d'
id: (int, optional) id to use for response tracking
endpoint... | python | def get_transaction(self, tx_hash, id=None, endpoint=None):
"""
Look up a transaction by hash.
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tx_hash: (str) hash in the form '58c634f81fbd4ae2733d7e3930a9849021840fc19dc6af064d6f2812a333f91d'
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CityOfZion/neo-python-rpc | neorpc/Client.py | RPCClient.get_storage | def get_storage(self, contract_hash, storage_key, id=None, endpoint=None):
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Returns a storage item of a specified contract
Args:
contract_hash: (str) hash of the contract to lookup, for example 'd7678dd97c000be3f33e9362e673101bac4ca654'
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"""
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contract_hash: (str) hash of the contract to lookup, for example 'd7678dd97c000be3f33e9362e673101bac4ca654'
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CityOfZion/neo-python-rpc | neorpc/Client.py | RPCClient.get_tx_out | def get_tx_out(self, tx_hash, vout_id, id=None, endpoint=None):
"""
Gets a transaction output by specified transaction hash and output index
Args:
tx_hash: (str) hash in the form '58c634f81fbd4ae2733d7e3930a9849021840fc19dc6af064d6f2812a333f91d'
vout_id: (int) index of th... | python | def get_tx_out(self, tx_hash, vout_id, id=None, endpoint=None):
"""
Gets a transaction output by specified transaction hash and output index
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tx_hash: (str) hash in the form '58c634f81fbd4ae2733d7e3930a9849021840fc19dc6af064d6f2812a333f91d'
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CityOfZion/neo-python-rpc | neorpc/Client.py | RPCClient.invoke_contract | def invoke_contract(self, contract_hash, params, id=None, endpoint=None):
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contract_hash: (str) hash of the contract, for example 'd7678dd97c000be3f33e9362e673101bac4ca654'
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CityOfZion/neo-python-rpc | neorpc/Client.py | RPCClient.invoke_contract_fn | def invoke_contract_fn(self, contract_hash, operation, params=None, id=None, endpoint=None):
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CityOfZion/neo-python-rpc | neorpc/Client.py | RPCClient.invoke_script | def invoke_script(self, script, id=None, endpoint=None):
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Invokes a script that has been assembled
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script: (str) a hexlified string of a contract invocation script, example '00c10b746f74616c537570706c796754a64cac1b1073e662933ef3e30b007cd98d67d7'
id: (int, optiona... | python | def invoke_script(self, script, id=None, endpoint=None):
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CityOfZion/neo-python-rpc | neorpc/Client.py | RPCClient.send_raw_tx | def send_raw_tx(self, serialized_tx, id=None, endpoint=None):
"""
Submits a serialized tx to the network
Args:
serialized_tx: (str) a hexlified string of a transaction
id: (int, optional) id to use for response tracking
endpoint: (RPCEndpoint, optional) endpoi... | python | def send_raw_tx(self, serialized_tx, id=None, endpoint=None):
"""
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CityOfZion/neo-python-rpc | neorpc/Client.py | RPCClient.validate_addr | def validate_addr(self, address, id=None, endpoint=None):
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address: (str) address to lookup ( in format 'AXjaFSP23Jkbe6Pk9pPGT6NBDs1HVdqaXK')
id: (int, optional) id to use for response tracking
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CityOfZion/neo-python-rpc | neorpc/Client.py | RPCClient.get_peers | def get_peers(self, id=None, endpoint=None):
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Get the current peers of a remote node
Args:
id: (int, optional) id to use for response tracking
endpoint: (RPCEndpoint, optional) endpoint to specify to use
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endpoint: (RPCEndpoint, optional) endpoint to specify to use
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CityOfZion/neo-python-rpc | neorpc/Client.py | RPCClient.get_validators | def get_validators(self, id=None, endpoint=None):
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Returns the current NEO consensus nodes information and voting status.
Args:
id: (int, optional) id to use for response tracking
endpoint: (RPCEndpoint, optional) endpoint to specify to use
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id: (int, optional) id to use for response tracking
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CityOfZion/neo-python-rpc | neorpc/Client.py | RPCClient.get_version | def get_version(self, id=None, endpoint=None):
"""
Get the current version of the endpoint.
Note: Not all endpoints currently implement this method
Args:
id: (int, optional) id to use for response tracking
endpoint: (RPCEndpoint, optional) endpoint to specify to ... | python | def get_version(self, id=None, endpoint=None):
"""
Get the current version of the endpoint.
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CityOfZion/neo-python-rpc | neorpc/Client.py | RPCClient.get_new_address | def get_new_address(self, id=None, endpoint=None):
"""
Create new address
Args:
id: (int, optional) id to use for response tracking
endpoint: (RPCEndpoint, optional) endpoint to specify to use
Returns:
json object of the result or the error encountered... | python | def get_new_address(self, id=None, endpoint=None):
"""
Create new address
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id: (int, optional) id to use for response tracking
endpoint: (RPCEndpoint, optional) endpoint to specify to use
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CityOfZion/neo-python-rpc | neorpc/Client.py | RPCClient.get_wallet_height | def get_wallet_height(self, id=None, endpoint=None):
"""
Get the current wallet index height.
Args:
id: (int, optional) id to use for response tracking
endpoint: (RPCEndpoint, optional) endpoint to specify to use
Returns:
json object of the result or t... | python | def get_wallet_height(self, id=None, endpoint=None):
"""
Get the current wallet index height.
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id: (int, optional) id to use for response tracking
endpoint: (RPCEndpoint, optional) endpoint to specify to use
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CityOfZion/neo-python-rpc | neorpc/Client.py | RPCClient.list_address | def list_address(self, id=None, endpoint=None):
"""
Lists all the addresses in the current wallet.
Args:
id: (int, optional) id to use for response tracking
endpoint: (RPCEndpoint, optional) endpoint to specify to use
Returns:
json object of the result... | python | def list_address(self, id=None, endpoint=None):
"""
Lists all the addresses in the current wallet.
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id: (int, optional) id to use for response tracking
endpoint: (RPCEndpoint, optional) endpoint to specify to use
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CityOfZion/neo-python-rpc | neorpc/Client.py | RPCClient.send_from | def send_from(self, asset_id, addr_from, to_addr, value, fee=None, change_addr=None, id=None, endpoint=None):
"""
Transfer from the specified address to the destination address.
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asset_id: (str) asset identifier (for NEO: 'c56f33fc6ecfcd0c225c4ab356fee59390af8560be0e930faebe74a6... | python | def send_from(self, asset_id, addr_from, to_addr, value, fee=None, change_addr=None, id=None, endpoint=None):
"""
Transfer from the specified address to the destination address.
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CityOfZion/neo-python-rpc | neorpc/Client.py | RPCClient.send_to_address | def send_to_address(self, asset_id, to_addr, value, fee=None, change_addr=None, id=None, endpoint=None):
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CityOfZion/neo-python-rpc | neorpc/Client.py | RPCClient.send_many | def send_many(self, outputs_array, fee=None, change_addr=None, id=None, endpoint=None):
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adrn/schwimmbad | schwimmbad/__init__.py | choose_pool | def choose_pool(mpi=False, processes=1, **kwargs):
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adrn/schwimmbad | schwimmbad/mpi.py | MPIPool.wait | def wait(self, callback=None):
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adrn/schwimmbad | schwimmbad/mpi.py | MPIPool.map | def map(self, worker, tasks, callback=None):
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adrn/schwimmbad | schwimmbad/mpi.py | MPIPool.close | def close(self):
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self.comm.send(None, worker, 0) | python | def close(self):
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adrn/schwimmbad | setup.py | update_git_devstr | def update_git_devstr(version, path=None):
"""
Updates the git revision string if and only if the path is being imported
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the version string is accurate.
"""
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adrn/schwimmbad | schwimmbad/serial.py | SerialPool.map | def map(self, func, iterable, callback=None):
"""A wrapper around the built-in ``map()`` function to provide a
consistent interface with the other ``Pool`` classes.
Parameters
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worker : callable
A function or callable object that is executed on each element... | python | def map(self, func, iterable, callback=None):
"""A wrapper around the built-in ``map()`` function to provide a
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openvax/varcode | varcode/effects/translate.py | translate_codon | def translate_codon(codon, aa_pos):
"""Translate a single codon into a single amino acid or stop '*'
Parameters
----------
codon : str
Expected to be of length 3
aa_pos : int
Codon/amino acid offset into the protein (starting from 0)
"""
# not handling rare Leucine or Valine... | python | def translate_codon(codon, aa_pos):
"""Translate a single codon into a single amino acid or stop '*'
Parameters
----------
codon : str
Expected to be of length 3
aa_pos : int
Codon/amino acid offset into the protein (starting from 0)
"""
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openvax/varcode | varcode/effects/translate.py | translate | def translate(
nucleotide_sequence,
first_codon_is_start=True,
to_stop=True,
truncate=False):
"""Translates cDNA coding sequence into amino acid protein sequence.
Should typically start with a start codon but allowing non-methionine
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first_codon_is_start=True,
to_stop=True,
truncate=False):
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openvax/varcode | varcode/effects/translate.py | find_first_stop_codon | def find_first_stop_codon(nucleotide_sequence):
"""
Given a sequence of codons (expected to have length multiple of three),
return index of first stop codon, or -1 if none is in the sequence.
"""
n_mutant_codons = len(nucleotide_sequence) // 3
for i in range(n_mutant_codons):
codon = nuc... | python | def find_first_stop_codon(nucleotide_sequence):
"""
Given a sequence of codons (expected to have length multiple of three),
return index of first stop codon, or -1 if none is in the sequence.
"""
n_mutant_codons = len(nucleotide_sequence) // 3
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openvax/varcode | varcode/effects/translate.py | translate_in_frame_mutation | def translate_in_frame_mutation(
transcript,
ref_codon_start_offset,
ref_codon_end_offset,
mutant_codons):
"""
Returns:
- mutant amino acid sequence
- offset of first stop codon in the mutant sequence (or -1 if there was none)
- boolean flag indicating whe... | python | def translate_in_frame_mutation(
transcript,
ref_codon_start_offset,
ref_codon_end_offset,
mutant_codons):
"""
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- offset of first stop codon in the mutant sequence (or -1 if there was none)
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openvax/varcode | varcode/cli/genes_script.py | main | def main(args_list=None):
"""
Script which loads variants and annotates them with overlapping genes.
Example usage:
varcode-genes
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--vcf strelka.vcf \
--maf tcga_brca.maf \
--variant chr1 498584 C G \
--json-variants more... | python | def main(args_list=None):
"""
Script which loads variants and annotates them with overlapping genes.
Example usage:
varcode-genes
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--vcf strelka.vcf \
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openvax/varcode | varcode/maf.py | load_maf_dataframe | def load_maf_dataframe(path, nrows=None, raise_on_error=True, encoding=None):
"""
Load the guaranteed columns of a TCGA MAF file into a DataFrame
Parameters
----------
path : str
Path to MAF file
nrows : int
Optional limit to number of rows loaded
raise_on_error : bool
... | python | def load_maf_dataframe(path, nrows=None, raise_on_error=True, encoding=None):
"""
Load the guaranteed columns of a TCGA MAF file into a DataFrame
Parameters
----------
path : str
Path to MAF file
nrows : int
Optional limit to number of rows loaded
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openvax/varcode | varcode/maf.py | load_maf | def load_maf(
path,
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sort_key=variant_ascending_position_sort_key,
distinct=True,
raise_on_error=True,
encoding=None):
"""
Load reference name and Variant objects from MAF filename.
Parameters
----------
path : str
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path,
optional_cols=[],
sort_key=variant_ascending_position_sort_key,
distinct=True,
raise_on_error=True,
encoding=None):
"""
Load reference name and Variant objects from MAF filename.
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openvax/varcode | varcode/effects/effect_ordering.py | apply_to_field_if_exists | def apply_to_field_if_exists(effect, field_name, fn, default):
"""
Apply function to specified field of effect if it is not None,
otherwise return default.
"""
value = getattr(effect, field_name, None)
if value is None:
return default
else:
return fn(value) | python | def apply_to_field_if_exists(effect, field_name, fn, default):
"""
Apply function to specified field of effect if it is not None,
otherwise return default.
"""
value = getattr(effect, field_name, None)
if value is None:
return default
else:
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openvax/varcode | varcode/effects/effect_ordering.py | apply_to_transcript_if_exists | def apply_to_transcript_if_exists(effect, fn, default):
"""
Apply function to transcript associated with effect,
if it exists, otherwise return default.
"""
return apply_to_field_if_exists(
effect=effect,
field_name="transcript",
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default=default) | python | def apply_to_transcript_if_exists(effect, fn, default):
"""
Apply function to transcript associated with effect,
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openvax/varcode | varcode/effects/effect_ordering.py | number_exons_in_associated_transcript | def number_exons_in_associated_transcript(effect):
"""
Number of exons on transcript associated with effect,
if there is one (otherwise return 0).
"""
return apply_to_transcript_if_exists(
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fn=lambda t: len(t.exons),
default=0) | python | def number_exons_in_associated_transcript(effect):
"""
Number of exons on transcript associated with effect,
if there is one (otherwise return 0).
"""
return apply_to_transcript_if_exists(
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openvax/varcode | varcode/effects/effect_ordering.py | cds_length_of_associated_transcript | def cds_length_of_associated_transcript(effect):
"""
Length of coding sequence of transcript associated with effect,
if there is one (otherwise return 0).
"""
return apply_to_transcript_if_exists(
effect=effect,
fn=lambda t: len(t.coding_sequence) if (t.complete and t.coding_sequence... | python | def cds_length_of_associated_transcript(effect):
"""
Length of coding sequence of transcript associated with effect,
if there is one (otherwise return 0).
"""
return apply_to_transcript_if_exists(
effect=effect,
fn=lambda t: len(t.coding_sequence) if (t.complete and t.coding_sequence... | [
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openvax/varcode | varcode/effects/effect_ordering.py | length_of_associated_transcript | def length_of_associated_transcript(effect):
"""
Length of spliced mRNA sequence of transcript associated with effect,
if there is one (otherwise return 0).
"""
return apply_to_transcript_if_exists(
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fn=lambda t: len(t.sequence),
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"""
Length of spliced mRNA sequence of transcript associated with effect,
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openvax/varcode | varcode/effects/effect_ordering.py | name_of_associated_transcript | def name_of_associated_transcript(effect):
"""
Name of transcript associated with effect,
if there is one (otherwise return "").
"""
return apply_to_transcript_if_exists(
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fn=lambda t: t.name,
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"""
Name of transcript associated with effect,
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"""
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openvax/varcode | varcode/effects/effect_ordering.py | gene_id_of_associated_transcript | def gene_id_of_associated_transcript(effect):
"""
Ensembl gene ID of transcript associated with effect, returns
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"""
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default=None) | python | def gene_id_of_associated_transcript(effect):
"""
Ensembl gene ID of transcript associated with effect, returns
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"""
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openvax/varcode | varcode/effects/effect_ordering.py | effect_has_complete_transcript | def effect_has_complete_transcript(effect):
"""
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effect : subclass of MutationEffect
Returns True if effect has transcript and that transcript has complete CDS
"""
return apply_to_transcript_if_exists(
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Parameters
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effect : subclass of MutationEffect
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openvax/varcode | varcode/effects/effect_ordering.py | effect_associated_with_protein_coding_gene | def effect_associated_with_protein_coding_gene(effect):
"""
Parameters
----------
effect : subclass of MutationEffect
Returns True if effect is associated with a gene and that gene
has a protein_coding biotype.
"""
return apply_to_gene_if_exists(
effect=effect,
fn=lambda... | python | def effect_associated_with_protein_coding_gene(effect):
"""
Parameters
----------
effect : subclass of MutationEffect
Returns True if effect is associated with a gene and that gene
has a protein_coding biotype.
"""
return apply_to_gene_if_exists(
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openvax/varcode | varcode/effects/effect_ordering.py | effect_associated_with_protein_coding_transcript | def effect_associated_with_protein_coding_transcript(effect):
"""
Parameters
----------
effect : subclass of MutationEffect
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"""
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openvax/varcode | varcode/effects/effect_ordering.py | parse_transcript_number | def parse_transcript_number(effect):
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Try to parse the number at the end of a transcript name associated with
an effect.
e.g. TP53-001 returns the integer 1.
Parameters
----------
effect : subclass of MutationEffect
Returns int
"""
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Try to parse the number at the end of a transcript name associated with
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openvax/varcode | varcode/effects/effect_ordering.py | select_between_exonic_splice_site_and_alternate_effect | def select_between_exonic_splice_site_and_alternate_effect(effect):
"""
If the given effect is an ExonicSpliceSite then it might contain
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alternate effect. Otherwise, this acts as an identity function.
"""
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If the given effect is an ExonicSpliceSite then it might contain
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openvax/varcode | varcode/effects/effect_ordering.py | keep_max_priority_effects | def keep_max_priority_effects(effects):
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Given a list of effects, only keep the ones with the maximum priority
effect type.
Parameters
----------
effects : list of MutationEffect subclasses
Returns list of same length or shorter
"""
priority_values = map(effect_priority, effects... | python | def keep_max_priority_effects(effects):
"""
Given a list of effects, only keep the ones with the maximum priority
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effects : list of MutationEffect subclasses
Returns list of same length or shorter
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openvax/varcode | varcode/effects/effect_ordering.py | filter_pipeline | def filter_pipeline(effects, filters):
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Apply each filter to the effect list sequentially. If any filter
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return it.
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----------
effects : list of MutationEffect subclass instances
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"""
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openvax/varcode | varcode/effects/effect_ordering.py | top_priority_effect_for_single_gene | def top_priority_effect_for_single_gene(effects):
"""
For effects which are from the same gene, check to see if there
is a canonical transcript with both the maximum length CDS
and maximum length full transcript sequence.
If not, then use number of exons and transcript name as tie-breaking
feat... | python | def top_priority_effect_for_single_gene(effects):
"""
For effects which are from the same gene, check to see if there
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openvax/varcode | varcode/effects/effect_ordering.py | top_priority_effect | def top_priority_effect(effects):
"""
Given a collection of variant transcript effects,
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and whatever else would happen to the exonic sequence if ... | python | def top_priority_effect(effects):
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openvax/varcode | varcode/variant_collection.py | VariantCollection.to_dict | def to_dict(self):
"""
Since Collection.to_dict() returns a state dictionary with an
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"""
return dict(
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distinct=self.distinct,
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sourc... | python | def to_dict(self):
"""
Since Collection.to_dict() returns a state dictionary with an
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return dict(
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openvax/varcode | varcode/variant_collection.py | VariantCollection.clone_with_new_elements | def clone_with_new_elements(self, new_elements):
"""
Create another VariantCollection of the same class and with
same state (including metadata) but possibly different entries.
Warning: metadata is a dictionary keyed by variants. This method
leaves that dictionary as-is, which m... | python | def clone_with_new_elements(self, new_elements):
"""
Create another VariantCollection of the same class and with
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openvax/varcode | varcode/variant_collection.py | VariantCollection.effects | def effects(self, raise_on_error=True):
"""
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raise_on_error : bool, optional
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"""
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raise_on_error : bool, optional
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openvax/varcode | varcode/variant_collection.py | VariantCollection.gene_counts | def gene_counts(self):
"""
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derived class (VariantCollection or EffectCollection) to have
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"""
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"""
Returns number of elements overlapping each gene name. Expects the
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openvax/varcode | varcode/variant_collection.py | VariantCollection.filter_by_transcript_expression | def filter_by_transcript_expression(
self,
transcript_expression_dict,
min_expression_value=0.0):
"""
Filters variants down to those which have overlap a transcript whose
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self,
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openvax/varcode | varcode/variant_collection.py | VariantCollection.filter_by_gene_expression | def filter_by_gene_expression(
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Filters variants down to those which have overlap a gene whose
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... | python | def filter_by_gene_expression(
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Filters variants down to those which have overlap a gene whose
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openvax/varcode | varcode/variant_collection.py | VariantCollection.exactly_equal | def exactly_equal(self, other):
'''
Comparison between VariantCollection instances that takes into account
the info field of Variant instances.
Returns
----------
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collection. The Variant.info... | python | def exactly_equal(self, other):
'''
Comparison between VariantCollection instances that takes into account
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openvax/varcode | varcode/variant_collection.py | VariantCollection._merge_metadata_dictionaries | def _merge_metadata_dictionaries(cls, dictionaries):
"""
Helper function for combining variant collections: given multiple
dictionaries mapping:
source name -> (variant -> (attribute -> value))
Returns dictionary with union of all variants and sources.
"""
#... | python | def _merge_metadata_dictionaries(cls, dictionaries):
"""
Helper function for combining variant collections: given multiple
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source name -> (variant -> (attribute -> value))
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openvax/varcode | varcode/variant_collection.py | VariantCollection._combine_variant_collections | def _combine_variant_collections(cls, combine_fn, variant_collections, kwargs):
"""
Create a single VariantCollection from multiple different collections.
Parameters
----------
cls : class
Should be VariantCollection
combine_fn : function
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Create a single VariantCollection from multiple different collections.
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cls : class
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openvax/varcode | varcode/variant_collection.py | VariantCollection.union | def union(self, *others, **kwargs):
"""
Returns the union of variants in a several VariantCollection objects.
"""
return self._combine_variant_collections(
combine_fn=set.union,
variant_collections=(self,) + others,
kwargs=kwargs) | python | def union(self, *others, **kwargs):
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Returns the union of variants in a several VariantCollection objects.
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openvax/varcode | varcode/variant_collection.py | VariantCollection.intersection | def intersection(self, *others, **kwargs):
"""
Returns the intersection of variants in several VariantCollection objects.
"""
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openvax/varcode | varcode/variant_collection.py | VariantCollection.to_dataframe | def to_dataframe(self):
"""Build a DataFrame from this variant collection"""
def row_from_variant(variant):
return OrderedDict([
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"""Build a DataFrame from this variant collection"""
def row_from_variant(variant):
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openvax/varcode | varcode/string_helpers.py | trim_shared_prefix | def trim_shared_prefix(ref, alt):
"""
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and alternate strings. Examples: C>CT (nucleotides) or GYFP>G (amino acids).
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"""
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openvax/varcode | varcode/string_helpers.py | trim_shared_suffix | def trim_shared_suffix(ref, alt):
"""
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"""
Reuse the `trim_shared_prefix` function above to implement similar
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openvax/varcode | varcode/string_helpers.py | trim_shared_flanking_strings | def trim_shared_flanking_strings(ref, alt):
"""
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if they have a common prefix, a common suffix, and return
their unique components along with the prefix and suffix.
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then the res... | python | def trim_shared_flanking_strings(ref, alt):
"""
Given two nucleotide or amino acid strings, identify
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openvax/varcode | varcode/cli/effects_script.py | main | def main(args_list=None):
"""
Script which loads variants and annotates them with overlapping genes
and predicted coding effects.
Example usage:
varcode
--vcf mutect.vcf \
--vcf strelka.vcf \
--maf tcga_brca.maf \
--variant chr1 498584 C G \
... | python | def main(args_list=None):
"""
Script which loads variants and annotates them with overlapping genes
and predicted coding effects.
Example usage:
varcode
--vcf mutect.vcf \
--vcf strelka.vcf \
--maf tcga_brca.maf \
--variant chr1 498584 C G \
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")",... | Script which loads variants and annotates them with overlapping genes
and predicted coding effects.
Example usage:
varcode
--vcf mutect.vcf \
--vcf strelka.vcf \
--maf tcga_brca.maf \
--variant chr1 498584 C G \
--json-variants more_variants.j... | [
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] | train | https://github.com/openvax/varcode/blob/981633db45ca2b31f76c06894a7360ea5d70a9b8/varcode/cli/effects_script.py#L48-L77 |
openvax/varcode | varcode/effects/effect_prediction_coding_in_frame.py | get_codons | def get_codons(
variant,
trimmed_cdna_ref,
trimmed_cdna_alt,
sequence_from_start_codon,
cds_offset):
"""
Returns indices of first and last reference codons affected by the variant,
as well as the actual sequence of the mutated codons which replace those
reference ... | python | def get_codons(
variant,
trimmed_cdna_ref,
trimmed_cdna_alt,
sequence_from_start_codon,
cds_offset):
"""
Returns indices of first and last reference codons affected by the variant,
as well as the actual sequence of the mutated codons which replace those
reference ... | [
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Parameters
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variant : Variant
trimmed_cdna_ref : str
Trimmed reference cDNA nucleotides affected by the varia... | [
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openvax/varcode | varcode/effects/effect_prediction_coding_in_frame.py | predict_in_frame_coding_effect | def predict_in_frame_coding_effect(
variant,
transcript,
trimmed_cdna_ref,
trimmed_cdna_alt,
sequence_from_start_codon,
cds_offset):
"""Coding effect of an in-frame nucleotide change
Parameters
----------
variant : Variant
transcript : Transcript
... | python | def predict_in_frame_coding_effect(
variant,
transcript,
trimmed_cdna_ref,
trimmed_cdna_alt,
sequence_from_start_codon,
cds_offset):
"""Coding effect of an in-frame nucleotide change
Parameters
----------
variant : Variant
transcript : Transcript
... | [
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Parameters
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variant : Variant
transcript : Transcript
trimmed_cdna_ref : str
Reference nucleotides from the coding sequence of the transcript
trimmed_cdna_alt : str
Nucleotides to insert in place of the reference nucleo... | [
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openvax/varcode | varcode/cli/variant_args.py | add_variant_args | def add_variant_args(arg_parser):
"""
Extends an ArgumentParser instance with the following commandline arguments:
--vcf
--genome
--maf
--variant
--json-variants
"""
variant_arg_group = arg_parser.add_argument_group(
title="Variants",
description="... | python | def add_variant_args(arg_parser):
"""
Extends an ArgumentParser instance with the following commandline arguments:
--vcf
--genome
--maf
--variant
--json-variants
"""
variant_arg_group = arg_parser.add_argument_group(
title="Variants",
description="... | [
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openvax/varcode | varcode/effects/mutate.py | insert_before | def insert_before(sequence, offset, new_residues):
"""Mutate the given sequence by inserting the string `new_residues` before
`offset`.
Parameters
----------
sequence : sequence
String of amino acids or DNA bases
offset : int
Base 0 offset from start of sequence, after which we... | python | def insert_before(sequence, offset, new_residues):
"""Mutate the given sequence by inserting the string `new_residues` before
`offset`.
Parameters
----------
sequence : sequence
String of amino acids or DNA bases
offset : int
Base 0 offset from start of sequence, after which we... | [
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Parameters
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sequence : sequence
String of amino acids or DNA bases
offset : int
Base 0 offset from start of sequence, after which we should insert
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new_residues :... | [
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