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eandersson/amqpstorm | amqpstorm/basic.py | Basic.ack | def ack(self, delivery_tag=0, multiple=False):
"""Acknowledge Message.
:param int/long delivery_tag: Server-assigned delivery tag
:param bool multiple: Acknowledge multiple messages
:raises AMQPInvalidArgument: Invalid Parameters
:raises AMQPChannelError: Raises if the channel ... | python | def ack(self, delivery_tag=0, multiple=False):
"""Acknowledge Message.
:param int/long delivery_tag: Server-assigned delivery tag
:param bool multiple: Acknowledge multiple messages
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eandersson/amqpstorm | amqpstorm/basic.py | Basic.nack | def nack(self, delivery_tag=0, multiple=False, requeue=True):
"""Negative Acknowledgement.
:param int/long delivery_tag: Server-assigned delivery tag
:param bool multiple: Negative acknowledge multiple messages
:param bool requeue: Re-queue the message
:raises AMQPInvalidArgume... | python | def nack(self, delivery_tag=0, multiple=False, requeue=True):
"""Negative Acknowledgement.
:param int/long delivery_tag: Server-assigned delivery tag
:param bool multiple: Negative acknowledge multiple messages
:param bool requeue: Re-queue the message
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eandersson/amqpstorm | amqpstorm/basic.py | Basic.reject | def reject(self, delivery_tag=0, requeue=True):
"""Reject Message.
:param int/long delivery_tag: Server-assigned delivery tag
:param bool requeue: Re-queue the message
:raises AMQPInvalidArgument: Invalid Parameters
:raises AMQPChannelError: Raises if the channel encountered an... | python | def reject(self, delivery_tag=0, requeue=True):
"""Reject Message.
:param int/long delivery_tag: Server-assigned delivery tag
:param bool requeue: Re-queue the message
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eandersson/amqpstorm | amqpstorm/basic.py | Basic._consume_add_and_get_tag | def _consume_add_and_get_tag(self, consume_rpc_result):
"""Add the tag to the channel and return it.
:param dict consume_rpc_result:
:rtype: str
"""
consumer_tag = consume_rpc_result['consumer_tag']
self._channel.add_consumer_tag(consumer_tag)
return consumer_ta... | python | def _consume_add_and_get_tag(self, consume_rpc_result):
"""Add the tag to the channel and return it.
:param dict consume_rpc_result:
:rtype: str
"""
consumer_tag = consume_rpc_result['consumer_tag']
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eandersson/amqpstorm | amqpstorm/basic.py | Basic._consume_rpc_request | def _consume_rpc_request(self, arguments, consumer_tag, exclusive, no_ack,
no_local, queue):
"""Create a Consume Frame and execute a RPC request.
:param str queue: Queue name
:param str consumer_tag: Consumer tag
:param bool no_local: Do not deliver own mess... | python | def _consume_rpc_request(self, arguments, consumer_tag, exclusive, no_ack,
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eandersson/amqpstorm | amqpstorm/basic.py | Basic._validate_publish_parameters | def _validate_publish_parameters(body, exchange, immediate, mandatory,
properties, routing_key):
"""Validate Publish Parameters.
:param bytes|str|unicode body: Message payload
:param str routing_key: Message routing key
:param str exchange: The excha... | python | def _validate_publish_parameters(body, exchange, immediate, mandatory,
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"""Validate Publish Parameters.
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eandersson/amqpstorm | amqpstorm/basic.py | Basic._handle_utf8_payload | def _handle_utf8_payload(body, properties):
"""Update the Body and Properties to the appropriate encoding.
:param bytes|str|unicode body: Message payload
:param dict properties: Message properties
:return:
"""
if 'content_encoding' not in properties:
propert... | python | def _handle_utf8_payload(body, properties):
"""Update the Body and Properties to the appropriate encoding.
:param bytes|str|unicode body: Message payload
:param dict properties: Message properties
:return:
"""
if 'content_encoding' not in properties:
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eandersson/amqpstorm | amqpstorm/basic.py | Basic._get_message | def _get_message(self, get_frame, auto_decode):
"""Get and return a message using a Basic.Get frame.
:param Basic.Get get_frame:
:param bool auto_decode: Auto-decode strings when possible.
:rtype: Message
"""
message_uuid = self._channel.rpc.register_request(
... | python | def _get_message(self, get_frame, auto_decode):
"""Get and return a message using a Basic.Get frame.
:param Basic.Get get_frame:
:param bool auto_decode: Auto-decode strings when possible.
:rtype: Message
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message_uuid = self._channel.rpc.register_request(
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eandersson/amqpstorm | amqpstorm/basic.py | Basic._publish_confirm | def _publish_confirm(self, frames_out):
"""Confirm that message was published successfully.
:param list frames_out:
:rtype: bool
"""
confirm_uuid = self._channel.rpc.register_request(['Basic.Ack',
'Basic.Nack'])
... | python | def _publish_confirm(self, frames_out):
"""Confirm that message was published successfully.
:param list frames_out:
:rtype: bool
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confirm_uuid = self._channel.rpc.register_request(['Basic.Ack',
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eandersson/amqpstorm | amqpstorm/basic.py | Basic._create_content_body | def _create_content_body(self, body):
"""Split body based on the maximum frame size.
This function is based on code from Rabbitpy.
https://github.com/gmr/rabbitpy
:param bytes|str|unicode body: Message payload
:rtype: collections.Iterable
"""
frames = i... | python | def _create_content_body(self, body):
"""Split body based on the maximum frame size.
This function is based on code from Rabbitpy.
https://github.com/gmr/rabbitpy
:param bytes|str|unicode body: Message payload
:rtype: collections.Iterable
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eandersson/amqpstorm | amqpstorm/basic.py | Basic._get_content_body | def _get_content_body(self, message_uuid, body_size):
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:param int body_size: Content Size.
:rtype: str
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:param str uuid_body: Rpc Identifier.
:param int body_size: Content Size.
:rtype: str
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eandersson/amqpstorm | amqpstorm/queue.py | Queue.declare | def declare(self, queue='', passive=False, durable=False,
exclusive=False, auto_delete=False, arguments=None):
"""Declare a Queue.
:param str queue: Queue name
:param bool passive: Do not create
:param bool durable: Durable queue
:param bool exclusive: Request ex... | python | def declare(self, queue='', passive=False, durable=False,
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eandersson/amqpstorm | amqpstorm/queue.py | Queue.delete | def delete(self, queue='', if_unused=False, if_empty=False):
"""Delete a Queue.
:param str queue: Queue name
:param bool if_unused: Delete only if unused
:param bool if_empty: Delete only if empty
:raises AMQPInvalidArgument: Invalid Parameters
:raises AMQPChannelError:... | python | def delete(self, queue='', if_unused=False, if_empty=False):
"""Delete a Queue.
:param str queue: Queue name
:param bool if_unused: Delete only if unused
:param bool if_empty: Delete only if empty
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eandersson/amqpstorm | amqpstorm/queue.py | Queue.purge | def purge(self, queue):
"""Purge a Queue.
:param str queue: Queue name
:raises AMQPInvalidArgument: Invalid Parameters
:raises AMQPChannelError: Raises if the channel encountered an error.
:raises AMQPConnectionError: Raises if the connection
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"""Purge a Queue.
:param str queue: Queue name
:raises AMQPInvalidArgument: Invalid Parameters
:raises AMQPChannelError: Raises if the channel encountered an error.
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eandersson/amqpstorm | amqpstorm/queue.py | Queue.bind | def bind(self, queue='', exchange='', routing_key='', arguments=None):
"""Bind a Queue.
:param str queue: Queue name
:param str exchange: Exchange name
:param str routing_key: The routing key to use
:param dict arguments: Bind key/value arguments
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:param str queue: Queue name
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:param str routing_key: The routing key to use
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eandersson/amqpstorm | amqpstorm/queue.py | Queue.unbind | def unbind(self, queue='', exchange='', routing_key='', arguments=None):
"""Unbind a Queue.
:param str queue: Queue name
:param str exchange: Exchange name
:param str routing_key: The routing key used
:param dict arguments: Unbind key/value arguments
:raises AMQPInvalid... | python | def unbind(self, queue='', exchange='', routing_key='', arguments=None):
"""Unbind a Queue.
:param str queue: Queue name
:param str exchange: Exchange name
:param str routing_key: The routing key used
:param dict arguments: Unbind key/value arguments
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eandersson/amqpstorm | amqpstorm/channel0.py | Channel0.on_frame | def on_frame(self, frame_in):
"""Handle frames sent to Channel0.
:param frame_in: Amqp frame.
:return:
"""
LOGGER.debug('Frame Received: %s', frame_in.name)
if frame_in.name == 'Heartbeat':
return
elif frame_in.name == 'Connection.Close':
... | python | def on_frame(self, frame_in):
"""Handle frames sent to Channel0.
:param frame_in: Amqp frame.
:return:
"""
LOGGER.debug('Frame Received: %s', frame_in.name)
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"""
self._set_connection_state(Stateful.CLOSED)
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eandersson/amqpstorm | amqpstorm/channel0.py | Channel0._blocked_connection | def _blocked_connection(self, frame_in):
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"""
self.is_blocked = True
LOGGER.warning(
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"""Connection is Blocked.
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"""
self.is_blocked = True
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eandersson/amqpstorm | amqpstorm/channel0.py | Channel0._send_start_ok | def _send_start_ok(self, frame_in):
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:return:
"""
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credentials ... | python | def _send_start_ok(self, frame_in):
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eandersson/amqpstorm | amqpstorm/channel0.py | Channel0._send_tune_ok | def _send_tune_ok(self, frame_in):
"""Send Tune OK frame.
:param specification.Connection.Tune frame_in: Tune frame.
:return:
"""
self.max_allowed_channels = self._negotiate(frame_in.channel_max,
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"""Send Tune OK frame.
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eandersson/amqpstorm | amqpstorm/channel0.py | Channel0._send_open_connection | def _send_open_connection(self):
"""Send Open Connection frame.
:return:
"""
open_frame = specification.Connection.Open(
virtual_host=self._parameters['virtual_host']
)
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"""Send Open Connection frame.
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"""
open_frame = specification.Connection.Open(
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eandersson/amqpstorm | amqpstorm/channel0.py | Channel0._write_frame | def _write_frame(self, frame_out):
"""Write a pamqp frame from Channel0.
:param frame_out: Amqp frame.
:return:
"""
self._connection.write_frame(0, frame_out)
LOGGER.debug('Frame Sent: %s', frame_out.name) | python | def _write_frame(self, frame_out):
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self._connection.write_frame(0, frame_out)
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eandersson/amqpstorm | amqpstorm/channel0.py | Channel0._client_properties | def _client_properties():
"""AMQPStorm Client Properties.
:rtype: dict
"""
return {
'product': 'AMQPStorm',
'platform': 'Python %s (%s)' % (platform.python_version(),
platform.python_implementation()),
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"""AMQPStorm Client Properties.
:rtype: dict
"""
return {
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eandersson/amqpstorm | amqpstorm/channel.py | Channel.build_inbound_messages | def build_inbound_messages(self, break_on_empty=False, to_tuple=False,
auto_decode=True):
"""Build messages in the inbound queue.
:param bool break_on_empty: Should we break the loop when there are
no more messages in our inbound queue.... | python | def build_inbound_messages(self, break_on_empty=False, to_tuple=False,
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eandersson/amqpstorm | amqpstorm/channel.py | Channel.close | def close(self, reply_code=200, reply_text=''):
"""Close Channel.
:param int reply_code: Close reply code (e.g. 200)
:param str reply_text: Close reply text
:raises AMQPInvalidArgument: Invalid Parameters
:raises AMQPChannelError: Raises if the channel encountered an error.
... | python | def close(self, reply_code=200, reply_text=''):
"""Close Channel.
:param int reply_code: Close reply code (e.g. 200)
:param str reply_text: Close reply text
:raises AMQPInvalidArgument: Invalid Parameters
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eandersson/amqpstorm | amqpstorm/channel.py | Channel.check_for_errors | def check_for_errors(self):
"""Check connection and channel for errors.
:raises AMQPChannelError: Raises if the channel encountered an error.
:raises AMQPConnectionError: Raises if the connection
encountered an error.
:return:
"""
try... | python | def check_for_errors(self):
"""Check connection and channel for errors.
:raises AMQPChannelError: Raises if the channel encountered an error.
:raises AMQPConnectionError: Raises if the connection
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:return:
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encountered an ... | python | def confirm_deliveries(self):
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eandersson/amqpstorm | amqpstorm/channel.py | Channel.on_frame | def on_frame(self, frame_in):
"""Handle frame sent to this specific channel.
:param pamqp.Frame frame_in: Amqp frame.
:return:
"""
if self.rpc.on_frame(frame_in):
return
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self._inbound.append(frame_in)
el... | python | def on_frame(self, frame_in):
"""Handle frame sent to this specific channel.
:param pamqp.Frame frame_in: Amqp frame.
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"""
if self.rpc.on_frame(frame_in):
return
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eandersson/amqpstorm | amqpstorm/channel.py | Channel.open | def open(self):
"""Open Channel.
:return:
"""
self._inbound = []
self._exceptions = []
self.set_state(self.OPENING)
self.rpc_request(specification.Channel.Open())
self.set_state(self.OPEN) | python | def open(self):
"""Open Channel.
:return:
"""
self._inbound = []
self._exceptions = []
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self.rpc_request(specification.Channel.Open())
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eandersson/amqpstorm | amqpstorm/channel.py | Channel.process_data_events | def process_data_events(self, to_tuple=False, auto_decode=True):
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:param bool to_tuple: Should incoming messages be converted to a
tuple before delivery.
:param bool auto_decode: Auto-decode strings when possible.
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eandersson/amqpstorm | amqpstorm/channel.py | Channel.rpc_request | def rpc_request(self, frame_out, connection_adapter=None):
"""Perform a RPC Request.
:param specification.Frame frame_out: Amqp frame.
:rtype: dict
"""
with self.rpc.lock:
uuid = self.rpc.register_request(frame_out.valid_responses)
self._connection.write_... | python | def rpc_request(self, frame_out, connection_adapter=None):
"""Perform a RPC Request.
:param specification.Frame frame_out: Amqp frame.
:rtype: dict
"""
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eandersson/amqpstorm | amqpstorm/channel.py | Channel.start_consuming | def start_consuming(self, to_tuple=False, auto_decode=True):
"""Start consuming messages.
:param bool to_tuple: Should incoming messages be converted to a
tuple before delivery.
:param bool auto_decode: Auto-decode strings when possible.
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eandersson/amqpstorm | amqpstorm/channel.py | Channel.stop_consuming | def stop_consuming(self):
"""Stop consuming messages.
:raises AMQPChannelError: Raises if the channel encountered an error.
:raises AMQPConnectionError: Raises if the connection
encountered an error.
:return:
"""
if not self.consumer... | python | def stop_consuming(self):
"""Stop consuming messages.
:raises AMQPChannelError: Raises if the channel encountered an error.
:raises AMQPConnectionError: Raises if the connection
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:return:
"""
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self.check_for_errors()
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eandersson/amqpstorm | amqpstorm/channel.py | Channel._basic_cancel | def _basic_cancel(self, frame_in):
"""Handle a Basic Cancel frame.
:param specification.Basic.Cancel frame_in: Amqp frame.
:return:
"""
LOGGER.warning(
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"""Handle a Basic Cancel frame.
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:return:
"""
LOGGER.warning(
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eandersson/amqpstorm | amqpstorm/channel.py | Channel._basic_return | def _basic_return(self, frame_in):
"""Handle a Basic Return Frame and treat it as an error.
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:return:
"""
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eandersson/amqpstorm | amqpstorm/channel.py | Channel._build_message | def _build_message(self, auto_decode):
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:param bool auto_decode: Auto-decode strings when possible.
:rtype: Message
"""
with self.lock:
if len(self._inbound) < 2:
return None
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:rtype: Message
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eandersson/amqpstorm | amqpstorm/channel.py | Channel._build_message_headers | def _build_message_headers(self):
"""Fetch Message Headers (Deliver & Header Frames).
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if not isinstance(basic_deliver, specification.Basic.Deliver):
LOGGER.warning(
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eandersson/amqpstorm | amqpstorm/channel.py | Channel._build_message_body | def _build_message_body(self, body_size):
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:rtype: str
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sleep(IDLE_WAIT)
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eandersson/amqpstorm | amqpstorm/channel.py | Channel._close_channel | def _close_channel(self, frame_in):
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:return:
"""
if frame_in.reply_code != 200:
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message = (
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if frame_in.reply_code != 200:
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eandersson/amqpstorm | amqpstorm/management/user.py | User.create | def create(self, username, password, tags=''):
"""Create User.
:param str username: Username
:param str password: Password
:param str tags: Comma-separate list of tags (e.g. monitoring)
:rtype: None
"""
user_payload = json.dumps({
'password': passwor... | python | def create(self, username, password, tags=''):
"""Create User.
:param str username: Username
:param str password: Password
:param str tags: Comma-separate list of tags (e.g. monitoring)
:rtype: None
"""
user_payload = json.dumps({
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eandersson/amqpstorm | amqpstorm/management/user.py | User.get_permission | def get_permission(self, username, virtual_host):
"""Get User permissions for the configured virtual host.
:param str username: Username
:param str virtual_host: Virtual host name
:raises ApiError: Raises if the remote server encountered an error.
:raises ApiConnectionError: Ra... | python | def get_permission(self, username, virtual_host):
"""Get User permissions for the configured virtual host.
:param str username: Username
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eandersson/amqpstorm | amqpstorm/management/user.py | User.set_permission | def set_permission(self, username, virtual_host, configure_regex='.*',
write_regex='.*', read_regex='.*'):
"""Set User permissions for the configured virtual host.
:param str username: Username
:param str virtual_host: Virtual host name
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eandersson/amqpstorm | amqpstorm/management/user.py | User.delete_permission | def delete_permission(self, username, virtual_host):
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eandersson/amqpstorm | examples/scalable_rpc_server.py | ScalableRpcServer.start_server | def start_server(self):
"""Start the RPC Server.
:return:
"""
self._stopped.clear()
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while not self._stopped.is_set():
try:
# Check our connection for ... | python | def start_server(self):
"""Start the RPC Server.
:return:
"""
self._stopped.clear()
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eandersson/amqpstorm | examples/scalable_rpc_server.py | ScalableRpcServer._update_consumers | def _update_consumers(self):
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eandersson/amqpstorm | amqpstorm/management/http_client.py | HTTPClient.get | def get(self, path, payload=None, headers=None):
"""HTTP GET operation.
:param path: URI Path
:param payload: HTTP Body
:param headers: HTTP Headers
:raises ApiError: Raises if the remote server encountered an error.
:raises ApiConnectionError: Raises if there was a con... | python | def get(self, path, payload=None, headers=None):
"""HTTP GET operation.
:param path: URI Path
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:param headers: HTTP Headers
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eandersson/amqpstorm | amqpstorm/management/http_client.py | HTTPClient.post | def post(self, path, payload=None, headers=None):
"""HTTP POST operation.
:param path: URI Path
:param payload: HTTP Body
:param headers: HTTP Headers
:raises ApiError: Raises if the remote server encountered an error.
:raises ApiConnectionError: Raises if there was a c... | python | def post(self, path, payload=None, headers=None):
"""HTTP POST operation.
:param path: URI Path
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eandersson/amqpstorm | amqpstorm/management/http_client.py | HTTPClient.delete | def delete(self, path, payload=None, headers=None):
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:param payload: HTTP Body
:param headers: HTTP Headers
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:raises ApiConnectionError: Raises if there was... | python | def delete(self, path, payload=None, headers=None):
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eandersson/amqpstorm | amqpstorm/management/http_client.py | HTTPClient.put | def put(self, path, payload=None, headers=None):
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eandersson/amqpstorm | amqpstorm/management/http_client.py | HTTPClient._request | def _request(self, method, path, payload=None, headers=None):
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eandersson/amqpstorm | amqpstorm/management/http_client.py | HTTPClient._check_for_errors | def _check_for_errors(response, json_response):
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:param response: HTTP response
:param json_response: Json response
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:return:
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... | python | def _check_for_errors(response, json_response):
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eandersson/amqpstorm | amqpstorm/management/healthchecks.py | HealthChecks.get | def get(self, node=None):
"""Run basic healthchecks against the current node, or against a given
node.
Example response:
> {"status":"ok"}
> {"status":"failed","reason":"string"}
:param node: Node name
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cggh/scikit-allel | allel/stats/diversity.py | mean_pairwise_difference | def mean_pairwise_difference(ac, an=None, fill=np.nan):
"""Calculate for each variant the mean number of pairwise differences
between chromosomes sampled from within a single population.
Parameters
----------
ac : array_like, int, shape (n_variants, n_alleles)
Allele counts array.
an :... | python | def mean_pairwise_difference(ac, an=None, fill=np.nan):
"""Calculate for each variant the mean number of pairwise differences
between chromosomes sampled from within a single population.
Parameters
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ac : array_like, int, shape (n_variants, n_alleles)
Allele counts array.
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cggh/scikit-allel | allel/stats/diversity.py | mean_pairwise_difference_between | def mean_pairwise_difference_between(ac1, ac2, an1=None, an2=None,
fill=np.nan):
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Parameters
----------
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cggh/scikit-allel | allel/stats/diversity.py | sequence_diversity | def sequence_diversity(pos, ac, start=None, stop=None,
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"""Estimate nucleotide diversity within a given region, which is the
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cggh/scikit-allel | allel/stats/diversity.py | sequence_divergence | def sequence_divergence(pos, ac1, ac2, an1=None, an2=None, start=None,
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cggh/scikit-allel | allel/stats/diversity.py | windowed_diversity | def windowed_diversity(pos, ac, size=None, start=None, stop=None, step=None,
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"""Estimate nucleotide diversity in windows over a single
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cggh/scikit-allel | allel/stats/diversity.py | windowed_divergence | def windowed_divergence(pos, ac1, ac2, size=None, start=None, stop=None,
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fill=np.nan):
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cggh/scikit-allel | allel/stats/diversity.py | windowed_df | def windowed_df(pos, ac1, ac2, size=None, start=None, stop=None, step=None,
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cggh/scikit-allel | allel/stats/diversity.py | watterson_theta | def watterson_theta(pos, ac, start=None, stop=None,
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"""Calculate the value of Watterson's estimator over a given region.
Parameters
----------
pos : array_like, int, shape (n_items,)
Variant positions, using 1-based coordinates, in ascending order.
... | python | def watterson_theta(pos, ac, start=None, stop=None,
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pos : array_like, int, shape (n_items,)
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cggh/scikit-allel | allel/stats/diversity.py | windowed_watterson_theta | def windowed_watterson_theta(pos, ac, size=None, start=None, stop=None,
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fill=np.nan):
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Parameters
----------
... | python | def windowed_watterson_theta(pos, ac, size=None, start=None, stop=None,
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cggh/scikit-allel | allel/stats/diversity.py | tajima_d | def tajima_d(ac, pos=None, start=None, stop=None, min_sites=3):
"""Calculate the value of Tajima's D over a given region.
Parameters
----------
ac : array_like, int, shape (n_variants, n_alleles)
Allele counts array.
pos : array_like, int, shape (n_items,), optional
Variant position... | python | def tajima_d(ac, pos=None, start=None, stop=None, min_sites=3):
"""Calculate the value of Tajima's D over a given region.
Parameters
----------
ac : array_like, int, shape (n_variants, n_alleles)
Allele counts array.
pos : array_like, int, shape (n_items,), optional
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cggh/scikit-allel | allel/stats/diversity.py | windowed_tajima_d | def windowed_tajima_d(pos, ac, size=None, start=None, stop=None,
step=None, windows=None, min_sites=3):
"""Calculate the value of Tajima's D in windows over a single
chromosome/contig.
Parameters
----------
pos : array_like, int, shape (n_items,)
Variant positions, usi... | python | def windowed_tajima_d(pos, ac, size=None, start=None, stop=None,
step=None, windows=None, min_sites=3):
"""Calculate the value of Tajima's D in windows over a single
chromosome/contig.
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pos : array_like, int, shape (n_items,)
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cggh/scikit-allel | allel/stats/diversity.py | moving_tajima_d | def moving_tajima_d(ac, size, start=0, stop=None, step=None, min_sites=3):
"""Calculate the value of Tajima's D in moving windows of `size` variants.
Parameters
----------
ac : array_like, int, shape (n_variants, n_alleles)
Allele counts array.
size : int
The window size (number of... | python | def moving_tajima_d(ac, size, start=0, stop=None, step=None, min_sites=3):
"""Calculate the value of Tajima's D in moving windows of `size` variants.
Parameters
----------
ac : array_like, int, shape (n_variants, n_alleles)
Allele counts array.
size : int
The window size (number of... | [
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cggh/scikit-allel | allel/stats/roh.py | roh_mhmm | def roh_mhmm(gv, pos, phet_roh=0.001, phet_nonroh=(0.0025, 0.01), transition=1e-6,
min_roh=0, is_accessible=None, contig_size=None):
"""Call ROH (runs of homozygosity) in a single individual given a genotype vector.
This function computes the likely ROH using a Multinomial HMM model. There are 3
... | python | def roh_mhmm(gv, pos, phet_roh=0.001, phet_nonroh=(0.0025, 0.01), transition=1e-6,
min_roh=0, is_accessible=None, contig_size=None):
"""Call ROH (runs of homozygosity) in a single individual given a genotype vector.
This function computes the likely ROH using a Multinomial HMM model. There are 3
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cggh/scikit-allel | allel/stats/roh.py | roh_poissonhmm | def roh_poissonhmm(gv, pos, phet_roh=0.001, phet_nonroh=(0.0025, 0.01), transition=1e-3,
window_size=1000, min_roh=0, is_accessible=None, contig_size=None):
"""Call ROH (runs of homozygosity) in a single individual given a genotype vector.
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window_size=1000, min_roh=0, is_accessible=None, contig_size=None):
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cggh/scikit-allel | allel/stats/sf.py | sfs | def sfs(dac, n=None):
"""Compute the site frequency spectrum given derived allele counts at
a set of biallelic variants.
Parameters
----------
dac : array_like, int, shape (n_variants,)
Array of derived allele counts.
n : int, optional
The total number of chromosomes called.
... | python | def sfs(dac, n=None):
"""Compute the site frequency spectrum given derived allele counts at
a set of biallelic variants.
Parameters
----------
dac : array_like, int, shape (n_variants,)
Array of derived allele counts.
n : int, optional
The total number of chromosomes called.
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cggh/scikit-allel | allel/stats/sf.py | sfs_folded | def sfs_folded(ac, n=None):
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Parameters
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ac : array_like, int, shape (n_variants, 2)
Allele counts array.
n : int, optional
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cggh/scikit-allel | allel/stats/sf.py | sfs_scaled | def sfs_scaled(dac, n=None):
"""Compute the site frequency spectrum scaled such that a constant value is
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Parameters
----------
dac : array_like, int, shape (n_variants,)
Array of derived allele counts.
... | python | def sfs_scaled(dac, n=None):
"""Compute the site frequency spectrum scaled such that a constant value is
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cggh/scikit-allel | allel/stats/sf.py | scale_sfs | def scale_sfs(s):
"""Scale a site frequency spectrum.
Parameters
----------
s : array_like, int, shape (n_chromosomes,)
Site frequency spectrum.
Returns
-------
sfs_scaled : ndarray, int, shape (n_chromosomes,)
Scaled site frequency spectrum.
"""
k = np.arange(s.si... | python | def scale_sfs(s):
"""Scale a site frequency spectrum.
Parameters
----------
s : array_like, int, shape (n_chromosomes,)
Site frequency spectrum.
Returns
-------
sfs_scaled : ndarray, int, shape (n_chromosomes,)
Scaled site frequency spectrum.
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cggh/scikit-allel | allel/stats/sf.py | sfs_folded_scaled | def sfs_folded_scaled(ac, n=None):
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population size.
Parameters
----------
ac : array_like, int, shape (n_variants, 2)
Allele counts array.
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cggh/scikit-allel | allel/stats/sf.py | scale_sfs_folded | def scale_sfs_folded(s, n):
"""Scale a folded site frequency spectrum.
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----------
s : array_like, int, shape (n_chromosomes//2,)
Folded site frequency spectrum.
n : int
Number of chromosomes called.
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"""Scale a folded site frequency spectrum.
Parameters
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s : array_like, int, shape (n_chromosomes//2,)
Folded site frequency spectrum.
n : int
Number of chromosomes called.
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cggh/scikit-allel | allel/stats/sf.py | joint_sfs | def joint_sfs(dac1, dac2, n1=None, n2=None):
"""Compute the joint site frequency spectrum between two populations.
Parameters
----------
dac1 : array_like, int, shape (n_variants,)
Derived allele counts for the first population.
dac2 : array_like, int, shape (n_variants,)
Derived al... | python | def joint_sfs(dac1, dac2, n1=None, n2=None):
"""Compute the joint site frequency spectrum between two populations.
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dac1 : array_like, int, shape (n_variants,)
Derived allele counts for the first population.
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cggh/scikit-allel | allel/stats/sf.py | joint_sfs_folded | def joint_sfs_folded(ac1, ac2, n1=None, n2=None):
"""Compute the joint folded site frequency spectrum between two
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Parameters
----------
ac1 : array_like, int, shape (n_variants, 2)
Allele counts for the first population.
ac2 : array_like, int, shape (n_variants, 2)
... | python | def joint_sfs_folded(ac1, ac2, n1=None, n2=None):
"""Compute the joint folded site frequency spectrum between two
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ac1 : array_like, int, shape (n_variants, 2)
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cggh/scikit-allel | allel/stats/sf.py | joint_sfs_scaled | def joint_sfs_scaled(dac1, dac2, n1=None, n2=None):
"""Compute the joint site frequency spectrum between two populations,
scaled such that a constant value is expected across the spectrum for
neutral variation, constant population size and unrelated populations.
Parameters
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dac1 : arr... | python | def joint_sfs_scaled(dac1, dac2, n1=None, n2=None):
"""Compute the joint site frequency spectrum between two populations,
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cggh/scikit-allel | allel/stats/sf.py | scale_joint_sfs | def scale_joint_sfs(s):
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Joint site frequency spectrum.
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Scaled joint site frequency spectrum.
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"""Scale a joint site frequency spectrum.
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s : array_like, int, shape (n1, n2)
Joint site frequency spectrum.
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cggh/scikit-allel | allel/stats/sf.py | joint_sfs_folded_scaled | def joint_sfs_folded_scaled(ac1, ac2, n1=None, n2=None):
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cggh/scikit-allel | allel/stats/sf.py | scale_joint_sfs_folded | def scale_joint_sfs_folded(s, n1, n2):
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Folded joint site frequency spectrum.
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cggh/scikit-allel | allel/stats/sf.py | fold_sfs | def fold_sfs(s, n):
"""Fold a site frequency spectrum.
Parameters
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s : array_like, int, shape (n_chromosomes,)
Site frequency spectrum
n : int
Total number of chromosomes called.
Returns
-------
sfs_folded : ndarray, int
Folded site frequency spectrum
... | python | def fold_sfs(s, n):
"""Fold a site frequency spectrum.
Parameters
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s : array_like, int, shape (n_chromosomes,)
Site frequency spectrum
n : int
Total number of chromosomes called.
Returns
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sfs_folded : ndarray, int
Folded site frequency spectrum
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cggh/scikit-allel | allel/stats/sf.py | fold_joint_sfs | def fold_joint_sfs(s, n1, n2):
"""Fold a joint site frequency spectrum.
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Joint site frequency spectrum.
n1, n2 : int, optional
The total number of chromosomes called in each population.
Returns
-... | python | def fold_joint_sfs(s, n1, n2):
"""Fold a joint site frequency spectrum.
Parameters
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Joint site frequency spectrum.
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cggh/scikit-allel | allel/stats/sf.py | plot_sfs | def plot_sfs(s, yscale='log', bins=None, n=None,
clip_endpoints=True, label=None, plot_kwargs=None,
ax=None):
"""Plot a site frequency spectrum.
Parameters
----------
s : array_like, int, shape (n_chromosomes,)
Site frequency spectrum.
yscale : string, optional
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ax=None):
"""Plot a site frequency spectrum.
Parameters
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s : array_like, int, shape (n_chromosomes,)
Site frequency spectrum.
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cggh/scikit-allel | allel/stats/sf.py | plot_sfs_folded | def plot_sfs_folded(*args, **kwargs):
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Site frequency spectrum.
yscale : string, optional
Y axis scale.
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cggh/scikit-allel | allel/stats/sf.py | plot_sfs_scaled | def plot_sfs_scaled(*args, **kwargs):
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Site frequency spectrum.
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Y axis scale.
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Site frequency spectrum.
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cggh/scikit-allel | allel/stats/sf.py | plot_sfs_folded_scaled | def plot_sfs_folded_scaled(*args, **kwargs):
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Site frequency spectrum.
yscale : string, optional
Y axis scale.
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cggh/scikit-allel | allel/stats/sf.py | plot_joint_sfs | def plot_joint_sfs(s, ax=None, imshow_kwargs=None):
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Joint site frequency spectrum.
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cggh/scikit-allel | allel/stats/sf.py | plot_joint_sfs_folded | def plot_joint_sfs_folded(*args, **kwargs):
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Joint site frequency spectrum.
ax : axes, optional
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Joint site frequency spectrum.
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cggh/scikit-allel | allel/stats/sf.py | plot_joint_sfs_scaled | def plot_joint_sfs_scaled(*args, **kwargs):
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Joint site frequency spectrum.
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Joint site frequency spectrum.
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cggh/scikit-allel | allel/stats/sf.py | plot_joint_sfs_folded_scaled | def plot_joint_sfs_folded_scaled(*args, **kwargs):
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Joint site frequency spectrum.
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s : array_like, int, shape (n_chromosomes_pop1/2, n_chromosomes_pop2/2)
Joint site frequency spectrum.
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Joint site frequency spectrum.
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Axes on which to draw. If not provided, a new figure will be created.
imshow_kwargs : ... | [
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] | train | https://github.com/cggh/scikit-allel/blob/3c979a57a100240ba959dd13f98839349530f215/allel/stats/sf.py#L779-L803 |
cggh/scikit-allel | allel/compat.py | memoryview_safe | def memoryview_safe(x):
"""Make array safe to run in a Cython memoryview-based kernel. These
kernels typically break down with the error ``ValueError: buffer source
array is read-only`` when running in dask distributed.
See Also
--------
https://github.com/dask/distributed/issues/1978
https... | python | def memoryview_safe(x):
"""Make array safe to run in a Cython memoryview-based kernel. These
kernels typically break down with the error ``ValueError: buffer source
array is read-only`` when running in dask distributed.
See Also
--------
https://github.com/dask/distributed/issues/1978
https... | [
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https://github.com/dask/distributed/issues/1978
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cggh/scikit-allel | allel/io/vcf_read.py | _prep_fields_param | def _prep_fields_param(fields):
"""Prepare the `fields` parameter, and determine whether or not to store samples."""
store_samples = False
if fields is None:
# add samples by default
return True, None
if isinstance(fields, str):
fields = [fields]
else:
fields = lis... | python | def _prep_fields_param(fields):
"""Prepare the `fields` parameter, and determine whether or not to store samples."""
store_samples = False
if fields is None:
# add samples by default
return True, None
if isinstance(fields, str):
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cggh/scikit-allel | allel/io/vcf_read.py | _chunk_iter_progress | def _chunk_iter_progress(it, log, prefix):
"""Wrap a chunk iterator for progress logging."""
n_variants = 0
before_all = time.time()
before_chunk = before_all
for chunk, chunk_length, chrom, pos in it:
after_chunk = time.time()
elapsed_chunk = after_chunk - before_chunk
elaps... | python | def _chunk_iter_progress(it, log, prefix):
"""Wrap a chunk iterator for progress logging."""
n_variants = 0
before_all = time.time()
before_chunk = before_all
for chunk, chunk_length, chrom, pos in it:
after_chunk = time.time()
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cggh/scikit-allel | allel/io/vcf_read.py | read_vcf | def read_vcf(input,
fields=None,
exclude_fields=None,
rename_fields=None,
types=None,
numbers=None,
alt_number=DEFAULT_ALT_NUMBER,
fills=None,
region=None,
tabix='tabix',
samples=None,
... | python | def read_vcf(input,
fields=None,
exclude_fields=None,
rename_fields=None,
types=None,
numbers=None,
alt_number=DEFAULT_ALT_NUMBER,
fills=None,
region=None,
tabix='tabix',
samples=None,
... | [
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.. versionchanged:: 1.12.0
Now returns None if no variants are found in the VCF file or matching the
requested region.
Parameters
----------
input : string or file-like
{input}
fields : list of strings, optional
{fields}
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cggh/scikit-allel | allel/io/vcf_read.py | vcf_to_npz | def vcf_to_npz(input, output,
compressed=True,
overwrite=False,
fields=None,
exclude_fields=None,
rename_fields=None,
types=None,
numbers=None,
alt_number=DEFAULT_ALT_NUMBER,
fills=None... | python | def vcf_to_npz(input, output,
compressed=True,
overwrite=False,
fields=None,
exclude_fields=None,
rename_fields=None,
types=None,
numbers=None,
alt_number=DEFAULT_ALT_NUMBER,
fills=None... | [
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.. versionchanged:: 1.12.0
Now will not create any output file if no variants are found in the VCF file or
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Parameters
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output : string
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cggh/scikit-allel | allel/io/vcf_read.py | vcf_to_hdf5 | def vcf_to_hdf5(input, output,
group='/',
compression='gzip',
compression_opts=1,
shuffle=False,
overwrite=False,
vlen=True,
fields=None,
exclude_fields=None,
rename_fields=Non... | python | def vcf_to_hdf5(input, output,
group='/',
compression='gzip',
compression_opts=1,
shuffle=False,
overwrite=False,
vlen=True,
fields=None,
exclude_fields=None,
rename_fields=Non... | [
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.. versionchanged:: 1.12.0
Now will not create any output file if no variants are found in the VCF file or
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Parameters
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input : string
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output : string
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cggh/scikit-allel | allel/io/vcf_read.py | vcf_to_zarr | def vcf_to_zarr(input, output,
group='/',
compressor='default',
overwrite=False,
fields=None,
exclude_fields=None,
rename_fields=None,
types=None,
numbers=None,
alt_number=DEFA... | python | def vcf_to_zarr(input, output,
group='/',
compressor='default',
overwrite=False,
fields=None,
exclude_fields=None,
rename_fields=None,
types=None,
numbers=None,
alt_number=DEFA... | [
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.. versionchanged:: 1.12.0
Now will not create any output files if no variants are found in the VCF file or
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Parameters
----------
input : string
{input}
output : string
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cggh/scikit-allel | allel/io/vcf_read.py | iter_vcf_chunks | def iter_vcf_chunks(input,
fields=None,
exclude_fields=None,
types=None,
numbers=None,
alt_number=DEFAULT_ALT_NUMBER,
fills=None,
region=None,
tabix='tabix',
... | python | def iter_vcf_chunks(input,
fields=None,
exclude_fields=None,
types=None,
numbers=None,
alt_number=DEFAULT_ALT_NUMBER,
fills=None,
region=None,
tabix='tabix',
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input : string
{input}
fields : list of strings, optional
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exclude_fields : list of strings, optional
{exclude_fields}
types : dict, optional
{types}
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cggh/scikit-allel | allel/io/vcf_read.py | vcf_to_dataframe | def vcf_to_dataframe(input,
fields=None,
exclude_fields=None,
types=None,
numbers=None,
alt_number=DEFAULT_ALT_NUMBER,
fills=None,
region=None,
tabix='t... | python | def vcf_to_dataframe(input,
fields=None,
exclude_fields=None,
types=None,
numbers=None,
alt_number=DEFAULT_ALT_NUMBER,
fills=None,
region=None,
tabix='t... | [
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Parameters
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input : string
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fields : list of strings, optional
{fields}
exclude_fields : list of strings, optional
{exclude_fields}
types : dict, optional
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