id int32 0 252k | repo stringlengths 7 55 | path stringlengths 4 127 | func_name stringlengths 1 88 | original_string stringlengths 75 19.8k | language stringclasses 1
value | code stringlengths 51 19.8k | code_tokens list | docstring stringlengths 3 17.3k | docstring_tokens list | sha stringlengths 40 40 | url stringlengths 87 242 |
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900 | eandersson/amqpstorm | amqpstorm/uri_connection.py | UriConnection._parse_uri_options | def _parse_uri_options(self, parsed_uri, use_ssl=False, ssl_options=None):
"""Parse the uri options.
:param parsed_uri:
:param bool use_ssl:
:return:
"""
ssl_options = ssl_options or {}
kwargs = urlparse.parse_qs(parsed_uri.query)
vhost = urlparse.unquote... | python | def _parse_uri_options(self, parsed_uri, use_ssl=False, ssl_options=None):
ssl_options = ssl_options or {}
kwargs = urlparse.parse_qs(parsed_uri.query)
vhost = urlparse.unquote(parsed_uri.path[1:]) or DEFAULT_VIRTUAL_HOST
options = {
'ssl': use_ssl,
'virtual_host'... | [
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901 | eandersson/amqpstorm | amqpstorm/uri_connection.py | UriConnection._parse_ssl_options | def _parse_ssl_options(self, ssl_kwargs):
"""Parse TLS Options.
:param ssl_kwargs:
:rtype: dict
"""
ssl_options = {}
for key in ssl_kwargs:
if key not in compatibility.SSL_OPTIONS:
LOGGER.warning('invalid option: %s', key)
cont... | python | def _parse_ssl_options(self, ssl_kwargs):
ssl_options = {}
for key in ssl_kwargs:
if key not in compatibility.SSL_OPTIONS:
LOGGER.warning('invalid option: %s', key)
continue
if 'ssl_version' in key:
value = self._get_ssl_version(ssl... | [
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902 | eandersson/amqpstorm | amqpstorm/uri_connection.py | UriConnection._get_ssl_version | def _get_ssl_version(self, value):
"""Get the TLS Version.
:param str value:
:return: TLS Version
"""
return self._get_ssl_attribute(value, compatibility.SSL_VERSIONS,
ssl.PROTOCOL_TLSv1,
'ssl_options:... | python | def _get_ssl_version(self, value):
return self._get_ssl_attribute(value, compatibility.SSL_VERSIONS,
ssl.PROTOCOL_TLSv1,
'ssl_options: ssl_version \'%s\' not '
'found falling back to PROTOCOL_TLS... | [
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903 | eandersson/amqpstorm | amqpstorm/uri_connection.py | UriConnection._get_ssl_validation | def _get_ssl_validation(self, value):
"""Get the TLS Validation option.
:param str value:
:return: TLS Certificate Options
"""
return self._get_ssl_attribute(value, compatibility.SSL_CERT_MAP,
ssl.CERT_NONE,
... | python | def _get_ssl_validation(self, value):
return self._get_ssl_attribute(value, compatibility.SSL_CERT_MAP,
ssl.CERT_NONE,
'ssl_options: cert_reqs \'%s\' not '
'found falling back to CERT_NONE.') | [
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904 | eandersson/amqpstorm | amqpstorm/uri_connection.py | UriConnection._get_ssl_attribute | def _get_ssl_attribute(value, mapping, default_value, warning_message):
"""Get the TLS attribute based on the compatibility mapping.
If no valid attribute can be found, fall-back on default and
display a warning.
:param str value:
:param dict mapping: Dictionary based m... | python | def _get_ssl_attribute(value, mapping, default_value, warning_message):
for key in mapping:
if not key.endswith(value.lower()):
continue
return mapping[key]
LOGGER.warning(warning_message, value)
return default_value | [
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905 | eandersson/amqpstorm | amqpstorm/management/api.py | ManagementApi.top | def top(self):
"""Top Processes.
:raises ApiError: Raises if the remote server encountered an error.
:raises ApiConnectionError: Raises if there was a connectivity issue.
:rtype: list
"""
nodes = []
for node in self.nodes():
nodes.append(self.http_cl... | python | def top(self):
nodes = []
for node in self.nodes():
nodes.append(self.http_client.get(API_TOP % node['name']))
return nodes | [
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906 | eandersson/amqpstorm | amqpstorm/basic.py | Basic.qos | def qos(self, prefetch_count=0, prefetch_size=0, global_=False):
"""Specify quality of service.
:param int prefetch_count: Prefetch window in messages
:param int/long prefetch_size: Prefetch window in octets
:param bool global_: Apply to entire connection
:raises AMQPInvalidArg... | python | def qos(self, prefetch_count=0, prefetch_size=0, global_=False):
if not compatibility.is_integer(prefetch_count):
raise AMQPInvalidArgument('prefetch_count should be an integer')
elif not compatibility.is_integer(prefetch_size):
raise AMQPInvalidArgument('prefetch_size should be ... | [
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907 | eandersson/amqpstorm | amqpstorm/basic.py | Basic.get | def get(self, queue='', no_ack=False, to_dict=False, auto_decode=True):
"""Fetch a single message.
:param str queue: Queue name
:param bool no_ack: No acknowledgement needed
:param bool to_dict: Should incoming messages be converted to a
dictionary before delivery.
... | python | def get(self, queue='', no_ack=False, to_dict=False, auto_decode=True):
if not compatibility.is_string(queue):
raise AMQPInvalidArgument('queue should be a string')
elif not isinstance(no_ack, bool):
raise AMQPInvalidArgument('no_ack should be a boolean')
elif self._chann... | [
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908 | eandersson/amqpstorm | amqpstorm/basic.py | Basic.recover | def recover(self, requeue=False):
"""Redeliver unacknowledged messages.
:param bool requeue: Re-queue the messages
:raises AMQPInvalidArgument: Invalid Parameters
:raises AMQPChannelError: Raises if the channel encountered an error.
:raises AMQPConnectionError: Raises if the co... | python | def recover(self, requeue=False):
if not isinstance(requeue, bool):
raise AMQPInvalidArgument('requeue should be a boolean')
recover_frame = specification.Basic.Recover(requeue=requeue)
return self._channel.rpc_request(recover_frame) | [
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909 | eandersson/amqpstorm | amqpstorm/basic.py | Basic.cancel | def cancel(self, consumer_tag=''):
"""Cancel a queue consumer.
:param str consumer_tag: Consumer tag
:raises AMQPInvalidArgument: Invalid Parameters
:raises AMQPChannelError: Raises if the channel encountered an error.
:raises AMQPConnectionError: Raises if the connection
... | python | def cancel(self, consumer_tag=''):
if not compatibility.is_string(consumer_tag):
raise AMQPInvalidArgument('consumer_tag should be a string')
cancel_frame = specification.Basic.Cancel(consumer_tag=consumer_tag)
result = self._channel.rpc_request(cancel_frame)
self._channel.re... | [
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910 | 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):
if not compatibility.is_integer(delivery_tag):
raise AMQPInvalidArgument('delivery_tag should be an integer')
elif not isinstance(requeue, bool):
raise AMQPInvalidArgument('requeue should be a boolean')
reject_frame = specif... | [
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:param int/long delivery_tag: Server-assigned delivery tag
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911 | 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):
consumer_tag = consume_rpc_result['consumer_tag']
self._channel.add_consumer_tag(consumer_tag)
return consumer_tag | [
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912 | 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,
no_local, queue):
consume_frame = specification.Basic.Consume(queue=queue,
consumer_tag=consumer_tag,
ex... | [
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:param bool no_ack: No acknowledgement needed
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913 | 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,
properties, routing_key):
if not compatibility.is_string(body):
raise AMQPInvalidArgument('body should be a string')
elif not compatibility.is_string(routing_key):
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:param bytes|str|unicode body: Message payload
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914 | 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):
if 'content_encoding' not in properties:
properties['content_encoding'] = 'utf-8'
encoding = properties['content_encoding']
if compatibility.is_unicode(body):
body = body.encode(encoding)
elif compatibility.PYTHON3 and i... | [
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915 | 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):
message_uuid = self._channel.rpc.register_request(
get_frame.valid_responses + ['ContentHeader', 'ContentBody']
)
try:
self._channel.write_frame(get_frame)
get_ok_frame = self._channel.rpc.get_request(message_uui... | [
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916 | 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_uuid = self._channel.rpc.register_request(['Basic.Ack',
'Basic.Nack'])
self._channel.write_frames(frames_out)
result = self._channel.rpc.get_request(confirm_uuid, raw=True)
self._ch... | [
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917 | 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):
frames = int(math.ceil(len(body) / float(self._max_frame_size)))
for offset in compatibility.RANGE(0, frames):
start_frame = self._max_frame_size * offset
end_frame = start_frame + self._max_frame_size
body_len = len(body)
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918 | eandersson/amqpstorm | amqpstorm/basic.py | Basic._get_content_body | def _get_content_body(self, message_uuid, body_size):
"""Get Content Body using RPC requests.
:param str uuid_body: Rpc Identifier.
:param int body_size: Content Size.
:rtype: str
"""
body = bytes()
while len(body) < body_size:
body_piece = self._cha... | python | def _get_content_body(self, message_uuid, body_size):
body = bytes()
while len(body) < body_size:
body_piece = self._channel.rpc.get_request(message_uuid, raw=True,
multiple=True)
if not body_piece.value:
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919 | 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):
LOGGER.debug('Frame Received: %s', frame_in.name)
if frame_in.name == 'Heartbeat':
return
elif frame_in.name == 'Connection.Close':
self._close_connection(frame_in)
elif frame_in.name == 'Connection.CloseOk':
self._close_c... | [
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920 | eandersson/amqpstorm | amqpstorm/channel0.py | Channel0._close_connection | def _close_connection(self, frame_in):
"""Connection Close.
:param specification.Connection.Close frame_in: Amqp frame.
:return:
"""
self._set_connection_state(Stateful.CLOSED)
if frame_in.reply_code != 200:
reply_text = try_utf8_decode(frame_in.reply_text)
... | python | def _close_connection(self, frame_in):
self._set_connection_state(Stateful.CLOSED)
if frame_in.reply_code != 200:
reply_text = try_utf8_decode(frame_in.reply_text)
message = (
'Connection was closed by remote server: %s' % reply_text
)
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921 | eandersson/amqpstorm | amqpstorm/channel0.py | Channel0._blocked_connection | def _blocked_connection(self, frame_in):
"""Connection is Blocked.
:param frame_in:
:return:
"""
self.is_blocked = True
LOGGER.warning(
'Connection is blocked by remote server: %s',
try_utf8_decode(frame_in.reason)
) | python | def _blocked_connection(self, frame_in):
self.is_blocked = True
LOGGER.warning(
'Connection is blocked by remote server: %s',
try_utf8_decode(frame_in.reason)
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922 | eandersson/amqpstorm | amqpstorm/channel0.py | Channel0._send_start_ok | def _send_start_ok(self, frame_in):
"""Send Start OK frame.
:param specification.Connection.Start frame_in: Amqp frame.
:return:
"""
mechanisms = try_utf8_decode(frame_in.mechanisms)
if 'EXTERNAL' in mechanisms:
mechanism = 'EXTERNAL'
credentials ... | python | def _send_start_ok(self, frame_in):
mechanisms = try_utf8_decode(frame_in.mechanisms)
if 'EXTERNAL' in mechanisms:
mechanism = 'EXTERNAL'
credentials = '\0\0'
elif 'PLAIN' in mechanisms:
mechanism = 'PLAIN'
credentials = self._plain_credentials()
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923 | 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,
MAX_CHANNELS)
self.max... | python | def _send_tune_ok(self, frame_in):
self.max_allowed_channels = self._negotiate(frame_in.channel_max,
MAX_CHANNELS)
self.max_frame_size = self._negotiate(frame_in.frame_max,
MAX_FRAME_SIZE)
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924 | 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']
)
self._write_frame(open_frame) | python | def _send_open_connection(self):
open_frame = specification.Connection.Open(
virtual_host=self._parameters['virtual_host']
)
self._write_frame(open_frame) | [
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925 | 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):
self._connection.write_frame(0, frame_out)
LOGGER.debug('Frame Sent: %s', frame_out.name) | [
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926 | 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()),
'capa... | python | def _client_properties():
return {
'product': 'AMQPStorm',
'platform': 'Python %s (%s)' % (platform.python_version(),
platform.python_implementation()),
'capabilities': {
'basic.nack': True,
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927 | 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,
auto_decode=True):
self.check_for_errors()
while not self.is_closed:
message = self._build_message(auto_decode=auto_decode)
if not message:
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928 | 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):
try:
self._connection.check_for_errors()
except AMQPConnectionError:
self.set_state(self.CLOSED)
raise
if self.exceptions:
exception = self.exceptions[0]
if self.is_open:
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929 | eandersson/amqpstorm | amqpstorm/channel.py | Channel.confirm_deliveries | def confirm_deliveries(self):
"""Set the channel to confirm that each message has been
successfully delivered.
:raises AMQPChannelError: Raises if the channel encountered an error.
:raises AMQPConnectionError: Raises if the connection
encountered an ... | python | def confirm_deliveries(self):
self._confirming_deliveries = True
confirm_frame = specification.Confirm.Select()
return self.rpc_request(confirm_frame) | [
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930 | 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
if frame_in.name in CONTENT_FRAME:
self._inbound.append(frame_in)
el... | python | def on_frame(self, frame_in):
if self.rpc.on_frame(frame_in):
return
if frame_in.name in CONTENT_FRAME:
self._inbound.append(frame_in)
elif frame_in.name == 'Basic.Cancel':
self._basic_cancel(frame_in)
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931 | eandersson/amqpstorm | amqpstorm/channel.py | Channel.process_data_events | def process_data_events(self, to_tuple=False, auto_decode=True):
"""Consume inbound messages.
:param bool to_tuple: Should incoming messages be converted to a
tuple before delivery.
:param bool auto_decode: Auto-decode strings when possible.
:raises AMQPCh... | python | def process_data_events(self, to_tuple=False, auto_decode=True):
if not self._consumer_callbacks:
raise AMQPChannelError('no consumer callback defined')
for message in self.build_inbound_messages(break_on_empty=True,
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932 | 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):
with self.rpc.lock:
uuid = self.rpc.register_request(frame_out.valid_responses)
self._connection.write_frame(self.channel_id, frame_out)
return self.rpc.get_request(
uuid, connection_adapter=connection... | [
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933 | 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.
:raises AMQPChanne... | python | def start_consuming(self, to_tuple=False, auto_decode=True):
while not self.is_closed:
self.process_data_events(
to_tuple=to_tuple,
auto_decode=auto_decode
)
if self.consumer_tags:
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continue
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934 | 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:
"""
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if not self.consumer_tags:
return
if not self.is_closed:
for tag in self.consumer_tags:
self.basic.cancel(tag)
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935 | eandersson/amqpstorm | amqpstorm/channel.py | Channel.write_frame | def write_frame(self, frame_out):
"""Write a pamqp frame from the current channel.
:param specification.Frame frame_out: A single pamqp frame.
:return:
"""
self.check_for_errors()
self._connection.write_frame(self.channel_id, frame_out) | python | def write_frame(self, frame_out):
self.check_for_errors()
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936 | eandersson/amqpstorm | amqpstorm/channel.py | Channel.write_frames | def write_frames(self, frames_out):
"""Write multiple pamqp frames from the current channel.
:param list frames_out: A list of pamqp frames.
:return:
"""
self.check_for_errors()
self._connection.write_frames(self.channel_id, frames_out) | python | def write_frames(self, frames_out):
self.check_for_errors()
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937 | 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(
'Received Basic.Cancel on consumer_tag: %s',
try_utf8_decode(frame_in.consumer_tag)
)
... | python | def _basic_cancel(self, frame_in):
LOGGER.warning(
'Received Basic.Cancel on consumer_tag: %s',
try_utf8_decode(frame_in.consumer_tag)
)
self.remove_consumer_tag(frame_in.consumer_tag) | [
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938 | 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.
:param specification.Basic.Return frame_in: Amqp frame.
:return:
"""
reply_text = try_utf8_decode(frame_in.reply_text)
message = (
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reply_text = try_utf8_decode(frame_in.reply_text)
message = (
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(
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... | [
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939 | eandersson/amqpstorm | amqpstorm/channel.py | Channel._build_message | def _build_message(self, auto_decode):
"""Fetch and build a complete Message from the inbound queue.
:param bool auto_decode: Auto-decode strings when possible.
:rtype: Message
"""
with self.lock:
if len(self._inbound) < 2:
return None
he... | python | def _build_message(self, auto_decode):
with self.lock:
if len(self._inbound) < 2:
return None
headers = self._build_message_headers()
if not headers:
return None
basic_deliver, content_header = headers
body = self._build... | [
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940 | eandersson/amqpstorm | amqpstorm/channel.py | Channel._build_message_body | def _build_message_body(self, body_size):
"""Build the Message body from the inbound queue.
:rtype: str
"""
body = bytes()
while len(body) < body_size:
if not self._inbound:
self.check_for_errors()
sleep(IDLE_WAIT)
cont... | python | def _build_message_body(self, body_size):
body = bytes()
while len(body) < body_size:
if not self._inbound:
self.check_for_errors()
sleep(IDLE_WAIT)
continue
body_piece = self._inbound.pop(0)
if not body_piece.value:
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941 | 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=''):
user_payload = json.dumps({
'password': password,
'tags': tags
})
return self.http_client.put(API_USER % username,
payload=user_payload) | [
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942 | 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):
virtual_host = quote(virtual_host, '')
return self.http_client.get(API_USER_VIRTUAL_HOST_PERMISSIONS %
(
virtual_host,
username
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943 | 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
:param str configure_regex:... | python | def set_permission(self, username, virtual_host, configure_regex='.*',
write_regex='.*', read_regex='.*'):
virtual_host = quote(virtual_host, '')
permission_payload = json.dumps({
"configure": configure_regex,
"read": read_regex,
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944 | eandersson/amqpstorm | amqpstorm/management/user.py | User.delete_permission | def delete_permission(self, username, virtual_host):
"""Delete 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 ApiConnectionErr... | python | def delete_permission(self, username, virtual_host):
virtual_host = quote(virtual_host, '')
return self.http_client.delete(
API_USER_VIRTUAL_HOST_PERMISSIONS %
(
virtual_host,
username
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945 | eandersson/amqpstorm | examples/scalable_rpc_server.py | ScalableRpcServer.start_server | def start_server(self):
"""Start the RPC Server.
:return:
"""
self._stopped.clear()
if not self._connection or self._connection.is_closed:
self._create_connection()
while not self._stopped.is_set():
try:
# Check our connection for ... | python | def start_server(self):
self._stopped.clear()
if not self._connection or self._connection.is_closed:
self._create_connection()
while not self._stopped.is_set():
try:
# Check our connection for errors.
self._connection.check_for_errors()
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946 | eandersson/amqpstorm | examples/scalable_rpc_server.py | ScalableRpcServer._update_consumers | def _update_consumers(self):
"""Update Consumers.
- Add more if requested.
- Make sure the consumers are healthy.
- Remove excess consumers.
:return:
"""
# Do we need to start more consumers.
consumer_to_start = \
min(max(self.num... | python | def _update_consumers(self):
# Do we need to start more consumers.
consumer_to_start = \
min(max(self.number_of_consumers - len(self._consumers), 0), 2)
for _ in range(consumer_to_start):
consumer = Consumer(self.rpc_queue)
self._start_consumer(consumer)
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947 | 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):
return self._request('get', path, payload, headers) | [
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948 | 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):
return self._request('post', path, payload, headers) | [
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949 | eandersson/amqpstorm | amqpstorm/management/http_client.py | HTTPClient.delete | def delete(self, path, payload=None, headers=None):
"""HTTP DELETE 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... | python | def delete(self, path, payload=None, headers=None):
return self._request('delete', path, payload, headers) | [
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950 | eandersson/amqpstorm | amqpstorm/management/http_client.py | HTTPClient.put | def put(self, path, payload=None, headers=None):
"""HTTP PUT 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 put(self, path, payload=None, headers=None):
return self._request('put', path, payload, headers) | [
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951 | eandersson/amqpstorm | amqpstorm/management/http_client.py | HTTPClient._request | def _request(self, method, path, payload=None, headers=None):
"""HTTP operation.
:param method: Operation type (e.g. post)
:param path: URI Path
:param payload: HTTP Body
:param headers: HTTP Headers
:raises ApiError: Raises if the remote server encountered an error.
... | python | def _request(self, method, path, payload=None, headers=None):
url = urlparse.urljoin(self._base_url, 'api/%s' % path)
headers = headers or {}
headers['content-type'] = 'application/json'
try:
response = requests.request(
method, url,
auth=self.... | [
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952 | eandersson/amqpstorm | amqpstorm/management/http_client.py | HTTPClient._check_for_errors | def _check_for_errors(response, json_response):
"""Check payload for errors.
:param response: HTTP response
:param json_response: Json response
:raises ApiError: Raises if the remote server encountered an error.
:return:
"""
status_code = response.status_code
... | python | def _check_for_errors(response, json_response):
status_code = response.status_code
try:
response.raise_for_status()
except requests.HTTPError as why:
raise ApiError(str(why), reply_code=status_code)
if isinstance(json_response, dict) and 'error' in json_response:
... | [
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953 | 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
:raises ApiError: Raises if the remote ... | python | def get(self, node=None):
if not node:
return self.http_client.get(HEALTHCHECKS)
return self.http_client.get(HEALTHCHECKS_NODE % node) | [
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954 | 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):
# This function calculates the mean number of pairwise differences
# between haplotypes within a single population, generalising to any number
# of alleles.
# check inputs
ac = asarray_ndim(ac, 2)
# total number of haplotypes
if an is... | [
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Allele counts array.
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955 | 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):
"""Calculate for each variant the mean number of pairwise differences
between chromosomes sampled from two different populations.
Parameters
----------
ac1 : array_like, int, shape... | python | def mean_pairwise_difference_between(ac1, ac2, an1=None, an2=None,
fill=np.nan):
# This function calculates the mean number of pairwise differences
# between haplotypes from two different populations, generalising to any
# number of alleles.
# check inputs
ac1 =... | [
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956 | cggh/scikit-allel | allel/stats/diversity.py | watterson_theta | def watterson_theta(pos, ac, start=None, stop=None,
is_accessible=None):
"""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,
is_accessible=None):
# check inputs
if not isinstance(pos, SortedIndex):
pos = SortedIndex(pos, copy=False)
is_accessible = asarray_ndim(is_accessible, 1, allow_none=True)
if not hasattr(ac, 'count_segregating'):
ac ... | [
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957 | 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):
# check inputs
if not hasattr(ac, 'count_segregating'):
ac = AlleleCountsArray(ac, copy=False)
# deal with subregion
if pos is not None and (start is not None or stop is not None):
if not isinstance(pos, SortedIndex):
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958 | 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):
d = moving_statistic(values=ac, statistic=tajima_d, size=size, start=start, stop=stop,
step=step, min_sites=min_sites)
return d | [
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959 | 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):
# check input
dac, n = _check_dac_n(dac, n)
# need platform integer for bincount
dac = dac.astype(int, copy=False)
# compute site frequency spectrum
x = n + 1
s = np.bincount(dac, minlength=x)
return s | [
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960 | cggh/scikit-allel | allel/stats/sf.py | sfs_folded | def sfs_folded(ac, n=None):
"""Compute the folded site frequency spectrum given reference and
alternate allele counts at a set of biallelic variants.
Parameters
----------
ac : array_like, int, shape (n_variants, 2)
Allele counts array.
n : int, optional
The total number of chro... | python | def sfs_folded(ac, n=None):
# check input
ac, n = _check_ac_n(ac, n)
# compute minor allele counts
mac = np.amin(ac, axis=1)
# need platform integer for bincount
mac = mac.astype(int, copy=False)
# compute folded site frequency spectrum
x = n//2 + 1
s = np.bincount(mac, minlength=... | [
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961 | 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
expected across the spectrum for neutral variation and constant
population size.
Parameters
----------
dac : array_like, int, shape (n_variants,)
Array of derived allele counts.
... | python | def sfs_scaled(dac, n=None):
# compute site frequency spectrum
s = sfs(dac, n=n)
# apply scaling
s = scale_sfs(s)
return s | [
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962 | 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):
k = np.arange(s.size)
out = s * k
return out | [
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963 | cggh/scikit-allel | allel/stats/sf.py | sfs_folded_scaled | def sfs_folded_scaled(ac, n=None):
"""Compute the folded site frequency spectrum scaled such that a constant
value is expected across the spectrum for neutral variation and constant
population size.
Parameters
----------
ac : array_like, int, shape (n_variants, 2)
Allele counts array.
... | python | def sfs_folded_scaled(ac, n=None):
# check input
ac, n = _check_ac_n(ac, n)
# compute the site frequency spectrum
s = sfs_folded(ac, n=n)
# apply scaling
s = scale_sfs_folded(s, n)
return s | [
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964 | cggh/scikit-allel | allel/stats/sf.py | scale_sfs_folded | def scale_sfs_folded(s, n):
"""Scale a folded site frequency spectrum.
Parameters
----------
s : array_like, int, shape (n_chromosomes//2,)
Folded site frequency spectrum.
n : int
Number of chromosomes called.
Returns
-------
sfs_folded_scaled : ndarray, int, shape (n_c... | python | def scale_sfs_folded(s, n):
k = np.arange(s.shape[0])
out = s * k * (n - k) / n
return out | [
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965 | 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):
# check inputs
dac1, n1 = _check_dac_n(dac1, n1)
dac2, n2 = _check_dac_n(dac2, n2)
# compute site frequency spectrum
x = n1 + 1
y = n2 + 1
# need platform integer for bincount
tmp = (dac1 * y + dac2).astype(int, copy=False)
s = np.bincoun... | [
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Derived allele counts for the first population.
dac2 : array_like, int, shape (n_variants,)
Derived allele counts for the second population.
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966 | 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
populations.
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):
# check inputs
ac1, n1 = _check_ac_n(ac1, n1)
ac2, n2 = _check_ac_n(ac2, n2)
# compute minor allele counts
mac1 = np.amin(ac1, axis=1)
mac2 = np.amin(ac2, axis=1)
# compute site frequency spectrum
x = n1//2 + 1
y = n2//2 + 1
tmp... | [
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Allele counts for the second population.
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967 | 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
----------
dac1 : arr... | python | def joint_sfs_scaled(dac1, dac2, n1=None, n2=None):
# compute site frequency spectrum
s = joint_sfs(dac1, dac2, n1=n1, n2=n2)
# apply scaling
s = scale_joint_sfs(s)
return s | [
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Derived allele co... | [
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968 | cggh/scikit-allel | allel/stats/sf.py | scale_joint_sfs | def scale_joint_sfs(s):
"""Scale a joint site frequency spectrum.
Parameters
----------
s : array_like, int, shape (n1, n2)
Joint site frequency spectrum.
Returns
-------
joint_sfs_scaled : ndarray, int, shape (n1, n2)
Scaled joint site frequency spectrum.
"""
i =... | python | def scale_joint_sfs(s):
i = np.arange(s.shape[0])[:, None]
j = np.arange(s.shape[1])[None, :]
out = (s * i) * j
return out | [
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969 | cggh/scikit-allel | allel/stats/sf.py | joint_sfs_folded_scaled | def joint_sfs_folded_scaled(ac1, ac2, n1=None, n2=None):
"""Compute the joint folded 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
---------... | python | def joint_sfs_folded_scaled(ac1, ac2, n1=None, n2=None):
# noqa
# check inputs
ac1, n1 = _check_ac_n(ac1, n1)
ac2, n2 = _check_ac_n(ac2, n2)
# compute site frequency spectrum
s = joint_sfs_folded(ac1, ac2, n1=n1, n2=n2)
# apply scaling
s = scale_joint_sfs_folded(s, n1, n2)
return... | [
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970 | cggh/scikit-allel | allel/stats/sf.py | scale_joint_sfs_folded | def scale_joint_sfs_folded(s, n1, n2):
"""Scale a folded joint site frequency spectrum.
Parameters
----------
s : array_like, int, shape (m_chromosomes//2, n_chromosomes//2)
Folded joint site frequency spectrum.
n1, n2 : int, optional
The total number of chromosomes called in each p... | python | def scale_joint_sfs_folded(s, n1, n2):
# noqa
out = np.empty_like(s)
for i in range(s.shape[0]):
for j in range(s.shape[1]):
out[i, j] = s[i, j] * i * j * (n1 - i) * (n2 - j)
return out | [
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971 | cggh/scikit-allel | allel/stats/sf.py | fold_sfs | def fold_sfs(s, n):
"""Fold a site frequency spectrum.
Parameters
----------
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):
# check inputs
s = asarray_ndim(s, 1)
assert s.shape[0] <= n + 1, 'invalid number of chromosomes'
# need to check s has all entries up to n
if s.shape[0] < n + 1:
sn = np.zeros(n + 1, dtype=s.dtype)
sn[:s.shape[0]] = s
s = sn
# fold
nf = (n + 1) ... | [
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972 | cggh/scikit-allel | allel/stats/sf.py | fold_joint_sfs | def fold_joint_sfs(s, n1, n2):
"""Fold a joint site frequency spectrum.
Parameters
----------
s : array_like, int, shape (m_chromosomes, n_chromosomes)
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):
# check inputs
s = asarray_ndim(s, 2)
assert s.shape[0] <= n1 + 1, 'invalid number of chromosomes'
assert s.shape[1] <= n2 + 1, 'invalid number of chromosomes'
# need to check s has all entries up to m
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Joint site frequency spectrum.
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973 | 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
... | python | def plot_sfs(s, yscale='log', bins=None, n=None,
clip_endpoints=True, label=None, plot_kwargs=None,
ax=None):
import matplotlib.pyplot as plt
import scipy
# check inputs
s = asarray_ndim(s, 1)
# setup axes
if ax is None:
fig, ax = plt.subplots()
# setup d... | [
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Site frequency spectrum.
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Y axis scale.
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Allele count bins.
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974 | cggh/scikit-allel | allel/stats/sf.py | plot_sfs_folded | def plot_sfs_folded(*args, **kwargs):
"""Plot a folded site frequency spectrum.
Parameters
----------
s : array_like, int, shape (n_chromosomes/2,)
Site frequency spectrum.
yscale : string, optional
Y axis scale.
bins : int or array_like, int, optional
Allele count bins.... | python | def plot_sfs_folded(*args, **kwargs):
ax = plot_sfs(*args, **kwargs)
n = kwargs.get('n', None)
if n:
ax.set_xlabel('minor allele frequency')
else:
ax.set_xlabel('minor allele count')
return ax | [
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Site frequency spectrum.
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975 | cggh/scikit-allel | allel/stats/sf.py | plot_sfs_scaled | def plot_sfs_scaled(*args, **kwargs):
"""Plot a scaled site frequency spectrum.
Parameters
----------
s : array_like, int, shape (n_chromosomes,)
Site frequency spectrum.
yscale : string, optional
Y axis scale.
bins : int or array_like, int, optional
Allele count bins.
... | python | def plot_sfs_scaled(*args, **kwargs):
kwargs.setdefault('yscale', 'linear')
ax = plot_sfs(*args, **kwargs)
ax.set_ylabel('scaled site frequency')
return ax | [
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976 | cggh/scikit-allel | allel/stats/sf.py | plot_sfs_folded_scaled | def plot_sfs_folded_scaled(*args, **kwargs):
"""Plot a folded scaled site frequency spectrum.
Parameters
----------
s : array_like, int, shape (n_chromosomes/2,)
Site frequency spectrum.
yscale : string, optional
Y axis scale.
bins : int or array_like, int, optional
Alle... | python | def plot_sfs_folded_scaled(*args, **kwargs):
kwargs.setdefault('yscale', 'linear')
ax = plot_sfs_folded(*args, **kwargs)
ax.set_ylabel('scaled site frequency')
n = kwargs.get('n', None)
if n:
ax.set_xlabel('minor allele frequency')
else:
ax.set_xlabel('minor allele count')
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977 | cggh/scikit-allel | allel/stats/sf.py | plot_joint_sfs_scaled | def plot_joint_sfs_scaled(*args, **kwargs):
"""Plot a scaled joint site frequency spectrum.
Parameters
----------
s : array_like, int, shape (n_chromosomes_pop1, n_chromosomes_pop2)
Joint site frequency spectrum.
ax : axes, optional
Axes on which to draw. If not provided, a new figu... | python | def plot_joint_sfs_scaled(*args, **kwargs):
imshow_kwargs = kwargs.get('imshow_kwargs', dict())
imshow_kwargs.setdefault('norm', None)
kwargs['imshow_kwargs'] = imshow_kwargs
ax = plot_joint_sfs(*args, **kwargs)
return ax | [
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978 | cggh/scikit-allel | allel/stats/sf.py | plot_joint_sfs_folded_scaled | def plot_joint_sfs_folded_scaled(*args, **kwargs):
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Parameters
----------
s : array_like, int, shape (n_chromosomes_pop1/2, n_chromosomes_pop2/2)
Joint site frequency spectrum.
ax : axes, optional
Axes on which to draw. If not pr... | python | def plot_joint_sfs_folded_scaled(*args, **kwargs):
imshow_kwargs = kwargs.get('imshow_kwargs', dict())
imshow_kwargs.setdefault('norm', None)
kwargs['imshow_kwargs'] = imshow_kwargs
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ax.set_xlabel('minor allele count (population 1)')
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979 | 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):
store_samples = False
if fields is None:
# add samples by default
return True, None
if isinstance(fields, str):
fields = [fields]
else:
fields = list(fields)
if 'samples' in fields:
fields.remove('samples')
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980 | 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):
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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981 | 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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982 | 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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983 | 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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984 | 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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output : string
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985 | 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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986 | 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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987 | cggh/scikit-allel | allel/io/vcf_read.py | vcf_to_recarray | def vcf_to_recarray(input,
fields=None,
exclude_fields=None,
types=None,
numbers=None,
alt_number=DEFAULT_ALT_NUMBER,
fills=None,
region=None,
tabix='tabix',
... | python | def vcf_to_recarray(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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988 | cggh/scikit-allel | allel/io/fasta.py | write_fasta | def write_fasta(path, sequences, names, mode='w', width=80):
"""Write nucleotide sequences stored as numpy arrays to a FASTA file.
Parameters
----------
path : string
File path.
sequences : sequence of arrays
One or more ndarrays of dtype 'S1' containing the sequences.
names : ... | python | def write_fasta(path, sequences, names, mode='w', width=80):
# check inputs
if isinstance(sequences, np.ndarray):
# single sequence
sequences = [sequences]
names = [names]
if len(sequences) != len(names):
raise ValueError('must provide the same number of sequences and names')... | [
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989 | cggh/scikit-allel | allel/stats/hw.py | heterozygosity_observed | def heterozygosity_observed(g, fill=np.nan):
"""Calculate the rate of observed heterozygosity for each variant.
Parameters
----------
g : array_like, int, shape (n_variants, n_samples, ploidy)
Genotype array.
fill : float, optional
Use this value for variants where all calls are mi... | python | def heterozygosity_observed(g, fill=np.nan):
# check inputs
if not hasattr(g, 'count_het') or not hasattr(g, 'count_called'):
g = GenotypeArray(g, copy=False)
# count hets
n_het = np.asarray(g.count_het(axis=1))
n_called = np.asarray(g.count_called(axis=1))
# calculate rate of observed... | [
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Genotype array.
fill : float, optional
Use this value for variants where all calls are missing.
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-------
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990 | cggh/scikit-allel | allel/stats/hw.py | heterozygosity_expected | def heterozygosity_expected(af, ploidy, fill=np.nan):
"""Calculate the expected rate of heterozygosity for each variant
under Hardy-Weinberg equilibrium.
Parameters
----------
af : array_like, float, shape (n_variants, n_alleles)
Allele frequencies array.
ploidy : int
Sample pl... | python | def heterozygosity_expected(af, ploidy, fill=np.nan):
# check inputs
af = asarray_ndim(af, 2)
# calculate expected heterozygosity
out = 1 - np.sum(np.power(af, ploidy), axis=1)
# fill values where allele frequencies could not be calculated
af_sum = np.sum(af, axis=1)
with ignore_invalid():... | [
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Allele frequencies array.
ploidy : int
Sample ploidy.
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991 | cggh/scikit-allel | allel/stats/hw.py | inbreeding_coefficient | def inbreeding_coefficient(g, fill=np.nan):
"""Calculate the inbreeding coefficient for each variant.
Parameters
----------
g : array_like, int, shape (n_variants, n_samples, ploidy)
Genotype array.
fill : float, optional
Use this value for variants where the expected heterozygosit... | python | def inbreeding_coefficient(g, fill=np.nan):
# check inputs
if not hasattr(g, 'count_het') or not hasattr(g, 'count_called'):
g = GenotypeArray(g, copy=False)
# calculate observed and expected heterozygosity
ho = heterozygosity_observed(g)
af = g.count_alleles().to_frequencies()
he = het... | [
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Genotype array.
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Use this value for variants where the expected heterozygosity is
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992 | cggh/scikit-allel | allel/stats/mendel.py | mendel_errors | def mendel_errors(parent_genotypes, progeny_genotypes):
"""Locate genotype calls not consistent with Mendelian transmission of
alleles.
Parameters
----------
parent_genotypes : array_like, int, shape (n_variants, 2, 2)
Genotype calls for the two parents.
progeny_genotypes : array_like, ... | python | def mendel_errors(parent_genotypes, progeny_genotypes):
# setup
parent_genotypes = GenotypeArray(parent_genotypes)
progeny_genotypes = GenotypeArray(progeny_genotypes)
check_ploidy(parent_genotypes.ploidy, 2)
check_ploidy(progeny_genotypes.ploidy, 2)
# transform into per-call allele counts
... | [
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Genotype calls for the two parents.
progeny_genotypes : array_like, int, shape (n_variants, n_progeny, 2)
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993 | cggh/scikit-allel | allel/stats/mendel.py | paint_transmission | def paint_transmission(parent_haplotypes, progeny_haplotypes):
"""Paint haplotypes inherited from a single diploid parent according to
their allelic inheritance.
Parameters
----------
parent_haplotypes : array_like, int, shape (n_variants, 2)
Both haplotypes from a single diploid parent.
... | python | def paint_transmission(parent_haplotypes, progeny_haplotypes):
# check inputs
parent_haplotypes = HaplotypeArray(parent_haplotypes)
progeny_haplotypes = HaplotypeArray(progeny_haplotypes)
if parent_haplotypes.n_haplotypes != 2:
raise ValueError('exactly two parental haplotypes should be provided... | [
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parent_haplotypes : array_like, int, shape (n_variants, 2)
Both haplotypes from a single diploid parent.
progeny_haplotypes : array_like, int, shape (n_variants, n_progeny)
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994 | cggh/scikit-allel | allel/stats/mendel.py | phase_progeny_by_transmission | def phase_progeny_by_transmission(g):
"""Phase progeny genotypes from a trio or cross using Mendelian
transmission.
Parameters
----------
g : array_like, int, shape (n_variants, n_samples, 2)
Genotype array, with parents as first two columns and progeny as
remaining columns.
Re... | python | def phase_progeny_by_transmission(g):
# setup
g = GenotypeArray(g, dtype='i1', copy=True)
check_ploidy(g.ploidy, 2)
check_min_samples(g.n_samples, 3)
# run the phasing
# N.B., a copy has already been made, so no need to make memoryview safe
is_phased = _opt_phase_progeny_by_transmission(g.v... | [
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g : array_like, int, shape (n_variants, n_samples, 2)
Genotype array, with parents as first two columns and progeny as
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-------
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995 | cggh/scikit-allel | allel/stats/mendel.py | phase_parents_by_transmission | def phase_parents_by_transmission(g, window_size):
"""Phase parent genotypes from a trio or cross, given progeny genotypes
already phased by Mendelian transmission.
Parameters
----------
g : GenotypeArray
Genotype array, with parents as first two columns and progeny as
remaining col... | python | def phase_parents_by_transmission(g, window_size):
# setup
check_type(g, GenotypeArray)
check_dtype(g.values, 'i1')
check_ploidy(g.ploidy, 2)
if g.is_phased is None:
raise ValueError('genotype array must first have progeny phased by transmission')
check_min_samples(g.n_samples, 3)
#... | [
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996 | cggh/scikit-allel | allel/stats/mendel.py | phase_by_transmission | def phase_by_transmission(g, window_size, copy=True):
"""Phase genotypes in a trio or cross where possible using Mendelian
transmission.
Parameters
----------
g : array_like, int, shape (n_variants, n_samples, 2)
Genotype array, with parents as first two columns and progeny as
remai... | python | def phase_by_transmission(g, window_size, copy=True):
# setup
g = np.asarray(g, dtype='i1')
g = GenotypeArray(g, copy=copy)
g._values = memoryview_safe(g.values)
check_ploidy(g.ploidy, 2)
check_min_samples(g.n_samples, 3)
# phase the progeny
is_phased = _opt_phase_progeny_by_transmissio... | [
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Genotype array, with parents as first two columns and progeny as
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997 | cggh/scikit-allel | allel/chunked/util.py | get_blen_array | def get_blen_array(data, blen=None):
"""Try to guess a reasonable block length to use for block-wise iteration
over `data`."""
if blen is None:
if hasattr(data, 'chunklen'):
# bcolz carray
return data.chunklen
elif hasattr(data, 'chunks') and \
hasa... | python | def get_blen_array(data, blen=None):
if blen is None:
if hasattr(data, 'chunklen'):
# bcolz carray
return data.chunklen
elif hasattr(data, 'chunks') and \
hasattr(data, 'shape') and \
hasattr(data.chunks, '__len__') and \
hasa... | [
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998 | cggh/scikit-allel | allel/chunked/storage_hdf5.py | h5fmem | def h5fmem(**kwargs):
"""Create an in-memory HDF5 file."""
# need a file name even tho nothing is ever written
fn = tempfile.mktemp()
# file creation args
kwargs['mode'] = 'w'
kwargs['driver'] = 'core'
kwargs['backing_store'] = False
# open HDF5 file
h5f = h5py.File(fn, **kwargs)
... | python | def h5fmem(**kwargs):
# need a file name even tho nothing is ever written
fn = tempfile.mktemp()
# file creation args
kwargs['mode'] = 'w'
kwargs['driver'] = 'core'
kwargs['backing_store'] = False
# open HDF5 file
h5f = h5py.File(fn, **kwargs)
return h5f | [
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999 | cggh/scikit-allel | allel/chunked/storage_hdf5.py | h5ftmp | def h5ftmp(**kwargs):
"""Create an HDF5 file backed by a temporary file."""
# create temporary file name
suffix = kwargs.pop('suffix', '.h5')
prefix = kwargs.pop('prefix', 'scikit_allel_')
tempdir = kwargs.pop('dir', None)
fn = tempfile.mktemp(suffix=suffix, prefix=prefix, dir=tempdir)
atex... | python | def h5ftmp(**kwargs):
# create temporary file name
suffix = kwargs.pop('suffix', '.h5')
prefix = kwargs.pop('prefix', 'scikit_allel_')
tempdir = kwargs.pop('dir', None)
fn = tempfile.mktemp(suffix=suffix, prefix=prefix, dir=tempdir)
atexit.register(os.remove, fn)
# file creation args
kw... | [
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