_id stringlengths 2 7 | title stringlengths 1 88 | partition stringclasses 3
values | text stringlengths 75 19.8k | language stringclasses 1
value | meta_information dict |
|---|---|---|---|---|---|
q900 | UriConnection._parse_uri_options | train | 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 | {
"resource": ""
} |
q901 | UriConnection._parse_ssl_options | train | 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 | {
"resource": ""
} |
q902 | UriConnection._get_ssl_version | train | 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 | {
"resource": ""
} |
q903 | UriConnection._get_ssl_validation | train | 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 | {
"resource": ""
} |
q904 | UriConnection._get_ssl_attribute | train | 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 | {
"resource": ""
} |
q905 | ManagementApi.top | train | 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 | {
"resource": ""
} |
q906 | Basic.qos | train | 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 | {
"resource": ""
} |
q907 | Basic.get | train | 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 | {
"resource": ""
} |
q908 | Basic.recover | train | 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 | {
"resource": ""
} |
q909 | Basic.cancel | train | 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 | {
"resource": ""
} |
q910 | Basic.reject | train | 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 | {
"resource": ""
} |
q911 | Basic._consume_add_and_get_tag | train | 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 | {
"resource": ""
} |
q912 | Basic._consume_rpc_request | train | 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 | {
"resource": ""
} |
q913 | Basic._validate_publish_parameters | train | 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 | {
"resource": ""
} |
q914 | Basic._handle_utf8_payload | train | 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 | {
"resource": ""
} |
q915 | Basic._get_message | train | 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 | {
"resource": ""
} |
q916 | Basic._publish_confirm | train | 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 | {
"resource": ""
} |
q917 | Basic._create_content_body | train | 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 | {
"resource": ""
} |
q918 | Basic._get_content_body | train | 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 | {
"resource": ""
} |
q919 | Channel0.on_frame | train | 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 | {
"resource": ""
} |
q920 | Channel0._close_connection | train | 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 | {
"resource": ""
} |
q921 | Channel0._blocked_connection | train | 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 | {
"resource": ""
} |
q922 | Channel0._send_start_ok | train | 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 | {
"resource": ""
} |
q923 | Channel0._send_tune_ok | train | 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 | {
"resource": ""
} |
q924 | Channel0._send_open_connection | train | 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 | {
"resource": ""
} |
q925 | Channel0._write_frame | train | 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 | {
"resource": ""
} |
q926 | Channel0._client_properties | train | def _client_properties():
"""AMQPStorm Client Properties.
:rtype: dict
"""
return {
'product': 'AMQPStorm',
'platform': 'Python %s (%s)' % (platform.python_version(),
platform.python_implementation()),
'capa... | python | {
"resource": ""
} |
q927 | Channel.build_inbound_messages | train | 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 | {
"resource": ""
} |
q928 | Channel.check_for_errors | train | 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 | {
"resource": ""
} |
q929 | Channel.confirm_deliveries | train | 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 | {
"resource": ""
} |
q930 | Channel.on_frame | train | 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 | {
"resource": ""
} |
q931 | Channel.process_data_events | train | 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 | {
"resource": ""
} |
q932 | Channel.rpc_request | train | 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 | {
"resource": ""
} |
q933 | Channel.start_consuming | train | 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 | {
"resource": ""
} |
q934 | Channel.stop_consuming | train | 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 | {
"resource": ""
} |
q935 | Channel.write_frame | train | 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 | {
"resource": ""
} |
q936 | Channel.write_frames | train | 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 | {
"resource": ""
} |
q937 | Channel._basic_cancel | train | 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 | {
"resource": ""
} |
q938 | Channel._basic_return | train | 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 = (
"Message not delivered: %s (%s) to ... | python | {
"resource": ""
} |
q939 | Channel._build_message | train | 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 | {
"resource": ""
} |
q940 | Channel._build_message_body | train | 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 | {
"resource": ""
} |
q941 | User.create | train | 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 | {
"resource": ""
} |
q942 | User.get_permission | train | 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 | {
"resource": ""
} |
q943 | User.set_permission | train | 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 | {
"resource": ""
} |
q944 | User.delete_permission | train | 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 | {
"resource": ""
} |
q945 | ScalableRpcServer.start_server | train | 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 | {
"resource": ""
} |
q946 | ScalableRpcServer._update_consumers | train | 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 | {
"resource": ""
} |
q947 | HTTPClient.get | train | 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 | {
"resource": ""
} |
q948 | HTTPClient.post | train | 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 | {
"resource": ""
} |
q949 | HTTPClient.delete | train | 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 | {
"resource": ""
} |
q950 | HTTPClient.put | train | 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 | {
"resource": ""
} |
q951 | HTTPClient._request | train | 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 | {
"resource": ""
} |
q952 | HTTPClient._check_for_errors | train | 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 | {
"resource": ""
} |
q953 | HealthChecks.get | train | 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 | {
"resource": ""
} |
q954 | mean_pairwise_difference | train | 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 | {
"resource": ""
} |
q955 | mean_pairwise_difference_between | train | 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 | {
"resource": ""
} |
q956 | watterson_theta | train | 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 | {
"resource": ""
} |
q957 | tajima_d | train | 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 | {
"resource": ""
} |
q958 | moving_tajima_d | train | 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 | {
"resource": ""
} |
q959 | sfs | train | 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 | {
"resource": ""
} |
q960 | sfs_folded | train | 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 | {
"resource": ""
} |
q961 | sfs_scaled | train | 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 | {
"resource": ""
} |
q962 | scale_sfs | train | 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 | {
"resource": ""
} |
q963 | sfs_folded_scaled | train | 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 | {
"resource": ""
} |
q964 | scale_sfs_folded | train | 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 | {
"resource": ""
} |
q965 | joint_sfs | train | 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 | {
"resource": ""
} |
q966 | joint_sfs_folded | train | 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 | {
"resource": ""
} |
q967 | joint_sfs_scaled | train | 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 | {
"resource": ""
} |
q968 | scale_joint_sfs | train | 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 | {
"resource": ""
} |
q969 | joint_sfs_folded_scaled | train | 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 | {
"resource": ""
} |
q970 | scale_joint_sfs_folded | train | 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 | {
"resource": ""
} |
q971 | fold_sfs | train | 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 | {
"resource": ""
} |
q972 | fold_joint_sfs | train | 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 | {
"resource": ""
} |
q973 | plot_sfs | train | 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 | {
"resource": ""
} |
q974 | plot_sfs_folded | train | 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 | {
"resource": ""
} |
q975 | plot_sfs_scaled | train | 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 | {
"resource": ""
} |
q976 | plot_sfs_folded_scaled | train | 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 | {
"resource": ""
} |
q977 | plot_joint_sfs_scaled | train | 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 | {
"resource": ""
} |
q978 | plot_joint_sfs_folded_scaled | train | def plot_joint_sfs_folded_scaled(*args, **kwargs):
"""Plot a scaled folded joint site frequency spectrum.
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 | {
"resource": ""
} |
q979 | _prep_fields_param | train | 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 | {
"resource": ""
} |
q980 | _chunk_iter_progress | train | 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 | {
"resource": ""
} |
q981 | read_vcf | train | 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 | {
"resource": ""
} |
q982 | vcf_to_npz | train | 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 | {
"resource": ""
} |
q983 | vcf_to_hdf5 | train | 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 | {
"resource": ""
} |
q984 | vcf_to_zarr | train | 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 | {
"resource": ""
} |
q985 | iter_vcf_chunks | train | 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 | {
"resource": ""
} |
q986 | vcf_to_dataframe | train | 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 | {
"resource": ""
} |
q987 | vcf_to_recarray | train | 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 | {
"resource": ""
} |
q988 | write_fasta | train | 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 | {
"resource": ""
} |
q989 | heterozygosity_observed | train | 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 | {
"resource": ""
} |
q990 | heterozygosity_expected | train | 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 | {
"resource": ""
} |
q991 | inbreeding_coefficient | train | 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 | {
"resource": ""
} |
q992 | mendel_errors | train | 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 | {
"resource": ""
} |
q993 | paint_transmission | train | 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 | {
"resource": ""
} |
q994 | phase_progeny_by_transmission | train | 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 | {
"resource": ""
} |
q995 | phase_parents_by_transmission | train | 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 | {
"resource": ""
} |
q996 | phase_by_transmission | train | 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 | {
"resource": ""
} |
q997 | get_blen_array | train | 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 | {
"resource": ""
} |
q998 | h5fmem | train | 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 | {
"resource": ""
} |
q999 | h5ftmp | train | 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 | {
"resource": ""
} |
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