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sprockets/sprockets-dynamodb | sprockets_dynamodb/client.py | Client.update_item | def update_item(self, table_name, key_dict,
condition_expression=None,
update_expression=None,
expression_attribute_names=None,
expression_attribute_values=None,
return_consumed_capacity=None,
return_... | python | def update_item(self, table_name, key_dict,
condition_expression=None,
update_expression=None,
expression_attribute_names=None,
expression_attribute_values=None,
return_consumed_capacity=None,
return_... | [
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Edits an existing item's attributes, or adds a new item to the table
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sprockets/sprockets-dynamodb | sprockets_dynamodb/client.py | Client.query | def query(self, table_name,
index_name=None,
consistent_read=None,
key_condition_expression=None,
filter_expression=None,
expression_attribute_names=None,
expression_attribute_values=None,
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index_name=None,
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key_condition_expression=None,
filter_expression=None,
expression_attribute_names=None,
expression_attribute_values=None,
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sprockets/sprockets-dynamodb | sprockets_dynamodb/client.py | Client.scan | def scan(self,
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tota... | python | def scan(self,
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If the total number of scanned items exceeds the maximum data set size
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sprockets/sprockets-dynamodb | sprockets_dynamodb/client.py | Client.execute | def execute(self, action, parameters):
"""
Execute a DynamoDB action with the given parameters. The method will
retry requests that failed due to OS level errors or when being
throttled by DynamoDB.
:param str action: DynamoDB action to invoke
:param dict parameters: par... | python | def execute(self, action, parameters):
"""
Execute a DynamoDB action with the given parameters. The method will
retry requests that failed due to OS level errors or when being
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:param str action: DynamoDB action to invoke
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sprockets/sprockets-dynamodb | sprockets_dynamodb/client.py | Client.set_error_callback | def set_error_callback(self, callback):
"""Assign a method to invoke when a request has encountered an
unrecoverable error in an action execution.
:param method callback: The method to invoke
"""
self.logger.debug('Setting error callback: %r', callback)
self._on_error =... | python | def set_error_callback(self, callback):
"""Assign a method to invoke when a request has encountered an
unrecoverable error in an action execution.
:param method callback: The method to invoke
"""
self.logger.debug('Setting error callback: %r', callback)
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sprockets/sprockets-dynamodb | sprockets_dynamodb/client.py | Client.set_instrumentation_callback | def set_instrumentation_callback(self, callback):
"""Assign a method to invoke when a request has completed gathering
measurements.
:param method callback: The method to invoke
"""
self.logger.debug('Setting instrumentation callback: %r', callback)
self._instrumentation... | python | def set_instrumentation_callback(self, callback):
"""Assign a method to invoke when a request has completed gathering
measurements.
:param method callback: The method to invoke
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self.logger.debug('Setting instrumentation callback: %r', callback)
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sprockets/sprockets-dynamodb | sprockets_dynamodb/client.py | Client._execute | def _execute(self, action, parameters, attempt, measurements):
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:param str action: DynamoDB action to invoke
:param dict parameters: parameters to send into the action
:param int attempt: Which attempt number this is
:param list measurements: A list fo... | python | def _execute(self, action, parameters, attempt, measurements):
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sprockets/sprockets-dynamodb | sprockets_dynamodb/client.py | Client._on_response | def _on_response(self, action, table, attempt, start, response, future,
measurements):
"""Invoked when the HTTP request to the DynamoDB has returned and
is responsible for setting the future result or exception based upon
the HTTP response provided.
:param str actio... | python | def _on_response(self, action, table, attempt, start, response, future,
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sprockets/sprockets-dynamodb | sprockets_dynamodb/client.py | Client._process_response | def _process_response(response):
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:param tornado.concurrent.Future response: The request future
:rtype: dict or list
:raises: sprockets_dynamodb.exceptions.DynamoDBException
... | python | def _process_response(response):
"""Process the raw AWS response, returning either the mapped exception
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oceanprotocol/oceandb-bigchaindb-driver | oceandb_bigchaindb_driver/plugin.py | Plugin.write | def write(self, obj, resource_id=None):
"""Write and obj in bdb.
:param obj: value to be written in bdb.
:param resource_id: id to make possible read and search for an resource.
:return: id of the transaction
"""
if resource_id is not None:
if self.read(resou... | python | def write(self, obj, resource_id=None):
"""Write and obj in bdb.
:param obj: value to be written in bdb.
:param resource_id: id to make possible read and search for an resource.
:return: id of the transaction
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oceanprotocol/oceandb-bigchaindb-driver | oceandb_bigchaindb_driver/plugin.py | Plugin._get | def _get(self, tx_id):
"""Read and obj in bdb using the tx_id.
:param resource_id: id of the transaction to be read.
:return: value with the data, transaction id and transaction.
"""
# tx_id=self._find_tx_id(resource_id)
value = [
{
'data': tr... | python | def _get(self, tx_id):
"""Read and obj in bdb using the tx_id.
:param resource_id: id of the transaction to be read.
:return: value with the data, transaction id and transaction.
"""
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oceanprotocol/oceandb-bigchaindb-driver | oceandb_bigchaindb_driver/plugin.py | Plugin._update | def _update(self, metadata, tx_id, resource_id):
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:param metadata: new metadata for the transaction.
:param tx_id: id of the transaction to be updated.
:return: id of the transaction.
"""
try:
if not tx_id:
... | python | def _update(self, metadata, tx_id, resource_id):
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oceanprotocol/oceandb-bigchaindb-driver | oceandb_bigchaindb_driver/plugin.py | Plugin.list | def list(self, search_from=None, search_to=None, limit=None):
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:param search_from: TBI
:param search_to: TBI
:param offset: TBI
:param limit: max number of values to be shows.
:return: list with transactions.
"... | python | def list(self, search_from=None, search_to=None, limit=None):
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:param search_from: TBI
:param search_to: TBI
:param offset: TBI
:param limit: max number of values to be shows.
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oceanprotocol/oceandb-bigchaindb-driver | oceandb_bigchaindb_driver/plugin.py | Plugin._list | def _list(self):
"""List all the objects saved in the namespace.
:param search_from: TBI
:param search_to: TBI
:param offset: TBI
:param limit: max number of values to be shows.
:return: list with transactions.
"""
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"""List all the objects saved in the namespace.
:param search_from: TBI
:param search_to: TBI
:param offset: TBI
:param limit: max number of values to be shows.
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oceanprotocol/oceandb-bigchaindb-driver | oceandb_bigchaindb_driver/plugin.py | Plugin.query | def query(self, search_model: QueryModel):
"""Query to bdb namespace.
:param query_string: query in string format.
:return: list of transactions that match with the query.
"""
self.logger.debug('bdb::get::{}'.format(search_model.query))
assets = json.loads(requests.post(... | python | def query(self, search_model: QueryModel):
"""Query to bdb namespace.
:param query_string: query in string format.
:return: list of transactions that match with the query.
"""
self.logger.debug('bdb::get::{}'.format(search_model.query))
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oceanprotocol/oceandb-bigchaindb-driver | oceandb_bigchaindb_driver/plugin.py | Plugin._delete | def _delete(self, tx_id):
"""Delete a transaction. Read documentation about CRAB model in https://blog.bigchaindb.com/crab-create-retrieve-append-burn-b9f6d111f460.
:param tx_id: transaction id
:return:
"""
txs = self.driver.instance.transactions.get(asset_id=self.get_asset_id(t... | python | def _delete(self, tx_id):
"""Delete a transaction. Read documentation about CRAB model in https://blog.bigchaindb.com/crab-create-retrieve-append-burn-b9f6d111f460.
:param tx_id: transaction id
:return:
"""
txs = self.driver.instance.transactions.get(asset_id=self.get_asset_id(t... | [
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oceanprotocol/oceandb-bigchaindb-driver | oceandb_bigchaindb_driver/plugin.py | Plugin.get_asset_id | def get_asset_id(self, tx_id):
"""Return the tx_id of the first transaction.
:param tx_id: Transaction id to start the recursive search.
:return Transaction id parent.
"""
tx = self.driver.instance.transactions.retrieve(txid=tx_id)
assert tx is not None
return tx... | python | def get_asset_id(self, tx_id):
"""Return the tx_id of the first transaction.
:param tx_id: Transaction id to start the recursive search.
:return Transaction id parent.
"""
tx = self.driver.instance.transactions.retrieve(txid=tx_id)
assert tx is not None
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johntruckenbrodt/spatialist | spatialist/envi.py | hdr | def hdr(data, filename):
"""
write ENVI header files
Parameters
----------
data: str or dict
the file or dictionary to get the info from
filename: str
the HDR file to write
Returns
-------
"""
hdrobj = data if isinstance(data, HDRobject) else HDRobject(data)
... | python | def hdr(data, filename):
"""
write ENVI header files
Parameters
----------
data: str or dict
the file or dictionary to get the info from
filename: str
the HDR file to write
Returns
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"""
hdrobj = data if isinstance(data, HDRobject) else HDRobject(data)
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johntruckenbrodt/spatialist | spatialist/envi.py | HDRobject.__hdr2dict | def __hdr2dict(self):
"""
read a HDR file into a dictionary
http://gis.stackexchange.com/questions/48618/how-to-read-write-envi-metadata-using-gdal
Returns
-------
dict
the hdr file metadata attributes
"""
with open(self.filename, 'r') as infil... | python | def __hdr2dict(self):
"""
read a HDR file into a dictionary
http://gis.stackexchange.com/questions/48618/how-to-read-write-envi-metadata-using-gdal
Returns
-------
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johntruckenbrodt/spatialist | spatialist/envi.py | HDRobject.write | def write(self, filename='same'):
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write object to an ENVI header file
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"""
write object to an ENVI header file
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filename = self.filename
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MLAB-project/pymlab | examples/I2CSPI_HBSTEP_CAMPAP.py | axis.MaxSpeed | def MaxSpeed(self, speed):
' Setup of maximum speed '
spi.SPI_write_byte(self.CS, 0x07) # Max Speed setup
spi.SPI_write_byte(self.CS, 0x00)
spi.SPI_write_byte(self.CS, speed) | python | def MaxSpeed(self, speed):
' Setup of maximum speed '
spi.SPI_write_byte(self.CS, 0x07) # Max Speed setup
spi.SPI_write_byte(self.CS, 0x00)
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MLAB-project/pymlab | examples/I2CSPI_HBSTEP_CAMPAP.py | axis.GoZero | def GoZero(self, speed):
' Go to Zero position '
self.ReleaseSW()
spi.SPI_write_byte(self.CS, 0x82 | (self.Dir & 1)) # Go to Zero
spi.SPI_write_byte(self.CS, 0x00)
spi.SPI_write_byte(self.CS, speed)
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time.sleep(0.3)
... | python | def GoZero(self, speed):
' Go to Zero position '
self.ReleaseSW()
spi.SPI_write_byte(self.CS, 0x82 | (self.Dir & 1)) # Go to Zero
spi.SPI_write_byte(self.CS, 0x00)
spi.SPI_write_byte(self.CS, speed)
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time.sleep(0.3)
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MLAB-project/pymlab | examples/I2CSPI_HBSTEP_CAMPAP.py | axis.Move | def Move(self, units):
' Move some distance units from current position '
steps = units * self.SPU # translate units to steps
if steps > 0: # look for direction
spi.SPI_write_byte(self.CS, 0x40 | (~self.Dir & 1))
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... | python | def Move(self, units):
' Move some distance units from current position '
steps = units * self.SPU # translate units to steps
if steps > 0: # look for direction
spi.SPI_write_byte(self.CS, 0x40 | (~self.Dir & 1))
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MLAB-project/pymlab | examples/I2CSPI_HBSTEP_CAMPAP.py | axis.ReadStatusBit | def ReadStatusBit(self, bit):
' Report given status bit '
spi.SPI_write_byte(self.CS, 0x39) # Read from address 0x19 (STATUS)
spi.SPI_write_byte(self.CS, 0x00)
data0 = spi.SPI_read_byte() # 1st byte
spi.SPI_write_byte(self.CS, 0x00)
data1 = spi.SPI_read_byte()... | python | def ReadStatusBit(self, bit):
' Report given status bit '
spi.SPI_write_byte(self.CS, 0x39) # Read from address 0x19 (STATUS)
spi.SPI_write_byte(self.CS, 0x00)
data0 = spi.SPI_read_byte() # 1st byte
spi.SPI_write_byte(self.CS, 0x00)
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MLAB-project/pymlab | src/pymlab/sensors/bus_translators.py | I2CSPI.SPI_write_byte | def SPI_write_byte(self, chip_select, data):
'Writes a data to a SPI device selected by chipselect bit. '
self.bus.write_byte_data(self.address, chip_select, data) | python | def SPI_write_byte(self, chip_select, data):
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MLAB-project/pymlab | src/pymlab/sensors/bus_translators.py | I2CSPI.SPI_write | def SPI_write(self, chip_select, data):
'Writes data to SPI device selected by chipselect bit. '
dat = list(data)
dat.insert(0, chip_select)
return self.bus.write_i2c_block(self.address, dat); | python | def SPI_write(self, chip_select, data):
'Writes data to SPI device selected by chipselect bit. '
dat = list(data)
dat.insert(0, chip_select)
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MLAB-project/pymlab | src/pymlab/sensors/bus_translators.py | I2CSPI.SPI_config | def SPI_config(self,config):
'Configure SPI interface parameters.'
self.bus.write_byte_data(self.address, 0xF0, config)
return self.bus.read_byte_data(self.address, 0xF0) | python | def SPI_config(self,config):
'Configure SPI interface parameters.'
self.bus.write_byte_data(self.address, 0xF0, config)
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MLAB-project/pymlab | src/pymlab/sensors/bus_translators.py | I2CSPI.GPIO_read | def GPIO_read(self):
'Reads logic state on GPIO enabled slave-selects pins.'
self.bus.write_byte_data(self.address, 0xF5, 0x0f)
status = self.bus.read_byte(self.address)
bits_values = dict([('SS0',status & 0x01 == 0x01),('SS1',status & 0x02 == 0x02),('SS2',status & 0x04 == 0x04),('SS3',s... | python | def GPIO_read(self):
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self.bus.write_byte_data(self.address, 0xF5, 0x0f)
status = self.bus.read_byte(self.address)
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MLAB-project/pymlab | src/pymlab/sensors/bus_translators.py | I2CSPI.GPIO_config | def GPIO_config(self, gpio_enable, gpio_config):
'Enable or disable slave-select pins as gpio.'
self.bus.write_byte_data(self.address, 0xF6, gpio_enable)
self.bus.write_byte_data(self.address, 0xF7, gpio_config)
return | python | def GPIO_config(self, gpio_enable, gpio_config):
'Enable or disable slave-select pins as gpio.'
self.bus.write_byte_data(self.address, 0xF6, gpio_enable)
self.bus.write_byte_data(self.address, 0xF7, gpio_config)
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MLAB-project/pymlab | src/pymlab/sensors/rps.py | RPS01.get_address | def get_address(self):
"""
Returns sensors I2C address.
"""
LOGGER.debug("Reading RPS01A sensor's address.",)
return self.bus.read_byte_data(self.address, self.address_reg) | python | def get_address(self):
"""
Returns sensors I2C address.
"""
LOGGER.debug("Reading RPS01A sensor's address.",)
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MLAB-project/pymlab | src/pymlab/sensors/rps.py | RPS01.get_zero_position | def get_zero_position(self):
"""
Returns programmed zero position in OTP memory.
"""
LSB = self.bus.read_byte_data(self.address, self.zero_position_MSB)
MSB = self.bus.read_byte_data(self.address, self.zero_position_LSB)
DATA = (MSB << 6) + LSB
return DATA | python | def get_zero_position(self):
"""
Returns programmed zero position in OTP memory.
"""
LSB = self.bus.read_byte_data(self.address, self.zero_position_MSB)
MSB = self.bus.read_byte_data(self.address, self.zero_position_LSB)
DATA = (MSB << 6) + LSB
return DATA | [
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MLAB-project/pymlab | src/pymlab/sensors/rps.py | RPS01.get_agc_value | def get_agc_value(self):
"""
Returns sensor's Automatic Gain Control actual value.
0 - Represents high magtetic field
0xFF - Represents low magnetic field
"""
LOGGER.debug("Reading RPS01A sensor's AGC settings",)
return self.bus.read_byte_data(self.a... | python | def get_agc_value(self):
"""
Returns sensor's Automatic Gain Control actual value.
0 - Represents high magtetic field
0xFF - Represents low magnetic field
"""
LOGGER.debug("Reading RPS01A sensor's AGC settings",)
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MLAB-project/pymlab | src/pymlab/sensors/rps.py | RPS01.get_diagnostics | def get_diagnostics(self):
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Reads diagnostic data from the sensor.
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"""
Reads diagnostic data from the sensor.
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MLAB-project/pymlab | src/pymlab/sensors/rps.py | RPS01.get_angle | def get_angle(self, verify = False):
"""
Retuns measured angle in degrees in range 0-360.
"""
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MSB = self.bus.read_byte_data(self.address, self.angle_MSB)
DATA = (MSB << 6) + LSB
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... | python | def get_angle(self, verify = False):
"""
Retuns measured angle in degrees in range 0-360.
"""
LSB = self.bus.read_byte_data(self.address, self.angle_LSB)
MSB = self.bus.read_byte_data(self.address, self.angle_MSB)
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vladsaveliev/TargQC | scripts/annotate_bed.py | main | def main(input_bed, output_file, output_features=False, genome=None,
only_canonical=False, short=False, extended=False, high_confidence=False,
ambiguities_method=False, coding_only=False, collapse_exons=False, work_dir=False, is_debug=False):
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MLAB-project/pymlab | src/pymlab/sensors/lioncell.py | LIONCELL.StateOfCharge | def StateOfCharge(self):
""" % of Full Charge """
return (self.bus.read_byte_data(self.address, 0x02) + self.bus.read_byte_data(self.address, 0x03) * 256) | python | def StateOfCharge(self):
""" % of Full Charge """
return (self.bus.read_byte_data(self.address, 0x02) + self.bus.read_byte_data(self.address, 0x03) * 256) | [
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MLAB-project/pymlab | src/pymlab/sensors/lioncell.py | LIONCELL.Chemistry | def Chemistry(self):
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chem = []
for n in range(length):
chem.append(self.bus.read_byte_data(self.address, 0x7A + n))
return chem | python | def Chemistry(self):
''' Get cells chemistry '''
length = self.bus.read_byte_data(self.address, 0x79)
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RI-imaging/ODTbrain | odtbrain/_alg2d_int.py | integrate_2d | def integrate_2d(uSin, angles, res, nm, lD=0, coords=None,
count=None, max_count=None, verbose=0):
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RI-imaging/ODTbrain | odtbrain/_alg2d_bpp.py | backpropagate_2d | def backpropagate_2d(uSin, angles, res, nm, lD=0, coords=None,
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svenkreiss/databench | logo/create.py | color | def color(x, y):
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"""
if (x-4) > (y-4) and -(y-4) <= (x-4):
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return "#CD845B"
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"""triangles.
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- http://paletton.com/#uid=70l150klllletuehUpNoMgTsdcs shade 2
"""
if (x-4) > (y-4) and -(y-4) <= (x-4):
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MLAB-project/pymlab | examples/I2CSPI_BRIDGEADC01.py | BRIDGEADC01.single_read | def single_read(self, register):
'''
Reads data from desired register only once.
'''
comm_reg = (0b00010 << 3) + register
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bytes_num = 1
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bytes_num = 3
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'''
Reads data from desired register only once.
'''
comm_reg = (0b00010 << 3) + register
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MLAB-project/pymlab | examples/I2CSPI_BRIDGEADC01.py | BRIDGEADC01.getStatus | def getStatus(self):
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MLAB-project/pymlab | examples/I2CSPI_BRIDGEADC01.py | BRIDGEADC01.setMode | def setMode(self
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vladsaveliev/TargQC | targqc/fastq.py | downsample | def downsample(work_dir, sample_name, fastq_left_fpath, fastq_right_fpath, downsample_to, num_pairs=None):
""" get N random headers from a fastq file without reading the
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modified from: http://www.biostars.org/p/6544/
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sample_name = sample_name or splitext(''.join(lc if lc ... | python | def downsample(work_dir, sample_name, fastq_left_fpath, fastq_right_fpath, downsample_to, num_pairs=None):
""" get N random headers from a fastq file without reading the
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MLAB-project/pymlab | src/pymlab/sensors/sht.py | SHT25.get_hum | def get_hum(self, raw = False):
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The physical value RH given above corresponds to the
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"""
self.bus.write_byte(self.address, self.TRIG_RH_noHOLD); # start humidity measurement
... | python | def get_hum(self, raw = False):
"""
The physical value RH given above corresponds to the
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self.bus.write_byte(self.address, self.TRIG_RH_noHOLD); # start humidity measurement
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johntruckenbrodt/spatialist | spatialist/explorer.py | RasterViewer.__reset_crosshair | def __reset_crosshair(self):
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redraw the cross-hair on the horizontal slice plot
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the x image coordinate
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y: int
the y image coordinate
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johntruckenbrodt/spatialist | spatialist/explorer.py | RasterViewer.__init_vertical_plot | def __init_vertical_plot(self):
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vladsaveliev/TargQC | targqc/utilz/jsontemplate/formatters.py | PythonPercentFormat | def PythonPercentFormat(format_str):
"""Use Python % format strings as template format specifiers."""
if format_str.startswith('printf '):
fmt = format_str[len('printf '):]
return lambda value: fmt % value
else:
return None | python | def PythonPercentFormat(format_str):
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vladsaveliev/TargQC | ensembl/__init__.py | get_merged_cds | def get_merged_cds(genome):
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return be... | python | def get_merged_cds(genome):
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vladsaveliev/TargQC | targqc/utilz/call_process.py | run | def run(cmd, output_fpath=None, input_fpath=None, checks=None, stdout_to_outputfile=True,
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vladsaveliev/TargQC | targqc/summarize.py | _correct_qualimap_genome_results | def _correct_qualimap_genome_results(samples):
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for s in samples:
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""" replacing Qualimap insert size histogram with Picard one.
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qualimap1_dirname = dirname(s.qualimap_ins_size_hist_fpath).replace('raw_data_qualimapReport', 'raw_data')
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RI-imaging/ODTbrain | odtbrain/_alg3d_bppt.py | norm_vec | def norm_vec(vector):
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RI-imaging/ODTbrain | odtbrain/_alg3d_bppt.py | rotation_matrix_from_point | def rotation_matrix_from_point(point, ret_inv=False):
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RI-imaging/ODTbrain | odtbrain/_alg3d_bppt.py | rotation_matrix_from_point_planerot | def rotation_matrix_from_point_planerot(point, plane_angle, ret_inv=False):
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RI-imaging/ODTbrain | odtbrain/_alg3d_bppt.py | sphere_points_from_angles_and_tilt | def sphere_points_from_angles_and_tilt(angles, tilted_axis):
"""
For a given tilt of the rotational axis `tilted_axis`, compute
the points on a unit sphere that correspond to the distribution
`angles` along the great circle about this axis.
Parameters
----------
angles: 1d ndarray
T... | python | def sphere_points_from_angles_and_tilt(angles, tilted_axis):
"""
For a given tilt of the rotational axis `tilted_axis`, compute
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`angles` along the great circle about this axis.
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angles: 1d ndarray
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RI-imaging/ODTbrain | odtbrain/_alg3d_bppt.py | backpropagate_3d_tilted | def backpropagate_3d_tilted(uSin, angles, res, nm, lD=0,
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retur... | python | def filenames_to_uniq(names,new_delim='.'):
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RI-imaging/ODTbrain | examples/example_helper.py | dl_file | def dl_file(url, dest, chunk_size=6553):
"""Download `url` to `dest`"""
import urllib3
http = urllib3.PoolManager()
r = http.request('GET', url, preload_content=False)
with dest.open('wb') as out:
while True:
data = r.read(chunk_size)
if data is None or len(data) == 0... | python | def dl_file(url, dest, chunk_size=6553):
"""Download `url` to `dest`"""
import urllib3
http = urllib3.PoolManager()
r = http.request('GET', url, preload_content=False)
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RI-imaging/ODTbrain | examples/example_helper.py | extract_lzma | def extract_lzma(path):
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tlfile = pathlib.Path(path)
# open lzma file
with tlfile.open("rb") as td:
data = lzma.decompress(td.read())
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fd, tmpname = tempfile.mkstemp(prefix="odt_ex_", suffix=".tar")
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"""Extract an lzma file and return the temporary file name"""
tlfile = pathlib.Path(path)
# open lzma file
with tlfile.open("rb") as td:
data = lzma.decompress(td.read())
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RI-imaging/ODTbrain | examples/example_helper.py | get_file | def get_file(fname, datapath=datapath):
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# download location
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RI-imaging/ODTbrain | examples/example_helper.py | load_tar_lzma_data | def load_tar_lzma_data(tlfile):
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RI-imaging/ODTbrain | examples/example_helper.py | load_zip_data | def load_zip_data(zipname, f_sino_real, f_sino_imag,
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RI-imaging/ODTbrain | odtbrain/_alg2d_fmp.py | fourier_map_2d | def fourier_map_2d(uSin, angles, res, nm, lD=0, semi_coverage=False,
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vladsaveliev/TargQC | targqc/utilz/file_utils.py | transform_to | def transform_to(ext):
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Takes functions like this to decorate:
f(in_file, out_dir=None, out_file=None) or,
f(in_file=in_file, out_dir=... | [
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Takes functions like this to decorate:
f(in_file, out_dir=None, out_file=None) or,
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examples:... | [
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vladsaveliev/TargQC | targqc/utilz/file_utils.py | filter_to | def filter_to(word):
"""
Decorator to create an output filename from an input filename by
adding a word onto the stem. in_file is filtered by the function
and the results are written to out_file. You would want to use
this over transform_to if you don't know the extension of the file
going in. T... | python | def filter_to(word):
"""
Decorator to create an output filename from an input filename by
adding a word onto the stem. in_file is filtered by the function
and the results are written to out_file. You would want to use
this over transform_to if you don't know the extension of the file
going in. T... | [
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vladsaveliev/TargQC | targqc/utilz/file_utils.py | chdir | def chdir(new_dir):
"""Context manager to temporarily change to a new directory.
http://lucentbeing.com/blog/context-managers-and-the-with-statement-in-python/
"""
cur_dir = os.getcwd()
safe_mkdir(new_dir)
os.chdir(new_dir)
try:
yield
finally:
os.chdir(cur_dir) | python | def chdir(new_dir):
"""Context manager to temporarily change to a new directory.
http://lucentbeing.com/blog/context-managers-and-the-with-statement-in-python/
"""
cur_dir = os.getcwd()
safe_mkdir(new_dir)
os.chdir(new_dir)
try:
yield
finally:
os.chdir(cur_dir) | [
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vladsaveliev/TargQC | targqc/utilz/file_utils.py | file_uptodate | def file_uptodate(fname, cmp_fname):
"""Check if a file exists, is non-empty and is more recent than cmp_fname.
"""
try:
return (file_exists(fname) and file_exists(cmp_fname) and
getmtime(fname) >= getmtime(cmp_fname))
except OSError:
return False | python | def file_uptodate(fname, cmp_fname):
"""Check if a file exists, is non-empty and is more recent than cmp_fname.
"""
try:
return (file_exists(fname) and file_exists(cmp_fname) and
getmtime(fname) >= getmtime(cmp_fname))
except OSError:
return False | [
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vladsaveliev/TargQC | targqc/utilz/file_utils.py | save_diskspace | def save_diskspace(fname, reason, config):
"""Overwrite a file in place with a short message to save disk.
This keeps files as a sanity check on processes working, but saves
disk by replacing them with a short message.
"""
if config["algorithm"].get("save_diskspace", False):
with open(fname... | python | def save_diskspace(fname, reason, config):
"""Overwrite a file in place with a short message to save disk.
This keeps files as a sanity check on processes working, but saves
disk by replacing them with a short message.
"""
if config["algorithm"].get("save_diskspace", False):
with open(fname... | [
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vladsaveliev/TargQC | targqc/utilz/file_utils.py | symlink_plus | def symlink_plus(orig, new):
"""Create relative symlinks and handle associated biological index files.
"""
for ext in ["", ".idx", ".gbi", ".tbi", ".bai"]:
if os.path.exists(orig + ext) and not os.path.lexists(new + ext):
with chdir(os.path.dirname(new)):
os.symlink(os.pa... | python | def symlink_plus(orig, new):
"""Create relative symlinks and handle associated biological index files.
"""
for ext in ["", ".idx", ".gbi", ".tbi", ".bai"]:
if os.path.exists(orig + ext) and not os.path.lexists(new + ext):
with chdir(os.path.dirname(new)):
os.symlink(os.pa... | [
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vladsaveliev/TargQC | targqc/utilz/file_utils.py | partition | def partition(pred, iterable):
'Use a predicate to partition entries into false entries and true entries'
# partition(is_odd, range(10)) --> 0 2 4 6 8 and 1 3 5 7 9
t1, t2 = itertools.tee(iterable)
try:
return itertools.ifilterfalse(pred, t1), itertools.ifilter(pred, t2)
except:
r... | python | def partition(pred, iterable):
'Use a predicate to partition entries into false entries and true entries'
# partition(is_odd, range(10)) --> 0 2 4 6 8 and 1 3 5 7 9
t1, t2 = itertools.tee(iterable)
try:
return itertools.ifilterfalse(pred, t1), itertools.ifilter(pred, t2)
except:
r... | [
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vladsaveliev/TargQC | targqc/utilz/file_utils.py | get_in | def get_in(d, t, default=None):
"""
look up if you can get a tuple of values from a nested dictionary,
each item in the tuple a deeper layer
example: get_in({1: {2: 3}}, (1, 2)) -> 3
example: get_in({1: {2: 3}}, (2, 3)) -> {}
"""
result = reduce(lambda d, t: d.get(t, {}), t, d)
if not r... | python | def get_in(d, t, default=None):
"""
look up if you can get a tuple of values from a nested dictionary,
each item in the tuple a deeper layer
example: get_in({1: {2: 3}}, (1, 2)) -> 3
example: get_in({1: {2: 3}}, (2, 3)) -> {}
"""
result = reduce(lambda d, t: d.get(t, {}), t, d)
if not r... | [
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vladsaveliev/TargQC | targqc/utilz/file_utils.py | which | def which(program):
"""
returns the path to an executable or None if it can't be found
"""
def is_exe(_fpath):
return os.path.isfile(_fpath) and os.access(_fpath, os.X_OK)
fpath, fname = os.path.split(program)
if fpath:
if is_exe(program):
return program
else:
... | python | def which(program):
"""
returns the path to an executable or None if it can't be found
"""
def is_exe(_fpath):
return os.path.isfile(_fpath) and os.access(_fpath, os.X_OK)
fpath, fname = os.path.split(program)
if fpath:
if is_exe(program):
return program
else:
... | [
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vladsaveliev/TargQC | targqc/utilz/file_utils.py | expanduser | def expanduser(path):
"""Expand ~ and ~user constructs.
If user or $HOME is unknown, do nothing."""
if path[:1] != '~':
return path
i, n = 1, len(path)
while i < n and path[i] not in '/\\':
i = i + 1
if 'HOME' in os.environ:
userhome = os.environ['HOME']
elif 'USERP... | python | def expanduser(path):
"""Expand ~ and ~user constructs.
If user or $HOME is unknown, do nothing."""
if path[:1] != '~':
return path
i, n = 1, len(path)
while i < n and path[i] not in '/\\':
i = i + 1
if 'HOME' in os.environ:
userhome = os.environ['HOME']
elif 'USERP... | [
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