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iotile/coretools | iotileship/iotile/ship/recipe.py | RecipeObject.prepare | def prepare(self, variables):
"""Initialize all steps in this recipe using their parameters.
Args:
variables (dict): A dictionary of global variable definitions
that may be used to replace or augment the parameters given
to each step.
Returns:
... | python | def prepare(self, variables):
"""Initialize all steps in this recipe using their parameters.
Args:
variables (dict): A dictionary of global variable definitions
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to each step.
Returns:
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iotile/coretools | iotileship/iotile/ship/recipe.py | RecipeObject._prepare_resources | def _prepare_resources(self, variables, overrides=None):
"""Create and optionally open all shared resources."""
if overrides is None:
overrides = {}
res_map = {}
own_map = {}
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... | python | def _prepare_resources(self, variables, overrides=None):
"""Create and optionally open all shared resources."""
if overrides is None:
overrides = {}
res_map = {}
own_map = {}
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iotile/coretools | iotileship/iotile/ship/recipe.py | RecipeObject._cleanup_resources | def _cleanup_resources(self, initialized_resources):
"""Cleanup all resources that we own that are open."""
cleanup_errors = []
# Make sure we clean up all resources that we can and don't error out at the
# first one.
for name, res in initialized_resources.items():
... | python | def _cleanup_resources(self, initialized_resources):
"""Cleanup all resources that we own that are open."""
cleanup_errors = []
# Make sure we clean up all resources that we can and don't error out at the
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iotile/coretools | iotileship/iotile/ship/recipe.py | RecipeObject.run | def run(self, variables=None, overrides=None):
"""Initialize and run this recipe.
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iotile/coretools | iotilebuild/iotile/build/config/scons-local-3.0.1/SCons/Tool/yacc.py | generate | def generate(env):
"""Add Builders and construction variables for yacc to an Environment."""
c_file, cxx_file = SCons.Tool.createCFileBuilders(env)
# C
c_file.add_action('.y', YaccAction)
c_file.add_emitter('.y', yEmitter)
c_file.add_action('.yacc', YaccAction)
c_file.add_emitter('.yacc', ... | python | def generate(env):
"""Add Builders and construction variables for yacc to an Environment."""
c_file, cxx_file = SCons.Tool.createCFileBuilders(env)
# C
c_file.add_action('.y', YaccAction)
c_file.add_emitter('.y', yEmitter)
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iotile/coretools | iotilebuild/iotile/build/config/scons-local-3.0.1/SCons/Tool/ilink32.py | generate | def generate(env):
"""Add Builders and construction variables for Borland ilink to an
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SCons.Tool.createSharedLibBuilder(env)
SCons.Tool.createProgBuilder(env)
env['LINK'] = '$CC'
env['LINKFLAGS'] = SCons.Util.CLVar('')
env['LINKCOM'] = '$LINK -q $LINKFLAGS -e$TA... | python | def generate(env):
"""Add Builders and construction variables for Borland ilink to an
Environment."""
SCons.Tool.createSharedLibBuilder(env)
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iotile/coretools | iotilebuild/iotile/build/config/scons-local-3.0.1/SCons/Tool/MSCommon/sdk.py | SDKDefinition.find_sdk_dir | def find_sdk_dir(self):
"""Try to find the MS SDK from the registry.
Return None if failed or the directory does not exist.
"""
if not SCons.Util.can_read_reg:
debug('find_sdk_dir(): can not read registry')
return None
hkey = self.HKEY_FMT % self.hkey_da... | python | def find_sdk_dir(self):
"""Try to find the MS SDK from the registry.
Return None if failed or the directory does not exist.
"""
if not SCons.Util.can_read_reg:
debug('find_sdk_dir(): can not read registry')
return None
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iotile/coretools | iotilebuild/iotile/build/config/scons-local-3.0.1/SCons/Tool/MSCommon/sdk.py | SDKDefinition.get_sdk_dir | def get_sdk_dir(self):
"""Return the MSSSDK given the version string."""
try:
return self._sdk_dir
except AttributeError:
sdk_dir = self.find_sdk_dir()
self._sdk_dir = sdk_dir
return sdk_dir | python | def get_sdk_dir(self):
"""Return the MSSSDK given the version string."""
try:
return self._sdk_dir
except AttributeError:
sdk_dir = self.find_sdk_dir()
self._sdk_dir = sdk_dir
return sdk_dir | [
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iotile/coretools | iotilebuild/iotile/build/config/scons-local-3.0.1/SCons/Tool/MSCommon/sdk.py | SDKDefinition.get_sdk_vc_script | def get_sdk_vc_script(self,host_arch, target_arch):
""" Return the script to initialize the VC compiler installed by SDK
"""
if (host_arch == 'amd64' and target_arch == 'x86'):
# No cross tools needed compiling 32 bits on 64 bit machine
host_arch=target_arch
arc... | python | def get_sdk_vc_script(self,host_arch, target_arch):
""" Return the script to initialize the VC compiler installed by SDK
"""
if (host_arch == 'amd64' and target_arch == 'x86'):
# No cross tools needed compiling 32 bits on 64 bit machine
host_arch=target_arch
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iotile/coretools | iotileemulate/iotile/emulate/utilities/format_rpc.py | format_rpc | def format_rpc(data):
"""Format an RPC call and response.
Args:
data (tuple): A tuple containing the address, rpc_id, argument and
response payloads and any error code.
Returns:
str: The formated RPC string.
"""
address, rpc_id, args, resp, _status = data
name = r... | python | def format_rpc(data):
"""Format an RPC call and response.
Args:
data (tuple): A tuple containing the address, rpc_id, argument and
response payloads and any error code.
Returns:
str: The formated RPC string.
"""
address, rpc_id, args, resp, _status = data
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iotile/coretools | transport_plugins/bled112/iotile_transport_bled112/server_bled112.py | BLED112Server.start | async def start(self):
"""Start serving access to devices over bluetooth."""
self._command_task.start()
try:
await self._cleanup_old_connections()
except Exception:
await self.stop()
raise
#FIXME: This is a temporary hack, get the actual dev... | python | async def start(self):
"""Start serving access to devices over bluetooth."""
self._command_task.start()
try:
await self._cleanup_old_connections()
except Exception:
await self.stop()
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iotile/coretools | transport_plugins/bled112/iotile_transport_bled112/server_bled112.py | BLED112Server.stop | async def stop(self):
"""Safely shut down this interface"""
await self._command_task.future_command(['_set_mode', 0, 0]) # Disable advertising
await self._cleanup_old_connections()
self._command_task.stop()
self._stream.stop()
self._serial_port.close()
await su... | python | async def stop(self):
"""Safely shut down this interface"""
await self._command_task.future_command(['_set_mode', 0, 0]) # Disable advertising
await self._cleanup_old_connections()
self._command_task.stop()
self._stream.stop()
self._serial_port.close()
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iotile/coretools | transport_plugins/bled112/iotile_transport_bled112/server_bled112.py | BLED112Server._call_rpc | async def _call_rpc(self, header):
"""Call an RPC given a header and possibly a previously sent payload
Args:
header (bytearray): The RPC header we should call
"""
length, _, cmd, feature, address = struct.unpack("<BBBBB", bytes(header))
rpc_id = (feature << 8) | cm... | python | async def _call_rpc(self, header):
"""Call an RPC given a header and possibly a previously sent payload
Args:
header (bytearray): The RPC header we should call
"""
length, _, cmd, feature, address = struct.unpack("<BBBBB", bytes(header))
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iotile/coretools | iotilesensorgraph/iotile/sg/output_formats/script.py | format_script | def format_script(sensor_graph):
"""Create a binary script containing this sensor graph.
This function produces a repeatable script by applying a known sorting
order to all constants and config variables when iterating over those
dictionaries.
Args:
sensor_graph (SensorGraph): the sensor g... | python | def format_script(sensor_graph):
"""Create a binary script containing this sensor graph.
This function produces a repeatable script by applying a known sorting
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iotile/coretools | iotilesensorgraph/iotile/sg/sensor_log.py | SensorLog.dump | def dump(self):
"""Dump the state of this SensorLog.
The purpose of this method is to be able to restore the same state
later. However there are links in the SensorLog for stream walkers.
So the dump process saves the state of each stream walker and upon
restore, it looks thro... | python | def dump(self):
"""Dump the state of this SensorLog.
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iotile/coretools | iotilesensorgraph/iotile/sg/sensor_log.py | SensorLog.set_rollover | def set_rollover(self, area, enabled):
"""Configure whether rollover is enabled for streaming or storage streams.
Normally a SensorLog is used in ring-buffer mode which means that old
readings are automatically overwritten as needed when new data is saved.
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"""Configure whether rollover is enabled for streaming or storage streams.
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iotile/coretools | iotilesensorgraph/iotile/sg/sensor_log.py | SensorLog.watch | def watch(self, selector, callback):
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selector (DataStreamSelector): The selector to watch.
If this is None, it is treated as a wildcard selector
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callback (callable): Th... | python | def watch(self, selector, callback):
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iotile/coretools | iotilesensorgraph/iotile/sg/sensor_log.py | SensorLog.create_walker | def create_walker(self, selector, skip_all=True):
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iotile/coretools | iotilesensorgraph/iotile/sg/sensor_log.py | SensorLog.destroy_walker | def destroy_walker(self, walker):
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Args:
walker (StreamWalker): The walker to remove from internal updating
lists.
"""
if walker.buffered:
self._queue_walkers.remove(walker)
else:
... | python | def destroy_walker(self, walker):
"""Destroy a previously created stream walker.
Args:
walker (StreamWalker): The walker to remove from internal updating
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"""
if walker.buffered:
self._queue_walkers.remove(walker)
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iotile/coretools | iotilesensorgraph/iotile/sg/sensor_log.py | SensorLog.restore_walker | def restore_walker(self, dumped_state):
"""Restore a stream walker that was previously serialized.
Since stream walkers need to be tracked in an internal list for
notification purposes, we need to be careful with how we restore
them to make sure they remain part of the right list.
... | python | def restore_walker(self, dumped_state):
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iotile/coretools | iotilesensorgraph/iotile/sg/sensor_log.py | SensorLog.clear | def clear(self):
"""Clear all data from this sensor_log.
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"""
for walker in self._virtual_walkers:
walker.skip_all()
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... | python | def clear(self):
"""Clear all data from this sensor_log.
All readings in all walkers are skipped and buffered data is
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"""
for walker in self._virtual_walkers:
walker.skip_all()
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iotile/coretools | iotilesensorgraph/iotile/sg/sensor_log.py | SensorLog.push | def push(self, stream, reading):
"""Push a reading into a stream, updating any associated stream walkers.
Args:
stream (DataStream): the stream to push the reading into
reading (IOTileReading): the reading to push
"""
# Make sure the stream is correct
re... | python | def push(self, stream, reading):
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stream (DataStream): the stream to push the reading into
reading (IOTileReading): the reading to push
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iotile/coretools | iotilesensorgraph/iotile/sg/sensor_log.py | SensorLog._erase_buffer | def _erase_buffer(self, output_buffer):
"""Erase readings in the specified buffer to make space."""
erase_size = self._model.get(u'buffer_erase_size')
buffer_type = u'storage'
if output_buffer:
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"""Erase readings in the specified buffer to make space."""
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iotile/coretools | iotilesensorgraph/iotile/sg/sensor_log.py | SensorLog.inspect_last | def inspect_last(self, stream, only_allocated=False):
"""Return the last value pushed into a stream.
This function works even if the stream is virtual and no
virtual walker has been created for it. It is primarily
useful to aid in debugging sensor graphs.
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str... | python | def inspect_last(self, stream, only_allocated=False):
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iotile/coretools | iotilebuild/iotile/build/config/scons-local-3.0.1/SCons/exitfuncs.py | _run_exitfuncs | def _run_exitfuncs():
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"""
while _exithandlers:
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"""run any registered exit functions
_exithandlers is traversed in reverse order so functions are executed
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iotile/coretools | iotilebuild/iotile/build/config/scons-local-3.0.1/SCons/Tool/mslink.py | _windowsLdmodTargets | def _windowsLdmodTargets(target, source, env, for_signature):
"""Get targets for loadable modules."""
return _dllTargets(target, source, env, for_signature, 'LDMODULE') | python | def _windowsLdmodTargets(target, source, env, for_signature):
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iotile/coretools | iotilebuild/iotile/build/config/scons-local-3.0.1/SCons/Tool/mslink.py | _dllEmitter | def _dllEmitter(target, source, env, paramtp):
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SCons.Tool.msvc.validate_vars(env)
extratargets = []
extrasources = []
dll = env.FindIxes(target, '%sPREFIX' % paramtp, '%sSUFFIX' % paramtp)
no_import_lib = env.get('no_import_lib', 0)
if not dll:
... | python | def _dllEmitter(target, source, env, paramtp):
"""Common implementation of dll emitter."""
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extratargets = []
extrasources = []
dll = env.FindIxes(target, '%sPREFIX' % paramtp, '%sSUFFIX' % paramtp)
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iotile/coretools | iotilebuild/iotile/build/config/scons-local-3.0.1/SCons/Tool/mslink.py | embedManifestDllCheck | def embedManifestDllCheck(target, source, env):
"""Function run by embedManifestDllCheckAction to check for existence of manifest
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if env.get('WINDOWS_EMBED_MANIFEST', 0):
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"""Function run by embedManifestDllCheckAction to check for existence of manifest
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iotile/coretools | iotilebuild/iotile/build/config/scons-local-3.0.1/SCons/Tool/dvips.py | generate | def generate(env):
"""Add Builders and construction variables for dvips to an Environment."""
global PSAction
if PSAction is None:
PSAction = SCons.Action.Action('$PSCOM', '$PSCOMSTR')
global DVIPSAction
if DVIPSAction is None:
DVIPSAction = SCons.Action.Action(DviPsFunction, strfun... | python | def generate(env):
"""Add Builders and construction variables for dvips to an Environment."""
global PSAction
if PSAction is None:
PSAction = SCons.Action.Action('$PSCOM', '$PSCOMSTR')
global DVIPSAction
if DVIPSAction is None:
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iotile/coretools | iotilebuild/iotile/build/config/site_scons/arm.py | build_library | def build_library(tile, libname, chip):
"""Build a static ARM cortex library"""
dirs = chip.build_dirs()
output_name = '%s_%s.a' % (libname, chip.arch_name())
# Support both firmware/src and just src locations for source code
if os.path.exists('firmware'):
VariantDir(dirs['build'], os.pat... | python | def build_library(tile, libname, chip):
"""Build a static ARM cortex library"""
dirs = chip.build_dirs()
output_name = '%s_%s.a' % (libname, chip.arch_name())
# Support both firmware/src and just src locations for source code
if os.path.exists('firmware'):
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iotile/coretools | iotilebuild/iotile/build/config/site_scons/arm.py | tb_h_file_creation | def tb_h_file_creation(target, source, env):
"""Compile tilebus file into only .h files corresponding to config variables for inclusion in a library"""
files = [str(x) for x in source]
try:
desc = TBDescriptor(files)
except pyparsing.ParseException as e:
raise BuildError("Could not par... | python | def tb_h_file_creation(target, source, env):
"""Compile tilebus file into only .h files corresponding to config variables for inclusion in a library"""
files = [str(x) for x in source]
try:
desc = TBDescriptor(files)
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iotile/coretools | iotilebuild/iotile/build/config/site_scons/arm.py | checksum_creation_action | def checksum_creation_action(target, source, env):
"""Create a linker command file for patching an application checksum into a firmware image"""
# Important Notes:
# There are apparently many ways to calculate a CRC-32 checksum, we use the following options
# Initial seed value prepended to the input: ... | python | def checksum_creation_action(target, source, env):
"""Create a linker command file for patching an application checksum into a firmware image"""
# Important Notes:
# There are apparently many ways to calculate a CRC-32 checksum, we use the following options
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iotile/coretools | iotilebuild/iotile/build/config/site_scons/arm.py | create_arg_file | def create_arg_file(target, source, env):
"""Create an argument file containing -I and -D arguments to gcc.
This file will be passed to gcc using @<path>.
"""
output_name = str(target[0])
with open(output_name, "w") as outfile:
for define in env.get('CPPDEFINES', []):
outfile.... | python | def create_arg_file(target, source, env):
"""Create an argument file containing -I and -D arguments to gcc.
This file will be passed to gcc using @<path>.
"""
output_name = str(target[0])
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iotile/coretools | iotilebuild/iotile/build/config/site_scons/arm.py | merge_hex_executables | def merge_hex_executables(target, source, env):
"""Combine all hex files into a singular executable file."""
output_name = str(target[0])
hex_final = IntelHex()
for image in source:
file = str(image)
root, ext = os.path.splitext(file)
file_format = ext[1:]
if file_format... | python | def merge_hex_executables(target, source, env):
"""Combine all hex files into a singular executable file."""
output_name = str(target[0])
hex_final = IntelHex()
for image in source:
file = str(image)
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iotile/coretools | iotilebuild/iotile/build/config/site_scons/arm.py | ensure_image_is_hex | def ensure_image_is_hex(input_path):
"""Return a path to a hex version of a firmware image.
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"""Return a path to a hex version of a firmware image.
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iotile/coretools | iotileemulate/iotile/emulate/virtual/emulated_device.py | EmulatedDevice._dispatch_rpc | def _dispatch_rpc(self, address, rpc_id, arg_payload):
"""Background work queue handler to dispatch RPCs."""
if self.emulator.is_tile_busy(address):
self._track_change('device.rpc_busy_response', (address, rpc_id, arg_payload, None, None), formatter=format_rpc)
raise BusyRPCResp... | python | def _dispatch_rpc(self, address, rpc_id, arg_payload):
"""Background work queue handler to dispatch RPCs."""
if self.emulator.is_tile_busy(address):
self._track_change('device.rpc_busy_response', (address, rpc_id, arg_payload, None, None), formatter=format_rpc)
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iotile/coretools | iotileemulate/iotile/emulate/virtual/emulated_device.py | EmulatedDevice.rpc | def rpc(self, address, rpc_id, *args, **kwargs):
"""Immediately dispatch an RPC inside this EmulatedDevice.
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iotile/coretools | iotileemulate/iotile/emulate/virtual/emulated_device.py | EmulatedDevice.trace_sync | def trace_sync(self, data, timeout=5.0):
"""Send tracing data and wait for it to finish.
This awaitable coroutine wraps VirtualIOTileDevice.trace() and turns
the callback into an awaitable object. The appropriate usage of this
method is by calling it inside the event loop as:
... | python | def trace_sync(self, data, timeout=5.0):
"""Send tracing data and wait for it to finish.
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iotile/coretools | iotileemulate/iotile/emulate/virtual/emulated_device.py | EmulatedDevice.stream_sync | def stream_sync(self, report, timeout=120.0):
"""Send a report and wait for it to finish.
This awaitable coroutine wraps VirtualIOTileDevice.stream() and turns
the callback into an awaitable object. The appropriate usage of this
method is by calling it inside the event loop as:
... | python | def stream_sync(self, report, timeout=120.0):
"""Send a report and wait for it to finish.
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iotile/coretools | iotileemulate/iotile/emulate/virtual/emulated_device.py | EmulatedDevice.synchronize_task | def synchronize_task(self, func, *args, **kwargs):
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iotile/coretools | iotileemulate/iotile/emulate/virtual/emulated_device.py | EmulatedDevice.load_metascenario | def load_metascenario(self, scenario_list):
"""Load one or more scenarios from a list.
Each entry in scenario_list should be a dict containing at least a
name key and an optional tile key and args key. If tile is present
and its value is not None, the scenario specified will be loaded ... | python | def load_metascenario(self, scenario_list):
"""Load one or more scenarios from a list.
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iotile/coretools | iotilebuild/iotile/build/config/scons-local-3.0.1/SCons/Tool/m4.py | generate | def generate(env):
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jobec/rfc5424-logging-handler | rfc5424logging/handler.py | Rfc5424SysLogHandler.encode_priority | def encode_priority(self, facility, priority):
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benedictpaten/sonLib | misc.py | sonTraceRootPath | def sonTraceRootPath():
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"""
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return 1, j, k | python | def linOriginRegression(points):
"""
computes a linear regression starting at zero
"""
j = sum([ i[0] for i in points ])
k = sum([ i[1] for i in points ])
if j != 0:
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benedictpaten/sonLib | misc.py | close | def close(i, j, tolerance):
"""
check two float values are within a bound of one another
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return i <= j + tolerance and i >= j - tolerance | python | def close(i, j, tolerance):
"""
check two float values are within a bound of one another
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benedictpaten/sonLib | misc.py | filterOverlappingAlignments | def filterOverlappingAlignments(alignments):
"""Filter alignments to be non-overlapping.
"""
l = []
alignments = alignments[:]
sortAlignments(alignments)
alignments.reverse()
for pA1 in alignments:
for pA2 in l:
if pA1.contig1 == pA2.contig1 and getPositiveCoordinateRange... | python | def filterOverlappingAlignments(alignments):
"""Filter alignments to be non-overlapping.
"""
l = []
alignments = alignments[:]
sortAlignments(alignments)
alignments.reverse()
for pA1 in alignments:
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benedictpaten/sonLib | tree.py | binaryTree_depthFirstNumbers | def binaryTree_depthFirstNumbers(binaryTree, labelTree=True, dontStopAtID=True):
"""
get mid-order depth first tree numbers
"""
traversalIDs = {}
def traverse(binaryTree, mid=0, leafNo=0):
if binaryTree.internal and (dontStopAtID or binaryTree.iD is None):
midStart = mid
... | python | def binaryTree_depthFirstNumbers(binaryTree, labelTree=True, dontStopAtID=True):
"""
get mid-order depth first tree numbers
"""
traversalIDs = {}
def traverse(binaryTree, mid=0, leafNo=0):
if binaryTree.internal and (dontStopAtID or binaryTree.iD is None):
midStart = mid
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benedictpaten/sonLib | tree.py | binaryTree_nodeNames | def binaryTree_nodeNames(binaryTree):
"""
creates names for the leave and internal nodes
of the newick tree from the leaf labels
"""
def fn(binaryTree, labels):
if binaryTree.internal:
fn(binaryTree.left, labels)
fn(binaryTree.right, labels)
labels[binaryT... | python | def binaryTree_nodeNames(binaryTree):
"""
creates names for the leave and internal nodes
of the newick tree from the leaf labels
"""
def fn(binaryTree, labels):
if binaryTree.internal:
fn(binaryTree.left, labels)
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benedictpaten/sonLib | tree.py | makeRandomBinaryTree | def makeRandomBinaryTree(leafNodeNumber=None):
"""Creates a random binary tree.
"""
while True:
nodeNo = [-1]
def fn():
nodeNo[0] += 1
if random.random() > 0.6:
i = str(nodeNo[0])
return BinaryTree(0.00001 + random.random()*0.8, True, f... | python | def makeRandomBinaryTree(leafNodeNumber=None):
"""Creates a random binary tree.
"""
while True:
nodeNo = [-1]
def fn():
nodeNo[0] += 1
if random.random() > 0.6:
i = str(nodeNo[0])
return BinaryTree(0.00001 + random.random()*0.8, True, f... | [
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benedictpaten/sonLib | tree.py | getRandomBinaryTreeLeafNode | def getRandomBinaryTreeLeafNode(binaryTree):
"""Get random binary tree node.
"""
if binaryTree.internal == True:
if random.random() > 0.5:
return getRandomBinaryTreeLeafNode(binaryTree.left)
else:
return getRandomBinaryTreeLeafNode(binaryTree.right)
else:
... | python | def getRandomBinaryTreeLeafNode(binaryTree):
"""Get random binary tree node.
"""
if binaryTree.internal == True:
if random.random() > 0.5:
return getRandomBinaryTreeLeafNode(binaryTree.left)
else:
return getRandomBinaryTreeLeafNode(binaryTree.right)
else:
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benedictpaten/sonLib | tree.py | transformByDistance | def transformByDistance(wV, subModel, alphabetSize=4):
"""
transform wV by given substitution matrix
"""
nc = [0.0]*alphabetSize
for i in xrange(0, alphabetSize):
j = wV[i]
k = subModel[i]
for l in xrange(0, alphabetSize):
nc[l] += j * k[l]
return nc | python | def transformByDistance(wV, subModel, alphabetSize=4):
"""
transform wV by given substitution matrix
"""
nc = [0.0]*alphabetSize
for i in xrange(0, alphabetSize):
j = wV[i]
k = subModel[i]
for l in xrange(0, alphabetSize):
nc[l] += j * k[l]
return nc | [
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benedictpaten/sonLib | tree.py | normaliseWV | def normaliseWV(wV, normFac=1.0):
"""
make char probs divisible by one
"""
f = sum(wV) / normFac
return [ i/f for i in wV ] | python | def normaliseWV(wV, normFac=1.0):
"""
make char probs divisible by one
"""
f = sum(wV) / normFac
return [ i/f for i in wV ] | [
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benedictpaten/sonLib | tree.py | felsensteins | def felsensteins(binaryTree, subMatrices, ancestorProbs, leaves, alphabetSize):
"""
calculates the un-normalised probabilties of each non-gap residue position
"""
l = {}
def upPass(binaryTree):
if binaryTree.internal: #is internal binaryTree
i = branchUp(binaryTree.left)
... | python | def felsensteins(binaryTree, subMatrices, ancestorProbs, leaves, alphabetSize):
"""
calculates the un-normalised probabilties of each non-gap residue position
"""
l = {}
def upPass(binaryTree):
if binaryTree.internal: #is internal binaryTree
i = branchUp(binaryTree.left)
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benedictpaten/sonLib | tree.py | annotateTree | def annotateTree(bT, fn):
"""
annotate a tree in an external array using the given function
"""
l = [None]*bT.traversalID.midEnd
def fn2(bT):
l[bT.traversalID.mid] = fn(bT)
if bT.internal:
fn2(bT.left)
fn2(bT.right)
fn2(bT)
return l | python | def annotateTree(bT, fn):
"""
annotate a tree in an external array using the given function
"""
l = [None]*bT.traversalID.midEnd
def fn2(bT):
l[bT.traversalID.mid] = fn(bT)
if bT.internal:
fn2(bT.left)
fn2(bT.right)
fn2(bT)
return l | [
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benedictpaten/sonLib | tree.py | remodelTreeRemovingRoot | def remodelTreeRemovingRoot(root, node):
"""
Node is mid order number
"""
import bioio
assert root.traversalID.mid != node
hash = {}
def fn(bT):
if bT.traversalID.mid == node:
assert bT.internal == False
return [ bT ]
elif bT.internal:
i = ... | python | def remodelTreeRemovingRoot(root, node):
"""
Node is mid order number
"""
import bioio
assert root.traversalID.mid != node
hash = {}
def fn(bT):
if bT.traversalID.mid == node:
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benedictpaten/sonLib | tree.py | moveRoot | def moveRoot(root, branch):
"""
Removes the old root and places the new root at the mid point along the given branch
"""
import bioio
if root.traversalID.mid == branch:
return bioio.newickTreeParser(bioio.printBinaryTree(root, True))
def fn2(tree, seq):
if seq is not None:
... | python | def moveRoot(root, branch):
"""
Removes the old root and places the new root at the mid point along the given branch
"""
import bioio
if root.traversalID.mid == branch:
return bioio.newickTreeParser(bioio.printBinaryTree(root, True))
def fn2(tree, seq):
if seq is not None:
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benedictpaten/sonLib | tree.py | checkGeneTreeMatchesSpeciesTree | def checkGeneTreeMatchesSpeciesTree(speciesTree, geneTree, processID):
"""
Function to check ids in gene tree all match nodes in species tree
"""
def fn(tree, l):
if tree.internal:
fn(tree.left, l)
fn(tree.right, l)
else:
l.append(processID(tree.iD))
... | python | def checkGeneTreeMatchesSpeciesTree(speciesTree, geneTree, processID):
"""
Function to check ids in gene tree all match nodes in species tree
"""
def fn(tree, l):
if tree.internal:
fn(tree.left, l)
fn(tree.right, l)
else:
l.append(processID(tree.iD))
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benedictpaten/sonLib | tree.py | calculateProbableRootOfGeneTree | def calculateProbableRootOfGeneTree(speciesTree, geneTree, processID=lambda x : x):
"""
Goes through each root possible branch making it the root.
Returns tree that requires the minimum number of duplications.
"""
#get all rooted trees
#run dup calc on each tree
#return tree with fewest num... | python | def calculateProbableRootOfGeneTree(speciesTree, geneTree, processID=lambda x : x):
"""
Goes through each root possible branch making it the root.
Returns tree that requires the minimum number of duplications.
"""
#get all rooted trees
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benedictpaten/sonLib | bioio.py | redirectLoggerStreamHandlers | def redirectLoggerStreamHandlers(oldStream, newStream):
"""Redirect the stream of a stream handler to a different stream
"""
for handler in list(logger.handlers): #Remove old handlers
if handler.stream == oldStream:
handler.close()
logger.removeHandler(handler)
for handle... | python | def redirectLoggerStreamHandlers(oldStream, newStream):
"""Redirect the stream of a stream handler to a different stream
"""
for handler in list(logger.handlers): #Remove old handlers
if handler.stream == oldStream:
handler.close()
logger.removeHandler(handler)
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benedictpaten/sonLib | bioio.py | popen | def popen(command, tempFile):
"""Runs a command and captures standard out in the given temp file.
"""
fileHandle = open(tempFile, 'w')
logger.debug("Running the command: %s" % command)
sts = subprocess.call(command, shell=True, stdout=fileHandle, bufsize=-1)
fileHandle.close()
if sts != 0:
... | python | def popen(command, tempFile):
"""Runs a command and captures standard out in the given temp file.
"""
fileHandle = open(tempFile, 'w')
logger.debug("Running the command: %s" % command)
sts = subprocess.call(command, shell=True, stdout=fileHandle, bufsize=-1)
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benedictpaten/sonLib | bioio.py | getTotalCpuTimeAndMemoryUsage | def getTotalCpuTimeAndMemoryUsage():
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childs = resource.getrusage(resource.RUSAGE_CHILDREN)
totalCpuTime = me.ru_utime+me.ru_stime+childs.ru_utime+childs.ru_stime
totalMemory... | python | def getTotalCpuTimeAndMemoryUsage():
"""Gives the total cpu time and memory usage of itself and its children.
"""
me = resource.getrusage(resource.RUSAGE_SELF)
childs = resource.getrusage(resource.RUSAGE_CHILDREN)
totalCpuTime = me.ru_utime+me.ru_stime+childs.ru_utime+childs.ru_stime
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benedictpaten/sonLib | bioio.py | saveInputs | def saveInputs(savedInputsDir, listOfFilesAndDirsToSave):
"""Copies the list of files to a directory created in the save inputs dir,
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"""
logger.info("Saving the inputs: %s to the directory: %s" % (" ".join(listOfFilesAndDirsToSave), savedInputsDir))
assert os.... | python | def saveInputs(savedInputsDir, listOfFilesAndDirsToSave):
"""Copies the list of files to a directory created in the save inputs dir,
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"""
logger.info("Saving the inputs: %s to the directory: %s" % (" ".join(listOfFilesAndDirsToSave), savedInputsDir))
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benedictpaten/sonLib | bioio.py | nameValue | def nameValue(name, value, valueType=str, quotes=False):
"""Little function to make it easier to make name value strings for commands.
"""
if valueType == bool:
if value:
return "--%s" % name
return ""
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"""Little function to make it easier to make name value strings for commands.
"""
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if value:
return "--%s" % name
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benedictpaten/sonLib | bioio.py | makeSubDir | def makeSubDir(dirName):
"""Makes a given subdirectory if it doesn't already exist, making sure it us public.
"""
if not os.path.exists(dirName):
os.mkdir(dirName)
os.chmod(dirName, 0777)
return dirName | python | def makeSubDir(dirName):
"""Makes a given subdirectory if it doesn't already exist, making sure it us public.
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os.mkdir(dirName)
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benedictpaten/sonLib | bioio.py | getTempFile | def getTempFile(suffix="", rootDir=None):
"""Returns a string representing a temporary file, that must be manually deleted
"""
if rootDir is None:
handle, tmpFile = tempfile.mkstemp(suffix)
os.close(handle)
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"""Returns a string representing a temporary file, that must be manually deleted
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os.close(handle)
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"""
if rootDir is None:
return tempfile.mkdtemp()
else:
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"""
returns a temporary directory that must be manually deleted. rootDir will be
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benedictpaten/sonLib | bioio.py | catFiles | def catFiles(filesToCat, catFile):
"""Cats a bunch of files into one file. Ensures a no more than maxCat files
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"""
if len(filesToCat) == 0: #We must handle this case or the cat call will hang waiting for input
open(catFile, 'w').close()
return
maxCat = ... | python | def catFiles(filesToCat, catFile):
"""Cats a bunch of files into one file. Ensures a no more than maxCat files
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"""
if len(filesToCat) == 0: #We must handle this case or the cat call will hang waiting for input
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benedictpaten/sonLib | bioio.py | prettyXml | def prettyXml(elem):
""" Return a pretty-printed XML string for the ElementTree Element.
"""
roughString = ET.tostring(elem, "utf-8")
reparsed = minidom.parseString(roughString)
return reparsed.toprettyxml(indent=" ") | python | def prettyXml(elem):
""" Return a pretty-printed XML string for the ElementTree Element.
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roughString = ET.tostring(elem, "utf-8")
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benedictpaten/sonLib | bioio.py | fastaEncodeHeader | def fastaEncodeHeader(attributes):
"""Decodes the fasta header
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for i in attributes:
assert len(str(i).split()) == 1
return "|".join([ str(i) for i in attributes ]) | python | def fastaEncodeHeader(attributes):
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benedictpaten/sonLib | bioio.py | fastaWrite | def fastaWrite(fileHandleOrFile, name, seq, mode="w"):
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valid_chars = {x for x in string.ascii_letters + "-"}
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r... | python | def fastaWrite(fileHandleOrFile, name, seq, mode="w"):
"""Writes out fasta file
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fileHandle = _getFileHandle(fileHandleOrFile, mode)
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benedictpaten/sonLib | bioio.py | fastqRead | def fastqRead(fileHandleOrFile):
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benedictpaten/sonLib | bioio.py | _getMultiFastaOffsets | def _getMultiFastaOffsets(fasta):
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j = f.read(1)
l = []
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i += 1
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j = f.read(1)
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benedictpaten/sonLib | bioio.py | fastaReadHeaders | def fastaReadHeaders(fasta):
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headers = []
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headers.append(line[1:-1])
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headers = []
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benedictpaten/sonLib | bioio.py | fastaAlignmentRead | def fastaAlignmentRead(fasta, mapFn=(lambda x : x), l=None):
"""
reads in columns of multiple alignment and returns them iteratively
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l = _getMultiFastaOffsets(fasta)
else:
l = l[:]
seqNo = len(l)
for i in xrange(0, seqNo):
j = open(fasta, 'r')
... | python | def fastaAlignmentRead(fasta, mapFn=(lambda x : x), l=None):
"""
reads in columns of multiple alignment and returns them iteratively
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if l is None:
l = _getMultiFastaOffsets(fasta)
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seqNo = len(l)
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benedictpaten/sonLib | bioio.py | fastaAlignmentWrite | def fastaAlignmentWrite(columnAlignment, names, seqNo, fastaFile,
filter=lambda x : True):
"""
Writes out column alignment to given file multi-fasta format
"""
fastaFile = open(fastaFile, 'w')
columnAlignment = [ i for i in columnAlignment if filter(i) ]
for seq in xrange... | python | def fastaAlignmentWrite(columnAlignment, names, seqNo, fastaFile,
filter=lambda x : True):
"""
Writes out column alignment to given file multi-fasta format
"""
fastaFile = open(fastaFile, 'w')
columnAlignment = [ i for i in columnAlignment if filter(i) ]
for seq in xrange... | [
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benedictpaten/sonLib | bioio.py | getRandomSequence | def getRandomSequence(length=500):
"""Generates a random name and sequence.
"""
fastaHeader = ""
for i in xrange(int(random.random()*100)):
fastaHeader = fastaHeader + random.choice([ 'A', 'C', '0', '9', ' ', '\t' ])
return (fastaHeader, \
"".join([ random.choice([ 'A', 'C', 'T',... | python | def getRandomSequence(length=500):
"""Generates a random name and sequence.
"""
fastaHeader = ""
for i in xrange(int(random.random()*100)):
fastaHeader = fastaHeader + random.choice([ 'A', 'C', '0', '9', ' ', '\t' ])
return (fastaHeader, \
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benedictpaten/sonLib | bioio.py | mutateSequence | def mutateSequence(seq, distance):
"""Mutates the DNA sequence for use in testing.
"""
subProb=distance
inProb=0.05*distance
deProb=0.05*distance
contProb=0.9
l = []
bases = [ 'A', 'C', 'T', 'G' ]
i=0
while i < len(seq):
if random.random() < subProb:
l.append(... | python | def mutateSequence(seq, distance):
"""Mutates the DNA sequence for use in testing.
"""
subProb=distance
inProb=0.05*distance
deProb=0.05*distance
contProb=0.9
l = []
bases = [ 'A', 'C', 'T', 'G' ]
i=0
while i < len(seq):
if random.random() < subProb:
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benedictpaten/sonLib | bioio.py | newickTreeParser | def newickTreeParser(newickTree, defaultDistance=DEFAULT_DISTANCE, \
sortNonBinaryNodes=False, reportUnaryNodes=False):
"""
lax newick tree parser
"""
newickTree = newickTree.replace("(", " ( ")
newickTree = newickTree.replace(")", " ) ")
newickTree = newickTree.replace(":",... | python | def newickTreeParser(newickTree, defaultDistance=DEFAULT_DISTANCE, \
sortNonBinaryNodes=False, reportUnaryNodes=False):
"""
lax newick tree parser
"""
newickTree = newickTree.replace("(", " ( ")
newickTree = newickTree.replace(")", " ) ")
newickTree = newickTree.replace(":",... | [
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benedictpaten/sonLib | bioio.py | pWMRead | def pWMRead(fileHandle, alphabetSize=4):
"""reads in standard position weight matrix format,
rows are different types of base, columns are individual residues
"""
lines = fileHandle.readlines()
assert len(lines) == alphabetSize
l = [ [ float(i) ] for i in lines[0].split() ]
for line in lines... | python | def pWMRead(fileHandle, alphabetSize=4):
"""reads in standard position weight matrix format,
rows are different types of base, columns are individual residues
"""
lines = fileHandle.readlines()
assert len(lines) == alphabetSize
l = [ [ float(i) ] for i in lines[0].split() ]
for line in lines... | [
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benedictpaten/sonLib | bioio.py | pWMWrite | def pWMWrite(fileHandle, pWM, alphabetSize=4):
"""Writes file in standard PWM format, is reverse of pWMParser
"""
for i in xrange(0, alphabetSize):
fileHandle.write("%s\n" % ' '.join([ str(pWM[j][i]) for j in xrange(0, len(pWM)) ])) | python | def pWMWrite(fileHandle, pWM, alphabetSize=4):
"""Writes file in standard PWM format, is reverse of pWMParser
"""
for i in xrange(0, alphabetSize):
fileHandle.write("%s\n" % ' '.join([ str(pWM[j][i]) for j in xrange(0, len(pWM)) ])) | [
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benedictpaten/sonLib | bioio.py | cigarRead | def cigarRead(fileHandleOrFile):
"""Reads a list of pairwise alignments into a pairwise alignment structure.
Query and target are reversed!
"""
fileHandle = _getFileHandle(fileHandleOrFile)
#p = re.compile("cigar:\\s+(.+)\\s+([0-9]+)\\s+([0-9]+)\\s+([\\+\\-\\.])\\s+(.+)\\s+([0-9]+)\\s+([0-9]+)\\s+(... | python | def cigarRead(fileHandleOrFile):
"""Reads a list of pairwise alignments into a pairwise alignment structure.
Query and target are reversed!
"""
fileHandle = _getFileHandle(fileHandleOrFile)
#p = re.compile("cigar:\\s+(.+)\\s+([0-9]+)\\s+([0-9]+)\\s+([\\+\\-\\.])\\s+(.+)\\s+([0-9]+)\\s+([0-9]+)\\s+(... | [
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benedictpaten/sonLib | bioio.py | cigarWrite | def cigarWrite(fileHandle, pairwiseAlignment, withProbs=True):
"""Writes out the pairwiseAlignment to the file stream.
Query and target are reversed from normal order.
"""
if len(pairwiseAlignment.operationList) == 0:
logger.info("Writing zero length pairwiseAlignment to file!")
strand1 = ... | python | def cigarWrite(fileHandle, pairwiseAlignment, withProbs=True):
"""Writes out the pairwiseAlignment to the file stream.
Query and target are reversed from normal order.
"""
if len(pairwiseAlignment.operationList) == 0:
logger.info("Writing zero length pairwiseAlignment to file!")
strand1 = ... | [
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benedictpaten/sonLib | bioio.py | getRandomPairwiseAlignment | def getRandomPairwiseAlignment():
"""Gets a random pairwiseAlignment.
"""
i, j, k, l = _getRandomSegment()
m, n, o, p = _getRandomSegment()
score = random.choice(xrange(-1000, 1000))
return PairwiseAlignment(i, j, k, l, m, n, o, p, score, getRandomOperationList(abs(k - j), abs(o - n))) | python | def getRandomPairwiseAlignment():
"""Gets a random pairwiseAlignment.
"""
i, j, k, l = _getRandomSegment()
m, n, o, p = _getRandomSegment()
score = random.choice(xrange(-1000, 1000))
return PairwiseAlignment(i, j, k, l, m, n, o, p, score, getRandomOperationList(abs(k - j), abs(o - n))) | [
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benedictpaten/sonLib | bioio.py | addEdgeToGraph | def addEdgeToGraph(parentNodeName, childNodeName, graphFileHandle, colour="black", length="10", weight="1", dir="none", label="", style=""):
"""Links two nodes in the graph together.
"""
graphFileHandle.write('edge[color=%s,len=%s,weight=%s,dir=%s,label="%s",style=%s];\n' % (colour, length, weight, dir, lab... | python | def addEdgeToGraph(parentNodeName, childNodeName, graphFileHandle, colour="black", length="10", weight="1", dir="none", label="", style=""):
"""Links two nodes in the graph together.
"""
graphFileHandle.write('edge[color=%s,len=%s,weight=%s,dir=%s,label="%s",style=%s];\n' % (colour, length, weight, dir, lab... | [
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