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Parse parameters.
Combine default and user-defined parameters.
def _parse_params(self, params=None):
"""
Parse parameters.
Combine default and user-defined parameters.
"""
prm = self.default_params.copy()
if params is not None:
prm.update(params)
... |
Run XXmotif and predict motifs from a FASTA file.
Parameters
----------
bin : str
Command used to run the tool.
fastafile : str
Name of the FASTA input file.
params : dict, optional
Optional parameters. For some of the tools required... |
Parse parameters.
Combine default and user-defined parameters.
def _parse_params(self, params=None):
"""
Parse parameters.
Combine default and user-defined parameters.
"""
prm = self.default_params.copy()
if params is not None:
prm.update(params)
... |
Run Homer and predict motifs from a FASTA file.
Parameters
----------
bin : str
Command used to run the tool.
fastafile : str
Name of the FASTA input file.
params : dict, optional
Optional parameters. For some of the tools required p... |
Convert BioProspector output to motifs
Parameters
----------
fo : file-like
File object containing BioProspector output.
Returns
-------
motifs : list
List of Motif instances.
def parse(self, fo):
"""
Convert BioProspecto... |
Run HMS and predict motifs from a FASTA file.
Parameters
----------
bin : str
Command used to run the tool.
fastafile : str
Name of the FASTA input file.
params : dict, optional
Optional parameters. For some of the tools required par... |
Convert HMS output to motifs
Parameters
----------
fo : file-like
File object containing HMS output.
Returns
-------
motifs : list
List of Motif instances.
def parse(self, fo):
"""
Convert HMS output to motifs
... |
Run AMD and predict motifs from a FASTA file.
Parameters
----------
bin : str
Command used to run the tool.
fastafile : str
Name of the FASTA input file.
params : dict, optional
Optional parameters. For some of the tools required par... |
Convert AMD output to motifs
Parameters
----------
fo : file-like
File object containing AMD output.
Returns
-------
motifs : list
List of Motif instances.
def parse(self, fo):
"""
Convert AMD output to motifs
... |
Convert Improbizer output to motifs
Parameters
----------
fo : file-like
File object containing Improbizer output.
Returns
-------
motifs : list
List of Motif instances.
def parse(self, fo):
"""
Convert Improbizer output ... |
Run Trawler and predict motifs from a FASTA file.
Parameters
----------
bin : str
Command used to run the tool.
fastafile : str
Name of the FASTA input file.
params : dict, optional
Optional parameters. For some of the tools required... |
Run Weeder and predict motifs from a FASTA file.
Parameters
----------
bin : str
Command used to run the tool.
fastafile : str
Name of the FASTA input file.
params : dict, optional
Optional parameters. For some of the tools required ... |
Parse parameters.
Combine default and user-defined parameters.
def _parse_params(self, params=None):
"""
Parse parameters.
Combine default and user-defined parameters.
"""
prm = self.default_params.copy()
if params is not None:
prm.update(params)
... |
Run MotifSampler and predict motifs from a FASTA file.
Parameters
----------
bin : str
Command used to run the tool.
fastafile : str
Name of the FASTA input file.
params : dict, optional
Optional parameters. For some of the tools req... |
Convert MotifSampler output to motifs
Parameters
----------
fo : file-like
File object containing MotifSampler output.
Returns
-------
motifs : list
List of Motif instances.
def parse(self, fo):
"""
Convert MotifSampler o... |
Convert MotifSampler output to motifs
Parameters
----------
fo : file-like
File object containing MotifSampler output.
Returns
-------
motifs : list
List of Motif instances.
def parse_out(self, fo):
"""
Convert MotifSampl... |
Run MDmodule and predict motifs from a FASTA file.
Parameters
----------
bin : str
Command used to run the tool.
fastafile : str
Name of the FASTA input file.
params : dict, optional
Optional parameters. For some of the tools require... |
Convert MDmodule output to motifs
Parameters
----------
fo : file-like
File object containing MDmodule output.
Returns
-------
motifs : list
List of Motif instances.
def parse(self, fo):
"""
Convert MDmodule output to mot... |
Parse parameters.
Combine default and user-defined parameters.
def _parse_params(self, params=None):
"""
Parse parameters.
Combine default and user-defined parameters.
"""
prm = self.default_params.copy()
if params is not None:
prm.update(params)
... |
Run ChIPMunk and predict motifs from a FASTA file.
Parameters
----------
bin : str
Command used to run the tool.
fastafile : str
Name of the FASTA input file.
params : dict, optional
Optional parameters. For some of the tools require... |
Convert ChIPMunk output to motifs
Parameters
----------
fo : file-like
File object containing ChIPMunk output.
Returns
-------
motifs : list
List of Motif instances.
def parse(self, fo):
"""
Convert ChIPMunk output to mot... |
Run Posmo and predict motifs from a FASTA file.
Parameters
----------
bin : str
Command used to run the tool.
fastafile : str
Name of the FASTA input file.
params : dict, optional
Optional parameters. For some of the tools required p... |
Convert Posmo output to motifs
Parameters
----------
fo : file-like
File object containing Posmo output.
Returns
-------
motifs : list
List of Motif instances.
def parse(self, fo, width, seed=None):
"""
Convert Posmo outp... |
Convert GADEM output to motifs
Parameters
----------
fo : file-like
File object containing GADEM output.
Returns
-------
motifs : list
List of Motif instances.
def parse(self, fo):
"""
Convert GADEM output to motifs
... |
Get enriched JASPAR motifs in a FASTA file.
Parameters
----------
bin : str
Command used to run the tool.
fastafile : str
Name of the FASTA input file.
params : dict, optional
Optional parameters. For some of the tools required param... |
Run MEME and predict motifs from a FASTA file.
Parameters
----------
bin : str
Command used to run the tool.
fastafile : str
Name of the FASTA input file.
params : dict, optional
Optional parameters. For some of the tools required pa... |
Convert MEME output to motifs
Parameters
----------
fo : file-like
File object containing MEME output.
Returns
-------
motifs : list
List of Motif instances.
def parse(self, fo):
"""
Convert MEME output to motifs
... |
Scan regions in input table with motifs.
Parameters
----------
input_table : str
Filename of input table. Can be either a text-separated tab file or a
feather file.
genome : str
Genome name. Can be either the name of a FASTA-formatted file or a
genomepy genome name... |
Run maelstrom on an input table.
Parameters
----------
infile : str
Filename of input table. Can be either a text-separated tab file or a
feather file.
genome : str
Genome name. Can be either the name of a FASTA-formatted file or a
genomepy genome name.
... |
Plot clustered heatmap of predicted motif activity.
Parameters
----------
kind : str, optional
Which data type to use for plotting. Default is 'final', which will plot the
result of the rang aggregation. Other options are 'freq' for the motif frequencies,
... |
Create motif scores boxplot of different clusters.
Motifs can be specified as either motif or factor names.
The motif scores will be scaled and plotted as z-scores.
Parameters
----------
motifs : iterable or str
List of motif or factor names.
... |
Return version of package on pypi.python.org using json. Adapted from https://stackoverflow.com/a/34366589
def get_version(package, url_pattern=URL_PATTERN):
"""Return version of package on pypi.python.org using json. Adapted from https://stackoverflow.com/a/34366589"""
req = requests.get(url_pattern.format(pa... |
Converts arguments extracted from a parser to a dict,
and will dismiss arguments which default to NOT_SET.
:param parser: an ``argparse.ArgumentParser`` instance.
:type parser: argparse.ArgumentParser
:return: Dictionary with the configs found in the parsed CLI arguments.
:rtype: dict
def get_args... |
Parse input string and return int, float or str depending on format.
@param val: Input string.
@param parsebool: If True parse yes / no, on / off as boolean.
@return: Value of type int, float or str.
def parse_value(val, parsebool=False):
"""Parse input string and return int, float ... |
Buffered read from socket. Reads all data available from socket.
@fp: File pointer for socket.
@return: String of characters read from buffer.
def socket_read(fp):
"""Buffered read from socket. Reads all data available from socket.
@fp: File pointer for socket.
@return: String of ... |
Convenience function that executes command and returns result.
@param args: Tuple of command and arguments.
@param env: Dictionary of environment variables.
(Environment is not modified if None.)
@return: Command output.
def exec_command(args, env=None):
"""Convenience functi... |
D.set_nested((k1, k2,k3, ...), v) -> D[k1][k2][k3] ... = v
def set_nested(self, klist, value):
"""D.set_nested((k1, k2,k3, ...), v) -> D[k1][k2][k3] ... = v"""
keys = list(klist)
if len(keys) > 0:
curr_dict = self
last_key = keys.pop()
for key in keys:
... |
Register filter on a column of table.
@param column: The column name.
@param patterns: A single pattern or a list of patterns used for
matching column values.
@param is_regex: The patterns will be treated as regex if True, the
... |
Unregister filter on a column of the table.
@param column: The column header.
def unregisterFilter(self, column):
"""Unregister filter on a column of the table.
@param column: The column header.
"""
if self._filters.has_key(column):
del sel... |
Register multiple filters at once.
@param **kwargs: Multiple filters are registered using keyword
variables. Each keyword must correspond to a field name
with an optional suffix:
field: Field equal to value or in list... |
Apply filter on ps command result.
@param headers: List of column headers.
@param table: Nested list of rows and columns.
@return: Nested list of rows and columns filtered using
registered filters.
def applyFilters(self, headers, table):
"""App... |
Connect to a host.
With a host argument, it connects the instance using TCP; port number
and timeout are optional, socket_file must be None. The port number
defaults to the standard telnet port (23).
With a socket_file argument, it connects the instance using
named soc... |
General analysis function that groups data by subject/list number and performs analysis.
Parameters
----------
egg : Egg data object
The data to be analyzed
subjgroup : list of strings or ints
String/int variables indicating how to group over subjects. Must be
the length of th... |
Private function that groups data by subject/list number and performs
analysis for a chunk of data.
Parameters
----------
data : Egg data object
The data to be analyzed
subjgroup : list of strings or ints
String/int variables indicating how to group over subjects. Must be
... |
Retrieve values for graphs.
def retrieveVals(self):
"""Retrieve values for graphs."""
if self.hasGraph('tomcat_memory'):
stats = self._tomcatInfo.getMemoryStats()
self.setGraphVal('tomcat_memory', 'used',
stats['total'] - stats['free'])
... |
Calculate the autocorrelation function for a 1D time series.
Parameters
----------
data : numpy.ndarray (N,)
The time series.
Returns
-------
rho : numpy.ndarray (N,)
An autocorrelation function.
def function(data, maxt=None):
"""
Calculate the autocorrelation function... |
Retrieve values for graphs.
def retrieveVals(self):
"""Retrieve values for graphs."""
nginxInfo = NginxInfo(self._host, self._port,
self._user, self._password,
self._statuspath, self._ssl)
stats = nginxInfo.getServerStats()
... |
Implements Munin Plugin Auto-Configuration Option.
@return: True if plugin can be auto-configured, False otherwise.
def autoconf(self):
"""Implements Munin Plugin Auto-Configuration Option.
@return: True if plugin can be auto-configured, False otherwise.
... |
Query and parse Web Server Status Page.
def getStats(self):
"""Query and parse Web Server Status Page.
"""
url = "%s://%s:%d/%s" % (self._proto, self._host, self._port,
self._monpath)
response = util.get_url(url, self._user, self._password)
... |
Retrieve values for graphs.
def retrieveVals(self):
"""Retrieve values for graphs."""
apcinfo = APCinfo(self._host, self._port, self._user, self._password,
self._monpath, self._ssl, self._extras)
stats = apcinfo.getAllStats()
if self.hasGraph('php_apc... |
Implements Munin Plugin Auto-Configuration Option.
@return: True if plugin can be auto-configured, False otherwise.
def autoconf(self):
"""Implements Munin Plugin Auto-Configuration Option.
@return: True if plugin can be auto-configured, False otherwise.
... |
Runs varnishstats command to get stats from Varnish Cache.
@return: Dictionary of stats.
def getStats(self):
"""Runs varnishstats command to get stats from Varnish Cache.
@return: Dictionary of stats.
"""
info_dict = {}
args = [varnishstatCmd, '-1']
... |
Returns description for stat entry.
@param entry: Entry name.
@return: Description for entry.
def getDesc(self, entry):
"""Returns description for stat entry.
@param entry: Entry name.
@return: Description for entry.
"""
if le... |
Retrieve values for graphs.
def retrieveVals(self):
"""Retrieve values for graphs."""
opcinfo = OPCinfo(self._host, self._port, self._user, self._password,
self._monpath, self._ssl)
stats = opcinfo.getAllStats()
if self.hasGraph('php_opc_memory') and ... |
Implements Munin Plugin Auto-Configuration Option.
@return: True if plugin can be auto-configured, False otherwise.
def autoconf(self):
"""Implements Munin Plugin Auto-Configuration Option.
@return: True if plugin can be auto-configured, False otherwise.
... |
Computes clustering along a set of feature dimensions
Parameters
----------
egg : quail.Egg
Data to analyze
dist_funcs : dict
Dictionary of distance functions for feature clustering analyses
Returns
----------
probabilities : Numpy array
Each number represents cluste... |
Compute clustering scores along a set of feature dimensions
Parameters
----------
pres_list : list
list of presented words
rec_list : list
list of recalled words
feature_list : list
list of feature dicts for presented words
distances : dict
dict of distance ma... |
Computes probabilities for each transition distance (probability that a word
recalled will be a given distance--in presentation order--from the previous
recalled word).
Parameters
----------
egg : quail.Egg
Data to analyze
match : str (exact, best or smooth)
Matching approach t... |
Retrieve values for graphs.
def retrieveVals(self):
"""Retrieve values for graphs."""
if self._diskList:
self._fetchDevAll('disk', self._diskList,
self._info.getDiskStats)
if self._mdList:
self._fetchDevAll('md', self._mdList,
... |
Generate configuration for I/O Request stats.
@param namestr: Field name component indicating device type.
@param titlestr: Title component indicating device type.
@param devlist: List of devices.
def _configDevRequests(self, namestr, titlestr, devlist):
"""Generate configura... |
Generate configuration for I/O Queue Length.
@param namestr: Field name component indicating device type.
@param titlestr: Title component indicating device type.
@param devlist: List of devices.
def _configDevActive(self, namestr, titlestr, devlist):
"""Generate configuratio... |
Initialize I/O stats for devices.
@param namestr: Field name component indicating device type.
@param devlist: List of devices.
@param statsfunc: Function for retrieving stats for device.
def _fetchDevAll(self, namestr, devlist, statsfunc):
"""Initialize I/O stats for devic... |
Retrieve values for graphs.
def retrieveVals(self):
"""Retrieve values for graphs."""
for graph_name in self.getGraphList():
for field_name in self.getGraphFieldList(graph_name):
self.setGraphVal(graph_name, field_name, self._stats.get(field_name)) |
Retrieve values for graphs.
def retrieveVals(self):
"""Retrieve values for graphs."""
if self.hasGraph('sys_loadavg'):
self._loadstats = self._sysinfo.getLoadAvg()
if self._loadstats:
self.setGraphVal('sys_loadavg', 'load15min', self._loadstats[2])
... |
Searches os.environ. If a key is found try evaluating its type else;
return the string.
returns: k->value (type as defined by ast.literal_eval)
def get(key, default=None):
"""
Searches os.environ. If a key is found try evaluating its type else;
return the string.
returns: ... |
Saves a list of keyword arguments as environment variables to a file.
If no filepath given will default to the default `.env` file.
def save(filepath=None, **kwargs):
"""
Saves a list of keyword arguments as environment variables to a file.
If no filepath given will default to the default `... |
Reads a .env file into os.environ.
For a set filepath, open the file and read contents into os.environ.
If filepath is not set then look in current dir for a .env file.
def load(filepath=None):
"""
Reads a .env file into os.environ.
For a set filepath, open the file and read conte... |
Gets each line from the file and parse the data.
Attempt to translate the value into a python type is possible
(falls back to string).
def _get_line_(filepath):
"""
Gets each line from the file and parse the data.
Attempt to translate the value into a python type is possible
(falls back to stri... |
Query and parse Apache Web Server Status Page.
def initStats(self):
"""Query and parse Apache Web Server Status Page."""
url = "%s://%s:%d/%s?auto" % (self._proto, self._host, self._port,
self._statuspath)
response = util.get_url(url, self._user, self._p... |
Returns a df of features for presented items
def get_pres_features(self, features=None):
"""
Returns a df of features for presented items
"""
if features is None:
features = self.dist_funcs.keys()
elif not isinstance(features, list):
features = [features]... |
Returns a df of features for recalled items
def get_rec_features(self, features=None):
"""
Returns a df of features for recalled items
"""
if features is None:
features = self.dist_funcs.keys()
elif not isinstance(features, list):
features = [features]
... |
Print info about the data egg
def info(self):
"""
Print info about the data egg
"""
print('Number of subjects: ' + str(self.n_subjects))
print('Number of lists per subject: ' + str(self.n_lists))
print('Number of words per list: ' + str(self.list_length))
print('... |
Save method for the Egg object
The data will be saved as a 'egg' file, which is a dictionary containing
the elements of a Egg saved in the hd5 format using
`deepdish`.
Parameters
----------
fname : str
A name for the file. If the file extension (.egg) is n... |
Save method for the FriedEgg object
The data will be saved as a 'fegg' file, which is a dictionary containing
the elements of a FriedEgg saved in the hd5 format using
`deepdish`.
Parameters
----------
fname : str
A name for the file. If the file extension ... |
Computes probability of a word being recalled nth (in the appropriate recall
list), given its presentation position. Note: zero indexed
Parameters
----------
egg : quail.Egg
Data to analyze
position : int
Position of item to be analyzed
match : str (exact, best or smooth)
... |
Retrieve values for graphs.
def retrieveVals(self):
"""Retrieve values for graphs."""
apacheInfo = ApacheInfo(self._host, self._port,
self._user, self._password,
self._statuspath, self._ssl)
stats = apacheInfo.getServerStats()
... |
Implements Munin Plugin Auto-Configuration Option.
@return: True if plugin can be auto-configured, False otherwise.
def autoconf(self):
"""Implements Munin Plugin Auto-Configuration Option.
@return: True if plugin can be auto-configured, False otherwise.
... |
Retrieve values for graphs.
def retrieveVals(self):
"""Retrieve values for graphs."""
ntpinfo = NTPinfo()
ntpstats = ntpinfo.getHostOffsets(self._remoteHosts)
if ntpstats:
for host in self._remoteHosts:
hostkey = re.sub('\.', '_', host)
hostst... |
Implements Munin Plugin Auto-Configuration Option.
@return: True if plugin can be auto-configured, False otherwise.
def autoconf(self):
"""Implements Munin Plugin Auto-Configuration Option.
@return: True if plugin can be auto-configured, False otherwise.
... |
Retrieve values for graphs.
def retrieveVals(self):
"""Retrieve values for graphs."""
lighttpdInfo = LighttpdInfo(self._host, self._port,
self._user, self._password,
self._statuspath, self._ssl)
stats = lighttpdInfo.getServerStats... |
Implements Munin Plugin Auto-Configuration Option.
@return: True if plugin can be auto-configured, False otherwise.
def autoconf(self):
"""Implements Munin Plugin Auto-Configuration Option.
@return: True if plugin can be auto-configured, False otherwise.
... |
Retrieve values for graphs.
def retrieveVals(self):
"""Retrieve values for graphs."""
name = 'diskspace'
if self.hasGraph(name):
for fspath in self._fslist:
if self._statsSpace.has_key(fspath):
self.setGraphVal(name, fspath,
... |
Perform symbolic object (symbolic LU decomposition) computation for a given
sparsity pattern.
def symbolic(self, mtx):
"""
Perform symbolic object (symbolic LU decomposition) computation for a given
sparsity pattern.
"""
self.free_symbolic()
indx = self._getIndx... |
Perform numeric object (LU decomposition) computation using the
symbolic decomposition. The symbolic decomposition is (re)computed
if necessary.
def numeric(self, mtx):
"""
Perform numeric object (LU decomposition) computation using the
symbolic decomposition. The symbolic decom... |
Free symbolic data
def free_symbolic(self):
"""Free symbolic data"""
if self._symbolic is not None:
self.funs.free_symbolic(self._symbolic)
self._symbolic = None
self.mtx = None |
Free numeric data
def free_numeric(self):
"""Free numeric data"""
if self._numeric is not None:
self.funs.free_numeric(self._numeric)
self._numeric = None
self.free_symbolic() |
Solution of system of linear equation using the Numeric object.
Parameters
----------
sys : constant
one of UMFPACK system description constants, like
UMFPACK_A, UMFPACK_At, see umfSys list and UMFPACK docs
mtx : scipy.sparse.csc_matrix or scipy.sparse.csr_matrix... |
One-shot solution of system of linear equation. Reuses Numeric object
if possible.
Parameters
----------
sys : constant
one of UMFPACK system description constants, like
UMFPACK_A, UMFPACK_At, see umfSys list and UMFPACK docs
mtx : scipy.sparse.csc_matrix... |
Perform LU decomposition.
For a given matrix A, the decomposition satisfies::
LU = PRAQ when do_recip is true
LU = P(R^-1)AQ when do_recip is false
Parameters
----------
mtx : scipy.sparse.csc_matrix or scipy.sparse.csr_matrix
Input... |
Reorders a list according to strategy
def order_stick(presenter, egg, dist_dict, strategy, fingerprint):
"""
Reorders a list according to strategy
"""
def compute_feature_stick(features, weights, alpha):
'''create a 'stick' of feature weights'''
feature_stick = []
for f, w in ... |
Computes weights for one reordering using stick-breaking method
def stick_perm(presenter, egg, dist_dict, strategy):
"""Computes weights for one reordering using stick-breaking method"""
# seed RNG
np.random.seed()
# unpack egg
egg_pres, egg_rec, egg_features, egg_dist_funcs = parse_egg(egg)
... |
Creates a nested dict of distances
def compute_distances_dict(egg):
""" Creates a nested dict of distances """
pres, rec, features, dist_funcs = parse_egg(egg)
pres_list = list(pres)
features_list = list(features)
# initialize dist dict
distances = {}
# for each word in the list
for i... |
Compute clustering scores along a set of feature dimensions
Parameters
----------
pres_list : list
list of presented words
rec_list : list
list of recalled words
feature_list : list
list of feature dicts for presented words
distances : dict
dict of distance matri... |
In-place method that updates fingerprint with new data
Parameters
----------
egg : quail.Egg
Data to update fingerprint
Returns
----------
None
def update(self, egg, permute=False, nperms=1000,
parallel=False):
"""
In-place m... |
Reorders a list of stimuli to match a fingerprint
Parameters
----------
egg : quail.Egg
Data to compute fingerprint
method : str
Method to re-sort list. Can be 'stick' or 'permute' (default: permute)
nperms : int
Number of permutations to us... |
Query and parse Web Server Status Page.
@param extras: Include extra metrics, which can be computationally more
expensive.
def initStats(self, extras=None):
"""Query and parse Web Server Status Page.
@param extras: Include extra metrics, which can be co... |
Return major and minor device number for block device path devpath.
@param devpath: Full path for block device.
@return: Tuple (major, minor).
def _getDevMajorMinor(self, devpath):
"""Return major and minor device number for block device path devpath.
@param devpath: Full path fo... |
Return unique device for any block device path.
@param devpath: Full path for block device.
@return: Unique device string without the /dev prefix.
def _getUniqueDev(self, devpath):
"""Return unique device for any block device path.
@param devpath: Full path for ... |
Parses /proc/devices to initialize device class - major number map
for block devices.
def _initBlockMajorMap(self):
"""Parses /proc/devices to initialize device class - major number map
for block devices.
"""
self._mapMajorDevclass = {}
try:
fp = ope... |
Check files in /dev/mapper to initialize data structures for
mappings between device-mapper devices, minor device numbers, VGs
and LVs.
def _initDMinfo(self):
"""Check files in /dev/mapper to initialize data structures for
mappings between device-mapper devices, minor device numbers,... |
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