def __init__(self, settingsFile, analysisId, genome=None, expType=None):
Analysis.__init__(self,
settingsFile,
analysisId=analysisId,
genome=genome)
if expType != None:
self.type = expType
self._resultsDir = None # Outside of galaxy and tmpDir struct. Same as inputFile location
self._stayWithinGalaxy = self._settings.getBoolean(
'stayWithinGalaxy', False)
self._galaxyInputs = {
} # May be in galaxy-dist/database/files or else symlinked lib
self._galaxyOutputs = {} # In galaxy-dist/database/files
self._nonGalaxyOutputs = {
} # In resultsDir (same as inputFiles location directory
self._fileSets = {
'galaxyInput': self._galaxyInputs,
'galaxyOutput': self._galaxyOutputs,
'nonGalaxyInput': self._inputFiles,
'nonGalaxyOutput': self._nonGalaxyOutputs,
'target': self._targetOutput,
'intermediate': self._interimFiles
}
self._deliverToGalaxyKeys = None
self.createAnalysisDir(
) # encode pipeline creates this via the manifest.
self.declareLogFile()
def __init__(self, verbose=False):
Analysis.__init__(self, verbose=verbose)
# Settings:
self.tries = 20 # number of repetitions for a certain signal height
self.min_percent = 0.001 # Quantiles
self.max_percent = 100 # Quantiles
self.binning = 100
self.minimum_statistics = 100
self.extremaconfiguration = "1.04 / 55 / 0.97 / 45"
def __init__(self, settingsFile,analysisId,genome=None,expType=None):
Analysis.__init__(self, settingsFile, analysisId=analysisId, genome=genome)
if expType != None:
self.type = expType
self._resultsDir = None # Outside of galaxy and tmpDir struct. Same as inputFile location
self._stayWithinGalaxy = self._settings.getBoolean('stayWithinGalaxy', False)
self._galaxyInputs = {} # May be in galaxy-dist/database/files or else symlinked lib
self._galaxyOutputs = {} # In galaxy-dist/database/files
self._nonGalaxyOutputs = {} # In resultsDir (same as inputFiles location directory
self._fileSets = { 'galaxyInput' : self._galaxyInputs,
'galaxyOutput': self._galaxyOutputs,
'nonGalaxyInput' : self._inputFiles,
'nonGalaxyOutput': self._nonGalaxyOutputs,
'target': self._targetOutput,
'intermediate': self._interimFiles }
self._deliverToGalaxyKeys = None
self.createAnalysisDir() # encode pipeline creates this via the manifest.
self.declareLogFile()
def __init__(self, settingsFile, manifestFile, resume=0):
manifest = Settings(manifestFile)
Analysis.__init__(self, settingsFile, manifest['expName'])
self.resume = resume
self.name = manifest['expName']
self.dataType = manifest['dataType']
self.readType = manifest['readType']
self.replicates = []
self.json = {}
if self.readType == 'single':
if 'fileRep1' in manifest:
self.replicates.append(1)
self.registerInputFile('tagsRep1.fastq', manifest['fileRep1'])
if 'fileRep2' in manifest:
self.replicates.append(2)
self.registerInputFile('tagsRep2.fastq', manifest['fileRep2'])
elif self.readType == 'paired':
if 'fileRd1Rep1' in manifest:
self.replicates.append(1)
self.registerInputFile('tagsRd1Rep1.fastq',
manifest['fileRd1Rep1'])
self.registerInputFile('tagsRd2Rep1.fastq',
manifest['fileRd2Rep1'])
if 'fileRd1Rep2' in manifest:
self.replicates.append(2)
self.registerInputFile('tagsRd1Rep2.fastq',
manifest['fileRd1Rep2'])
self.registerInputFile('tagsRd2Rep2.fastq',
manifest['fileRd2Rep2'])
self.interimDir = None
self.targetDir = None
self.pipeline = None
if self.dataType == 'DNAse':
self.pipeline = DnasePipeline(self)
else:
pass
def __init__(self, settingsFile, manifestFile, resume=0):
manifest = Settings(manifestFile)
Analysis.__init__(self, settingsFile, manifest['expName'])
self.resume = resume
self.name = manifest['expName']
self.dataType = manifest['dataType']
self.readType = manifest['readType']
self.replicates = []
self.json = {}
if self.readType == 'single':
if 'fileRep1' in manifest:
self.replicates.append(1)
self.registerInputFile('tagsRep1.fastq', manifest['fileRep1'])
if 'fileRep2' in manifest:
self.replicates.append(2)
self.registerInputFile('tagsRep2.fastq', manifest['fileRep2'])
elif self.readType == 'paired':
if 'fileRd1Rep1' in manifest:
self.replicates.append(1)
self.registerInputFile('tagsRd1Rep1.fastq', manifest['fileRd1Rep1'])
self.registerInputFile('tagsRd2Rep1.fastq', manifest['fileRd2Rep1'])
if 'fileRd1Rep2' in manifest:
self.replicates.append(2)
self.registerInputFile('tagsRd1Rep2.fastq', manifest['fileRd1Rep2'])
self.registerInputFile('tagsRd2Rep2.fastq', manifest['fileRd2Rep2'])
self.interimDir = None
self.targetDir = None
self.pipeline = None
if self.dataType == 'DNAse':
self.pipeline = DnasePipeline(self)
else:
pass
def __init__(self, analysis=None, test_campaign=None, dut=None, begin=None, end=None, averaging=None, verbose=None):
Analysis.__init__(self, test_campaign if analysis is None else analysis.TCString, verbose=verbose, sub_dir='currents')
# Settings
self.Averaging = averaging
self.TimeZone = timezone('Europe/Zurich')
self.DataDir = join(self.TCDir, 'hv')
# Config
self.Ana = analysis
self.IsCollection = hasattr(analysis, 'Runs')
self.Type = self.Ana.Type if analysis is not None and self.IsCollection else 'None'
self.RunSelection = RunSelector(testcampaign=self.TCString)
self.RunLogs = self.RunSelection.RunInfos
self.Run = self.RunSelection.Run if analysis is None else self.Ana.FirstAnalysis.Run if self.IsCollection else self.Ana.Run
if self.IsCollection:
self.Runs = self.Ana.Runs # required for plotting
self.RunPlan = self.load_run_plan() # required for plotting
self.HVConfig = self.load_parser()
self.Bias = self.Ana.Bias if hasattr(self.Ana, 'Bias') else None
self.Draw.ServerDir = analysis.Draw.ServerDir if analysis is not None else None
# Times
self.Begin, self.End = self.load_times(begin, end, dut)
# DUT
self.DUT = self.init_dut(dut)
# HV Device Info
self.Number = self.load_device_number()
self.Channel = self.load_device_channel()
self.Name = self.HVConfig.get('HV{}'.format(self.Number), 'name')
self.Brand = remove_digits(self.Name.split('-')[0])
self.Model = self.HVConfig.get('HV{}'.format(self.Number), 'model')
self.Precision = .005 if '237' in self.Name else .05
# data
self.IgnoreJumps = True
self.Data = self.load_data()
