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, 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()