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validateAlignments.TrackSplittingValidation Class Reference
Inheritance diagram for validateAlignments.TrackSplittingValidation:
validateAlignments.GenericValidation

Public Member Functions

def __init__
 
def createConfiguration
 
def createScript
 
- Public Member Functions inherited from validateAlignments.GenericValidation
def __init__
 
def createConfiguration
 
def createFiles
 
def createScript
 
def getCompareStrings
 
def getRepMap
 

Additional Inherited Members

- Public Attributes inherited from validateAlignments.GenericValidation
 alignmentToValidate
 
 configFiles
 
 filesToCompare
 
 randomWorkdirPart
 
 scriptFiles
 
- Static Public Attributes inherited from validateAlignments.GenericValidation
string defaultReferenceName = "DEFAULT"
 

Detailed Description

Definition at line 494 of file validateAlignments.py.

Constructor & Destructor Documentation

def validateAlignments.TrackSplittingValidation.__init__ (   self,
  alignment,
  config 
)

Definition at line 495 of file validateAlignments.py.

496  def __init__(self, alignment, config):
497  GenericValidation.__init__(self, alignment, config)

Member Function Documentation

def validateAlignments.TrackSplittingValidation.createConfiguration (   self,
  path 
)

Definition at line 498 of file validateAlignments.py.

References validateAlignments.GenericValidation.filesToCompare, and validateAlignments.replaceByMap().

499  def createConfiguration(self, path ):
500  cfgName = "TkAlTrackSplitting.%s_cfg.py"%( self.alignmentToValidate.name )
501  repMap = GenericValidation.getRepMap(self)
502  repMap.update({
503  "APE": configTemplates.APETemplate,
504  "outputFile": replaceByMap( ".oO[workdir]Oo./TrackSplitting_.oO[name]Oo..root", repMap )
505  })
506  repMap["outputFile"] = os.path.expandvars( repMap["outputFile"] )
507  repMap["outputFile"] = os.path.abspath( repMap["outputFile"] )
508  cfgs = {cfgName:replaceByMap( configTemplates.TrackSplittingTemplate, repMap)}
509  self.filesToCompare[ GenericValidation.defaultReferenceName ] = repMap["outputFile"]
510  GenericValidation.createConfiguration(self, cfgs, path)
def replaceByMap
— Helpers —############################ replaces .oO[id]Oo.
def validateAlignments.TrackSplittingValidation.createScript (   self,
  path 
)

Definition at line 511 of file validateAlignments.py.

References validateAlignments.GenericValidation.configFiles, and validateAlignments.replaceByMap().

512  def createScript(self, path):
513  scriptName = "TkAlTrackSplitting.%s.sh"%( self.alignmentToValidate.name )
514  repMap = GenericValidation.getRepMap(self)
515  repMap["CommandLine"]=""
516  for cfg in self.configFiles:
517  repMap["CommandLine"]+= repMap["CommandLineTemplate"]%{"cfgFile":cfg,
518  "postProcess":""
519  }
520 
521  scripts = {scriptName: replaceByMap( configTemplates.scriptTemplate, repMap ) }
522  return GenericValidation.createScript(self, scripts, path)
def replaceByMap
— Helpers —############################ replaces .oO[id]Oo.