89 lines
2.5 KiB
Python
89 lines
2.5 KiB
Python
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class Walker:
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"""Represents a functional walking object to be applied to SAM records.
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Actually useful programs will inherit from this walker object to implement
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one or more of the blank operators provided by this module. Effectly, this
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engine applies a walker object in a standard order to each record in a SAM/BAM
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file:
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walker = MyWalker(args)
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samRecords = parseReadsInFiles( files ):
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results = []
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foreach record in files:
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if walker.filterfunc( record ):
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x = walker.mapfunc( record )
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results.append(x)
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reduced = reduce( walker.reducefunc, results, walker.reduceDefault )
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where:
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filterfunc( data ) -> returns true or false if the data should be
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included or excluded from mapping
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mapfunc( data ) -> applied to each record, locus, or pair of records, depending
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on the walker type
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reducefunc( x, sum ) -> combines partial results x with the accumulating
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results sum across all the data
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"""
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def __init__(self, walkerType, options, name = None, desc = None ):
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self.options = options
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self.setOption( 'walkerType', walkerType )
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self.setOption( 'name', name )
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self.setOption( 'desc', desc )
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print self.options
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reduceDefault = 0
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#
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# walker types
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#
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def isRecordWalker( self ):
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return self.getOption('walkerType') == 'byRecord'
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def isPairedRecordWalker( self ):
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return self.getOption('walkerType') == 'byRecordPairs'
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def isLociWalker( self ):
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return self.getOption('walkerType') == 'byLoci'
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#
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# Option processing
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#
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def getOption( self, flag ):
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if self.hasOption( flag ):
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return self.options[flag]
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else:
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return None
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def setOption( self, flag, value ):
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self.options[flag] = value
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def hasOption(self, flag):
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return flag in self.options
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def optionEnabled(self, flag):
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return flag in self.options and self.options[flag] <> False
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def optionDisabled(self, flag):
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return not self.optionEnabled(flag)
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#
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# Default functions
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#
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def filterfunc( self, datum ):
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return True
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def mapfunc( self, datum ):
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return datum
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def reducefunc( self, mapResult, sum ):
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return sum + 1
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if __name__ == "__main__":
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main()
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