32 lines
873 B
Python
Executable File
32 lines
873 B
Python
Executable File
#!/util/bin/python
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#from SamWalk import *
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from SimpleSAM import *
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import Walker
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class SamWalkTest(object, Walker.Walker):
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def __init__(self):
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Walker.Walker.__init__( self, 'byRecord', {}, name = 'SamWalkTest' )
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def filterfunc( self, read ):
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"""Return true if you want to keep the read for mapping"""
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return True
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#return datum.getPos() % 2 == 0
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def mapfunc( self, read ):
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"""Do something to the read, and return a result for reduction"""
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#print datum
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return 1
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#return len(datum.getSeq())
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#return datum.getSeq() + '/'
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#return "\n>%s\n%s" % (datum.getQName(), datum.getSeq())
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#reduceDefault = ''
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def reducefunc( self, x, sum ):
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"""Take the result of mapping, and previous reduce results in sum, and combine them"""
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#print x
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return x + sum
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