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import numpy as np
old_settings = np.seterr(all='ignore')
def compute_ratio(value1, value2, args):
value1 = value1 + args['pseudocount'][0]
value2 = value2 + args['pseudocount'][1]
ratio = float(value1) / value2
if args['valueType'] == 'log2':
ratio = np.log2(ratio)
elif args['valueType'] == 'reciprocal_ratio':
# the reciprocal ratio of a/b
# is a/b if a/b > 1 else -1* b/a
ratio = ratio if ratio >= 1 else -1.0 / ratio
return ratio
def getRatio(tileCoverage, args):
r"""
The mapreduce method calls this function
for each tile. The parameters (args) are fixed
in the main method.
>>> funcArgs= {'valueType': 'ratio', 'scaleFactors': (1,1), 'pseudocount': [1, 1]}
>>> getRatio([9, 19], funcArgs)
0.5
>>> getRatio([0, 0], funcArgs)
1.0
>>> getRatio([np.nan, np.nan], funcArgs)
nan
>>> getRatio([np.nan, 1.0], funcArgs)
nan
>>> funcArgs['valueType'] ='subtract'
>>> getRatio([20, 10], funcArgs)
10
>>> funcArgs['scaleFactors'] = (1, 0.5)
>>> getRatio([10, 20], funcArgs)
0.0
The reciprocal ratio is of a and b is:
is a/b if a/b > 1 else -1* b/a
>>> funcArgs['valueType'] ='reciprocal_ratio'
>>> funcArgs['scaleFactors'] = (1, 1)
>>> funcArgs['pseudocount'] = [0, 0]
>>> getRatio([2, 1], funcArgs)
2.0
>>> getRatio([1, 2], funcArgs)
-2.0
>>> getRatio([1, 1], funcArgs)
1.0
"""
value1 = args['scaleFactors'][0] * tileCoverage[0]
value2 = args['scaleFactors'][1] * tileCoverage[1]
# if any of the two values to compare
# is nan, return nan
if np.isnan(value1) or np.isnan(value2):
return np.nan
# ratio case
if args['valueType'] in ['ratio', 'log2', 'reciprocal_ratio']:
bin_value = compute_ratio(value1, value2, args)
# non ratio case (diff, sum etc)
else:
if args['valueType'] == 'subtract':
bin_value = value1 - value2
elif args['valueType'] == 'add':
bin_value = value1 + value2
elif args['valueType'] == 'first':
bin_value = value1
elif args['valueType'] == 'second':
bin_value = value2
elif args['valueType'] == 'mean':
bin_value = (value1 + value2) / 2.0
return bin_value
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