Source code for deeptools.getRatio

import numpy as np

old_settings = np.seterr(all='ignore')


[docs] 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
[docs] 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