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comparison galaxy_micropita/src/breadcrumbs/src/UtilityMath.py @ 3:8fb4630ab314 draft default tip

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author sagun98
date Thu, 03 Jun 2021 17:07:36 +0000
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2:1c5736dc85ab 3:8fb4630ab314
1 """
2 Author: Timothy Tickle
3 Description: Utility class for generic math functions.
4 """
5
6 #####################################################################################
7 #Copyright (C) <2012>
8 #
9 #Permission is hereby granted, free of charge, to any person obtaining a copy of
10 #this software and associated documentation files (the "Software"), to deal in the
11 #Software without restriction, including without limitation the rights to use, copy,
12 #modify, merge, publish, distribute, sublicense, and/or sell copies of the Software,
13 #and to permit persons to whom the Software is furnished to do so, subject to
14 #the following conditions:
15 #
16 #The above copyright notice and this permission notice shall be included in all copies
17 #or substantial portions of the Software.
18 #
19 #THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
20 #INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
21 #PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
22 #HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
23 #OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
24 #SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
25 #####################################################################################
26
27 __author__ = "Timothy Tickle"
28 __copyright__ = "Copyright 2012"
29 __credits__ = ["Timothy Tickle"]
30 __license__ = "MIT"
31 __maintainer__ = "Timothy Tickle"
32 __email__ = "ttickle@sph.harvard.edu"
33 __status__ = "Development"
34
35 #Import libaries
36 import itertools
37 import numpy as np
38 import operator
39 import random
40 from ValidateData import ValidateData
41
42 class UtilityMath():
43 """
44 Class to perform misc math methods.
45 """
46
47 ##
48 #Happy path test 2
49 @staticmethod
50 def funcConvertToBHQValue(ldPValues, iNumberOfTests=None):
51 """
52 Convert a list of p-value to a list of q-values.
53
54 :param ldPValues: List of doubles (p-values) to convert.
55 :type List
56 :param iNumberOfTests: Number of (multiple) tests if different than the ldValue length. If not set the length of ldPValues is used.
57 :type Integer
58 :return List: List of Q-values made with a BH modification.
59 """
60
61 #If the number of tests is not specified, use the number of pvalues
62 if(iNumberOfTests == None):
63 iNumberOfTests = len(ldPValues)
64 #Used to hold the pvalues as they are being manipulated
65 lsConvertToQValues = list()
66 #Is used to set the ordr of the pvalues as they are placed in the lsConvertToQValues
67 dOrder = 1
68 for dValue in ldPValues:
69 lsConvertToQValues.append([dValue,dOrder,None])
70 dOrder = dOrder + 1
71
72 #Sort by pvalue
73 lsConvertToQValues.sort(key=lambda x: x[0])
74
75 #Used to keep track of the current test number
76 iTest = 1
77 for dConvValue in lsConvertToQValues:
78 dConvValue[2] = dConvValue[0] * iNumberOfTests / iTest
79 iTest = iTest + 1
80
81 #Sort by original order
82 lsConvertToQValues.sort(key=lambda x: x[1])
83
84 #return just 1 dimension (the qvalue)
85 return [ldValues[2] for ldValues in lsConvertToQValues]
86
87 #Happy path tested 5
88 @staticmethod
89 def funcSampleWithReplacement(aData, iSelect):
90 """
91 Sample from a vector of data (aData) with replacement iSelect many objects.
92
93 :param aData: Data to sample from with replacement.
94 :type List
95 :param iSelect: Amount of data to select from the original data population.
96 :type Integer.
97 :return List: List of sampled data.
98 Returns an empty list on error.
99 """
100
101 if iSelect and aData:
102 iDataSize = len(aData)
103 funcRandom, funcInt = random.random, int
104 lsSampling = operator.itemgetter(*[funcInt(funcRandom() * iDataSize) for selected in itertools.repeat(None, iSelect)])(aData)
105 if isinstance(lsSampling, basestring):
106 lsSampling = [lsSampling]
107 return lsSampling
108 return []
109
110 #Happy Path Tested 2
111 @staticmethod
112 def funcSumRowsOfColumns(npaAbundance, lsSampleNames):
113 """
114 Takes the column names of a npArray and sums the rows into one column.
115
116 :param npaAbundance: Array of data to sum.
117 :type Numpy Array
118 :param lsSampleNames: List of sample names.
119 :type List List of strings.
120 :return List List of data summed at each row.
121 """
122
123 #Compress by data name
124 npPooledSample = npaAbundance[lsSampleNames[0]]
125 for strSampleName in lsSampleNames[1:]:
126 #When combining, combine counts by summing
127 npPooledSample = npPooledSample + npaAbundance[strSampleName]
128 return list(npPooledSample)
129
130 #Testing Status: Light happy path testing 2
131 @staticmethod
132 def funcTransposeDataMatrix(npaMatrix, fRemoveAdornments=False):
133 """
134 Transposes a numpy array.
135
136 :param npaMatrix: Data matrix to transpose.
137 :type Numpy Array
138 :param fRemoveAdornments: Remove the first column before transposing.
139 :type Boolean True indicates removing the column.
140 :return Boolean or Numpy Array: Transposed array or a boolean indicating error.
141 Boolean False is returned on error.
142 """
143
144 #Validate parameters
145 if(not ValidateData.funcIsValidNPArray(npaMatrix)):
146 print "".join(["Utility_Math:transposeDataMatrix::Error, transposeDataMatrix was an invalid structured array. Value =",str(npaMatrix)])
147 return False
148 if(not ValidateData.funcIsValidBoolean(fRemoveAdornments)):
149 print "".join(["Utility_Math:transposeDataMatrix::Error, fRemoveAdornments was an invalid boolean. Value =",str(fRemoveAdornments)])
150 return False
151
152 #Change to samples x taxa as is needed for the compute method below
153 #Also remove the first row which is taxa identification
154 conversionMatrix = [list(row)[fRemoveAdornments:] for row in npaMatrix]
155 return np.array(conversionMatrix).transpose()
156