annotate MicroPITA.py @ 1:cd71e90abfab draft

Updated version that suppresses the future warnings option that was causing a problem
author george-weingart
date Sun, 08 Feb 2015 18:27:54 -0500
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1 #!/usr/bin/env python
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2 """
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3 Author: Timothy Tickle
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4 Description: Class to Run analysis for the microPITA paper
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5 """
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6
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7 #####################################################################################
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8 #Copyright (C) <2012>
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9 #
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10 #Permission is hereby granted, free of charge, to any person obtaining a copy of
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11 #this software and associated documentation files (the "Software"), to deal in the
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12 #Software without restriction, including without limitation the rights to use, copy,
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13 #modify, merge, publish, distribute, sublicense, and/or sell copies of the Software,
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14 #and to permit persons to whom the Software is furnished to do so, subject to
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15 #the following conditions:
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16 #
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17 #The above copyright notice and this permission notice shall be included in all copies
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18 #or substantial portions of the Software.
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19 #
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20 #THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
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21 #INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
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22 #PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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23 #HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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24 #OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
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25 #SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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26 #####################################################################################
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27
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28 __author__ = "Timothy Tickle"
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29 __copyright__ = "Copyright 2012"
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30 __credits__ = ["Timothy Tickle"]
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31 __license__ = "MIT"
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32 __maintainer__ = "Timothy Tickle"
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33 __email__ = "ttickle@sph.harvard.edu"
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34 __status__ = "Development"
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35
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36 import sys
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37 import argparse
1
cd71e90abfab Updated version that suppresses the future warnings option that was causing a problem
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38 import warnings
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39 warnings.simplefilter(action = "ignore", category = FutureWarning)
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40 from src.breadcrumbs.src.AbundanceTable import AbundanceTable
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41 from src.breadcrumbs.src.ConstantsBreadCrumbs import ConstantsBreadCrumbs
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42 from src.breadcrumbs.src.Metric import Metric
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43 from src.breadcrumbs.src.KMedoids import Kmedoids
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44 from src.breadcrumbs.src.MLPYDistanceAdaptor import MLPYDistanceAdaptor
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45 from src.breadcrumbs.src.SVM import SVM
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46 from src.breadcrumbs.src.UtilityMath import UtilityMath
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47
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48 from src.ConstantsMicropita import ConstantsMicropita
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49 import csv
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50 import logging
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51 import math
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52 import mlpy
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53 import numpy as np
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54 import operator
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55 import os
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56 import random
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57 import scipy.cluster.hierarchy as hcluster
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58 import scipy.spatial.distance
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59 from types import *
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60
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61 class MicroPITA:
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62 """
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63 Selects samples from a first tier of a multi-tiered study to be used in a second tier.
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64 Different methods can be used for selection.
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65 The expected input is an abundance table (and potentially a text file of targeted features,
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66 if using the targeted features option). Output is a list of samples exhibiting the
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67 characteristics of interest.
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68 """
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69
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70 #Constants
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71 #Diversity metrics Alpha
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72 c_strInverseSimpsonDiversity = Metric.c_strInvSimpsonDiversity
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73 c_strChao1Diversity = Metric.c_strChao1Diversity
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74
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75 #Diversity metrics Beta
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76 c_strBrayCurtisDissimilarity = Metric.c_strBrayCurtisDissimilarity
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77
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78 #Additive inverses of diversity metrics beta
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79 c_strInvBrayCurtisDissimilarity = Metric.c_strInvBrayCurtisDissimilarity
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80
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81 #Technique Names
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82 ConstantsMicropita.c_strDiversity2 = ConstantsMicropita.c_strDiversity+"_C"
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83
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84 #Targeted feature settings
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85 c_strTargetedRanked = ConstantsMicropita.c_strTargetedRanked
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86 c_strTargetedAbundance = ConstantsMicropita.c_strTargetedAbundance
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87
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88 #Technique groupings
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89 # c_lsDiversityMethods = [ConstantsMicropita.c_strDiversity,ConstantsMicropita.c_strDiversity2]
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90
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91 #Converts ecology metrics into standardized method selection names
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92 dictConvertAMetricDiversity = {c_strInverseSimpsonDiversity:ConstantsMicropita.c_strDiversity, c_strChao1Diversity:ConstantsMicropita.c_strDiversity2}
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93 # dictConvertMicroPITAToAMetric = {ConstantsMicropita.c_strDiversity:c_strInverseSimpsonDiversity, ConstantsMicropita.c_strDiversity2:c_strChao1Diversity}
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94 dictConvertBMetricToMethod = {c_strBrayCurtisDissimilarity:ConstantsMicropita.c_strRepresentative}
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95 dictConvertInvBMetricToMethod = {c_strBrayCurtisDissimilarity:ConstantsMicropita.c_strExtreme}
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96
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97 #Linkage used in the Hierarchical clustering
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98 c_strHierarchicalClusterMethod = 'average'
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99
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100 ####Group 1## Diversity
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101 #Testing: Happy path Testing (8)
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102 def funcGetTopRankedSamples(self, lldMatrix = None, lsSampleNames = None, iTopAmount = None):
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103 """
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104 Given a list of lists of measurements, for each list the indices of the highest values are returned. If lsSamplesNames is given
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105 it is treated as a list of string names that is in the order of the measurements in each list. Indices are returned or the sample
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106 names associated with the indices.
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107
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108 :param lldMatrix: List of lists [[value,value,value,value],[value,value,value,value]].
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109 :type: List of lists List of measurements. Each list is a different measurement. Each measurement in positionally related to a sample.
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110 :param lsSampleNames: List of sample names positionally related (the same) to each list (Optional).
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111 :type: List of strings List of strings.
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112 :param iTopAmount: The amount of top measured samples (assumes the higher measurements are better).
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113 :type: integer Integer amount of sample names/ indices to return.
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114 :return List: List of samples to be selected.
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115 """
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116 topRankListRet = []
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117 for rowMetrics in lldMatrix:
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118 #Create 2 d array to hold value and index and sort
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119 liIndexX = [rowMetrics,range(len(rowMetrics))]
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120 liIndexX[1].sort(key = liIndexX[0].__getitem__,reverse = True)
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121
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122 if lsSampleNames:
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123 topRankListRet.append([lsSampleNames[iIndex] for iIndex in liIndexX[1][:iTopAmount]])
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124 else:
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125 topRankListRet.append(liIndexX[1][:iTopAmount])
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126
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127 return topRankListRet
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128
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129 ####Group 2## Representative Dissimilarity
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130 #Testing: Happy path tested 1
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131 def funcGetCentralSamplesByKMedoids(self, npaMatrix=None, sMetric=None, lsSampleNames=None, iNumberSamplesReturned=0, istmBetaMatrix=None, istrmTree=None, istrmEnvr=None):
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132 """
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133 Gets centroid samples by k-medoids clustering of a given matrix.
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134
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135 :param npaMatrix: Numpy array where row=features and columns=samples
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136 :type: Numpy array Abundance Data.
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137 :param sMetric: String name of beta metric used as the distance metric.
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138 :type: String String name of beta metric.
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139 :param lsSampleNames: The names of the sample
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140 :type: List List of strings
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141 :param iNumberSamplesReturned: Number of samples to return, each will be a centroid of a sample.
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142 :type: Integer Number of samples to return
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143 :return List: List of selected samples.
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144 :param istmBetaMatrix: File with beta-diversity matrix
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145 :type: File stream or file path string
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146 """
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147
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148 #Count of how many rows
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149 sampleCount = npaMatrix.shape[0]
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150 if iNumberSamplesReturned > sampleCount:
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151 logging.error("MicroPITA.funcGetCentralSamplesByKMedoids:: There are not enough samples to return the amount of samples specified. Return sample count = "+str(iNumberSamplesReturned)+". Sample number = "+str(sampleCount)+".")
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152 return False
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153
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154 #If the cluster count is equal to the sample count return all samples
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155 if sampleCount == iNumberSamplesReturned:
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156 return list(lsSampleNames)
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157
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158 #Get distance matrix
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159 distanceMatrix=scipy.spatial.distance.squareform(Metric.funcReadMatrixFile(istmMatrixFile=istmBetaMatrix,lsSampleOrder=lsSampleNames)[0]) if istmBetaMatrix else Metric.funcGetBetaMetric(npadAbundancies=npaMatrix, sMetric=sMetric, istrmTree=istrmTree, istrmEnvr=istrmEnvr, lsSampleOrder=lsSampleNames)
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160 if type(distanceMatrix) is BooleanType:
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161 logging.error("MicroPITA.funcGetCentralSamplesByKMedoids:: Could not read in the supplied distance matrix, returning false.")
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162 return False
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163
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164 # Handle unifrac output
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165 if sMetric in [Metric.c_strUnifracUnweighted,Metric.c_strUnifracWeighted]:
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166 distanceMatrix = distanceMatrix[0]
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167
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168 #Log distance matrix
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169 logging.debug("MicroPITA.funcGetCentralSamplesByKMedoids:: Distance matrix for representative selection using metric="+str(sMetric))
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170
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171 distance = MLPYDistanceAdaptor(npaDistanceMatrix=distanceMatrix, fIsCondensedMatrix=True)
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172
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173 #Create object to determine clusters/medoids
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174 medoidsMaker = Kmedoids(k=iNumberSamplesReturned, dist=distance)
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175 #medoidsData includes(1d numpy array, medoids indexes;
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176 # 1d numpy array, non-medoids indexes;
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177 # 1d numpy array, cluster membership for non-medoids;
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178 # double, cost of configuration)
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179 #npaMatrix is samples x rows
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180 #Build a matrix of lists of indicies to pass to the distance matrix
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181 lliIndicesMatrix = [[iIndexPosition] for iIndexPosition in xrange(0,len(npaMatrix))]
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182 medoidsData = medoidsMaker.compute(np.array(lliIndicesMatrix))
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183 logging.debug("MicroPITA.funcGetCentralSamplesByKMedoids:: Results from the kmedoid method in representative selection:")
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184 logging.debug(str(medoidsData))
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185
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186 #If returning the same amount of clusters and samples
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187 #Return centroids
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188 selectedIndexes = medoidsData[0]
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189 return [lsSampleNames[selectedIndexes[index]] for index in xrange(0,iNumberSamplesReturned)]
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190
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191 ####Group 3## Highest Dissimilarity
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192 #Testing: Happy path tested
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193 def funcSelectExtremeSamplesFromHClust(self, strBetaMetric, npaAbundanceMatrix, lsSampleNames, iSelectSampleCount, istmBetaMatrix=None, istrmTree=None, istrmEnvr=None):
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194 """
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195 Select extreme samples from HClustering.
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196
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197 :param strBetaMetric: The beta metric to use for distance matrix generation.
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198 :type: String The name of the beta metric to use.
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199 :param npaAbundanceMatrix: Numpy array where row=samples and columns=features.
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200 :type: Numpy Array Abundance data.
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201 :param lsSampleNames: The names of the sample.
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202 :type: List List of strings.
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203 :param iSelectSampleCount: Number of samples to select (return).
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204 :type: Integer Integer number of samples returned.
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205 :return Samples: List of samples.
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206 :param istmBetaMatrix: File with beta-diversity matrix
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207 :type: File stream or file path string
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208 """
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209
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210 #If they want all the sample count, return all sample names
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211 iSampleCount=len(npaAbundanceMatrix[:,0])
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212 if iSelectSampleCount==iSampleCount:
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213 return lsSampleNames
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214
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215 #Holds the samples to be returned
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216 lsReturnSamplesRet = []
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217
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218 #Generate beta matrix
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219 #Returns condensed matrix
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220 tempDistanceMatrix = scipy.spatial.distance.squareform(Metric.funcReadMatrixFile(istmMatrixFile=istmBetaMatrix,lsSampleOrder=lsSampleNames)[0]) if istmBetaMatrix else Metric.funcGetBetaMetric(npadAbundancies=npaAbundanceMatrix, sMetric=strBetaMetric, istrmTree=istrmTree, istrmEnvr=istrmEnvr, lsSampleOrder=lsSampleNames, fAdditiveInverse = True)
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221
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222 if strBetaMetric in [Metric.c_strUnifracUnweighted,Metric.c_strUnifracWeighted]:
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223 tempDistanceMatrix = tempDistanceMatrix[0]
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224
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225 if type(tempDistanceMatrix) is BooleanType:
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226 logging.error("MicroPITA.funcSelectExtremeSamplesFromHClust:: Could not read in the supplied distance matrix, returning false.")
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227 return False
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228
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229 if istmBetaMatrix:
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230 tempDistanceMatrix = 1-tempDistanceMatrix
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231
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232 #Feed beta matrix to linkage to cluster
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233 #Send condensed matrix
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234 linkageMatrix = hcluster.linkage(tempDistanceMatrix, method=self.c_strHierarchicalClusterMethod)
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235
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236 #Extract cluster information from dendrogram
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237 #The linakge matrix is of the form
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238 #[[int1 int2 doube int3],...]
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239 #int1 and int1 are the paired samples indexed at 0 and up.
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240 #each list is an entry for a branch that is number starting with the first
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241 #list being sample count index + 1
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242 #each list is then named by an increment as they appear
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243 #this means that if a number is in the list and is = sample count or greater it is not
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244 #terminal and is instead a branch.
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245 #This method just takes the lowest metric measurement (highest distance pairs/clusters)
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246 #Works much better than the original technique
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247 #get total number of samples
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248
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249 iCurrentSelectCount = 0
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250 for row in linkageMatrix:
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251 #Get nodes ofthe lowest pairing (so the furthest apart pair)
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252 iNode1 = int(row[0])
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253 iNode2 = int(row[1])
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254 #Make sure the nodes are a terminal node (sample) and not a branch in the dendrogram
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255 #The branching in the dendrogram will start at the number of samples and increment higher.
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256 #Add each of the pair one at a time breaking when enough samples are selected.
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257 if iNode1<iSampleCount:
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258 lsReturnSamplesRet.append(lsSampleNames[iNode1])
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259 iCurrentSelectCount = iCurrentSelectCount + 1
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260 if iCurrentSelectCount == iSelectSampleCount:
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261 break
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262 if iNode2<iSampleCount:
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263 lsReturnSamplesRet.append(lsSampleNames[iNode2])
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264 iCurrentSelectCount = iCurrentSelectCount + 1
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265 if iCurrentSelectCount == iSelectSampleCount:
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266 break
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267
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268 #Return selected samples
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269 return lsReturnSamplesRet
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270
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271 ####Group 4## Rank Average of user Defined Taxa
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272 #Testing: Happy Path Tested
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273 def funcGetAverageAbundanceSamples(self, abndTable, lsTargetedFeature, fRank=False):
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274 """
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275 Averages feature abundance or ranked abundance. Expects a column 0 of taxa id that is skipped.
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276
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277 :param abndTable: Abundance Table to analyse
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278 :type: AbundanceTable Abundance Table
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279 :param lsTargetedFeature: String names
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280 :type: list list of string names of features (bugs) which are measured after ranking against the full sample
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281 :param fRank: Indicates to rank the abundance before getting the average abundance of the features (default false)
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282 :type: boolean Flag indicating ranking abundance before calculating average feature measurement (false= no ranking)
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283 :return List of lists or boolean: List of lists or False on error. One internal list per sample indicating the sample,
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284 feature average abundance or ranked abundance. Lists will already be sorted.
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285 For not Ranked [[sample,average abundance of selected feature,1]]
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286 For Ranked [[sample,average ranked abundance, average abundance of selected feature]]
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287 Error Returns false
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288 """
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289
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290 llAbundance = abndTable.funcGetAverageAbundancePerSample(lsTargetedFeature)
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291 if not llAbundance:
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292 logging.error("MicroPITA.funcGetAverageAbundanceSamples:: Could not get average abundance, returned false. Make sure the features (bugs) are spelled correctly and in the abundance table.")
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293 return False
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294 #Add a space for ranking if needed
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295 #Not ranked will be [[sSample,average abundance,1]]
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296 #(where 1 will not discriminant ties if used in later functions, so this generalizes)
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297 #Ranked will be [[sSample, average rank, average abundance]]
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298 llRetAbundance = [[llist[0],-1,llist[1]] for llist in llAbundance]
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299 #Rank if needed
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300 if fRank:
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301 abndRanked = abndTable.funcRankAbundance()
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302 if abndRanked == None:
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303 logging.error("MicroPITA.funcGetAverageAbundanceSamples:: Could not rank the abundance table, returned false.")
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304 return False
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305 llRetRank = abndRanked.funcGetAverageAbundancePerSample(lsTargetedFeature)
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306 if not llRetRank:
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307 logging.error("MicroPITA.funcGetAverageAbundanceSamples:: Could not get average ranked abundance, returned false. Make sure the features (bugs) are spelled correctly and in the abundance table.")
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308 return False
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309 dictRanks = dict(llRetRank)
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310 llRetAbundance = [[a[0],dictRanks[a[0]],a[2]] for a in llRetAbundance]
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311
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312 #Sort first for ties and then for the main feature
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313 if not fRank or ConstantsMicropita.c_fBreakRankTiesByDiversity:
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314 llRetAbundance = sorted(llRetAbundance, key = lambda sampleData: sampleData[2], reverse = not fRank)
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315 if fRank:
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316 llRetAbundance = sorted(llRetAbundance, key = lambda sampleData: sampleData[1], reverse = not fRank)
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317 return llRetAbundance
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318
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319 #Testing: Happy Path Tested
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320 def funcSelectTargetedTaxaSamples(self, abndMatrix, lsTargetedTaxa, iSampleSelectionCount, sMethod = ConstantsMicropita.lsTargetedFeatureMethodValues[0]):
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321 """
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322 Selects samples with the highest ranks or abundance of targeted features.
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323 If ranked, select the highest abundance for tie breaking
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324
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325 :param abndMatrix: Abundance table to analyse
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326 :type: AbundanceTable Abundance table
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327 :param lsTargetedTaxa: List of features
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328 :type: list list of strings
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329 :param iSampleSelectionCount: Number of samples to select
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330 :type: integer integer
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331 :param sMethod: Method to select targeted features
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332 :type: string String (Can be values found in ConstantsMicropita.lsTargetedFeatureMethodValues)
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333 :return List of strings: List of sample names which were selected
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334 List of strings Empty list is returned on an error.
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335 """
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336
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337 #Check data
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338 if(len(lsTargetedTaxa) < 1):
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339 logging.error("MicroPITA.funcSelectTargetedTaxaSamples. Taxa defined selection was requested but no features were given.")
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340 return []
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341
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342 lsTargetedSamples = self.funcGetAverageAbundanceSamples(abndTable=abndMatrix, lsTargetedFeature=lsTargetedTaxa,
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343 fRank=sMethod.lower() == self.c_strTargetedRanked.lower())
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344 #If an error occured or the key word for the method was not recognized
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345 if lsTargetedSamples == False:
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346 logging.error("MicroPITA.funcSelectTargetedTaxaSamples:: Was not able to select for the features given. So targeted feature selection was performed. Check to make sure the features are spelled correctly and exist in the abundance file.")
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347 return []
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348
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349 #Select from results
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350 return [sSample[0] for sSample in lsTargetedSamples[:iSampleSelectionCount]]
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351
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352 ####Group 5## Random
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353 #Testing: Happy path Tested
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354 def funcGetRandomSamples(self, lsSamples=None, iNumberOfSamplesToReturn=0):
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355 """
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356 Returns random sample names of the number given. No replacement.
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357
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358 :param lsSamples: List of sample names
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359 :type: list list of strings
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360 :param iNumberOfSamplesToReturn: Number of samples to select
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361 :type: integer integer.
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362 :return List: List of selected samples (strings).
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363 """
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364
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365 #Input matrix sample count
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366 sampleCount = len(lsSamples)
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367
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368 #Return the full matrix if they ask for a return matrix where length == original
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369 if(iNumberOfSamplesToReturn >= sampleCount):
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370 return lsSamples
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371
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372 #Get the random indices for the sample (without replacement)
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373 liRandomIndices = random.sample(range(sampleCount), iNumberOfSamplesToReturn)
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374
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375 #Create a boolean array of if indexes are to be included in the reduced array
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376 return [sSample for iIndex, sSample in enumerate(lsSamples) if iIndex in liRandomIndices]
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377
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378 #Happy path tested (case 3)
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379 def funcGetAveragePopulation(self, abndTable, lfCompress):
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380 """
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381 Get the average row per column in the abndtable.
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382
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383 :param abndTable: AbundanceTable of data to be averaged
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384 :type: AbudanceTable
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385 :param lfCompress: List of boolean flags (false means to remove sample before averaging
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386 :type: List of floats
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387 :return List of doubles:
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388 """
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389 if sum(lfCompress) == 0:
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390 return []
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391
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392 #Get the average populations
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393 lAverageRet = []
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394
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395 for sFeature in abndTable.funcGetAbundanceCopy():
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396 sFeature = list(sFeature)[1:]
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397 sFeature=np.compress(lfCompress,sFeature,axis=0)
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398 lAverageRet.append(sum(sFeature)/float(len(sFeature)))
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399 return lAverageRet
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400
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401 #Happy path tested (2 cases)
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402 def funcGetDistanceFromAverage(self, abndTable,ldAverage,lsSamples,lfSelected):
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403 """
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404 Given an abundance table and an average sample, this returns the distance of each sample
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405 (measured using brays-curtis dissimilarity) from the average.
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406 The distances are reduced by needing to be in the lsSamples and being a true in the lfSelected
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407 (which is associated with the samples in the order of the samples in the abundance table;
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408 use abundancetable.funcGetSampleNames() to see the order if needed).
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409
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410 :param abndTable: Abundance table holding the data to be analyzed.
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411 :type: AbundanceTable
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412 :param ldAverage: Average population (Average features of the abundance table of samples)
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413 :type: List of doubles which represent the average population
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414 :param lsSamples: These are the only samples used in the analysis
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415 :type: List of strings (sample ids)
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416 :param lfSelected: Samples to be included in the analysis
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417 :type: List of boolean (true means include)
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418 :return: List of distances (doubles)
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419 """
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420 #Get the distance from label 1 of all samples in label0 splitting into selected and not selected lists
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421 ldSelectedDistances = []
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422
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423 for sSampleName in [sSample for iindex, sSample in enumerate(lsSamples) if lfSelected[iindex]]:
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424 #Get the sample measurements
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425 ldSelectedDistances.append(Metric.funcGetBrayCurtisDissimilarity(np.array([abndTable.funcGetSample(sSampleName),ldAverage]))[0])
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426 return ldSelectedDistances
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427
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428 #Happy path tested (1 case)
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429 def funcMeasureDistanceFromLabelToAverageOtherLabel(self, abndTable, lfGroupOfInterest, lfGroupOther):
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430 """
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431 Get the distance of samples from one label from the average sample of not the label.
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432 Note: This assumes 2 classes.
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433
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434 :param abndTable: Table of data to work out of.
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435 :type: Abundace Table
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436 :param lfGroupOfInterest: Boolean indicator of the sample being in the first group.
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437 :type: List of floats, true indicating an individual in the group of interest.
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438 :param lfGroupOther: Boolean indicator of the sample being in the other group.
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439 :type: List of floats, true indicating an individual in the
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440 :return List of List of doubles: [list of tuples (string sample name,double distance) for the selected population, list of tuples for the not selected population]
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441 """
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442 #Get all sample names
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443 lsAllSamples = abndTable.funcGetSampleNames()
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444
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445 #Get average populations
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446 lAverageOther = self.funcGetAveragePopulation(abndTable=abndTable, lfCompress=lfGroupOther)
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447
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448 #Get the distance from the average of the other label (label 1)
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449 ldSelectedDistances = self.funcGetDistanceFromAverage(abndTable=abndTable, ldAverage=lAverageOther,
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450 lsSamples=lsAllSamples, lfSelected=lfGroupOfInterest)
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451
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452 return zip([lsAllSamples[iindex] for iindex, fGroup in enumerate(lfGroupOfInterest) if fGroup],ldSelectedDistances)
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diff changeset
453
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diff changeset
454 #Happy path tested (1 test case)
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455 def funcPerformDistanceSelection(self, abndTable, iSelectionCount, sLabel, sValueOfInterest):
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parents:
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456 """
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457 Given metadata, metadata of one value (sValueOfInterest) is measured from the average (centroid) value of another label group.
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458 An iSelectionCount of samples is selected from the group of interest closest to and furthest from the centroid of the other group.
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459
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460 :params abndTable: Abundance of measurements
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diff changeset
461 :type: AbundanceTable
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diff changeset
462 :params iSelectionCount: The number of samples selected per sample.
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parents:
diff changeset
463 :type: Integer Integer greater than 0
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diff changeset
464 :params sLabel: ID of the metadata which is the supervised label
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diff changeset
465 :type: String
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diff changeset
466 :params sValueOfInterest: Metadata value in the sLabel metadta row of the abundance table which defines the group of interest.
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467 :type: String found in the abundance table metadata row indicated by sLabel.
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468 :return list list of tuples (samplename, distance) [[iSelectionCount of tuples closest to the other centroid], [iSelectionCount of tuples farthest from the other centroid], [all tuples of samples not selected]]
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469 """
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470
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471 lsMetadata = abndTable.funcGetMetadata(sLabel)
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parents:
diff changeset
472 #Other metadata values
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473 lsUniqueOtherValues = list(set(lsMetadata)-set(sValueOfInterest))
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474
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475 #Get boolean indicator of values of interest
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476 lfLabelsInterested = [sValueOfInterest == sValue for sValue in lsMetadata]
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477
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478 #Get the distances of the items of interest from the other metadata values
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479 dictDistanceAverages = {}
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480 for sOtherLabel in lsUniqueOtherValues:
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481 #Get boolean indicator of labels not of interest
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482 lfLabelsOther = [sOtherLabel == sValue for sValue in lsMetadata]
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483
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484 #Get the distances of data from two different groups to the average of the other
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485 ldValueDistances = dict(self.funcMeasureDistanceFromLabelToAverageOtherLabel(abndTable, lfLabelsInterested, lfLabelsOther))
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diff changeset
486
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487 for sKey in ldValueDistances:
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488 dictDistanceAverages[sKey] = ldValueDistances[sKey] + dictDistanceAverages[sKey] if sKey in dictDistanceAverages else ldValueDistances[sKey]
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489
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diff changeset
490 #Finish average by dividing by length of lsUniqueOtherValues
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491 ltpleAverageDistances = [(sKey, dictDistanceAverages[sKey]/float(len(lsUniqueOtherValues))) for sKey in dictDistanceAverages]
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parents:
diff changeset
492
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parents:
diff changeset
493 #Sort to extract extremes
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494 ltpleAverageDistances = sorted(ltpleAverageDistances,key=operator.itemgetter(1))
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495
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496 #Get the closest and farthest distances
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497 ltupleDiscriminantSamples = ltpleAverageDistances[:iSelectionCount]
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498 ltupleDistinctSamples = ltpleAverageDistances[iSelectionCount*-1:]
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499
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parents:
diff changeset
500 #Remove the selected samples from the larger population of distances (better visualization)
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parents:
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501 ldSelected = [tpleSelected[0] for tpleSelected in ltupleDiscriminantSamples+ltupleDistinctSamples]
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parents:
diff changeset
502
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george-weingart
parents:
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503 #Return discriminant tuples, distinct tuples, other tuples
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parents:
diff changeset
504 return [ltupleDiscriminantSamples, ltupleDistinctSamples,
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505 [tplData for tplData in ltpleAverageDistances if tplData[0] not in ldSelected]]
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george-weingart
parents:
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506
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parents:
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507 #Run the supervised method surrounding distance from centroids
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george-weingart
parents:
diff changeset
508 #Happy path tested (3 test cases)
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parents:
diff changeset
509 def funcRunSupervisedDistancesFromCentroids(self, abundanceTable, fRunDistinct, fRunDiscriminant,
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parents:
diff changeset
510 xOutputSupFile, xPredictSupFile, strSupervisedMetadata,
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george-weingart
parents:
diff changeset
511 iSampleSupSelectionCount, lsOriginalSampleNames, lsOriginalLabels, fAppendFiles = False):
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george-weingart
parents:
diff changeset
512 """
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george-weingart
parents:
diff changeset
513 Runs supervised methods based on measuring distances of one label from the centroid of another. NAs are evaluated as theirown group.
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george-weingart
parents:
diff changeset
514
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george-weingart
parents:
diff changeset
515 :param abundanceTable: AbundanceTable
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george-weingart
parents:
diff changeset
516 :type: AbudanceTable Data to analyze
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george-weingart
parents:
diff changeset
517 :param fRunDistinct: Run distinct selection method
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george-weingart
parents:
diff changeset
518 :type: Boolean boolean (true runs method)
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george-weingart
parents:
diff changeset
519 :param fRunDiscriminant: Run discriminant method
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
520 :type: Boolean boolean (true runs method)
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george-weingart
parents:
diff changeset
521 :param xOutputSupFile: File output from supervised methods detailing data going into the method.
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george-weingart
parents:
diff changeset
522 :type: String or FileStream
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george-weingart
parents:
diff changeset
523 :param xPredictSupFile: File output from supervised methods distance results from supervised methods.
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george-weingart
parents:
diff changeset
524 :type: String or FileStream
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george-weingart
parents:
diff changeset
525 :param strSupervisedMetadata: The metadata that will be used to group samples.
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george-weingart
parents:
diff changeset
526 :type: String
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george-weingart
parents:
diff changeset
527 :param iSampleSupSelectionCount: Number of samples to select
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george-weingart
parents:
diff changeset
528 :type: Integer int sample selection count
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george-weingart
parents:
diff changeset
529 :param lsOriginalSampleNames: List of the sample names, order is important and should be preserved from the abundanceTable.
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george-weingart
parents:
diff changeset
530 :type: List of samples
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george-weingart
parents:
diff changeset
531 :param fAppendFiles: Indicates that output files already exist and appending is occuring.
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george-weingart
parents:
diff changeset
532 :type: Boolean
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george-weingart
parents:
diff changeset
533 :return Selected Samples: A dictionary of selected samples by selection ID
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george-weingart
parents:
diff changeset
534 Dictionary {"Selection Method":["SampleID","SampleID"...]}
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george-weingart
parents:
diff changeset
535 """
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george-weingart
parents:
diff changeset
536 #Get labels and run one label against many
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george-weingart
parents:
diff changeset
537 lstrMetadata = abundanceTable.funcGetMetadata(strSupervisedMetadata)
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george-weingart
parents:
diff changeset
538 dictlltpleDistanceMeasurements = {}
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george-weingart
parents:
diff changeset
539 for sMetadataValue in set(lstrMetadata):
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george-weingart
parents:
diff changeset
540
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george-weingart
parents:
diff changeset
541 #For now perform the selection here for the label of interest against the other labels
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george-weingart
parents:
diff changeset
542 dictlltpleDistanceMeasurements.setdefault(sMetadataValue,[]).extend(self.funcPerformDistanceSelection(abndTable=abundanceTable,
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george-weingart
parents:
diff changeset
543 iSelectionCount=iSampleSupSelectionCount, sLabel=strSupervisedMetadata, sValueOfInterest=sMetadataValue))
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george-weingart
parents:
diff changeset
544
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george-weingart
parents:
diff changeset
545 #Make expected output files for supervised methods
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george-weingart
parents:
diff changeset
546 #1. Output file which is similar to an input file for SVMs
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george-weingart
parents:
diff changeset
547 #2. Output file that is similar to the probabilitic output of a SVM (LibSVM)
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george-weingart
parents:
diff changeset
548 #Manly for making output of supervised methods (Distance from Centroid) similar
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george-weingart
parents:
diff changeset
549 #MicropitaVis needs some of these files
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george-weingart
parents:
diff changeset
550 if xOutputSupFile:
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george-weingart
parents:
diff changeset
551 if fAppendFiles:
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george-weingart
parents:
diff changeset
552 SVM.funcUpdateSVMFileWithAbundanceTable(abndAbundanceTable=abundanceTable, xOutputSVMFile=xOutputSupFile,
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george-weingart
parents:
diff changeset
553 lsOriginalLabels=lsOriginalLabels, lsSampleOrdering=lsOriginalSampleNames)
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george-weingart
parents:
diff changeset
554 else:
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george-weingart
parents:
diff changeset
555 SVM.funcConvertAbundanceTableToSVMFile(abndAbundanceTable=abundanceTable, xOutputSVMFile=xOutputSupFile,
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
556 sMetadataLabel=strSupervisedMetadata, lsOriginalLabels=lsOriginalLabels, lsSampleOrdering=lsOriginalSampleNames)
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george-weingart
parents:
diff changeset
557
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george-weingart
parents:
diff changeset
558 #Will contain the samples selected to return
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george-weingart
parents:
diff changeset
559 #One or more of the methods may be active so this is why I am extending instead of just returning the result of each method type
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george-weingart
parents:
diff changeset
560 dictSelectedSamplesRet = dict()
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george-weingart
parents:
diff changeset
561 for sKey, ltplDistances in dictlltpleDistanceMeasurements.items():
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george-weingart
parents:
diff changeset
562 if fRunDistinct:
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george-weingart
parents:
diff changeset
563 dictSelectedSamplesRet.setdefault(ConstantsMicropita.c_strDistinct,[]).extend([ltple[0] for ltple in ltplDistances[1]])
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george-weingart
parents:
diff changeset
564 if fRunDiscriminant:
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george-weingart
parents:
diff changeset
565 dictSelectedSamplesRet.setdefault(ConstantsMicropita.c_strDiscriminant,[]).extend([ltple[0] for ltple in ltplDistances[0]])
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george-weingart
parents:
diff changeset
566
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george-weingart
parents:
diff changeset
567 if xPredictSupFile:
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george-weingart
parents:
diff changeset
568 dictFlattenedDistances = dict()
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george-weingart
parents:
diff changeset
569 [dictFlattenedDistances.setdefault(sKey, []).append(tple)
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
570 for sKey, lltple in dictlltpleDistanceMeasurements.items()
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
571 for ltple in lltple for tple in ltple]
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george-weingart
parents:
diff changeset
572 if fAppendFiles:
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george-weingart
parents:
diff changeset
573 self._updatePredictFile(xPredictSupFile=xPredictSupFile, xInputLabelsFile=xOutputSupFile,
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george-weingart
parents:
diff changeset
574 dictltpleDistanceMeasurements=dictFlattenedDistances, abundanceTable=abundanceTable, lsOriginalSampleNames=lsOriginalSampleNames)
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george-weingart
parents:
diff changeset
575 else:
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george-weingart
parents:
diff changeset
576 self._writeToPredictFile(xPredictSupFile=xPredictSupFile, xInputLabelsFile=xOutputSupFile,
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george-weingart
parents:
diff changeset
577 dictltpleDistanceMeasurements=dictFlattenedDistances, abundanceTable=abundanceTable, lsOriginalSampleNames=lsOriginalSampleNames)
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george-weingart
parents:
diff changeset
578 return dictSelectedSamplesRet
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george-weingart
parents:
diff changeset
579
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
580 #Two happy path test cases
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
581 def _updatePredictFile(self, xPredictSupFile, xInputLabelsFile, dictltpleDistanceMeasurements, abundanceTable, lsOriginalSampleNames):
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
582 """
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
583 Manages updating the predict file.
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
584
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
585 :param xPredictSupFile: File that has predictions (distances) from the supervised method.
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
586 :type: FileStream or String file path
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
587 :param xInputLabelsFile: File that as input to the supervised methods.
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
588 :type: FileStream or String file path
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
589 :param dictltpleDistanceMeasurements:
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
590 :type: Dictionary of lists of tuples {"labelgroup":[("SampleName",dDistance)...], "labelgroup":[("SampleName",dDistance)...]}
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
591 """
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
592
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
593 if not isinstance(xPredictSupFile, str):
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
594 xPredictSupFile.close()
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
595 xPredictSupFile = xPredictSupFile.name
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
596 csvr = open(xPredictSupFile,'r')
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
597
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
598 f = csv.reader(csvr,delimiter=ConstantsBreadCrumbs.c_strBreadCrumbsSVMSpace)
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
599 lsHeader = f.next()[1:]
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
600 dictlltpleRead = dict([(sHeader,[]) for sHeader in lsHeader])
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
601
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
602 #Read data in
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
603 iSampleIndex = 0
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
604 for sRow in f:
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
605 sLabel = sRow[0]
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
606 [dictlltpleRead[lsHeader[iDistanceIndex]].append((lsOriginalSampleNames[iSampleIndex],dDistance)) for iDistanceIndex, dDistance in enumerate(sRow[1:])
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
607 if not dDistance == ConstantsMicropita.c_sEmptyPredictFileValue]
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
608 iSampleIndex += 1
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
609
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
610 #Combine dictltpleDistanceMeasurements with new data
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
611 #If they share a key then merge keeping parameter data
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
612 #If they do not share the key, keep the full data
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
613 dictNew = {}
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
614 for sKey in dictltpleDistanceMeasurements.keys():
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
615 lsSamples = [tple[0] for tple in dictltpleDistanceMeasurements[sKey]]
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
616 dictNew[sKey] = dictltpleDistanceMeasurements[sKey]+[tple for tple in dictlltpleRead[sKey] if tple[0] not in lsSamples] if sKey in dictlltpleRead.keys() else dictltpleDistanceMeasurements[sKey]
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
617 for sKey in dictlltpleRead:
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
618 if sKey not in dictltpleDistanceMeasurements.keys():
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
619 dictNew[sKey] = dictlltpleRead[sKey]
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
620
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
621 #Call writer
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
622 self._writeToPredictFile(xPredictSupFile=xPredictSupFile, xInputLabelsFile=xInputLabelsFile,
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
623 dictltpleDistanceMeasurements=dictNew, abundanceTable=abundanceTable,
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
624 lsOriginalSampleNames=lsOriginalSampleNames, fFromUpdate=True)
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
625
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
626 #2 happy path test cases
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
627 def _writeToPredictFile(self, xPredictSupFile, xInputLabelsFile, dictltpleDistanceMeasurements, abundanceTable, lsOriginalSampleNames, fFromUpdate=False):
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
628 """
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
629 Write to the predict file.
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
630
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
631 :param xPredictSupFile: File that has predictions (distances) from the supervised method.
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
632 :type: FileStream or String file path
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
633 :param xInputLabelsFile: File that as input to the supervised methods.
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
634 :type: FileStream or String file path
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
635 :param dictltpleDistanceMeasurements:
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
636 :type: Dictionary of lists of tuples {"labelgroup":[("SampleName",dDistance)...], "labelgroup":[("SampleName",dDistance)...]}
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
637 :param abundanceTable: An abundance table of the sample data.
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
638 :type: AbundanceTable
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
639 :param lsOriginalSampleNames: Used if the file is being updated as the sample names so that it may be passed in and consistent with other writing.
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
640 Otherwise will use the sample names from the abundance table.
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
641 :type: List of strings
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
642 :param fFromUpdate: Indicates if this is part of an update to the file or not.
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
643 :type: Boolean
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
644 """
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
645
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
646 xInputLabelsFileName = xInputLabelsFile
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
647 if not isinstance(xInputLabelsFile,str):
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
648 xInputLabelsFileName = xInputLabelsFile.name
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
649 f = csv.writer(open(xPredictSupFile,"w") if isinstance(xPredictSupFile, str) else xPredictSupFile,delimiter=ConstantsBreadCrumbs.c_strBreadCrumbsSVMSpace)
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
650
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
651 lsAllSampleNames = abundanceTable.funcGetSampleNames()
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george-weingart
parents:
diff changeset
652 lsLabels = SVM.funcReadLabelsFromFile(xSVMFile=xInputLabelsFileName, lsAllSampleNames= lsOriginalSampleNames if fFromUpdate else lsAllSampleNames,
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
653 isPredictFile=False)
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
654 dictLabels = dict([(sSample,sLabel) for sLabel in lsLabels.keys() for sSample in lsLabels[sLabel]])
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
655
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
656 #Dictionay keys will be used to order the predict file
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
657 lsMeasurementKeys = dictltpleDistanceMeasurements.keys()
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
658 #Make header
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
659 f.writerow(["labels"]+lsMeasurementKeys)
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
660
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
661 #Reformat dictionary to make it easier to use
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
662 for sKey in dictltpleDistanceMeasurements:
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
663 dictltpleDistanceMeasurements[sKey] = dict([ltpl for ltpl in dictltpleDistanceMeasurements[sKey]])
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
664
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
665 for sSample in lsOriginalSampleNames:
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
666 #Make body of file
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
667 f.writerow([dictLabels.get(sSample,ConstantsMicropita.c_sEmptyPredictFileValue)]+
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
668 [str(dictltpleDistanceMeasurements[sKey].get(sSample,ConstantsMicropita.c_sEmptyPredictFileValue))
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
669 for sKey in lsMeasurementKeys])
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
670
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george-weingart
parents:
diff changeset
671 def _funcRunNormalizeSensitiveMethods(self, abndData, iSampleSelectionCount, dictSelectedSamples, lsAlphaMetrics, lsBetaMetrics, lsInverseBetaMetrics,
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
672 fRunDiversity, fRunRepresentative, fRunExtreme, strAlphaMetadata=None,
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george-weingart
parents:
diff changeset
673 istmBetaMatrix=None, istrmTree=None, istrmEnvr=None, fInvertDiversity=False):
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
674 """
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
675 Manages running methods that are sensitive to normalization. This is called twice, once for the set of methods which should not be normalized and the other
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
676 for the set that should be normalized.
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
677
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
678 :param abndData: Abundance table object holding the samples to be measured.
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
679 :type: AbundanceTable
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
680 :param iSampleSelectionCount The number of samples to select per method.
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
681 :type: Integer
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
682 :param dictSelectedSamples Will be added to as samples are selected {"Method:["strSelectedSampleID","strSelectedSampleID"...]}.
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
683 :type: Dictionary
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
684 :param lsAlphaMetrics: List of alpha metrics to use on alpha metric dependent assays (like highest diversity).
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
685 :type: List of strings
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
686 :param lsBetaMetrics: List of beta metrics to use on beta metric dependent assays (like most representative).
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
687 :type: List of strings
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
688 :param lsInverseBetaMetrics: List of inverse beta metrics to use on inverse beta metric dependent assays (like most dissimilar).
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
689 :type: List of strings
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
690 :param fRunDiversity: Run Diversity based methods (true indicates run).
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
691 :type: Boolean
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
692 :param fRunRepresentative: Run Representative based methods (true indicates run).
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
693 :type: Boolean
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
694 :param fRunExtreme: Run Extreme based methods (true indicates run).
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
695 :type: Boolean
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
696 :param istmBetaMatrix: File that has a precalculated beta matrix
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
697 :type: File stream or File path string
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
698 :return Selected Samples: Samples selected by methods.
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
699 Dictionary {"Selection Method":["SampleID","SampleID","SampleID",...]}
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
700 """
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
701
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
702 #Sample ids/names
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
703 lsSampleNames = abndData.funcGetSampleNames()
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
704
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
705 #Generate alpha metrics and get most diverse
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
706 if fRunDiversity:
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
707
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
708 #Get Alpha metrics matrix
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
709 internalAlphaMatrix = None
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
710 #Name of technique
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
711 strMethod = [strAlphaMetadata] if strAlphaMetadata else lsAlphaMetrics
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
712
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
713 #If given an alpha-diversity metadata
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
714 if strAlphaMetadata:
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
715 internalAlphaMatrix = [[float(strNum) for strNum in abndData.funcGetMetadata(strAlphaMetadata)]]
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
716 else:
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
717 #Expects Observations (Taxa (row) x sample (column))
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
718 #Returns [[metric1-sample1, metric1-sample2, metric1-sample3],[metric1-sample1, metric1-sample2, metric1-sample3]]
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
719 internalAlphaMatrix = Metric.funcBuildAlphaMetricsMatrix(npaSampleAbundance = abndData.funcGetAbundanceCopy()
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
720 if not abndData.funcIsSummed()
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
721 else abndData.funcGetFeatureAbundanceTable(abndData.funcGetTerminalNodes()).funcGetAbundanceCopy(),
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
722 lsSampleNames = lsSampleNames, lsDiversityMetricAlpha = lsAlphaMetrics)
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
723
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
724 if internalAlphaMatrix:
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
725 #Invert measurments
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
726 if fInvertDiversity:
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
727 lldNewDiversity = []
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
728 for lsLine in internalAlphaMatrix:
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
729 lldNewDiversity.append([1/max(dValue,ConstantsMicropita.c_smallNumber) for dValue in lsLine])
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
730 internalAlphaMatrix = lldNewDiversity
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
731 #Get top ranked alpha diversity by most diverse
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
732 #Expects [[sample1,sample2,sample3...],[sample1,sample2,sample3..],...]
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
733 #Returns [[sampleName1, sampleName2, sampleNameN],[sampleName1, sampleName2, sampleNameN]]
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
734 mostDiverseAlphaSamplesIndexes = self.funcGetTopRankedSamples(lldMatrix=internalAlphaMatrix, lsSampleNames=lsSampleNames, iTopAmount=iSampleSelectionCount)
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
735
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
736 #Add to results
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
737 for index in xrange(0,len(strMethod)):
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
738 strSelectionMethod = self.dictConvertAMetricDiversity.get(strMethod[index],ConstantsMicropita.c_strDiversity+"="+strMethod[index])
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
739 dictSelectedSamples.setdefault(strSelectionMethod,[]).extend(mostDiverseAlphaSamplesIndexes[index])
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
740
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
741 logging.info("MicroPITA.funcRunNormalizeSensitiveMethods:: Selected Samples 1b")
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
742 logging.info(dictSelectedSamples)
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
743
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
744 #Generate beta metrics and
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
745 if fRunRepresentative or fRunExtreme:
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
746
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
747 #Abundance matrix transposed
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
748 npaTransposedAbundance = UtilityMath.funcTransposeDataMatrix(abndData.funcGetAbundanceCopy(), fRemoveAdornments=True)
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
749
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
750 #Get center selection using clusters/tiling
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
751 #This will be for beta metrics in normalized space
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
752 if fRunRepresentative:
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
753
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
754 if istmBetaMatrix:
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
755 #Get representative dissimilarity samples
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
756 medoidSamples=self.funcGetCentralSamplesByKMedoids(npaMatrix=npaTransposedAbundance, sMetric=ConstantsMicropita.c_custom, lsSampleNames=lsSampleNames, iNumberSamplesReturned=iSampleSelectionCount, istmBetaMatrix=istmBetaMatrix, istrmTree=istrmTree, istrmEnvr=istrmEnvr)
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
757
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
758 if medoidSamples:
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
759 dictSelectedSamples.setdefault(ConstantsMicropita.c_strRepresentative+"="+ConstantsMicropita.c_custom,[]).extend(medoidSamples)
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
760 else:
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
761 logging.info("MicroPITA.funcRunNormalizeSensitiveMethods:: Performing representative selection on normalized data.")
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
762 for bMetric in lsBetaMetrics:
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
763
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
764 #Get representative dissimilarity samples
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
765 medoidSamples=self.funcGetCentralSamplesByKMedoids(npaMatrix=npaTransposedAbundance, sMetric=bMetric, lsSampleNames=lsSampleNames, iNumberSamplesReturned=iSampleSelectionCount, istmBetaMatrix=istmBetaMatrix, istrmTree=istrmTree, istrmEnvr=istrmEnvr)
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
766
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
767 if medoidSamples:
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
768 dictSelectedSamples.setdefault(self.dictConvertBMetricToMethod.get(bMetric,ConstantsMicropita.c_strRepresentative+"="+bMetric),[]).extend(medoidSamples)
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
769
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
770 #Get extreme selection using clusters, tiling
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
771 if fRunExtreme:
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
772 logging.info("MicroPITA.funcRunNormalizeSensitiveMethods:: Performing extreme selection on normalized data.")
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
773 if istmBetaMatrix:
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
774
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
775 #Samples for representative dissimilarity
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
776 #This involves inverting the distance metric,
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
777 #Taking the dendrogram level of where the number cluster == the number of samples to select
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
778 #Returning a repersentative sample from each cluster
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
779 extremeSamples = self.funcSelectExtremeSamplesFromHClust(strBetaMetric=ConstantsMicropita.c_custom, npaAbundanceMatrix=npaTransposedAbundance, lsSampleNames=lsSampleNames, iSelectSampleCount=iSampleSelectionCount, istmBetaMatrix=istmBetaMatrix, istrmTree=istrmTree, istrmEnvr=istrmEnvr)
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
780
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
781 #Add selected samples
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
782 if extremeSamples:
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
783 dictSelectedSamples.setdefault(ConstantsMicropita.c_strExtreme+"="+ConstantsMicropita.c_custom,[]).extend(extremeSamples)
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
784
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
785 else:
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
786 #Run KMedoids with inverse custom distance metric in normalized space
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
787 for bMetric in lsInverseBetaMetrics:
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
788
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
789 #Samples for representative dissimilarity
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
790 #This involves inverting the distance metric,
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
791 #Taking the dendrogram level of where the number cluster == the number of samples to select
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
792 #Returning a repersentative sample from each cluster
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
793 extremeSamples = self.funcSelectExtremeSamplesFromHClust(strBetaMetric=bMetric, npaAbundanceMatrix=npaTransposedAbundance, lsSampleNames=lsSampleNames, iSelectSampleCount=iSampleSelectionCount, istmBetaMatrix=istmBetaMatrix, istrmTree=istrmTree, istrmEnvr=istrmEnvr)
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
794
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
795 #Add selected samples
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
796 if extremeSamples:
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
797 dictSelectedSamples.setdefault(self.dictConvertInvBMetricToMethod.get(bMetric,ConstantsMicropita.c_strExtreme+"="+bMetric),[]).extend(extremeSamples)
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
798
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
799 logging.info("MicroPITA.funcRunNormalizeSensitiveMethods:: Selected Samples 2,3b")
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
800 logging.info(dictSelectedSamples)
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
801 return dictSelectedSamples
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
802
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
803 def funcRun(self, strIDName, strLastMetadataName, istmInput,
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
804 ostmInputPredictFile, ostmPredictFile, ostmCheckedFile, ostmOutput,
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
805 cDelimiter, cFeatureNameDelimiter, strFeatureSelection,
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
806 istmFeatures, iCount, lstrMethods, strLastRowMetadata = None, strLabel = None, strStratify = None,
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
807 strCustomAlpha = None, strCustomBeta = None, strAlphaMetadata = None, istmBetaMatrix = None, istrmTree = None, istrmEnvr = None,
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
808 iMinSeqs = ConstantsMicropita.c_liOccurenceFilter[0], iMinSamples = ConstantsMicropita.c_liOccurenceFilter[1], fInvertDiversity = False):
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
809 """
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
810 Manages the selection of samples given different metrics.
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
811
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
812 :param strIDName: Sample Id metadata row
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
813 :type: String
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
814 :param strLastMetadataName: The id of the metadata positioned last in the abundance table.
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
815 :type: String String metadata id.
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
816 :param istmInput: File to store input data to supervised methods.
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
817 :type: FileStream of String file path
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
818 :param ostmInputPredictFile: File to store distances from supervised methods.
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
819 :type: FileStream or String file path
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
820 :param ostmCheckedFile: File to store the AbundanceTable data after it is being checked.
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
821 :type: FileStream or String file path
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
822 :param ostmOutPut: File to store sample selection by methods of interest.
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
823 :type: FileStream or String file path
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
824 :param cDelimiter: Delimiter of abundance table.
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
825 :type: Character Char (default TAB).
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
826 :param cFeatureNameDelimiter: Delimiter of the name of features (for instance if they contain consensus lineages indicating clades).
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
827 :type: Character (default |).
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
828 :param stFeatureSelectionMethod: Which method to use to select features in a targeted manner (Using average ranked abundance or average abundance).
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
829 :type: String (specific values indicated in ConstantsMicropita.lsTargetedFeatureMethodValues).
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
830 :param istmFeatures: File which holds the features of interest if using targeted feature methodology.
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
831 :type: FileStream or String file path
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
832 :param iCount: Number of samples to select in each methods, supervised methods select this amount per label if possible.
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
833 :type: Integer integer.
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
834 :param lstrMethods: List of strings indicating selection techniques.
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
835 :type: List of string method names
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
836 :param strLabel: The metadata used for supervised labels.
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
837 :type: String
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
838 :param strStratify: The metadata used to stratify unsupervised data.
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
839 :type: String
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
840 :param strCustomAlpha: Custom alpha diversity metric
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
841 :type: String
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
842 :param strCustomBeta: Custom beta diversity metric
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
843 :type: String
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
844 :param strAlphaMetadata: Metadata id which is a diveristy metric to use in highest diversity sampling
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
845 :type: String
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
846 :param istmBetaMatrix: File containing precalculated beta-diversity matrix for representative sampling
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
847 :type: FileStream or String file path
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
848 :param istrmTree: File containing tree for phylogentic beta-diversity analysis
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
849 :type: FileStream or String file path
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
850 :param istrmEnvr: File containing environment for phylogentic beta-diversity analysis
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
851 :type: FileStream or String file path
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
852 :param iMinSeqs: Minimum sequence in the occurence filter which filters all features not with a minimum number of sequences in each of a minimum number of samples.
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
853 :type: Integer
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
854 :param iMinSamples: Minimum sample count for the occurence filter.
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
855 :type: Integer
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
856 :param fInvertDiversity: When true will invert diversity measurements before using.
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
857 :type: boolean
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
858 :return Selected Samples: Samples selected by methods.
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
859 Dictionary {"Selection Method":["SampleID","SampleID","SampleID",...]}
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
860 """
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
861
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
862 #Holds the top ranked samples from different metrics
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
863 #dict[metric name] = [samplename,samplename...]
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
864 selectedSamples = dict()
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
865
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
866 #If a target feature file is given make sure that targeted feature is in the selection methods, if not add
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
867 if ConstantsMicropita.c_strFeature in lstrMethods:
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
868 if not istmFeatures:
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
869 logging.error("MicroPITA.funcRun:: Did not receive both the Targeted feature file and the feature selection method. MicroPITA did not run.")
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
870 return False
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
871
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
872 #Diversity metrics to run
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
873 #Use custom metrics if specified
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
874 #Custom beta metrics set to normalized only, custom alpha metrics set to count only
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
875 diversityMetricsAlpha = [] if strCustomAlpha or strAlphaMetadata else [MicroPITA.c_strInverseSimpsonDiversity]
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
876 diversityMetricsBeta = [] if istmBetaMatrix else [strCustomBeta] if strCustomBeta else [MicroPITA.c_strBrayCurtisDissimilarity]
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
877 # inverseDiversityMetricsBeta = [MicroPITA.c_strInvBrayCurtisDissimilarity]
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
878 diversityMetricsAlphaNoNormalize = [strAlphaMetadata] if strAlphaMetadata else [strCustomAlpha] if strCustomAlpha else []
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
879 diversityMetricsBetaNoNormalize = []
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
880 # inverseDiversityMetricsBetaNoNormalize = []
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
881
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
882 #Targeted taxa
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
883 userDefinedTaxa = []
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
884
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
885 #Perform different flows flags
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
886 c_RUN_MAX_DIVERSITY_1 = ConstantsMicropita.c_strDiversity in lstrMethods
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
887 c_RUN_REPRESENTIVE_DISSIMILARITY_2 = ConstantsMicropita.c_strRepresentative in lstrMethods
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
888 c_RUN_MAX_DISSIMILARITY_3 = ConstantsMicropita.c_strExtreme in lstrMethods
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
889 c_RUN_RANK_AVERAGE_USER_4 = False
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
890 if ConstantsMicropita.c_strFeature in lstrMethods:
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
891 c_RUN_RANK_AVERAGE_USER_4 = True
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
892 if not istmFeatures:
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
893 logging.error("MicroPITA.funcRun:: No taxa file was given for taxa selection.")
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
894 return False
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
895 #Read in taxa list, break down to lines and filter out empty strings
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
896 userDefinedTaxa = filter(None,(s.strip( ) for s in istmFeatures.readlines()))
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
897 c_RUN_RANDOM_5 = ConstantsMicropita.c_strRandom in lstrMethods
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
898 c_RUN_DISTINCT = ConstantsMicropita.c_strDistinct in lstrMethods
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
899 c_RUN_DISCRIMINANT = ConstantsMicropita.c_strDiscriminant in lstrMethods
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
900
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
901 #Read in abundance data
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
902 #Abundance is a structured array. Samples (column) by Taxa (rows) with the taxa id row included as the column index=0
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
903 #Abundance table object to read in and manage data
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
904 totalAbundanceTable = AbundanceTable.funcMakeFromFile(xInputFile=istmInput, lOccurenceFilter = [iMinSeqs, iMinSamples],
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
905 cDelimiter=cDelimiter, sMetadataID=strIDName, sLastMetadataRow=strLastRowMetadata,
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
906 sLastMetadata=strLastMetadataName, cFeatureNameDelimiter=cFeatureNameDelimiter, xOutputFile=ostmCheckedFile)
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
907 if not totalAbundanceTable:
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
908 logging.error("MicroPITA.funcRun:: Could not read in the abundance table. Analysis was not performed."+
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
909 " This often occurs when the Last Metadata is not specified correctly."+
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
910 " Please check to make sure the Last Metadata selection is the row of the last metadata,"+
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
911 " all values after this selection should be microbial measurements and should be numeric.")
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
912 return False
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
913
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
914 lsOriginalLabels = SVM.funcMakeLabels(totalAbundanceTable.funcGetMetadata(strLabel)) if strLabel else strLabel
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
915
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
916 dictTotalMetadata = totalAbundanceTable.funcGetMetadataCopy()
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
917 logging.debug("MicroPITA.funcRun:: Received metadata=" + str(dictTotalMetadata))
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
918 #If there is only 1 unique value for the labels, do not run the Supervised methods
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
919 if strLabel and ( len(set(dictTotalMetadata.get(strLabel,[]))) < 2 ):
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
920 logging.error("The label " + strLabel + " did not have 2 or more values. Labels found=" + str(dictTotalMetadata.get(strLabel,[])))
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
921 return False
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
922
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
923 #Run unsupervised methods###
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
924 #Stratify the data if need be and drop the old data
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
925 lStratifiedAbundanceTables = totalAbundanceTable.funcStratifyByMetadata(strStratify) if strStratify else [totalAbundanceTable]
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
926
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
927 #For each stratified abundance block or for the unstratfified abundance
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
928 #Run the unsupervised blocks
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
929 fAppendSupFiles = False
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
930 for stratAbundanceTable in lStratifiedAbundanceTables:
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
931 logging.info("MicroPITA.funcRun:: Running abundance block:"+stratAbundanceTable.funcGetName())
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
932
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
933 ###NOT SUMMED, NOT NORMALIZED
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
934 #Only perform if the data is not yet normalized
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
935 if not stratAbundanceTable.funcIsNormalized( ):
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
936 #Need to first work with unnormalized data
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
937 if c_RUN_MAX_DIVERSITY_1 or c_RUN_REPRESENTIVE_DISSIMILARITY_2 or c_RUN_MAX_DISSIMILARITY_3:
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
938
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
939 self._funcRunNormalizeSensitiveMethods(abndData=stratAbundanceTable, iSampleSelectionCount=iCount,
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
940 dictSelectedSamples=selectedSamples, lsAlphaMetrics=diversityMetricsAlphaNoNormalize,
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
941 lsBetaMetrics=diversityMetricsBetaNoNormalize,
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
942 lsInverseBetaMetrics=diversityMetricsBetaNoNormalize,
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
943 fRunDiversity=c_RUN_MAX_DIVERSITY_1,fRunRepresentative=c_RUN_REPRESENTIVE_DISSIMILARITY_2,
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
944 fRunExtreme=c_RUN_MAX_DISSIMILARITY_3, strAlphaMetadata=strAlphaMetadata,
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
945 istrmTree=istrmTree, istrmEnvr=istrmEnvr, fInvertDiversity=fInvertDiversity)
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
946
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
947
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
948 #Generate selection by the rank average of user defined taxa
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
949 #Expects (Taxa (row) by Samples (column))
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
950 #Expects a column 0 of taxa id that is skipped
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
951 #Returns [(sample name,average,rank)]
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
952 #SUMMED AND NORMALIZED
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
953 stratAbundanceTable.funcSumClades()
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
954 #Normalize data at this point
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
955 stratAbundanceTable.funcNormalize()
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
956 if c_RUN_RANK_AVERAGE_USER_4:
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
957 selectedSamples[ConstantsMicropita.c_strFeature] = self.funcSelectTargetedTaxaSamples(abndMatrix=stratAbundanceTable,
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
958 lsTargetedTaxa=userDefinedTaxa, iSampleSelectionCount=iCount, sMethod=strFeatureSelection)
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
959 logging.info("MicroPITA.funcRun:: Selected Samples Rank")
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
960 logging.info(selectedSamples)
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
961
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
962 ###SUMMED AND NORMALIZED analysis block
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
963 #Diversity based metric will move reduce to terminal taxa as needed
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
964 if c_RUN_MAX_DIVERSITY_1 or c_RUN_REPRESENTIVE_DISSIMILARITY_2 or c_RUN_MAX_DISSIMILARITY_3:
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
965
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
966 self._funcRunNormalizeSensitiveMethods(abndData=stratAbundanceTable, iSampleSelectionCount=iCount,
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
967 dictSelectedSamples=selectedSamples, lsAlphaMetrics=diversityMetricsAlpha,
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
968 lsBetaMetrics=diversityMetricsBeta,
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
969 lsInverseBetaMetrics=diversityMetricsBeta,
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
970 fRunDiversity=c_RUN_MAX_DIVERSITY_1,fRunRepresentative=c_RUN_REPRESENTIVE_DISSIMILARITY_2,
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
971 fRunExtreme=c_RUN_MAX_DISSIMILARITY_3,
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
972 istmBetaMatrix=istmBetaMatrix, istrmTree=istrmTree, istrmEnvr=istrmEnvr, fInvertDiversity=fInvertDiversity)
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
973
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
974 #5::Select randomly
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
975 #Expects sampleNames = List of sample names [name, name, name...]
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
976 if(c_RUN_RANDOM_5):
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
977 #Select randomly from sample names
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
978 selectedSamples[ConstantsMicropita.c_strRandom] = self.funcGetRandomSamples(lsSamples=stratAbundanceTable.funcGetSampleNames(), iNumberOfSamplesToReturn=iCount)
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
979 logging.info("MicroPITA.funcRun:: Selected Samples Random")
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
980 logging.info(selectedSamples)
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
981
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
982 #Perform supervised selection
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
983 if c_RUN_DISTINCT or c_RUN_DISCRIMINANT:
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
984 if strLabel:
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
985 dictSelectionRet = self.funcRunSupervisedDistancesFromCentroids(abundanceTable=stratAbundanceTable,
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
986 fRunDistinct=c_RUN_DISTINCT, fRunDiscriminant=c_RUN_DISCRIMINANT,
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
987 xOutputSupFile=ostmInputPredictFile,xPredictSupFile=ostmPredictFile,
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
988 strSupervisedMetadata=strLabel, iSampleSupSelectionCount=iCount,
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
989 lsOriginalSampleNames = totalAbundanceTable.funcGetSampleNames(),
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
990 lsOriginalLabels = lsOriginalLabels,
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
991 fAppendFiles=fAppendSupFiles)
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
992
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
993 [selectedSamples.setdefault(sKey,[]).extend(lValue) for sKey,lValue in dictSelectionRet.items()]
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
994
2f4f6f08c8c4 Uploaded
george-weingart
parents:
diff changeset
995 if not fAppendSupFiles:
2f4f6f08c8c4 Uploaded
george-weingart
parents:
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996 fAppendSupFiles = True
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997 logging.info("MicroPITA.funcRun:: Selected Samples Unsupervised")
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998 logging.info(selectedSamples)
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999 return selectedSamples
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1000
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parents:
diff changeset
1001 #Testing: Happy path tested
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diff changeset
1002 @staticmethod
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1003 def funcWriteSelectionToFile(dictSelection,xOutputFilePath):
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1004 """
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1005 Writes the selection of samples by method to an output file.
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1006
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1007 :param dictSelection: The dictionary of selections by method to be written to a file.
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1008 :type: Dictionary The dictionary of selections by method {"method":["sample selected","sample selected"...]}
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1009 :param xOutputFilePath: FileStream or String path to file inwhich the dictionary is written.
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1010 :type: String FileStream or String path to file
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1011 """
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1012
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1013 if not dictSelection:
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1014 return
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1015
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1016 #Open file
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1017 f = csv.writer(open(xOutputFilePath,"w") if isinstance(xOutputFilePath, str) else xOutputFilePath, delimiter=ConstantsMicropita.c_outputFileDelim )
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1018
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1019 #Create output content from dictionary
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1020 for sKey in dictSelection:
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1021 f.writerow([sKey]+dictSelection[sKey])
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1022 logging.debug("MicroPITA.funcRun:: Selected samples output to file:"+str(dictSelection[sKey]))
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1023
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diff changeset
1024 #Testing: Happy Path tested
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diff changeset
1025 @staticmethod
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1026 def funcReadSelectionFileToDictionary(xInputFile):
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1027 """
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1028 Reads in an output selection file from micropita and formats it into a dictionary.
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1029
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1030 :param xInputFile: String path to file or file stream to read and translate into a dictionary.
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1031 {"method":["sample selected","sample selected"...]}
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1032 :type: FileStream or String Path to file
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1033 :return Dictionary: Samples selected by methods.
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1034 Dictionary {"Selection Method":["SampleID","SampleID","SampleID",...]}
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1035 """
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1036
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1037 #Open file
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1038 istmReader = csv.reader(open(xInputFile,'r') if isinstance(xInputFile, str) else xInputFile, delimiter = ConstantsMicropita.c_outputFileDelim)
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1039
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1040 #Dictionary to hold selection data
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1041 return dict([(lsLine[0], lsLine[1:]) for lsLine in istmReader])
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1042
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1043 #Set up arguments reader
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1044 argp = argparse.ArgumentParser( prog = "MicroPITA.py",
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1045 description = """Selects samples from abundance tables based on various selection schemes.""" )
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1046
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1047 args = argp.add_argument_group( "Common", "Commonly modified options" )
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1048 args.add_argument(ConstantsMicropita.c_strCountArgument,"--num", dest="iCount", metavar = "samples", default = 10, type = int, help = ConstantsMicropita.c_strCountHelp)
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1049 args.add_argument("-m","--method", dest = "lstrMethods", metavar = "method", default = [], help = ConstantsMicropita.c_strSelectionTechniquesHelp,
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1050 choices = ConstantsMicropita.c_lsAllMethods, action = "append")
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1051
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1052 args = argp.add_argument_group( "Custom", "Selecting and inputing custom metrics" )
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1053 args.add_argument("-a","--alpha", dest = "strAlphaDiversity", metavar = "AlphaDiversity", default = None, help = ConstantsMicropita.c_strCustomAlphaDiversityHelp, choices = Metric.setAlphaDiversities)
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1054 args.add_argument("-b","--beta", dest = "strBetaDiversity", metavar = "BetaDiversity", default = None, help = ConstantsMicropita.c_strCustomBetaDiversityHelp, choices = list(Metric.setBetaDiversities)+[Metric.c_strUnifracUnweighted,Metric.c_strUnifracWeighted])
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1055 args.add_argument("-q","--alphameta", dest = "strAlphaMetadata", metavar = "AlphaDiversityMetadata", default = None, help = ConstantsMicropita.c_strCustomAlphaDiversityMetadataHelp)
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1056 args.add_argument("-x","--betamatrix", dest = "istmBetaMatrix", metavar = "BetaDiversityMatrix", default = None, help = ConstantsMicropita.c_strCustomBetaDiversityMatrixHelp)
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1057 args.add_argument("-o","--tree", dest = "istrmTree", metavar = "PhylogeneticTree", default = None, help = ConstantsMicropita.c_strCustomPhylogeneticTreeHelp)
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1058 args.add_argument("-i","--envr", dest = "istrmEnvr", metavar = "EnvironmentFile", default = None, help = ConstantsMicropita.c_strCustomEnvironmentFileHelp)
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1059 args.add_argument("-f","--invertDiversity", dest = "fInvertDiversity", action="store_true", default = False, help = ConstantsMicropita.c_strInvertDiversityHelp)
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1060
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1061 args = argp.add_argument_group( "Miscellaneous", "Row/column identifiers and feature targeting options" )
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1062 args.add_argument("-d",ConstantsMicropita.c_strIDNameArgument, dest="strIDName", metavar="sample_id", help= ConstantsMicropita.c_strIDNameHelp)
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1063 args.add_argument("-l",ConstantsMicropita.c_strLastMetadataNameArgument, dest="strLastMetadataName", metavar = "metadata_id", default = None,
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1064 help= ConstantsMicropita.c_strLastMetadataNameHelp)
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1065 args.add_argument("-r",ConstantsMicropita.c_strTargetedFeatureMethodArgument, dest="strFeatureSelection", metavar="targeting_method", default=ConstantsMicropita.lsTargetedFeatureMethodValues[0],
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1066 choices=ConstantsMicropita.lsTargetedFeatureMethodValues, help= ConstantsMicropita.c_strTargetedFeatureMethodHelp)
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1067 args.add_argument("-t",ConstantsMicropita.c_strTargetedSelectionFileArgument, dest="istmFeatures", metavar="feature_file", type=argparse.FileType("rU"), help=ConstantsMicropita.c_strTargetedSelectionFileHelp)
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1068 args.add_argument("-w",ConstantsMicropita.c_strFeatureMetadataArgument, dest="strLastFeatureMetadata", metavar="Last_Feature_Metadata", default=None, help=ConstantsMicropita.c_strFeatureMetadataHelp)
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1069
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1070 args = argp.add_argument_group( "Data labeling", "Metadata IDs for strata and supervised label values" )
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1071 args.add_argument("-e",ConstantsMicropita.c_strSupervisedLabelArgument, dest="strLabel", metavar= "supervised_id", help=ConstantsMicropita.c_strSupervisedLabelHelp)
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1072 args.add_argument("-s",ConstantsMicropita.c_strUnsupervisedStratifyMetadataArgument, dest="strUnsupervisedStratify", metavar="stratify_id",
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1073 help= ConstantsMicropita.c_strUnsupervisedStratifyMetadataHelp)
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1074
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1075 args = argp.add_argument_group( "File formatting", "Rarely modified file formatting options" )
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1076 args.add_argument("-j",ConstantsMicropita.c_strFileDelimiterArgument, dest="cFileDelimiter", metavar="column_delimiter", default="\t", help=ConstantsMicropita.c_strFileDelimiterHelp)
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1077 args.add_argument("-k",ConstantsMicropita.c_strFeatureNameDelimiterArgument, dest="cFeatureNameDelimiter", metavar="taxonomy_delimiter", default="|", help=ConstantsMicropita.c_strFeatureNameDelimiterHelp)
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1078
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1079 args = argp.add_argument_group( "Debugging", "Debugging options - modify at your own risk!" )
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1080 args.add_argument("-v",ConstantsMicropita.c_strLoggingArgument, dest="strLogLevel", metavar = "log_level", default="WARNING",
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1081 choices=ConstantsMicropita.c_lsLoggingChoices, help= ConstantsMicropita.c_strLoggingHelp)
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1082 args.add_argument("-c",ConstantsMicropita.c_strCheckedAbundanceFileArgument, dest="ostmCheckedFile", metavar = "output_qc", type = argparse.FileType("w"), help = ConstantsMicropita.c_strCheckedAbundanceFileHelp)
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diff changeset
1083 args.add_argument("-g",ConstantsMicropita.c_strLoggingFileArgument, dest="ostmLoggingFile", metavar = "output_log", type = argparse.FileType("w"), help = ConstantsMicropita.c_strLoggingFileHelp)
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diff changeset
1084 args.add_argument("-u",ConstantsMicropita.c_strSupervisedInputFile, dest="ostmInputPredictFile", metavar = "output_scaled", type = argparse.FileType("w"), help = ConstantsMicropita.c_strSupervisedInputFileHelp)
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diff changeset
1085 args.add_argument("-p",ConstantsMicropita.c_strSupervisedPredictedFile, dest="ostmPredictFile", metavar = "output_labels", type = argparse.FileType("w"), help = ConstantsMicropita.c_strSupervisedPredictedFileHelp)
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diff changeset
1086
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diff changeset
1087 argp.add_argument("istmInput", metavar = "input.pcl/biome", type = argparse.FileType("rU"), help = ConstantsMicropita.c_strAbundanceFileHelp,
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diff changeset
1088 default = sys.stdin)
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diff changeset
1089 argp.add_argument("ostmOutput", metavar = "output.txt", type = argparse.FileType("w"), help = ConstantsMicropita.c_strGenericOutputDataFileHelp,
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diff changeset
1090 default = sys.stdout)
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1091
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1092 __doc__ = "::\n\n\t" + argp.format_help( ).replace( "\n", "\n\t" ) + __doc__
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1093
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1094 def _main( ):
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1095 args = argp.parse_args( )
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diff changeset
1096
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diff changeset
1097 #Set up logger
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diff changeset
1098 iLogLevel = getattr(logging, args.strLogLevel.upper(), None)
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1099 logging.basicConfig(stream = args.ostmLoggingFile if args.ostmLoggingFile else sys.stderr, filemode = 'w', level=iLogLevel)
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1100
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diff changeset
1101 #Run micropita
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1102 logging.info("MicroPITA:: Start microPITA")
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1103 microPITA = MicroPITA()
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1104
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1105 #Argparse will append to the default but will not remove the default so I do this here
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1106 if not len(args.lstrMethods):
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1107 args.lstrMethods = [ConstantsMicropita.c_strRepresentative]
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1108
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1109 dictSelectedSamples = microPITA.funcRun(
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1110 strIDName = args.strIDName,
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1111 strLastMetadataName = args.strLastMetadataName,
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1112 istmInput = args.istmInput,
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1113 ostmInputPredictFile = args.ostmInputPredictFile,
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1114 ostmPredictFile = args.ostmPredictFile,
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1115 ostmCheckedFile = args.ostmCheckedFile,
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1116 ostmOutput = args.ostmOutput,
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1117 cDelimiter = args.cFileDelimiter,
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1118 cFeatureNameDelimiter = args.cFeatureNameDelimiter,
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1119 istmFeatures = args.istmFeatures,
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1120 strFeatureSelection = args.strFeatureSelection,
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1121 iCount = args.iCount,
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1122 strLastRowMetadata = args.strLastFeatureMetadata,
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1123 strLabel = args.strLabel,
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1124 strStratify = args.strUnsupervisedStratify,
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1125 strCustomAlpha = args.strAlphaDiversity,
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1126 strCustomBeta = args.strBetaDiversity,
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1127 strAlphaMetadata = args.strAlphaMetadata,
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1128 istmBetaMatrix = args.istmBetaMatrix,
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1129 istrmTree = args.istrmTree,
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1130 istrmEnvr = args.istrmEnvr,
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1131 lstrMethods = args.lstrMethods,
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1132 fInvertDiversity = args.fInvertDiversity
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1133 )
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1134
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1135 if not dictSelectedSamples:
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diff changeset
1136 logging.error("MicroPITA:: Error, did not get a result from analysis.")
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1137 return -1
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1138 logging.info("End microPITA")
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1139
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1140 #Log output for debugging
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1141 logging.debug("MicroPITA:: Returned the following samples:"+str(dictSelectedSamples))
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1142
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diff changeset
1143 #Write selection to file
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1144 microPITA.funcWriteSelectionToFile(dictSelection=dictSelectedSamples, xOutputFilePath=args.ostmOutput)
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george-weingart
parents:
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1145
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george-weingart
parents:
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1146 if __name__ == "__main__":
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george-weingart
parents:
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1147 _main( )