Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/stat/Stat.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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0
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 import math |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 |
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3 class Stat(object): |
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4 |
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5 def __init__(self, lValues = []): |
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6 self.reset() |
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7 if lValues != []: |
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8 self.fill(lValues) |
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9 |
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10 def __eq__(self, o): |
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11 self._lValues.sort() |
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12 o._lValues.sort() |
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13 return self._lValues == o._lValues and round(self._sum, 6) == round(o._sum, 6) \ |
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14 and round(self._sumOfSquares, 6) == round(o._sumOfSquares, 6) and self._n == self._n \ |
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15 and round(self._min, 6) == round(o._min, 6) and round(self._max, 6) == round(o._max, 6) |
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16 |
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17 def getValuesList(self): |
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18 return self._lValues |
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19 |
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20 def getSum(self): |
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21 return self._sum |
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22 |
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23 def getSumOfSquares(self): |
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24 return self._sumOfSquares |
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25 |
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26 def getValuesNumber(self): |
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27 return self._n |
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28 |
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29 def getMin(self): |
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30 return self._min |
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31 |
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32 def getMax(self): |
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33 return self._max |
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34 |
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35 ## Reset all attributes |
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36 # |
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37 def reset(self): |
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38 self._lValues = [] |
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39 self._sum = 0.0 |
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40 self._sumOfSquares = 0.0 |
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41 self._n = 0 |
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42 self._max = 0.0 |
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43 self._min = 0.0 |
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44 |
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45 ## Add a value to Stat instance list and update attributes |
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46 # |
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47 # @param v float value to add |
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48 # |
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49 def add(self, v): |
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50 self._lValues.append( float(v) ) |
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51 self._sum += float(v) |
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52 self._sumOfSquares += float(v) * float(v) |
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53 self._n = self._n + 1 |
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54 if v > self._max: |
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55 self._max = float(v) |
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56 if self._n == 1: |
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57 self._min = float(v) |
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58 elif v < self._min: |
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59 self._min = float(v) |
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60 |
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61 ## Add a list of values to Stat instance list and update attributes |
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62 # |
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63 # @param lValues list of float list to add |
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64 # |
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65 def fill(self, lValues): |
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66 for v in lValues: |
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67 self.add(v) |
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68 |
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69 ## Get the arithmetic mean of the Stat instance list |
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70 # |
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71 # @return float |
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72 # |
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73 def mean(self): |
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74 if self._n == 0: |
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75 return 0 |
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76 else: |
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77 return self._sum / float(self._n) |
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78 |
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79 ## Get the variance of the sample |
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80 # @note we consider a sample, not a population. So for calculation, we use n-1 |
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81 # |
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82 # @return float |
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83 # |
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84 def var(self): |
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85 if self._n < 2 or self.mean() == 0.0: |
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86 return 0 |
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87 else: |
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88 variance = self._sumOfSquares/float(self._n - 1) - self._n/float(self._n - 1) * self.mean()*self.mean() |
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89 if round(variance, 10) == 0: |
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90 variance = 0 |
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91 return variance |
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92 |
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93 ## Get the standard deviation of the sample |
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94 # |
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95 # @return float |
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96 # |
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97 def sd(self): |
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98 return math.sqrt( self.var() ) |
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99 |
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100 ## Get the coefficient of variation of the sample |
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101 # |
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102 # @return float |
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103 # |
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104 def cv(self): |
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105 if self._n < 2 or self.mean() == 0.0: |
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106 return 0 |
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107 else: |
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108 return self.sd() / self.mean() |
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109 |
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110 ## Get the median of the sample |
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111 # |
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112 # @return number or "NA" (Not available) |
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113 # |
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114 def median( self ): |
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115 if len(self._lValues) == 0: |
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116 return "NA" |
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117 if len(self._lValues) == 1: |
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118 return self._lValues[0] |
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119 self._lValues.sort() |
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120 m = int( math.ceil( len(self._lValues) / 2.0 ) ) |
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121 if len(self._lValues) % 2: |
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122 return self._lValues[m-1] |
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123 else: |
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124 return ( self._lValues[m-1] + self._lValues[m] ) / 2.0 |
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125 |
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126 ## Get the kurtosis (measure of whether the data are peaked or flat relative to a normal distribution, 'coef d'aplatissement ' in french)). |
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127 # k = 0 -> completely flat |
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128 # k = 3 -> same as normal distribution |
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129 # k >> 3 -> peak |
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130 # |
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131 # @return float |
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132 # |
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133 def kurtosis(self): |
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134 numerator = 0 |
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135 for i in self._lValues: |
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136 numerator += math.pow( i - self.mean(), 4 ) |
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137 return numerator / float(self._n - 1) * self.sd() |
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138 |
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139 ## Prepare a string with calculations on your values |
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140 # |
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141 # @return string |
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142 # |
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143 def string(self): |
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144 msg = "" |
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145 msg += "n=%d" % ( self._n ) |
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146 msg += " mean=%5.3f" % ( self.mean() ) |
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147 msg += " var=%5.3f" % ( self.var() ) |
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148 msg += " sd=%5.3f" % ( self.sd() ) |
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149 msg += " min=%5.3f" % ( self.getMin() ) |
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150 median = self.median() |
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151 if median == "NA": |
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152 msg += " med=%s" % (median) |
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153 else: |
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154 msg += " med=%5.3f" % (median) |
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155 msg += " max=%5.3f" % ( self.getMax() ) |
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156 return msg |
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157 |
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158 ## Print descriptive statistics |
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159 # |
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160 def view(self): |
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161 print self.string() |
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162 |
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163 ## Return sorted list of values, ascending (default) or descending |
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164 # |
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165 # @return list |
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166 # |
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167 def sort( self, isReverse = False ): |
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168 self._lValues.sort(reverse = isReverse) |
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169 return self._lValues |
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170 |
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171 ## Give the quantile corresponding to the chosen percentage |
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172 # |
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173 # @return number |
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174 # |
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175 def quantile( self, percentage ): |
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176 if self._n == 0: |
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177 return 0 |
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178 elif percentage == 1: |
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179 return self.getMax() |
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180 else: |
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181 return self.sort()[int(self._n * percentage)] |
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182 |
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183 ## Prepare a string with quantile values |
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184 # |
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185 # @return string |
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186 # |
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187 def stringQuantiles( self ): |
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188 return "n=%d min=%5.3f Q1=%5.3f median=%5.3f Q3=%5.3f max=%5.3f" % \ |
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189 (self._n, self.quantile(0), self.quantile(0.25), self.quantile(0.5), self.quantile(0.75), self.quantile(1)) |
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190 |
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191 ## Print quantiles string |
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192 # |
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193 def viewQuantiles( self ): |
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194 print self.stringQuantiles() |
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195 |
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196 ## Compute N50 |
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197 # @return number |
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198 def N50(self ): |
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199 lSorted = self.sort(True) |
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200 midlValues = self.getSum() / 2 |
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201 cumul = 0 |
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202 index = 0 |
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203 while cumul < midlValues: |
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204 cumul = cumul + lSorted[index] |
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205 index += 1 |
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206 if (index == 0): |
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207 return lSorted[index] |
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208 else : |
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209 return lSorted[index - 1] |