|
0
|
1 NAME
|
|
|
2 AnalyzeSDFilesData.pl - Analyze numerical data field values in SDFile(s)
|
|
|
3
|
|
|
4 SYNOPSIS
|
|
|
5 AnalyzeSDFilesData.pl SDFile(s)...
|
|
|
6
|
|
|
7 AnalyzeSDFilesData.pl [--datafields "fieldlabel,[fieldlabel,...]" | All]
|
|
|
8 [--datafieldpairs "fieldlabel,fieldlabel,[fieldlabel,fieldlabel,...]" |
|
|
|
9 AllPairs] [-d, --detail infolevel] [-f, --fast] [--frequencybins number
|
|
|
10 | "number,number,[number,...]"] [-h, --help] [--klargest number]
|
|
|
11 [--ksmallest number] [-m, --mode DescriptiveStatisticsBasic |
|
|
|
12 DescriptiveStatisticsAll | All | "function1, [function2,...]"]
|
|
|
13 [--trimfraction number] [-w, --workingdir dirname] SDFiles(s)...
|
|
|
14
|
|
|
15 DESCRIPTION
|
|
|
16 Analyze numerical data field values in *SDFile(s)* using a combination
|
|
|
17 of various statistical functions; Non-numerical values are simply
|
|
|
18 ignored. For *Correlation, RSquare, and Covariance* analysis, the count
|
|
|
19 of valid values in specified data field pairs must be same; otherwise,
|
|
|
20 column data field pair is ignored. The file names are separated by
|
|
|
21 space.The valid file extensions are *.sdf* and *.sd*. All other file
|
|
|
22 names are ignored. All the SD files in a current directory can be
|
|
|
23 specified either by **.sdf* or the current directory name.
|
|
|
24
|
|
|
25 OPTIONS
|
|
|
26 --datafields *"fieldlabel,[fieldlabel,...]" | Common | All*
|
|
|
27 Data fields to use for analysis. Possible values: list of comma
|
|
|
28 separated data field labels, data fields common to all records, or
|
|
|
29 all data fields. Default value: *Common*. Examples:
|
|
|
30
|
|
|
31 ALogP,MolWeight,EC50
|
|
|
32 "MolWeight,PSA"
|
|
|
33
|
|
|
34 --datafieldpairs *"fieldlabel,fieldlabel,[fieldlabel,fieldlabel,...]" |
|
|
|
35 CommonPairs | AllPairs*
|
|
|
36 This value is mode specific and is only used for *Correlation,
|
|
|
37 PearsonCorrelation, or Covariance* value of -m, --mode option. It
|
|
|
38 specifies data field label pairs to use for data analysis during
|
|
|
39 *Correlation* and *Covariance* calculations. Possible values: comma
|
|
|
40 delimited list of data field label pairs, data field label pairs
|
|
|
41 common to all records, or all data field pairs. Default
|
|
|
42 value:*CommonPairs*. Example:
|
|
|
43
|
|
|
44 MolWeight,EC50,NumN+O,PSA
|
|
|
45
|
|
|
46 For *AllPairs* value of --datafieldpairs option, all data field
|
|
|
47 label pairs are used for *Correlation* and *Covariance*
|
|
|
48 calculations.
|
|
|
49
|
|
|
50 -d, --detail *infolevel*
|
|
|
51 Level of information to print about column values being ignored.
|
|
|
52 Default: *0*. Possible values: 0, 1, 2, 3, or 4.
|
|
|
53
|
|
|
54 -f, --fast
|
|
|
55 In this mode, all the data field values specified for analysis are
|
|
|
56 assumed to contain numerical data and no checking is performed
|
|
|
57 before analysis. By default, only numerical data is used for
|
|
|
58 analysis; other types of column data is ignored.
|
|
|
59
|
|
|
60 --frequencybins *number | "number,number,[number,...]"*
|
|
|
61 Specify number of bins or bin range to use for frequency analysis.
|
|
|
62 Default value: *10*
|
|
|
63
|
|
|
64 Number of bins value along with the smallest and largest value for a
|
|
|
65 column is used to group the column values into different groups.
|
|
|
66
|
|
|
67 The bin range list is used to group values for a column into
|
|
|
68 different groups; It must contain values in ascending order.
|
|
|
69 Examples:
|
|
|
70
|
|
|
71 10,20,30
|
|
|
72 0.1,0.2,0.3,0.4,0.5
|
|
|
73
|
|
|
74 The frequency value calculated for a specific bin corresponds to all
|
|
|
75 the column values which are greater than the previous bin value and
|
|
|
76 less than or equal to the current bin value.
|
|
|
77
|
|
|
78 -h, --help
|
|
|
79 Print this help message.
|
|
|
80
|
|
|
81 --klargest *number*
|
|
|
82 Kth largest value to find by *KLargest* function. Default value:
|
|
|
83 *2*. Valid values: positive integers.
|
|
|
84
|
|
|
85 --ksmallest *number*
|
|
|
86 Kth smallest value to find by *KSmallest* function. Default values:
|
|
|
87 *2*. Valid values: positive integers.
|
|
|
88
|
|
|
89 -m, --mode *DescriptiveStatisticsBasic | DescriptiveStatisticsAll | All
|
|
|
90 | "function1, [function2,...]"*
|
|
|
91 Specify how to analyze data in SDFile(s): calculate basic or all
|
|
|
92 descriptive statistics; or use a comma delimited list of supported
|
|
|
93 statistical functions. Possible values: *DescriptiveStatisticsBasic
|
|
|
94 | DescriptiveStatisticsAll | "function1,[function2]..."*. Default
|
|
|
95 value: *DescriptiveStatisticsBasic*
|
|
|
96
|
|
|
97 *DescriptiveStatisticsBasic* includes these functions: *Count,
|
|
|
98 Maximum, Minimum, Mean, Median, Sum, StandardDeviation,
|
|
|
99 StandardError, Variance*.
|
|
|
100
|
|
|
101 *DescriptiveStatisticsAll*, in addition to
|
|
|
102 *DescriptiveStatisticsBasic* functions, includes: *GeometricMean,
|
|
|
103 Frequency, HarmonicMean, KLargest, KSmallest, Kurtosis, Mode,
|
|
|
104 RSquare, Skewness, TrimMean*.
|
|
|
105
|
|
|
106 *All* uses complete list of supported functions: *Average,
|
|
|
107 AverageDeviation, Correlation, Count, Covariance, GeometricMean,
|
|
|
108 Frequency, HarmonicMean, KLargest, KSmallest, Kurtosis, Maximum,
|
|
|
109 Minimum, Mean, Median, Mode, RSquare, Skewness, Sum, SumOfSquares,
|
|
|
110 StandardDeviation, StandardDeviationN, StandardError,
|
|
|
111 StandardScores, StandardScoresN, TrimMean, Variance, VarianceN*. The
|
|
|
112 function names ending with N calculate corresponding values assuming
|
|
|
113 an entire population instead of a population sample. Here are the
|
|
|
114 formulas for these functions:
|
|
|
115
|
|
|
116 Average: See Mean
|
|
|
117
|
|
|
118 AverageDeviation: SUM( ABS(x[i] - Xmean) ) / n
|
|
|
119
|
|
|
120 Correlation: See Pearson Correlation
|
|
|
121
|
|
|
122 Covariance: SUM( (x[i] - Xmean)(y[i] - Ymean) ) / n
|
|
|
123
|
|
|
124 GeometricMean: NthROOT( PRODUCT(x[i]) )
|
|
|
125
|
|
|
126 HarmonicMean: 1 / ( SUM(1/x[i]) / n )
|
|
|
127
|
|
|
128 Mean: SUM( x[i] ) / n
|
|
|
129
|
|
|
130 Median: Xsorted[(n - 1)/2 + 1] for even values of n; (Xsorted[n/2] +
|
|
|
131 Xsorted[n/2 + 1])/2 for odd values of n.
|
|
|
132
|
|
|
133 Kurtosis: [ {n(n + 1)/(n - 1)(n - 2)(n - 3)} SUM{ ((x[i] -
|
|
|
134 Xmean)/STDDEV)^4 } ] - {3((n - 1)^2)}/{(n - 2)(n-3)}
|
|
|
135
|
|
|
136 PearsonCorrelation: SUM( (x[i] - Xmean)(y[i] - Ymean) ) / SQRT( SUM(
|
|
|
137 (x[i] - Xmean)^2 ) (SUM( (y[i] - Ymean)^2 )) )
|
|
|
138
|
|
|
139 RSquare: PearsonCorrelation^2
|
|
|
140
|
|
|
141 Skewness: {n/(n - 1)(n - 2)} SUM{ ((x[i] - Xmean)/STDDEV)^3 }
|
|
|
142
|
|
|
143 StandardDeviation: SQRT ( SUM( (x[i] - Mean)^2 ) / (n - 1) )
|
|
|
144
|
|
|
145 StandardDeviationN: SQRT ( SUM( (x[i] - Mean)^2 ) / n )
|
|
|
146
|
|
|
147 StandardError: StandardDeviation / SQRT( n )
|
|
|
148
|
|
|
149 StandardScore: (x[i] - Mean) / (n - 1)
|
|
|
150
|
|
|
151 StandardScoreN: (x[i] - Mean) / n
|
|
|
152
|
|
|
153 Variance: SUM( (x[i] - Xmean)^2 / (n - 1) )
|
|
|
154
|
|
|
155 VarianceN: SUM( (x[i] - Xmean)^2 / n )
|
|
|
156
|
|
|
157 -o, --overwrite
|
|
|
158 Overwrite existing files.
|
|
|
159
|
|
|
160 --outdelim *comma | tab | semicolon*
|
|
|
161 Output text file delimiter. Possible values: *comma, tab, or
|
|
|
162 semicolon* Default value: *comma*.
|
|
|
163
|
|
|
164 -p, --precision *number*
|
|
|
165 Precision of calculated values in the output file. Default: up to
|
|
|
166 *2* decimal places. Valid values: positive integers.
|
|
|
167
|
|
|
168 -q, --quote *yes | no*
|
|
|
169 Put quotes around column values in output text file. Possible
|
|
|
170 values: *yes or no*. Default value: *yes*.
|
|
|
171
|
|
|
172 -r, --root *rootname*
|
|
|
173 New text file name is generated using the root: <Root>.<Ext>.
|
|
|
174 Default new file name: <InitialSDFileName><Mode>.<Ext>. Based on the
|
|
|
175 specified analysis, <Mode> corresponds to one of these values:
|
|
|
176 DescriptiveStatisticsBasic, DescriptiveStatisticsAll, AllStatistics,
|
|
|
177 SpecifiedStatistics, Covariance, Correlation, Frequency, or
|
|
|
178 StandardScores. The csv, and tsv <Ext> values are used for
|
|
|
179 comma/semicolon, and tab delimited text files respectively. This
|
|
|
180 option is ignored for multiple input files.
|
|
|
181
|
|
|
182 --trimfraction *number*
|
|
|
183 Fraction of data to exclude from the top and bottom of the data set
|
|
|
184 during *TrimMean* calculation. Default value: *0.1* Valid values: >
|
|
|
185 0 and < 1.
|
|
|
186
|
|
|
187 -w --workingdir *text*
|
|
|
188 Location of working directory. Default: current directory.
|
|
|
189
|
|
|
190 EXAMPLES
|
|
|
191 To calculate basic statistics for data in all common data fields and
|
|
|
192 generate a NewSample1DescriptiveStatisticsBasic.csv file, type:
|
|
|
193
|
|
|
194 % AnalyzeSDFilesData.pl -o -r NewSample1 Sample1.sdf
|
|
|
195
|
|
|
196 To calculate basic statistics for MolWeight data field and generate a
|
|
|
197 NewSample1DescriptiveStatisticsBasic.csv file, type:
|
|
|
198
|
|
|
199 % AnalyzeSDFilesData.pl --datafields MolWeight -o -r NewSample1
|
|
|
200 Sample1.sdf
|
|
|
201
|
|
|
202 To calculate all available statistics for MolWeight data field and all
|
|
|
203 data field pairs, and generate NewSample1DescriptiveStatisticsAll.csv,
|
|
|
204 NewSample1CorrelationMatrix.csv, NewSample1CorrelationMatrix.csv, and
|
|
|
205 NewSample1MolWeightFrequencyAnalysis.csv files, type:
|
|
|
206
|
|
|
207 % AnalyzeSDFilesData.pl -m DescriptiveStatisticsAll --datafields
|
|
|
208 MolWeight -o --datafieldpairs AllPairs -r NewSample1 Sample1.sdf
|
|
|
209
|
|
|
210 To compute frequency distribution of MolWeight data field into five bins
|
|
|
211 and generate NewSample1MolWeightFrequencyAnalysis.csv, type:
|
|
|
212
|
|
|
213 % AnalyzeSDFilesData.pl -m Frequency --frequencybins 5 --datafields
|
|
|
214 MolWeight -o -r NewSample1 Sample1.sdf
|
|
|
215
|
|
|
216 To compute frequency distribution of data in MolWeight data field into
|
|
|
217 specified bin range values, and generate
|
|
|
218 NewSample1MolWeightFrequencyAnalysis.csv, type:
|
|
|
219
|
|
|
220 % AnalyzeSDFilesData.pl -m Frequency --frequencybins "100,200,400"
|
|
|
221 --datafields MolWeight -o -r NewSample1 Sample1.sdf
|
|
|
222
|
|
|
223 To calculate all available statistics for data in all data fields and
|
|
|
224 pairs, type:
|
|
|
225
|
|
|
226 % AnalyzeSDFilesData.pl -m All --datafields All --datafieldpairs
|
|
|
227 AllPairs -o -r NewSample1 Sample1.sdf
|
|
|
228
|
|
|
229 AUTHOR
|
|
|
230 Manish Sud <msud@san.rr.com>
|
|
|
231
|
|
|
232 SEE ALSO
|
|
|
233 FilterSDFiles.pl, InfoSDFiles.pl, SplitSDFiles.pl,
|
|
|
234 MergeTextFilesWithSD.pl
|
|
|
235
|
|
|
236 COPYRIGHT
|
|
|
237 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
238
|
|
|
239 This file is part of MayaChemTools.
|
|
|
240
|
|
|
241 MayaChemTools is free software; you can redistribute it and/or modify it
|
|
|
242 under the terms of the GNU Lesser General Public License as published by
|
|
|
243 the Free Software Foundation; either version 3 of the License, or (at
|
|
|
244 your option) any later version.
|
|
|
245
|
