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1 NAME
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2 ElementalAnalysisTextFiles.pl - Perform elemental analysis using formula
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3 column in TextFile(s)
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4
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5 SYNOPSIS
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6 ElementalAnalysisTextFiles.pl TextFile(s)...
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7
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8 ElementalAnalysisTextFiles.pl [-c, --colmode colnum | collabel] [-d,
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9 --detail infolevel] [-f, --fast] [-f, --formulacol colnum | collabel]
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10 [-h, --help] [--indelim comma | semicolon] [-m, --mode All |
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11 "ElementalAnysis, [MolecularWeight, ExactMass]"] [-o, --overwrite]
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12 [--outdelim comma | tab | semicolon] [-p, --precision number] [-q,
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13 --quote yes | no] [-r, --root rootname] [-s, --startcol colnum |
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14 collabel] [--startcolmode before | after] -v --valuecollabels [Name,
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15 Label, [Name, Label,...]] [-w, --workingdir dirname] TextFile(s)...
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16
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17 DESCRIPTION
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18 Perform elemental analysis using molecular formula column specified by a
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19 column number or label in *TextFile(s)*.
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20
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21 In addition to straightforward molecular formulas - H2O, HCl, C3H7O2N -
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22 other supported variations are: Ca3(PO4)2, [PCl4]+, [Fe(CN)6]4-,
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23 C37H42N2O6+2, Na2CO3.10H2O, 8H2S.46H2O, and so on. Charges are simply
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24 ignored. Isotope symbols in formulas specification, including D and T,
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25 are not supported.
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26
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27 The valid file extensions are *.csv* and *.tsv* for comma/semicolon and
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28 tab delimited text files respectively. All other file names are ignored.
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29 All the text files in a current directory can be specified by **.csv*,
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30 **.tsv*, or the current directory name. The --indelim option determines
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31 the format of *TextFile(s)*. Any file which doesn't correspond to the
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32 format indicated by --indelim option is ignored.
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33
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34 OPTIONS
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35 -c, --colmode *colnum | collabel*
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36 Specify how columns are identified in *TextFile(s)*: using column
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37 number or column label. Possible values: *colnum or collabel*.
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38 Default value: *colnum*.
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39
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40 -d, --detail *infolevel*
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41 Level of information to print about lines being ignored. Default:
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42 *1*. Possible values: *1, 2 or 3*.
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43
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44 -h, --help
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45 Print this help message.
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46
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47 --fast
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48 In this mode, the formula column specified using -f, --formulacol
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49 option is assumed to contain valid molecular formula data and
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50 initial formula validation check is skipped.
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51
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52 -f, --formulacol *col number | col name*
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53 This value is mode specific. It specifies molecular formula column
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54 to use for performing elemental analysis on *TextFile(s)*. Possible
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55 values: *col number or col label*. Default value: *first column
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56 containing the word formula in its column label*.
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57
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58 -m, --mode *All | "ElementalAnalysis,[MolecularWeight,ExactMass]"*
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59 Specify what values to calculate using molecular formula in
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60 *TextFile(s)*: calculate all supported values or specify a comma
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61 delimited list of values. Possible values: *All |
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62 "ElementalAnalysis, [MolecularWeight, ExactMass]"*. Default: *All*
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63
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64 --indelim *comma | semicolon*
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65 Input delimiter for CSV *TextFile(s)*. Possible values: *comma or
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66 semicolon*. Default value: *comma*. For TSV files, this option is
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67 ignored and *tab* is used as a delimiter.
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68
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69 -o, --overwrite
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70 Overwrite existing files.
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71
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72 --outdelim *comma | tab | semicolon*
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73 Output text file delimiter. Possible values: *comma, tab, or
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74 semicolon* Default value: *comma*.
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75
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76 -p, --precision *number*
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77 Precision of calculated values in the output file. Default: up to
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78 *2* decimal places. Valid values: positive integers.
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79
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80 -q, --quote *yes | no*
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81 Put quotes around column values in output text file. Possible
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82 values: *yes or no*. Default value: *yes*.
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83
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84 -r, --root *rootname*
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85 New text file name is generated using the root: <Root>.<Ext>.
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86 Default new file name: <InitialTextFileName>ElementalAnalysis.<Ext>.
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87 The csv, and tsv <Ext> values are used for comma/semicolon, and tab
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88 delimited text files respectively. This option is ignored for
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89 multiple input files.
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90
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91 -s, --startcol *colnum | collabel*
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92 This value is mode specific. It specifies the column in text files
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93 which is used for start adding calculated column values. For
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94 *colnum* mode, specify column number and for *collabel* mode,
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95 specify column label.
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96
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97 Default value: *last*. Start merge after the last column.
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98
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99 --startcolmode *before | after*
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100 Start adding calculated column values after the -s, --startcol
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101 value. Possible values: *before or after*. Default value: *after*.
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102
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103 -v --valuecollabels *Name,Label,[Name,Label,...]*
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104 Specify column labels to use for calculated values. In general, it's
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105 a comma delimited list of value name and column label pairs.
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106 Supported value names: *ElementalAnalysis, MolecularWeight, and
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107 ExactMass*. Default labels: *ElementalAnalysis, MolecularWeight, and
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108 ExactMass*.
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109
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110 -w, --workingdir *dirname*
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111 Location of working directory. Default: current directory.
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112
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113 EXAMPLES
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114 To perform elemental analysis, calculate molecular weight and exact mass
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115 using formulas in a column with the word Formula in its column label and
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116 generate a new CSV text file NewSample1.csv, type:
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117
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118 % ElementalAnalysisTextFiles.pl -o -r NewSample1 Sample1.csv
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119
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120 To perform elemental analysis using formulas in column number two, use
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121 column label Analysis for calculated data, and generate a new CSV text
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122 file NewSample1.csv, type:
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123
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124 % ElementalAnalysisTextFiles.pl --m ElementalAnalysis --formulacol 2
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125 --valuecollabels "ElementalAnalysis,Analysis" -o -r NewSample1
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126 Sample1.csv
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127
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128 To calculate molecular weight using formula in column label Formula with
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129 four decimal precision and generate a new CSV text file NewSample1.csv,
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130 type
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131
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132 % ElementalAnalysisTextFiles.pl --m MolecularWeight --colmode collabel
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133 --formulacol Formula --precision 4 -o -r NewSample1 Sample1.csv
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134
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135 To calculate exact mass using formula in column label Formula with four
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136 decimal precision, adding column for exact mass right after Formula
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137 column, and generate a new CSV text file NewSample1.csv, type
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138
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139 % ElementalAnalysisTextFiles.pl --m ExactMass --colmode collabel
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140 --formulacol Formula --precision 4 --startcolmode after
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141 --startcol Formula -o -r NewSample1 Sample1.csv
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142
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143 AUTHOR
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144 Manish Sud <msud@san.rr.com>
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145
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146 SEE ALSO
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147 AnalyzeTextFilesData.pl, InfoTextFiles.pl, ExtractFromTextFiles.pl
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148
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149 COPYRIGHT
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150 Copyright (C) 2015 Manish Sud. All rights reserved.
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151
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152 This file is part of MayaChemTools.
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153
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154 MayaChemTools is free software; you can redistribute it and/or modify it
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155 under the terms of the GNU Lesser General Public License as published by
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156 the Free Software Foundation; either version 3 of the License, or (at
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157 your option) any later version.
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158
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