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3 <title>MayaChemTools:Documentation:ElementalAnalysisTextFiles.pl</title>
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14 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./ElementalAnalysisSDFiles.html" title="ElementalAnalysisSDFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./EStateIndiciesFingerprints.html" title="EStateIndiciesFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>ElementalAnalysisTextFiles.pl</strong></td><td width="33%" align="right"><a href="././code/ElementalAnalysisTextFiles.html" title="View source code">Code</a> | <a href="./../pdf/ElementalAnalysisTextFiles.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/ElementalAnalysisTextFiles.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/ElementalAnalysisTextFiles.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/ElementalAnalysisTextFiles.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
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16 </table>
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17 </div>
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18 <p>
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19 </p>
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20 <h2>NAME</h2>
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21 <p>ElementalAnalysisTextFiles.pl - Perform elemental analysis using formula column in TextFile(s)</p>
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22 <p>
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23 </p>
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24 <h2>SYNOPSIS</h2>
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25 <p>ElementalAnalysisTextFiles.pl TextFile(s)...</p>
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26 <p>ElementalAnalysisTextFiles.pl [<strong>-c, --colmode</strong> colnum | collabel] [<strong>-d, --detail</strong> infolevel] [<strong>-f, --fast</strong>]
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27 [<strong>-f, --formulacol</strong> colnum | collabel] [<strong>-h, --help</strong>] [<strong>--indelim</strong> comma | semicolon]
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28 [<strong>-m, --mode</strong> All | "ElementalAnysis, [MolecularWeight, ExactMass]"] [<strong>-o, --overwrite</strong>]
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29 [<strong>--outdelim</strong> comma | tab | semicolon] [<strong>-p, --precision</strong> number] [<strong>-q, --quote</strong> yes | no]
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30 [<strong>-r, --root</strong> rootname] [<strong>-s, --startcol</strong> colnum | collabel] [<strong>--startcolmode</strong> before | after]
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31 <strong>-v --valuecollabels</strong> [Name, Label, [Name, Label,...]] [<strong>-w, --workingdir</strong> dirname] TextFile(s)...</p>
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32 <p>
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33 </p>
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34 <h2>DESCRIPTION</h2>
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35 <p>Perform elemental analysis using molecular formula column specified by a column number or label in
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36 <em>TextFile(s)</em>.</p>
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37 <p>In addition to straightforward molecular formulas - H2O, HCl, C3H7O2N -
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38 other supported variations are: Ca3(PO4)2, [PCl4]+, [Fe(CN)6]4-, C37H42N2O6+2, Na2CO3.10H2O,
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39 8H2S.46H2O, and so on. Charges are simply ignored. Isotope symbols in formulas specification, including
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40 D and T, are not supported.</p>
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41 <p>The valid file extensions are <em>.csv</em> and <em>.tsv</em> for comma/semicolon and tab delimited
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42 text files respectively. All other file names are ignored. All the text files in a
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43 current directory can be specified by <em>*.csv</em>, <em>*.tsv</em>, or the current directory
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44 name. The <strong>--indelim</strong> option determines the format of <em>TextFile(s)</em>. Any file
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45 which doesn't correspond to the format indicated by <strong>--indelim</strong> option is ignored.</p>
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46 <p>
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47 </p>
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48 <h2>OPTIONS</h2>
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49 <dl>
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50 <dt><strong><strong>-c, --colmode</strong> <em>colnum | collabel</em></strong></dt>
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51 <dd>
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52 <p>Specify how columns are identified in <em>TextFile(s)</em>: using column number or column
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53 label. Possible values: <em>colnum or collabel</em>. Default value: <em>colnum</em>.</p>
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54 </dd>
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55 <dt><strong><strong>-d, --detail</strong> <em>infolevel</em></strong></dt>
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56 <dd>
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57 <p>Level of information to print about lines being ignored. Default: <em>1</em>. Possible values:
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58 <em>1, 2 or 3</em>.</p>
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59 </dd>
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60 <dt><strong><strong>-h, --help</strong></strong></dt>
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61 <dd>
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62 <p>Print this help message.</p>
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63 </dd>
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64 <dt><strong><strong>--fast</strong></strong></dt>
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65 <dd>
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66 <p>In this mode, the formula column specified using <strong>-f, --formulacol</strong> option is assumed
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67 to contain valid molecular formula data and initial formula validation check is skipped.</p>
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68 </dd>
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69 <dt><strong><strong>-f, --formulacol</strong> <em>col number | col name</em></strong></dt>
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70 <dd>
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71 <p>This value is mode specific. It specifies molecular formula column to use for performing
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72 elemental analysis on <em>TextFile(s)</em>. Possible values: <em>col number or col label</em>.
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73 Default value: <em>first column containing the word formula in its column label</em>.</p>
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74 </dd>
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75 <dt><strong><strong>-m, --mode</strong> <em>All | "ElementalAnalysis,[MolecularWeight,ExactMass]"</em></strong></dt>
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76 <dd>
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77 <p>Specify what values to calculate using molecular formula in <em>TextFile(s)</em>: calculate all supported
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78 values or specify a comma delimited list of values. Possible values: <em>All | "ElementalAnalysis,
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79 [MolecularWeight, ExactMass]"</em>. Default: <em>All</em></p>
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80 </dd>
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81 <dt><strong><strong>--indelim</strong> <em>comma | semicolon</em></strong></dt>
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82 <dd>
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83 <p>Input delimiter for CSV <em>TextFile(s)</em>. Possible values: <em>comma or semicolon</em>.
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84 Default value: <em>comma</em>. For TSV files, this option is ignored and <em>tab</em> is used as a
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85 delimiter.</p>
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86 </dd>
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87 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
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88 <dd>
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89 <p>Overwrite existing files.</p>
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90 </dd>
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91 <dt><strong><strong>--outdelim</strong> <em>comma | tab | semicolon</em></strong></dt>
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92 <dd>
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93 <p>Output text file delimiter. Possible values: <em>comma, tab, or semicolon</em>
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94 Default value: <em>comma</em>.</p>
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95 </dd>
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96 <dt><strong><strong>-p, --precision</strong> <em>number</em></strong></dt>
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97 <dd>
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98 <p>Precision of calculated values in the output file. Default: up to <em>2</em> decimal places.
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99 Valid values: positive integers.</p>
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100 </dd>
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101 <dt><strong><strong>-q, --quote</strong> <em>yes | no</em></strong></dt>
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102 <dd>
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103 <p>Put quotes around column values in output text file. Possible values: <em>yes or
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104 no</em>. Default value: <em>yes</em>.</p>
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105 </dd>
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106 <dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt>
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107 <dd>
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108 <p>New text file name is generated using the root: <Root>.<Ext>. Default new file
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109 name: <InitialTextFileName>ElementalAnalysis.<Ext>. The csv, and tsv
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110 <Ext> values are used for comma/semicolon, and tab delimited text files
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111 respectively. This option is ignored for multiple input files.</p>
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112 </dd>
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113 <dt><strong><strong>-s, --startcol</strong> <em>colnum | collabel</em></strong></dt>
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114 <dd>
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115 <p>This value is mode specific. It specifies the column in text files which is
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116 used for start adding calculated column values. For <em>colnum</em> mode, specify
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117 column number and for <em>collabel</em> mode, specify column label.</p>
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118 <p>Default value: <em>last</em>. Start merge after the last column.</p>
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119 </dd>
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120 <dt><strong><strong>--startcolmode</strong> <em>before | after</em></strong></dt>
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121 <dd>
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122 <p>Start adding calculated column values after the <strong>-s, --startcol</strong> value. Possible values: <em>before or after</em>.
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123 Default value: <em>after</em>.</p>
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124 </dd>
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125 <dt><strong><strong>-v --valuecollabels</strong> <em>Name,Label,[Name,Label,...]</em></strong></dt>
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126 <dd>
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127 <p>Specify column labels to use for calculated values. In general, it's a comma delimited
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128 list of value name and column label pairs. Supported value names: <em>ElementalAnalysis,
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129 MolecularWeight, and ExactMass</em>. Default labels: <em>ElementalAnalysis, MolecularWeight,
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130 and ExactMass</em>.</p>
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131 </dd>
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132 <dt><strong><strong>-w, --workingdir</strong> <em>dirname</em></strong></dt>
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133 <dd>
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134 <p>Location of working directory. Default: current directory.</p>
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135 </dd>
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136 </dl>
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137 <p>
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138 </p>
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139 <h2>EXAMPLES</h2>
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140 <p>To perform elemental analysis, calculate molecular weight and exact mass using formulas
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141 in a column with the word Formula in its column label and generate a new CSV text
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142 file NewSample1.csv, type:</p>
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143 <div class="ExampleBox">
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144 % ElementalAnalysisTextFiles.pl -o -r NewSample1 Sample1.csv</div>
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145 <p>To perform elemental analysis using formulas in column number two, use column label
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146 Analysis for calculated data, and generate a new CSV text file NewSample1.csv, type:</p>
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147 <div class="ExampleBox">
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148 % ElementalAnalysisTextFiles.pl --m ElementalAnalysis --formulacol 2
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149 --valuecollabels "ElementalAnalysis,Analysis" -o -r NewSample1
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150 Sample1.csv</div>
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151 <p>To calculate molecular weight using formula in column label Formula with four decimal
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152 precision and generate a new CSV text file NewSample1.csv, type</p>
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153 <div class="ExampleBox">
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154 % ElementalAnalysisTextFiles.pl --m MolecularWeight --colmode collabel
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155 --formulacol Formula --precision 4 -o -r NewSample1 Sample1.csv</div>
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156 <p>To calculate exact mass using formula in column label Formula with four decimal
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157 precision, adding column for exact mass right after Formula column, and generate a
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158 new CSV text file NewSample1.csv, type</p>
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159 <div class="ExampleBox">
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160 % ElementalAnalysisTextFiles.pl --m ExactMass --colmode collabel
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161 --formulacol Formula --precision 4 --startcolmode after
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162 --startcol Formula -o -r NewSample1 Sample1.csv</div>
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163 <p>
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164 </p>
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165 <h2>AUTHOR</h2>
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166 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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167 <p>
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168 </p>
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169 <h2>SEE ALSO</h2>
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170 <p><a href="./AnalyzeTextFilesData.html">AnalyzeTextFilesData.pl</a>, <a href="./InfoTextFiles.html">InfoTextFiles.pl</a>, <a href="./ExtractFromTextFiles.html">ExtractFromTextFiles.pl</a>
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171 </p>
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172 <p>
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173 </p>
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174 <h2>COPYRIGHT</h2>
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175 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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176 <p>This file is part of MayaChemTools.</p>
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177 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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178 the terms of the GNU Lesser General Public License as published by the Free
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179 Software Foundation; either version 3 of the License, or (at your option)
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180 any later version.</p>
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181 <p> </p><p> </p><div class="DocNav">
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182 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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183 <tr align="left" valign="top"><td width="33%" align="left"><a href="./ElementalAnalysisSDFiles.html" title="ElementalAnalysisSDFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./EStateIndiciesFingerprints.html" title="EStateIndiciesFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>ElementalAnalysisTextFiles.pl</strong></td></tr>
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184 </table>
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185 </div>
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186 <br />
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187 <center>
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188 <img src="../../images/h2o2.png">
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189 </center>
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191 </html>
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