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