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<html> <head> <title>MayaChemTools:Documentation:ElementalAnalysisTextFiles.pl</title> <meta http-equiv="content-type" content="text/html;charset=utf-8"> <link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css"> </head> <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> <br/> <center> <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> </center> <br/> <div class="DocNav"> <table width="100%" border=0 cellpadding=0 cellspacing=2> <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> </table> </div> <p> </p> <h2>NAME</h2> <p>ElementalAnalysisTextFiles.pl - Perform elemental analysis using formula column in TextFile(s)</p> <p> </p> <h2>SYNOPSIS</h2> <p>ElementalAnalysisTextFiles.pl TextFile(s)...</p> <p>ElementalAnalysisTextFiles.pl [<strong>-c, --colmode</strong> colnum | collabel] [<strong>-d, --detail</strong> infolevel] [<strong>-f, --fast</strong>] [<strong>-f, --formulacol</strong> colnum | collabel] [<strong>-h, --help</strong>] [<strong>--indelim</strong> comma | semicolon] [<strong>-m, --mode</strong> All | "ElementalAnysis, [MolecularWeight, ExactMass]"] [<strong>-o, --overwrite</strong>] [<strong>--outdelim</strong> comma | tab | semicolon] [<strong>-p, --precision</strong> number] [<strong>-q, --quote</strong> yes | no] [<strong>-r, --root</strong> rootname] [<strong>-s, --startcol</strong> colnum | collabel] [<strong>--startcolmode</strong> before | after] <strong>-v --valuecollabels</strong> [Name, Label, [Name, Label,...]] [<strong>-w, --workingdir</strong> dirname] TextFile(s)...</p> <p> </p> <h2>DESCRIPTION</h2> <p>Perform elemental analysis using molecular formula column specified by a column number or label in <em>TextFile(s)</em>.</p> <p>In addition to straightforward molecular formulas - H2O, HCl, C3H7O2N - other supported variations are: Ca3(PO4)2, [PCl4]+, [Fe(CN)6]4-, C37H42N2O6+2, Na2CO3.10H2O, 8H2S.46H2O, and so on. Charges are simply ignored. Isotope symbols in formulas specification, including D and T, are not supported.</p> <p>The valid file extensions are <em>.csv</em> and <em>.tsv</em> for comma/semicolon and tab delimited text files respectively. All other file names are ignored. All the text files in a current directory can be specified by <em>*.csv</em>, <em>*.tsv</em>, or the current directory name. The <strong>--indelim</strong> option determines the format of <em>TextFile(s)</em>. Any file which doesn't correspond to the format indicated by <strong>--indelim</strong> option is ignored.</p> <p> </p> <h2>OPTIONS</h2> <dl> <dt><strong><strong>-c, --colmode</strong> <em>colnum | collabel</em></strong></dt> <dd> <p>Specify how columns are identified in <em>TextFile(s)</em>: using column number or column label. Possible values: <em>colnum or collabel</em>. Default value: <em>colnum</em>.</p> </dd> <dt><strong><strong>-d, --detail</strong> <em>infolevel</em></strong></dt> <dd> <p>Level of information to print about lines being ignored. Default: <em>1</em>. Possible values: <em>1, 2 or 3</em>.</p> </dd> <dt><strong><strong>-h, --help</strong></strong></dt> <dd> <p>Print this help message.</p> </dd> <dt><strong><strong>--fast</strong></strong></dt> <dd> <p>In this mode, the formula column specified using <strong>-f, --formulacol</strong> option is assumed to contain valid molecular formula data and initial formula validation check is skipped.</p> </dd> <dt><strong><strong>-f, --formulacol</strong> <em>col number | col name</em></strong></dt> <dd> <p>This value is mode specific. It specifies molecular formula column to use for performing elemental analysis on <em>TextFile(s)</em>. Possible values: <em>col number or col label</em>. Default value: <em>first column containing the word formula in its column label</em>.</p> </dd> <dt><strong><strong>-m, --mode</strong> <em>All | "ElementalAnalysis,[MolecularWeight,ExactMass]"</em></strong></dt> <dd> <p>Specify what values to calculate using molecular formula in <em>TextFile(s)</em>: calculate all supported values or specify a comma delimited list of values. Possible values: <em>All | "ElementalAnalysis, [MolecularWeight, ExactMass]"</em>. Default: <em>All</em></p> </dd> <dt><strong><strong>--indelim</strong> <em>comma | semicolon</em></strong></dt> <dd> <p>Input delimiter for CSV <em>TextFile(s)</em>. Possible values: <em>comma or semicolon</em>. Default value: <em>comma</em>. For TSV files, this option is ignored and <em>tab</em> is used as a delimiter.</p> </dd> <dt><strong><strong>-o, --overwrite</strong></strong></dt> <dd> <p>Overwrite existing files.</p> </dd> <dt><strong><strong>--outdelim</strong> <em>comma | tab | semicolon</em></strong></dt> <dd> <p>Output text file delimiter. Possible values: <em>comma, tab, or semicolon</em> Default value: <em>comma</em>.</p> </dd> <dt><strong><strong>-p, --precision</strong> <em>number</em></strong></dt> <dd> <p>Precision of calculated values in the output file. Default: up to <em>2</em> decimal places. Valid values: positive integers.</p> </dd> <dt><strong><strong>-q, --quote</strong> <em>yes | no</em></strong></dt> <dd> <p>Put quotes around column values in output text file. Possible values: <em>yes or no</em>. Default value: <em>yes</em>.</p> </dd> <dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt> <dd> <p>New text file name is generated using the root: <Root>.<Ext>. Default new file name: <InitialTextFileName>ElementalAnalysis.<Ext>. The csv, and tsv <Ext> values are used for comma/semicolon, and tab delimited text files respectively. This option is ignored for multiple input files.</p> </dd> <dt><strong><strong>-s, --startcol</strong> <em>colnum | collabel</em></strong></dt> <dd> <p>This value is mode specific. It specifies the column in text files which is used for start adding calculated column values. For <em>colnum</em> mode, specify column number and for <em>collabel</em> mode, specify column label.</p> <p>Default value: <em>last</em>. Start merge after the last column.</p> </dd> <dt><strong><strong>--startcolmode</strong> <em>before | after</em></strong></dt> <dd> <p>Start adding calculated column values after the <strong>-s, --startcol</strong> value. Possible values: <em>before or after</em>. Default value: <em>after</em>.</p> </dd> <dt><strong><strong>-v --valuecollabels</strong> <em>Name,Label,[Name,Label,...]</em></strong></dt> <dd> <p>Specify column labels to use for calculated values. In general, it's a comma delimited list of value name and column label pairs. Supported value names: <em>ElementalAnalysis, MolecularWeight, and ExactMass</em>. Default labels: <em>ElementalAnalysis, MolecularWeight, and ExactMass</em>.</p> </dd> <dt><strong><strong>-w, --workingdir</strong> <em>dirname</em></strong></dt> <dd> <p>Location of working directory. Default: current directory.</p> </dd> </dl> <p> </p> <h2>EXAMPLES</h2> <p>To perform elemental analysis, calculate molecular weight and exact mass using formulas in a column with the word Formula in its column label and generate a new CSV text file NewSample1.csv, type:</p> <div class="ExampleBox"> % ElementalAnalysisTextFiles.pl -o -r NewSample1 Sample1.csv</div> <p>To perform elemental analysis using formulas in column number two, use column label Analysis for calculated data, and generate a new CSV text file NewSample1.csv, type:</p> <div class="ExampleBox"> % ElementalAnalysisTextFiles.pl --m ElementalAnalysis --formulacol 2 --valuecollabels "ElementalAnalysis,Analysis" -o -r NewSample1 Sample1.csv</div> <p>To calculate molecular weight using formula in column label Formula with four decimal precision and generate a new CSV text file NewSample1.csv, type</p> <div class="ExampleBox"> % ElementalAnalysisTextFiles.pl --m MolecularWeight --colmode collabel --formulacol Formula --precision 4 -o -r NewSample1 Sample1.csv</div> <p>To calculate exact mass using formula in column label Formula with four decimal precision, adding column for exact mass right after Formula column, and generate a new CSV text file NewSample1.csv, type</p> <div class="ExampleBox"> % ElementalAnalysisTextFiles.pl --m ExactMass --colmode collabel --formulacol Formula --precision 4 --startcolmode after --startcol Formula -o -r NewSample1 Sample1.csv</div> <p> </p> <h2>AUTHOR</h2> <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p> <p> </p> <h2>SEE ALSO</h2> <p><a href="./AnalyzeTextFilesData.html">AnalyzeTextFilesData.pl</a>, <a href="./InfoTextFiles.html">InfoTextFiles.pl</a>, <a href="./ExtractFromTextFiles.html">ExtractFromTextFiles.pl</a> </p> <p> </p> <h2>COPYRIGHT</h2> <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p> <p>This file is part of MayaChemTools.</p> <p>MayaChemTools is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.</p> <p> </p><p> </p><div class="DocNav"> <table width="100%" border=0 cellpadding=0 cellspacing=2> <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> </table> </div> <br /> <center> <img src="../../images/h2o2.png"> </center> </body> </html>