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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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<html> <head> <title>MayaChemTools:Documentation:ExtractFromTextFiles.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="./ExtractFromSequenceFiles.html" title="ExtractFromSequenceFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./FilterSDFiles.html" title="FilterSDFiles.html">Next</a></td><td width="34%" align="middle"><strong>ExtractFromTextFiles.pl</strong></td><td width="33%" align="right"><a href="././code/ExtractFromTextFiles.html" title="View source code">Code</a> | <a href="./../pdf/ExtractFromTextFiles.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/ExtractFromTextFiles.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/ExtractFromTextFiles.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/ExtractFromTextFiles.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> </table> </div> <p> </p> <h2>NAME</h2> <p>ExtractFromTextFiles.pl - Extract specific data from TextFile(s)</p> <p> </p> <h2>SYNOPSIS</h2> <p>ExtractFromTextFiles.pl TextFile(s)...</p> <p>ExtractFromTextFiles.pl [<strong>-c, --colmode</strong> colnum | collabel] [<strong>--categorycol </strong> number | string] [<strong>--columns</strong> "colnum,[colnum]..." | "collabel,[collabel]..."] [<strong>-h, --help</strong>] [<strong>--indelim</strong> <em>comma | semicolon</em>] [<strong>-m, --mode </strong> <em>columns | rows | categories</em>] [<strong>-o, --overwrite</strong>] [<strong>--outdelim</strong> <em>comma | tab | semicolon</em>] [<strong>-q, --quote</strong> <em>yes | no</em>] [<strong>--rows</strong> "colid,value,criteria..." | "colid,value..." | "colid,mincolvalue,maxcolvalue" | "rownum,rownum,..." | colid | "minrownum,maxrownum"] [ <strong>--rowsmode</strong> rowsbycolvalue | rowsbycolvaluelist | rowsbycolvaluerange | rowbymincolvalue | rowbymaxcolvalue | rownums | rownumrange] [<strong>-r, --root</strong> <em>rootname</em>] [<strong>-w, --workingdir</strong> <em>dirname</em>] TextFile(s)...</p> <p> </p> <h2>DESCRIPTION</h2> <p>Extract column(s)/row(s) data from <em>TextFile(s)</em> identified by column numbers or labels. Or categorize data using a specified column category. During categorization, a summary text file is generated containing category name and count; an additional text file, containing data for for each category, is also generated. The file names are separated by space. 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>--categorycol </strong> <em>number | string</em></strong></dt> <dd> <p>Column used to categorize data. Default value: First column.</p> <p>For <em>colnum</em> value of <strong>-c, --colmode</strong> option, input value is a column number. Example: <em>1</em>.</p> <p>For <em>collabel</em> value of <strong>-c, --colmode</strong> option, input value is a column label. Example: <em>Mol_ID</em>.</p> </dd> <dt><strong><strong>--columns</strong> <em>"colnum,[colnum]..." | "collabel,[collabel]..."</em></strong></dt> <dd> <p>List of comma delimited columns to extract. Default value: First column.</p> <p>For <em>colnum</em> value of <strong>-c, --colmode</strong> option, input values format is: <em>colnum,colnum,...</em>. Example: <em>1,3,5</em></p> <p>For <em>collabel</em> value of <strong>-c, --colmode</strong> option, input values format is: <em>collabel,collabel,..</em>. Example: <em>Mol_ID,MolWeight</em></p> </dd> <dt><strong><strong>-h, --help</strong></strong></dt> <dd> <p>Print this help message.</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>-m, --mode </strong> <em>columns | rows | categories</em></strong></dt> <dd> <p>Specify what to extract from <em>TextFile(s)</em>. Possible values: <em>columns, rows, or categories</em>. Default value: <em>columns</em>.</p> <p>For <em>columns</em> mode, data for appropriate columns specified by <strong>--columns</strong> option is extracted from <em>TextFile(s)</em> and placed into new text files.</p> <p>For <em>rows</em> mode, appropriate rows specified in conjuction with <strong>--rowsmode</strong> and <strong>rows</strong> options are extracted from <em>TextFile(s)</em> and placed into new text files.</p> <p>For <em>categories</em> mode, coulmn specified by <strong>--categorycol</strong> is used to categorize data, and a summary text file is generated containing category name and count; an additional text file, containing data for for each category, is also generated.</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>-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 file name is generated using the root: <Root>.<Ext>. Default for new file names: <TextFile>CategoriesSummary.<Ext>, <TextFile>ExtractedColumns.<Ext>, and <TextFile>ExtractedRows.<Ext> for <em>categories</em>, <em>columns</em>, and <em>rows</em> mode respectively. And <TextFile>Category<CategoryName>.<Ext> for each category retrieved from each text file. The output file type determines <Ext> value: csv and tsv for CSV, and TSV files respectively.</p> <p>This option is ignored for multiple input files.</p> </dd> <dt><strong><strong>--rows</strong> <em>"colid,value,criteria..." | "colid,value..." | "colid,mincolvalue,maxcolvalue" | "rownum,rownum,..." | colid | "minrownum,maxrownum"</em></strong></dt> <dd> <p>This value is <strong>--rowsmode</strong> specific. In general, it's a list of comma separated column ids and associated mode specific value. Based on Column ids specification, column label or number, is controlled by <strong>-c, --colmode</strong> option.</p> <p>First line containing column labels is always written out. And value comparisons assume numerical column data.</p> <p>For <em>rowsbycolvalue</em> mode, input value format contains these triplets: <em>colid,value, criteria...</em>. Possible values for criteria: <em>le, ge or eq</em>. Examples:</p> <div class="OptionsBox"> MolWt,450,le <br/> MolWt,450,le,LogP,5,le,SumNumNO,10,le,SumNHOH,5,le</div> <p>For <em>rowsbycolvaluelist</em> mode, input value format is: <em>colid,value...</em>. Examples:</p> <div class="OptionsBox"> Mol_ID,20 <br/> Mol_ID,20,1002,1115</div> <p>For <em>rowsbycolvaluerange</em> mode, input value format is: <em>colid,mincolvalue,maxcolvalue</em>. Examples:</p> <div class="OptionsBox"> MolWt,100,450</div> <p>For <em>rowbymincolvalue, rowbymaxcolvalue</em> modes, input value format is: <em>colid</em>.</p> <p>For <em>rownum</em> mode, input value format is: <em>rownum</em>. Default value: <em>2</em>.</p> <p>For <em>rownumrange</em> mode, input value format is: <em>minrownum, maxrownum</em>. Examples:</p> <div class="OptionsBox"> 10,40</div> </dd> <dt><strong><strong>--rowsmode</strong> <em>rowsbycolvalue | rowsbycolvaluelist | rowsbycolvaluerange | rowbymincolvalue | rowbymaxcolvalue | rownums | rownumrange</em></strong></dt> <dd> <p>Specify how to extract rows from <em>TextFile(s)</em>. Possible values: <em>rowsbycolvalue, rowsbycolvaluelist, rowsbycolvaluerange, rowbymincolvalue, rowbymaxcolvalue, rownum, rownumrange</em>. Default value: <em>rownum</em>.</p> <p>Use <strong>--rows</strong> option to list rows criterion used for extraction of rows from <em>TextFile(s)</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 extract first column from a text file and generate a new CSV text file NewSample1.csv, type:</p> <div class="ExampleBox"> % ExtractFromTextFiles.pl -r NewSample1 -o Sample1.csv</div> <p>To extract columns Mol_ID, MolWeight, and NAME from Sample1.csv and generate a new textfile NewSample1.tsv with no quotes, type:</p> <div class="ExampleBox"> % ExtractFromTextFiles.pl -m columns -c collabel --columns "Mol_ID, MolWeight,NAME" --outdelim tab --quote no -r NewSample1 -o Sample1.csv</div> <p>To extract rows containing values for MolWeight column of less than 450 from Sample1.csv and generate a new textfile NewSample1.csv, type:</p> <div class="ExampleBox"> % ExtractFromTextFiles.pl -m rows --rowsmode rowsbycolvalue -c collabel --rows MolWeight,450,le -r NewSample1 -o Sample1.csv</div> <p>To extract rows containing values for MolWeight column between 400 and 500 from Sample1.csv and generate a new textfile NewSample1.csv, type:</p> <div class="ExampleBox"> % ExtractFromTextFiles.pl -m rows --rowsmode rowsbycolvaluerange -c collabel --rows MolWeight,450,500 -r NewSample1 -o Sample1.csv</div> <p>To extract a row containing minimum value for column MolWeight from Sample1.csv and generate a new textfile NewSample1.csv, type:</p> <div class="ExampleBox"> % ExtractFromTextFiles.pl -m rows --rowsmode rowbymincolvalue -c collabel --rows MolWeight -r NewSample1 -o 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="./JoinTextFiles.html">JoinTextFiles.pl</a>, <a href="./MergeTextFilesWithSD.html">MergeTextFilesWithSD.pl</a>, <a href="./ModifyTextFilesFormat.html">ModifyTextFilesFormat.pl</a>, <a href="./SplitTextFiles.html">SplitTextFiles.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="./ExtractFromSequenceFiles.html" title="ExtractFromSequenceFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./FilterSDFiles.html" title="FilterSDFiles.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>ExtractFromTextFiles.pl</strong></td></tr> </table> </div> <br /> <center> <img src="../../images/h2o2.png"> </center> </body> </html>