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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/scripts/html/ExtractFromTextFiles.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,214 @@ +<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>