Mercurial > repos > deepakjadmin > mayatool3_test3
view mayachemtools/docs/scripts/html/MergeTextFilesWithSD.html @ 2:dfff2614510e draft
Deleted selected files
| author | deepakjadmin |
|---|---|
| date | Wed, 20 Jan 2016 12:15:15 -0500 |
| parents | 73ae111cf86f |
| children |
line wrap: on
line source
<html> <head> <title>MayaChemTools:Documentation:MergeTextFilesWithSD.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="./MergeTextFiles.html" title="MergeTextFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./ModifyNewLineChar.html" title="ModifyNewLineChar.html">Next</a></td><td width="34%" align="middle"><strong>MergeTextFilesWithSD.pl</strong></td><td width="33%" align="right"><a href="././code/MergeTextFilesWithSD.html" title="View source code">Code</a> | <a href="./../pdf/MergeTextFilesWithSD.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/MergeTextFilesWithSD.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/MergeTextFilesWithSD.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/MergeTextFilesWithSD.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> </table> </div> <p> </p> <h2>NAME</h2> <p>MergeTextFilesWithSD.pl - Merge CSV or TSV TextFile(s) into SDFile</p> <p> </p> <h2>SYNOPSIS</h2> <p>MergeTextFilesWithSD.pl SDFile TextFile(s)...</p> <p>MergeTextFilesWithSD.pl [<strong>-h, --help</strong>] [<strong>--indelim</strong> comma | semicolon] [<strong>-c, --columns</strong> colnum,...;... | collabel,...;...] [<strong>-k, --keys</strong> colkeynum;... | colkeylabel;...] [<strong>-m, --mode</strong> colnum | collabel] [<strong>-o, --overwrite</strong>] [<strong>-r, --root</strong> rootname] [<strong>-s, --sdkey</strong> sdfieldname] [<strong>-w, --workingdir</strong> dirname] SDFile TextFile(s)...</p> <p> </p> <h2>DESCRIPTION</h2> <p>Merge multiple CSV or TSV <em>TextFile(s)</em> into <em>SDFile</em>. Unless <strong>-k --keys</strong> option is used, data rows from all <em>TextFile(s)</em> are added to <em>SDFile</em> in a sequential order, and the number of compounds in <em>SDFile</em> is used to determine how many rows of data are added from <em>TextFile(s)</em>.</p> <p>Multiple <em>TextFile(s)</em> names are separated by spaces. 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>-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>-c, --columns</strong> <em>colnum,...;... | collabel,...;...</em></strong></dt> <dd> <p>This value is mode specific. It is a list of columns to merge into <em>SDFile</em> specified by column numbers or labels for each text file delimited by ";". All <em>TextFile(s)</em> are merged into <em>SDFile</em>.</p> <p>Default value: <em>all;all;...</em>. By default, all columns from TextFile(s) are merged into <em>SDFile</em>.</p> <p>For <em>colnum</em> mode, input value format is: <em>colnum,...;colnum,...;...</em>. Example:</p> <div class="OptionsBox"> "1,2;1,3,4;7,8,9"</div> <p>For <em>collabel</em> mode, input value format is: <em>collabel,...;collabel,...;...</em>. Example:</p> <div class="OptionsBox"> "MW,SumNO;SumNHOH,ClogP,PSA;MolName,Mol_Id,Extreg"</div> </dd> <dt><strong><strong>-k, --keys</strong> <em>colkeynum;... | colkeylabel;...</em></strong></dt> <dd> <p>This value is mode specific. It specifies column keys to use for merging <em>TextFile(s)</em> into <em>SDFile</em>. The column keys, delimited by ";", are specified by column numbers or labels for <em>TextFile(s)</em>.</p> <p>By default, data rows from <em>TextFile(s)</em> are merged into <em>SDFile</em> in the order they appear.</p> <p>For <em>colnum</em> mode, input value format is:<em>colkeynum, colkeynum;...</em>. Example:</p> <div class="OptionsBox"> "1;3;7"</div> <p>For <em>collabel</em> mode, input value format is:<em>colkeylabel, colkeylabel;...</em>. Example:</p> <div class="OptionsBox"> "Mol_Id;Mol_Id;Cmpd_Id"</div> </dd> <dt><strong><strong>-m, --mode</strong> <em>colnum | collabel</em></strong></dt> <dd> <p>Specify how to merge <em>TextFile(s)</em> into <em>SDFile</em>: using column numbers or column labels. Possible values: <em>colnum or collabel</em>. Default value: <em>colnum</em>.</p> </dd> <dt><strong><strong>-o, --overwrite</strong></strong></dt> <dd> <p>Overwrite existing files.</p> </dd> <dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt> <dd> <p>New SD file name is generated using the root: <Root>.sdf. Default file name: <InitialSDFileName>MergedWith<FirstTextFileName>1To<Count>.sdf.</p> </dd> <dt><strong><strong>-s, --sdkey</strong> <em>sdfieldname</em></strong></dt> <dd> <p><em>SDFile</em> data field name used as a key to merge data from TextFile(s). By default, data rows from <em>TextFile(s)</em> are merged into <em>SDFile</em> in the order they appear.</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 merge Sample1.csv and Sample2.csv into Sample.sdf and generate NewSample.sdf, type:</p> <div class="ExampleBox"> % MergeTextFileswithSD.pl -r NewSample -o Sample.sdf Sample1.csv Sample2.csv</div> <p>To merge all Sample*.tsv into Sample.sdf and generate NewSample.sdf file, type:</p> <div class="ExampleBox"> % MergeTextFilesWithSD.pl -r NewSample -o Sample.sdf Sample*.tsv</div> <p>To merge column numbers "1,2" and "3,4,5" from Sample2.csv and Sample3.csv into Sample.sdf and to generate NewSample.sdf, type:</p> <div class="ExampleBox"> % MergeTextFilesWithSD.pl -r NewSample -m colnum -c "1,2;3,4,5" -o Sample.sdf Sample1.csv Sample2.csv</div> <p>To merge column "Mol_ID,Formula,MolWeight" and "Mol_ID,ChemBankID,NAME" from Sample1.csv and Sample2.csv into Sample.sdf using "Mol_ID" as SD and column keys to generate NewSample.sdf, type:</p> <div class="ExampleBox"> % MergeTextFilesWithSD.pl -r NewSample -s Mol_ID -k "Mol_ID;Mol_ID" -m collabel -c "Mol_ID,Formula,MolWeight;Mol_ID,ChemBankID,NAME" -o Sample1.sdf Sample1.csv Sample2.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="./ExtractFromSDFiles.html">ExtractFromSDFiles.pl</a>, <a href="./FilterSDFiles.html">FilterSDFiles.pl</a>, <a href="./InfoSDFiles.html">InfoSDFiles.pl</a>, <a href="./JoinSDFiles.html">JoinSDFiles.pl</a>, <a href="./JoinTextFiles.html">JoinTextFiles.pl</a>,  <a href="./MergeTextFiles.html">MergeTextFiles.pl</a>, <a href="./ModifyTextFilesFormat.html">ModifyTextFilesFormat.pl</a>, <a href="./SplitSDFiles.html">SplitSDFiles.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="./MergeTextFiles.html" title="MergeTextFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./ModifyNewLineChar.html" title="ModifyNewLineChar.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>MergeTextFilesWithSD.pl</strong></td></tr> </table> </div> <br /> <center> <img src="../../images/h2o2.png"> </center> </body> </html>