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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/scripts/html/InfoNucleicAcids.html Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,224 @@ +<html> +<head> +<title>MayaChemTools:Documentation:InfoNucleicAcids.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="./InfoFingerprintsFiles.html" title="InfoFingerprintsFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./InfoPDBFiles.html" title="InfoPDBFiles.html">Next</a></td><td width="34%" align="middle"><strong>InfoNucleicAcids.pl</strong></td><td width="33%" align="right"><a href="././code/InfoNucleicAcids.html" title="View source code">Code</a> | <a href="./../pdf/InfoNucleicAcids.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/InfoNucleicAcids.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/InfoNucleicAcids.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/InfoNucleicAcids.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> +</table> +</div> +<p> +</p> +<h2>NAME</h2> +<p>InfoNucleicAcids.pl - List properties of nucleic acids</p> +<p> +</p> +<h2>SYNOPSIS</h2> +<p>InfoNucleicAcids.pl NucleicAcidIDs...</p> +<p>InfoNucleicAcids.pl [<strong>-h, --help</strong>] [<strong>-m, --mode</strong> NucleicAcidID | NucleicAcidType] +[<strong>--OutDelim</strong> comma | tab | semicolon] +[<strong>--output</strong> STDOUT | File] [<strong>--OutputStyle</strong> NucleicAcidBlock | NucleicAcidRows] +[<strong>-o, --overwrite</strong>] [<strong>--precision</strong> number] [<strong>--PropertiesMode</strong> Categories | Names | All] +[<strong>-p, --properties</strong> CategoryName, [CategoryName,...] | PropertyName, [PropertyName,...]] +[<strong>--PropertiesListing</strong> ByGroup | Alphabetical] [<strong>-q, --quote</strong> yes | no] [<strong>-r, --root</strong> rootname] +[<strong>-w, --WorkingDir</strong> dirname] NucleicAcidIDs...</p> +<p> +</p> +<h2>DESCRIPTION</h2> +<p>List nucleic acid properties. Nucleic acids identification supports two types of IDs: code +or name. Nucleic acid properties data, in addition to basic information about nucleic acids - code, +name, type, chemical formula and molecular weight - include information about exact mass and +elemental composition.</p> +<p> +</p> +<h2>PARAMETERS</h2> +<dl> +<dt><strong><strong>NucleicAcidIDs</strong> <em>Code [NucleicAcidName...] | NucleicAcidType [NucleicAcidType...]</em></strong></dt> +<dd> +<p><em>NucleicAcidIDs</em> is a space delimited list of values to identify nucleic acids.</p> +<p>For <em>NucleicAcidID</em> mode, input value format is: <em>Code [NucleicAcidName...]</em>. Default: <em>A</em>. +Examples:</p> +<div class="OptionsBox"> + A +<br/> dG AMP +<br/> Cytidine T UDP dpppA "5'-dATP"</div> +<p>For <em>NucleicAcidType</em> mode, input value format is: <em>NucleicAcidType [NucleicAcidType...]</em>. +Default: <em>A</em>. Possible values are: <em>Nucleobase, Nucleoside, Deoxynucleoside, Nucleotide, +Deoxynucleotide</em>. Default: <em>Nucleoside</em>. +Examples:</p> +<div class="OptionsBox"> + Deoxynucleoside +<br/> Nucleobase Nucleotide</div> +</dd> +</dl> +<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>-m, --mode</strong> <em>NucleicAcidID | NucleicAcidType</em></strong></dt> +<dd> +<p>Specify nucleic acids for listing properties using one of these methods: nucleic acid +code and/or names or nucleic acid type.</p> +<p>Possible values: <em>NucleicAcidID or NucleicAcidType</em>. Default: <em>NucleicAcidID</em></p> +<p>For <em>NucleicAcidType</em>, command line parameters support these type: <em>Nucleobase, +Nucleoside, Deoxynucleoside, Nucleotide, Deoxynucleotide</em>.</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>--output</strong> <em>STDOUT | File</em></strong></dt> +<dd> +<p>List information at STDOUT or write it to a file. Possible values: <em>STDOUT or File</em>. Default: +<em>STDOUT</em>. <strong>-r, --root</strong> option is used to generate output file name.</p> +</dd> +<dt><strong><strong>--OutputStyle</strong> <em>NucleicAcidBlock | NucleicAcidRows</em></strong></dt> +<dd> +<p>Specify how to list nucleic acid information: add a new line for each property and present it as a block +for each nucleic acid; or include all properties in one line and show it as a single line.</p> +<p>Possible values: <em>NucleicAcidBlock | NucleicAcidRows</em>. Default: <em>NucleicAcidBlock</em></p> +<p>An example for <em>NucleicAcidBlock</em> output style:</p> +<div class="OptionsBox"> + Code: Ado +<br/> OtherCodes: A +<br/> Name: Adenosine +<br/> Type: Nucleoside +<br/> MolecularFormula: C10H13O4N5 +<br/> MolecularWeight: 267.2413 +<br/> ... ...</div> +<p>An example for <em>NucleicAcidRows</em> output style:</p> +<div class="OptionsBox"> + Code,OtherCodes,Name,Type,MolecularFormula,MolecularWeight</div> +</dd> +<dt><strong><strong>-o, --overwrite</strong></strong></dt> +<dd> +<p>Overwrite existing files.</p> +</dd> +<dt><strong><strong>--precision</strong> <em>number</em></strong></dt> +<dd> +<p>Precision for listing numerical values. Default: up to <em>4</em> decimal places. +Valid values: positive integers.</p> +</dd> +<dt><strong><strong>--PropertiesMode</strong> <em>Categories | Names | All</em></strong></dt> +<dd> +<p>Specify how property names are specified: use category names; explicit list of property names; or +use all available properties. Possible values: <em>Categories, Names, or All</em>. Default: <em>Categories</em>.</p> +<p>This option is used in conjunction with <strong>-p, --properties</strong> option to specify properties of +interest.</p> +</dd> +<dt><strong><strong>-p, --properties</strong> <em>CategoryName,[CategoryName,...] | PropertyName,[PropertyName,...]</em></strong></dt> +<dd> +<p>This option is <strong>--propertiesmode</strong> specific. In general, it's a list of comma separated category or +property names.</p> +<p>Specify which nucleic acid properties information to list for the nucleic acid IDs specified using +command line parameters: list basic information; list all available information; or specify a comma +separated list of nucleic acid property names.</p> +<p>Possible values: <em>Basic | BasicPlus | PropertyName,[PropertyName,...]</em>. +Default: <em>Basic</em>.</p> +<p><em>Basic</em> includes: <em>Code, OtherCodes, Name, Type, MolecularFormula, MolecularWeight</em></p> +<p><em>BasicPlus</em> includes: <em>Code, OtherCodes, Name, Type, MolecularFormula, MolecularWeight, ExactMass, +ElementalComposition</em></p> +<p>Here is a complete list of available properties: <em>Code, OtherCodes, BasePair, Name, Type, MolecularFormula, +MolecularFormulaAtpH7.5, MolecularWeight, ExactMass, ElementalComposition</em>.</p> +</dd> +<dt><strong><strong>--PropertiesListing</strong> <em>ByGroup | Alphabetical</em></strong></dt> +<dd> +<p>Specify how to list properties for nucleic acids: group by category or an alphabetical by +property names. Possible values: <em>ByGroup or Alphabetical</em>. Default: <em>ByGroup</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 text file name is generated using the root: <Root>.<Ext>. File name is only +used during <em>File</em> value of <strong>-o, --output</strong> option.</p> +<p>Default file name: NucleicAcidInfo<mode>.<Ext>. The csv, and tsv +<Ext> values are used for comma/semicolon, and tab delimited text files respectively.</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 list basic properties information for nucleoside A, type:</p> +<div class="ExampleBox"> + % InfoNucleicAcids.pl</div> +<p>To list all available properties information for nucleoside A, type:</p> +<div class="ExampleBox"> + % InfoNucleicAcids.pl --propertiesmode all A</div> +<p>To list all available information for all available nucleic acids, type:</p> +<div class="ExampleBox"> + % InfoNucleicAcids.pl --propertiesmode All All</div> +<p>To list basic properties information for all nucleobases, type:</p> +<div class="ExampleBox"> + % InfoNucleicAcids.pl -m NucleicAcidType Nucleoside</div> +<p>To list basic properties information for all nucleotides and deoxynulceotides, type:</p> +<div class="ExampleBox"> + % InfoNucleicAcids.pl -m NucleicAcidType Nucleotide Deoxynucleotide</div> +<p>To list basic properties information for variety of nucleic acids, type:</p> +<div class="ExampleBox"> + % InfoNucleicAcids.pl A dG AMP Cytidine T UDP "5'-dATP"</div> +<p>To list code and molecular weights for nucleosides A, G, C and T, type:</p> +<div class="ExampleBox"> + % InfoNucleicAcids.pl --PropertiesMode Names --properties + Code,MolecularWeight A G C T</div> +<p>To alphabetically list all the available properties for nucleotides dAMP, dGMP, +dCMP, and dTMP in rows instead of nucleic acid blocks with quotes around the values, type:</p> +<div class="ExampleBox"> + % InfoNucleicAcids.pl --PropertiesMode All --PropertiesListing + Alphabetical --OutputStyle NucleicAcidRows -q yes dAMP dGMP + dCMP dTMP</div> +<p>To alphabetically list all the available properties for all available nucleic acids to +a file names NucleicAcidsProperties.csv with quotes around the values, type</p> +<div class="ExampleBox"> + % InfoNucleicAcids.pl --PropertiesMode All --PropertiesListing + Alphabetical --output File --OutputStyle NucleicAcidRows -r + NucleicAcidsProperties -o -q Yes All</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="./InfoAminoAcids.html">InfoAminoAcids.pl</a>, <a href="./InfoPeriodicTableElements.html">InfoPeriodicTableElements.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="./InfoFingerprintsFiles.html" title="InfoFingerprintsFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./InfoPDBFiles.html" title="InfoPDBFiles.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>InfoNucleicAcids.pl</strong></td></tr> +</table> +</div> +<br /> +<center> +<img src="../../images/h2o2.png"> +</center> +</body> +</html>