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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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| 1 <html> | |
| 2 <head> | |
| 3 <title>MayaChemTools:Documentation:InfoNucleicAcids.pl</title> | |
| 4 <meta http-equiv="content-type" content="text/html;charset=utf-8"> | |
| 5 <link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css"> | |
| 6 </head> | |
| 7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> | |
| 8 <br/> | |
| 9 <center> | |
| 10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> | |
| 11 </center> | |
| 12 <br/> | |
| 13 <div class="DocNav"> | |
| 14 <table width="100%" border=0 cellpadding=0 cellspacing=2> | |
| 15 <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> | |
| 16 </table> | |
| 17 </div> | |
| 18 <p> | |
| 19 </p> | |
| 20 <h2>NAME</h2> | |
| 21 <p>InfoNucleicAcids.pl - List properties of nucleic acids</p> | |
| 22 <p> | |
| 23 </p> | |
| 24 <h2>SYNOPSIS</h2> | |
| 25 <p>InfoNucleicAcids.pl NucleicAcidIDs...</p> | |
| 26 <p>InfoNucleicAcids.pl [<strong>-h, --help</strong>] [<strong>-m, --mode</strong> NucleicAcidID | NucleicAcidType] | |
| 27 [<strong>--OutDelim</strong> comma | tab | semicolon] | |
| 28 [<strong>--output</strong> STDOUT | File] [<strong>--OutputStyle</strong> NucleicAcidBlock | NucleicAcidRows] | |
| 29 [<strong>-o, --overwrite</strong>] [<strong>--precision</strong> number] [<strong>--PropertiesMode</strong> Categories | Names | All] | |
| 30 [<strong>-p, --properties</strong> CategoryName, [CategoryName,...] | PropertyName, [PropertyName,...]] | |
| 31 [<strong>--PropertiesListing</strong> ByGroup | Alphabetical] [<strong>-q, --quote</strong> yes | no] [<strong>-r, --root</strong> rootname] | |
| 32 [<strong>-w, --WorkingDir</strong> dirname] NucleicAcidIDs...</p> | |
| 33 <p> | |
| 34 </p> | |
| 35 <h2>DESCRIPTION</h2> | |
| 36 <p>List nucleic acid properties. Nucleic acids identification supports two types of IDs: code | |
| 37 or name. Nucleic acid properties data, in addition to basic information about nucleic acids - code, | |
| 38 name, type, chemical formula and molecular weight - include information about exact mass and | |
| 39 elemental composition.</p> | |
| 40 <p> | |
| 41 </p> | |
| 42 <h2>PARAMETERS</h2> | |
| 43 <dl> | |
| 44 <dt><strong><strong>NucleicAcidIDs</strong> <em>Code [NucleicAcidName...] | NucleicAcidType [NucleicAcidType...]</em></strong></dt> | |
| 45 <dd> | |
| 46 <p><em>NucleicAcidIDs</em> is a space delimited list of values to identify nucleic acids.</p> | |
| 47 <p>For <em>NucleicAcidID</em> mode, input value format is: <em>Code [NucleicAcidName...]</em>. Default: <em>A</em>. | |
| 48 Examples:</p> | |
| 49 <div class="OptionsBox"> | |
| 50 A | |
| 51 <br/> dG AMP | |
| 52 <br/> Cytidine T UDP dpppA "5'-dATP"</div> | |
| 53 <p>For <em>NucleicAcidType</em> mode, input value format is: <em>NucleicAcidType [NucleicAcidType...]</em>. | |
| 54 Default: <em>A</em>. Possible values are: <em>Nucleobase, Nucleoside, Deoxynucleoside, Nucleotide, | |
| 55 Deoxynucleotide</em>. Default: <em>Nucleoside</em>. | |
| 56 Examples:</p> | |
| 57 <div class="OptionsBox"> | |
| 58 Deoxynucleoside | |
| 59 <br/> Nucleobase Nucleotide</div> | |
| 60 </dd> | |
| 61 </dl> | |
| 62 <p> | |
| 63 </p> | |
| 64 <h2>OPTIONS</h2> | |
| 65 <dl> | |
| 66 <dt><strong><strong>-h, --help</strong></strong></dt> | |
| 67 <dd> | |
| 68 <p>Print this help message.</p> | |
| 69 </dd> | |
| 70 <dt><strong><strong>-m, --mode</strong> <em>NucleicAcidID | NucleicAcidType</em></strong></dt> | |
| 71 <dd> | |
| 72 <p>Specify nucleic acids for listing properties using one of these methods: nucleic acid | |
| 73 code and/or names or nucleic acid type.</p> | |
| 74 <p>Possible values: <em>NucleicAcidID or NucleicAcidType</em>. Default: <em>NucleicAcidID</em></p> | |
| 75 <p>For <em>NucleicAcidType</em>, command line parameters support these type: <em>Nucleobase, | |
| 76 Nucleoside, Deoxynucleoside, Nucleotide, Deoxynucleotide</em>.</p> | |
| 77 </dd> | |
| 78 <dt><strong><strong>--OutDelim</strong> <em>comma | tab | semicolon</em></strong></dt> | |
| 79 <dd> | |
| 80 <p>Output text file delimiter. Possible values: <em>comma, tab, or semicolon</em> | |
| 81 Default value: <em>comma</em>.</p> | |
| 82 </dd> | |
| 83 <dt><strong><strong>--output</strong> <em>STDOUT | File</em></strong></dt> | |
| 84 <dd> | |
| 85 <p>List information at STDOUT or write it to a file. Possible values: <em>STDOUT or File</em>. Default: | |
| 86 <em>STDOUT</em>. <strong>-r, --root</strong> option is used to generate output file name.</p> | |
| 87 </dd> | |
| 88 <dt><strong><strong>--OutputStyle</strong> <em>NucleicAcidBlock | NucleicAcidRows</em></strong></dt> | |
| 89 <dd> | |
| 90 <p>Specify how to list nucleic acid information: add a new line for each property and present it as a block | |
| 91 for each nucleic acid; or include all properties in one line and show it as a single line.</p> | |
| 92 <p>Possible values: <em>NucleicAcidBlock | NucleicAcidRows</em>. Default: <em>NucleicAcidBlock</em></p> | |
| 93 <p>An example for <em>NucleicAcidBlock</em> output style:</p> | |
| 94 <div class="OptionsBox"> | |
| 95 Code: Ado | |
| 96 <br/> OtherCodes: A | |
| 97 <br/> Name: Adenosine | |
| 98 <br/> Type: Nucleoside | |
| 99 <br/> MolecularFormula: C10H13O4N5 | |
| 100 <br/> MolecularWeight: 267.2413 | |
| 101 <br/> ... ...</div> | |
| 102 <p>An example for <em>NucleicAcidRows</em> output style:</p> | |
| 103 <div class="OptionsBox"> | |
| 104 Code,OtherCodes,Name,Type,MolecularFormula,MolecularWeight</div> | |
| 105 </dd> | |
| 106 <dt><strong><strong>-o, --overwrite</strong></strong></dt> | |
| 107 <dd> | |
| 108 <p>Overwrite existing files.</p> | |
| 109 </dd> | |
| 110 <dt><strong><strong>--precision</strong> <em>number</em></strong></dt> | |
| 111 <dd> | |
| 112 <p>Precision for listing numerical values. Default: up to <em>4</em> decimal places. | |
| 113 Valid values: positive integers.</p> | |
| 114 </dd> | |
| 115 <dt><strong><strong>--PropertiesMode</strong> <em>Categories | Names | All</em></strong></dt> | |
| 116 <dd> | |
| 117 <p>Specify how property names are specified: use category names; explicit list of property names; or | |
| 118 use all available properties. Possible values: <em>Categories, Names, or All</em>. Default: <em>Categories</em>.</p> | |
| 119 <p>This option is used in conjunction with <strong>-p, --properties</strong> option to specify properties of | |
| 120 interest.</p> | |
| 121 </dd> | |
| 122 <dt><strong><strong>-p, --properties</strong> <em>CategoryName,[CategoryName,...] | PropertyName,[PropertyName,...]</em></strong></dt> | |
| 123 <dd> | |
| 124 <p>This option is <strong>--propertiesmode</strong> specific. In general, it's a list of comma separated category or | |
| 125 property names.</p> | |
| 126 <p>Specify which nucleic acid properties information to list for the nucleic acid IDs specified using | |
| 127 command line parameters: list basic information; list all available information; or specify a comma | |
| 128 separated list of nucleic acid property names.</p> | |
| 129 <p>Possible values: <em>Basic | BasicPlus | PropertyName,[PropertyName,...]</em>. | |
| 130 Default: <em>Basic</em>.</p> | |
| 131 <p><em>Basic</em> includes: <em>Code, OtherCodes, Name, Type, MolecularFormula, MolecularWeight</em></p> | |
| 132 <p><em>BasicPlus</em> includes: <em>Code, OtherCodes, Name, Type, MolecularFormula, MolecularWeight, ExactMass, | |
| 133 ElementalComposition</em></p> | |
| 134 <p>Here is a complete list of available properties: <em>Code, OtherCodes, BasePair, Name, Type, MolecularFormula, | |
| 135 MolecularFormulaAtpH7.5, MolecularWeight, ExactMass, ElementalComposition</em>.</p> | |
| 136 </dd> | |
| 137 <dt><strong><strong>--PropertiesListing</strong> <em>ByGroup | Alphabetical</em></strong></dt> | |
| 138 <dd> | |
| 139 <p>Specify how to list properties for nucleic acids: group by category or an alphabetical by | |
| 140 property names. Possible values: <em>ByGroup or Alphabetical</em>. Default: <em>ByGroup</em></p> | |
| 141 </dd> | |
| 142 <dt><strong><strong>-q, --quote</strong> <em>yes | no</em></strong></dt> | |
| 143 <dd> | |
| 144 <p>Put quotes around column values in output text file. Possible values: <em>yes or | |
| 145 no</em>. Default value: <em>yes</em>.</p> | |
| 146 </dd> | |
| 147 <dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt> | |
| 148 <dd> | |
| 149 <p>New text file name is generated using the root: <Root>.<Ext>. File name is only | |
| 150 used during <em>File</em> value of <strong>-o, --output</strong> option.</p> | |
| 151 <p>Default file name: NucleicAcidInfo<mode>.<Ext>. The csv, and tsv | |
| 152 <Ext> values are used for comma/semicolon, and tab delimited text files respectively.</p> | |
| 153 </dd> | |
| 154 <dt><strong><strong>-w, --WorkingDir</strong> <em>dirname</em></strong></dt> | |
| 155 <dd> | |
| 156 <p>Location of working directory. Default: current directory.</p> | |
| 157 </dd> | |
| 158 </dl> | |
| 159 <p> | |
| 160 </p> | |
| 161 <h2>EXAMPLES</h2> | |
| 162 <p>To list basic properties information for nucleoside A, type:</p> | |
| 163 <div class="ExampleBox"> | |
| 164 % InfoNucleicAcids.pl</div> | |
| 165 <p>To list all available properties information for nucleoside A, type:</p> | |
| 166 <div class="ExampleBox"> | |
| 167 % InfoNucleicAcids.pl --propertiesmode all A</div> | |
| 168 <p>To list all available information for all available nucleic acids, type:</p> | |
| 169 <div class="ExampleBox"> | |
| 170 % InfoNucleicAcids.pl --propertiesmode All All</div> | |
| 171 <p>To list basic properties information for all nucleobases, type:</p> | |
| 172 <div class="ExampleBox"> | |
| 173 % InfoNucleicAcids.pl -m NucleicAcidType Nucleoside</div> | |
| 174 <p>To list basic properties information for all nucleotides and deoxynulceotides, type:</p> | |
| 175 <div class="ExampleBox"> | |
| 176 % InfoNucleicAcids.pl -m NucleicAcidType Nucleotide Deoxynucleotide</div> | |
| 177 <p>To list basic properties information for variety of nucleic acids, type:</p> | |
| 178 <div class="ExampleBox"> | |
| 179 % InfoNucleicAcids.pl A dG AMP Cytidine T UDP "5'-dATP"</div> | |
| 180 <p>To list code and molecular weights for nucleosides A, G, C and T, type:</p> | |
| 181 <div class="ExampleBox"> | |
| 182 % InfoNucleicAcids.pl --PropertiesMode Names --properties | |
| 183 Code,MolecularWeight A G C T</div> | |
| 184 <p>To alphabetically list all the available properties for nucleotides dAMP, dGMP, | |
| 185 dCMP, and dTMP in rows instead of nucleic acid blocks with quotes around the values, type:</p> | |
| 186 <div class="ExampleBox"> | |
| 187 % InfoNucleicAcids.pl --PropertiesMode All --PropertiesListing | |
| 188 Alphabetical --OutputStyle NucleicAcidRows -q yes dAMP dGMP | |
| 189 dCMP dTMP</div> | |
| 190 <p>To alphabetically list all the available properties for all available nucleic acids to | |
| 191 a file names NucleicAcidsProperties.csv with quotes around the values, type</p> | |
| 192 <div class="ExampleBox"> | |
| 193 % InfoNucleicAcids.pl --PropertiesMode All --PropertiesListing | |
| 194 Alphabetical --output File --OutputStyle NucleicAcidRows -r | |
| 195 NucleicAcidsProperties -o -q Yes All</div> | |
| 196 <p> | |
| 197 </p> | |
| 198 <h2>AUTHOR</h2> | |
| 199 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p> | |
| 200 <p> | |
| 201 </p> | |
| 202 <h2>SEE ALSO</h2> | |
| 203 <p><a href="./InfoAminoAcids.html">InfoAminoAcids.pl</a>, <a href="./InfoPeriodicTableElements.html">InfoPeriodicTableElements.pl</a> | |
| 204 </p> | |
| 205 <p> | |
| 206 </p> | |
| 207 <h2>COPYRIGHT</h2> | |
| 208 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p> | |
| 209 <p>This file is part of MayaChemTools.</p> | |
| 210 <p>MayaChemTools is free software; you can redistribute it and/or modify it under | |
| 211 the terms of the GNU Lesser General Public License as published by the Free | |
| 212 Software Foundation; either version 3 of the License, or (at your option) | |
| 213 any later version.</p> | |
| 214 <p> </p><p> </p><div class="DocNav"> | |
| 215 <table width="100%" border=0 cellpadding=0 cellspacing=2> | |
| 216 <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> | |
| 217 </table> | |
| 218 </div> | |
| 219 <br /> | |
| 220 <center> | |
| 221 <img src="../../images/h2o2.png"> | |
| 222 </center> | |
| 223 </body> | |
| 224 </html> |