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