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<html> <head> <title>MayaChemTools:Code:NucleicAcids.pm</title> <meta http-equiv="content-type" content="text/html;charset=utf-8"> <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.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/> <pre> <a name="package-NucleicAcids-"></a> 1 <span class="k">package </span><span class="i">NucleicAcids</span><span class="sc">;</span> 2 <span class="c">#</span> 3 <span class="c"># $RCSfile: NucleicAcids.pm,v $</span> 4 <span class="c"># $Date: 2015/02/28 20:47:18 $</span> 5 <span class="c"># $Revision: 1.25 $</span> 6 <span class="c">#</span> 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> 8 <span class="c">#</span> 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> 10 <span class="c">#</span> 11 <span class="c"># This file is part of MayaChemTools.</span> 12 <span class="c">#</span> 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> 16 <span class="c"># later version.</span> 17 <span class="c">#</span> 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> 21 <span class="c"># details.</span> 22 <span class="c">#</span> 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> 27 <span class="c">#</span> 28 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span> 31 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span> 32 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span> 33 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span> 34 35 <span class="k">use</span> <span class="w">vars</span> <span class="q">qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS)</span><span class="sc">;</span> 36 37 <span class="i">@ISA</span> = <span class="q">qw(Exporter)</span><span class="sc">;</span> 38 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> 39 <span class="i">@EXPORT_OK</span> = <span class="q">qw(GetNucleicAcids GetNucleicAcidsByType GetNucleicAcidPropertiesData GetNucleicAcidPropertiesNames IsNucleicAcid IsNucleicAcidProperty IsNucleicAcidType)</span><span class="sc">;</span> 40 41 <span class="i">%EXPORT_TAGS</span> = <span class="s">(</span><span class="w">all</span> <span class="cm">=></span> <span class="s">[</span><span class="i">@EXPORT</span><span class="cm">,</span> <span class="i">@EXPORT_OK</span><span class="s">]</span><span class="s">)</span><span class="sc">;</span> 42 43 <span class="c">#</span> 44 <span class="c"># Load nucleic acids data...</span> 45 <span class="c">#</span> 46 <span class="k">my</span><span class="s">(</span><span class="i">%NucleicAcidDataMap</span><span class="cm">,</span> <span class="i">%NucleicAcidCodeMap</span><span class="cm">,</span> <span class="i">%NucleicAcidOtherCodeMap</span><span class="cm">,</span> <span class="i">%NucleicAcidNameMap</span><span class="cm">,</span> <span class="i">@NucleicAcidCodes</span><span class="cm">,</span> <span class="i">@NucleicAcidPropertyNames</span><span class="cm">,</span> <span class="i">%NucleicAcidPropertyNamesMap</span><span class="cm">,</span> <span class="i">%NucleicAcidTypesMap</span><span class="s">)</span><span class="sc">;</span> 47 <span class="i">_LoadNucleicAcidsData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 48 49 <span class="c">#</span> 50 <span class="c"># Get a list of all known nucleic acids as one of these values:</span> 51 <span class="c"># code or nucleic acid name...</span> 52 <span class="c">#</span> <a name="GetNucleicAcids-"></a> 53 <span class="k">sub </span><span class="m">GetNucleicAcids</span> <span class="s">{</span> 54 <span class="k">my</span><span class="s">(</span><span class="i">$NameType</span><span class="cm">,</span> <span class="i">$Code</span><span class="cm">,</span> <span class="i">$Name</span><span class="cm">,</span> <span class="i">@NucleicAcidNames</span><span class="s">)</span><span class="sc">;</span> 55 56 <span class="i">$NameType</span> = <span class="q">'Code'</span><span class="sc">;</span> 57 <span class="k">if</span> <span class="s">(</span><span class="i">@_</span> >= <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 58 <span class="s">(</span><span class="i">$NameType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 59 <span class="s">}</span> 60 61 <span class="c"># Collect names...</span> 62 <span class="i">@NucleicAcidNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 63 <span class="k">for</span> <span class="i">$Code</span> <span class="s">(</span><span class="i">@NucleicAcidCodes</span><span class="s">)</span> <span class="s">{</span> 64 <span class="j">NAME :</span> <span class="s">{</span> 65 <span class="k">if</span> <span class="s">(</span><span class="i">$NameType</span> =~ <span class="q">/^Name$/i</span><span class="s">)</span> <span class="s">{</span><span class="i">$Name</span> = <span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}{<span class="w">Name</span>}<span class="sc">;</span> <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> <span class="s">}</span> 66 <span class="i">$Name</span> = <span class="i">$Code</span><span class="sc">;</span> 67 <span class="s">}</span> 68 <span class="k">push</span> <span class="i">@NucleicAcidNames</span><span class="cm">,</span> <span class="i">$Name</span><span class="sc">;</span> 69 <span class="s">}</span> 70 71 <span class="k">return</span> <span class="s">(</span><span class="k">wantarray</span> ? <span class="i">@NucleicAcidNames</span> <span class="co">:</span> \<span class="i">@NucleicAcidNames</span><span class="s">)</span><span class="sc">;</span> 72 <span class="s">}</span> 73 74 <span class="c">#</span> 75 <span class="c"># Get a list of all known nucleic acids by one of these specified types:</span> 76 <span class="c"># Nucleobase, Nucleoside, Deoxynucleoside, Nucleotide, Deoxynucleotide. Default: Nucleoside</span> 77 <span class="c">#</span> <a name="GetNucleicAcidsByType-"></a> 78 <span class="k">sub </span><span class="m">GetNucleicAcidsByType</span> <span class="s">{</span> 79 <span class="k">my</span><span class="s">(</span><span class="i">$NameType</span><span class="cm">,</span> <span class="i">$Type</span><span class="cm">,</span> <span class="i">$Code</span><span class="cm">,</span> <span class="i">$Name</span><span class="cm">,</span> <span class="i">@NucleicAcidNames</span><span class="s">)</span><span class="sc">;</span> 80 81 <span class="i">$Type</span> = <span class="q">'Nucleoside'</span><span class="sc">;</span> 82 <span class="i">$NameType</span> = <span class="q">'Code'</span><span class="sc">;</span> 83 <span class="k">if</span> <span class="s">(</span><span class="i">@_</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span> 84 <span class="s">(</span><span class="i">$Type</span><span class="cm">,</span> <span class="i">$NameType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 85 <span class="s">}</span> 86 <span class="k">elsif</span> <span class="s">(</span><span class="i">@_</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 87 <span class="s">(</span><span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 88 <span class="s">}</span> 89 90 <span class="c"># Collect names...</span> 91 <span class="i">@NucleicAcidNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 92 <span class="j">CODE:</span> <span class="k">for</span> <span class="i">$Code</span> <span class="s">(</span><span class="i">@NucleicAcidCodes</span><span class="s">)</span> <span class="s">{</span> 93 <span class="k">if</span> <span class="s">(</span><span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}{<span class="w">Type</span>} !~ <span class="q">/^$Type$/i</span> <span class="s">)</span> <span class="s">{</span> 94 <span class="k">next</span> <span class="j">CODE</span><span class="sc">;</span> 95 <span class="s">}</span> 96 <span class="j">NAME :</span> <span class="s">{</span> 97 <span class="k">if</span> <span class="s">(</span><span class="i">$NameType</span> =~ <span class="q">/^Name$/i</span><span class="s">)</span> <span class="s">{</span><span class="i">$Name</span> = <span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}{<span class="w">Name</span>}<span class="sc">;</span> <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> <span class="s">}</span> 98 <span class="i">$Name</span> = <span class="i">$Code</span><span class="sc">;</span> 99 <span class="s">}</span> 100 <span class="k">push</span> <span class="i">@NucleicAcidNames</span><span class="cm">,</span> <span class="i">$Name</span><span class="sc">;</span> 101 <span class="s">}</span> 102 103 <span class="k">return</span> <span class="s">(</span><span class="k">wantarray</span> ? <span class="i">@NucleicAcidNames</span> <span class="co">:</span> \<span class="i">@NucleicAcidNames</span><span class="s">)</span><span class="sc">;</span> 104 <span class="s">}</span> 105 106 <span class="c">#</span> 107 <span class="c"># Get all available properties data for an nucleic acid using any of these symbols:</span> 108 <span class="c"># code, other code or name.</span> 109 <span class="c">#</span> 110 <span class="c"># A reference to a hash array is returned with keys and values representing property</span> 111 <span class="c"># name and its values respectively.</span> 112 <span class="c">#</span> <a name="GetNucleicAcidPropertiesData-"></a> 113 <span class="k">sub </span><span class="m">GetNucleicAcidPropertiesData</span> <span class="s">{</span> 114 <span class="k">my</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 115 <span class="k">my</span><span class="s">(</span><span class="i">$Code</span><span class="s">)</span><span class="sc">;</span> 116 117 <span class="k">if</span> <span class="s">(</span><span class="i">$Code</span> = <span class="i">_ValidateNucleicAcidID</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 118 <span class="k">return</span> \<span class="i">%</span>{<span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}}<span class="sc">;</span> 119 <span class="s">}</span> 120 <span class="k">else</span> <span class="s">{</span> 121 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 122 <span class="s">}</span> 123 <span class="s">}</span> 124 125 <span class="c">#</span> 126 <span class="c"># Get names of all available nucleic acid properties. A reference to an array containing</span> 127 <span class="c"># names of all available properties is returned.</span> 128 <span class="c">#</span> <a name="GetNucleicAcidPropertiesNames-"></a> 129 <span class="k">sub </span><span class="m">GetNucleicAcidPropertiesNames</span> <span class="s">{</span> 130 <span class="k">my</span><span class="s">(</span><span class="i">$Mode</span><span class="s">)</span><span class="sc">;</span> 131 <span class="k">my</span><span class="s">(</span><span class="i">$PropertyName</span><span class="cm">,</span> <span class="i">@PropertyNames</span><span class="s">)</span><span class="sc">;</span> 132 133 <span class="i">$Mode</span> = <span class="q">'ByGroup'</span><span class="sc">;</span> 134 <span class="k">if</span> <span class="s">(</span><span class="i">@_</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 135 <span class="s">(</span><span class="i">$Mode</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 136 <span class="s">}</span> 137 138 <span class="i">@PropertyNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 139 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^Alphabetical$/i</span><span class="s">)</span> <span class="s">{</span> 140 <span class="k">my</span><span class="s">(</span><span class="i">$PropertyName</span><span class="s">)</span><span class="sc">;</span> 141 <span class="c"># Code, OtherCodes and Name are always listed first...</span> 142 <span class="k">push</span> <span class="i">@PropertyNames</span><span class="cm">,</span> <span class="q">qw(Code OtherCodes Name)</span><span class="sc">;</span> 143 <span class="k">for</span> <span class="i">$PropertyName</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%NucleicAcidPropertyNamesMap</span><span class="s">)</span> <span class="s">{</span> 144 <span class="k">if</span> <span class="s">(</span><span class="i">$PropertyName</span> !~ <span class="q">/^(Code|OtherCodes|Name)$/</span><span class="s">)</span> <span class="s">{</span> 145 <span class="k">push</span> <span class="i">@PropertyNames</span><span class="cm">,</span> <span class="i">$PropertyName</span><span class="sc">;</span> 146 <span class="s">}</span> 147 <span class="s">}</span> 148 <span class="s">}</span> 149 <span class="k">else</span> <span class="s">{</span> 150 <span class="k">push</span> <span class="i">@PropertyNames</span><span class="cm">,</span> <span class="i">@NucleicAcidPropertyNames</span><span class="sc">;</span> 151 <span class="s">}</span> 152 <span class="k">return</span> <span class="s">(</span><span class="k">wantarray</span> ? <span class="i">@PropertyNames</span> <span class="co">:</span> \<span class="i">@PropertyNames</span><span class="s">)</span><span class="sc">;</span> 153 <span class="s">}</span> 154 155 <span class="c">#</span> 156 <span class="c"># Is it a known nucleic acid? Input is either a code or a name</span> 157 <span class="c">#</span> <a name="IsNucleicAcid-"></a> 158 <span class="k">sub </span><span class="m">IsNucleicAcid</span> <span class="s">{</span> 159 <span class="k">my</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 160 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="s">)</span><span class="sc">;</span> 161 162 <span class="i">$Status</span> = <span class="s">(</span><span class="i">_ValidateNucleicAcidID</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 163 164 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span> 165 <span class="s">}</span> 166 167 <span class="c">#</span> 168 <span class="c"># Is it an available nucleic acid property?</span> 169 <span class="c">#</span> <a name="IsNucleicAcidProperty-"></a> 170 <span class="k">sub </span><span class="m">IsNucleicAcidProperty</span> <span class="s">{</span> 171 <span class="k">my</span><span class="s">(</span><span class="i">$PropertyName</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 172 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="s">)</span><span class="sc">;</span> 173 174 <span class="i">$Status</span> = <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$NucleicAcidPropertyNamesMap</span>{<span class="i">$PropertyName</span>}<span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 175 176 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span> 177 <span class="s">}</span> 178 179 <span class="c">#</span> 180 <span class="c"># Is it an available nucleic acid type?</span> 181 <span class="c">#</span> <a name="IsNucleicAcidType-"></a> 182 <span class="k">sub </span><span class="m">IsNucleicAcidType</span> <span class="s">{</span> 183 <span class="k">my</span><span class="s">(</span><span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 184 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="s">)</span><span class="sc">;</span> 185 186 <span class="i">$Status</span> = <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$NucleicAcidTypesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$Type</span><span class="s">)</span>}<span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 187 188 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span> 189 <span class="s">}</span> 190 191 <span class="c">#</span> 192 <span class="c"># Implents GetNucleicAcid<PropertyName> for a valid proprty name.</span> 193 <span class="c">#</span> <a name="AUTOLOAD-"></a> 194 <span class="k">sub </span><span class="m">AUTOLOAD</span> <span class="s">{</span> 195 <span class="k">my</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 196 <span class="k">my</span><span class="s">(</span><span class="i">$FunctionName</span><span class="cm">,</span> <span class="i">$PropertyName</span><span class="cm">,</span> <span class="i">$PropertyValue</span><span class="cm">,</span> <span class="i">$Code</span><span class="s">)</span><span class="sc">;</span> 197 198 <span class="i">$PropertyValue</span> = <span class="k">undef</span><span class="sc">;</span> 199 200 <span class="k">use</span> <span class="w">vars</span> <span class="q">qw($AUTOLOAD)</span><span class="sc">;</span> 201 <span class="i">$FunctionName</span> = <span class="i">$AUTOLOAD</span><span class="sc">;</span> 202 <span class="i">$FunctionName</span> =~ <span class="q">s/.*:://</span><span class="sc">;</span> 203 204 <span class="c"># Only Get<PropertyName> functions are supported...</span> 205 <span class="k">if</span> <span class="s">(</span><span class="i">$FunctionName</span> !~ <span class="q">/^Get/</span><span class="s">)</span> <span class="s">{</span> 206 <span class="w">croak</span> <span class="q">"Error: Function, NucleicAcid::$FunctionName, is not supported by AUTOLOAD in NucleicAcid module: Only Get<PropertyName> functions are implemented..."</span><span class="sc">;</span> 207 <span class="s">}</span> 208 209 <span class="i">$PropertyName</span> = <span class="i">$FunctionName</span><span class="sc">;</span> 210 <span class="i">$PropertyName</span> =~ <span class="q">s/^GetNucleicAcid//</span><span class="sc">;</span> 211 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NucleicAcidPropertyNamesMap</span>{<span class="i">$PropertyName</span>}<span class="s">)</span> <span class="s">{</span> 212 <span class="w">croak</span> <span class="q">"Error: Function, NucleicAcid::$FunctionName, is not supported by AUTOLOAD in NucleicAcid module: Unknown nucleic acid property name, $PropertyName, specified..."</span><span class="sc">;</span> 213 <span class="s">}</span> 214 215 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$Code</span> = <span class="i">_ValidateNucleicAcidID</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 216 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 217 <span class="s">}</span> 218 <span class="i">$PropertyValue</span> = <span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}{<span class="i">$PropertyName</span>}<span class="sc">;</span> 219 <span class="k">return</span> <span class="i">$PropertyValue</span><span class="sc">;</span> 220 <span class="s">}</span> 221 222 <span class="c">#</span> 223 <span class="c"># Load NucleicAcidsData.csv files from <MayaChemTools>/lib directory...</span> 224 <span class="c">#</span> <a name="_LoadNucleicAcidsData-"></a> 225 <span class="k">sub </span><span class="m">_LoadNucleicAcidsData</span> <span class="s">{</span> 226 <span class="k">my</span><span class="s">(</span><span class="i">$NucleicAcidsDataFile</span><span class="cm">,</span> <span class="i">$MayaChemToolsLibDir</span><span class="s">)</span><span class="sc">;</span> 227 228 <span class="i">$MayaChemToolsLibDir</span> = <span class="i">GetMayaChemToolsLibDirName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 229 230 <span class="i">$NucleicAcidsDataFile</span> = <span class="q">"$MayaChemToolsLibDir"</span> . <span class="q">"/data/NucleicAcidsData.csv"</span><span class="sc">;</span> 231 232 <span class="k">if</span> <span class="s">(</span>! <span class="k">-e</span> <span class="q">"$NucleicAcidsDataFile"</span><span class="s">)</span> <span class="s">{</span> 233 <span class="w">croak</span> <span class="q">"Error: MayaChemTools package file, $NucleicAcidsDataFile, is missing: Possible installation problems..."</span><span class="sc">;</span> 234 <span class="s">}</span> 235 236 <span class="i">_LoadData</span><span class="s">(</span><span class="i">$NucleicAcidsDataFile</span><span class="s">)</span><span class="sc">;</span> 237 <span class="s">}</span> 238 239 <span class="c">#</span> 240 <span class="c"># Load NucleicAcidsData.csv file from <MayaChemTools>/lib directory...</span> 241 <span class="c">#</span> <a name="_LoadData-"></a> 242 <span class="k">sub </span><span class="m">_LoadData</span> <span class="s">{</span> 243 <span class="k">my</span><span class="s">(</span><span class="i">$NucleicAcidsDataFile</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 244 245 <span class="i">%NucleicAcidDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 246 <span class="i">@NucleicAcidCodes</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 247 <span class="i">@NucleicAcidPropertyNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 248 <span class="i">%NucleicAcidPropertyNamesMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 249 <span class="i">%NucleicAcidCodeMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 250 <span class="i">%NucleicAcidOtherCodeMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 251 <span class="i">%NucleicAcidNameMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 252 <span class="i">%NucleicAcidTypesMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 253 254 <span class="c"># Load property data for all nucleic acids...</span> 255 <span class="c">#</span> 256 <span class="c"># File Format:</span> 257 <span class="c"># "Code","OtherCodes","BasePair","Name","Type","ChemicalFormula","ChemicalFormulaAtpH7.5","MolecularWeight","ExactMass","ElementalComposition"</span> 258 <span class="c">#</span> 259 <span class="k">my</span><span class="s">(</span><span class="i">$Code</span><span class="cm">,</span> <span class="i">$OtherCodes</span><span class="cm">,</span> <span class="i">$NucleicAcidName</span><span class="cm">,</span> <span class="i">$Line</span><span class="cm">,</span> <span class="i">$NumOfCols</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">$Units</span><span class="cm">,</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">@ColLabels</span><span class="s">)</span><span class="sc">;</span> 260 261 <span class="i">$InDelim</span> = <span class="q">"\,"</span><span class="sc">;</span> 262 <span class="k">open</span> <span class="w">NUCLEICACIDSDATAFILE</span><span class="cm">,</span> <span class="q">"$NucleicAcidsDataFile"</span> <span class="k">or</span> <span class="w">croak</span> <span class="q">"Couldn't open $NucleicAcidsDataFile: $! ..."</span><span class="sc">;</span> 263 264 <span class="c"># Skip lines up to column labels...</span> 265 <span class="j">LINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*NUCLEICACIDSDATAFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 266 <span class="k">if</span> <span class="s">(</span><span class="i">$Line</span> !~ <span class="q">/^#/</span><span class="s">)</span> <span class="s">{</span> 267 <span class="k">last</span> <span class="j">LINE</span><span class="sc">;</span> 268 <span class="s">}</span> 269 <span class="s">}</span> 270 <span class="i">@ColLabels</span>= <span class="i">quotewords</span><span class="s">(</span><span class="i">$InDelim</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="i">$Line</span><span class="s">)</span><span class="sc">;</span> 271 <span class="i">$NumOfCols</span> = <span class="i">@ColLabels</span><span class="sc">;</span> 272 273 <span class="c"># Extract property names from column labels...</span> 274 <span class="i">@NucleicAcidPropertyNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 275 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#ColLabels</span><span class="s">)</span> <span class="s">{</span> 276 <span class="i">$Name</span> = <span class="i">$ColLabels</span>[<span class="i">$Index</span>]<span class="sc">;</span> 277 <span class="k">push</span> <span class="i">@NucleicAcidPropertyNames</span><span class="cm">,</span> <span class="i">$Name</span><span class="sc">;</span> 278 279 <span class="c"># Store property names...</span> 280 <span class="i">$NucleicAcidPropertyNamesMap</span>{<span class="i">$Name</span>} = <span class="i">$Name</span><span class="sc">;</span> 281 <span class="s">}</span> 282 283 <span class="c"># Process nucleic acid data...</span> 284 <span class="j">LINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*NUCLEICACIDSDATAFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 285 <span class="k">if</span> <span class="s">(</span><span class="i">$Line</span> =~ <span class="q">/^#/</span><span class="s">)</span> <span class="s">{</span> 286 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span> 287 <span class="s">}</span> 288 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 289 <span class="i">@LineWords</span> = <span class="i">quotewords</span><span class="s">(</span><span class="i">$InDelim</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="i">$Line</span><span class="s">)</span><span class="sc">;</span> 290 <span class="k">if</span> <span class="s">(</span><span class="i">@LineWords</span> != <span class="i">$NumOfCols</span><span class="s">)</span> <span class="s">{</span> 291 <span class="w">croak</span> <span class="q">"Error: The number of data fields, @LineWords, in $NucleicAcidsDataFile must be $NumOfCols.\nLine: $Line..."</span><span class="sc">;</span> 292 <span class="s">}</span> 293 <span class="i">$Code</span> = <span class="i">$LineWords</span>[<span class="n">0</span>]<span class="sc">;</span> <span class="i">$OtherCodes</span> = <span class="i">$LineWords</span>[<span class="n">1</span>]<span class="sc">;</span> <span class="i">$NucleicAcidName</span> = <span class="i">$LineWords</span>[<span class="n">3</span>]<span class="sc">;</span> 294 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}<span class="s">)</span> <span class="s">{</span> 295 <span class="w">carp</span> <span class="q">"Warning: Ignoring data for nucleic acid $Code: It has already been loaded.\nLine: $Line...."</span><span class="sc">;</span> 296 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span> 297 <span class="s">}</span> 298 299 <span class="c"># Store all the values...</span> 300 <span class="k">push</span> <span class="i">@NucleicAcidCodes</span><span class="cm">,</span> <span class="i">$Code</span><span class="sc">;</span> 301 <span class="i">%</span>{<span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 302 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#LineWords</span><span class="s">)</span> <span class="s">{</span> 303 <span class="i">$Name</span> = <span class="i">$NucleicAcidPropertyNames</span>[<span class="i">$Index</span>]<span class="sc">;</span> 304 <span class="i">$Value</span> = <span class="i">$LineWords</span>[<span class="i">$Index</span>]<span class="sc">;</span> 305 <span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}{<span class="i">$Name</span>} = <span class="i">$Value</span><span class="sc">;</span> 306 <span class="s">}</span> 307 <span class="s">}</span> 308 <span class="k">close</span> <span class="w">NUCLEICACIDSDATAFILE</span><span class="sc">;</span> 309 310 <span class="c"># Setup one letter and nucleic acid name maps...</span> 311 <span class="i">_SetupNucleicAcidIDMap</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 312 <span class="s">}</span> 313 314 <span class="c">#</span> 315 <span class="c"># Setup lowercase other codes and name maps pointing</span> 316 <span class="c"># to code as show in data file.</span> 317 <span class="c">#</span> <a name="_SetupNucleicAcidIDMap-"></a> 318 <span class="k">sub </span><span class="m">_SetupNucleicAcidIDMap</span> <span class="s">{</span> 319 <span class="k">my</span><span class="s">(</span><span class="i">$Code</span><span class="cm">,</span> <span class="i">@OtherCodes</span><span class="cm">,</span> <span class="i">$OtherCode</span><span class="cm">,</span> <span class="i">$NucleicAcidName</span><span class="cm">,</span> <span class="i">$NucleicAcidType</span><span class="s">)</span><span class="sc">;</span> 320 321 <span class="i">%NucleicAcidCodeMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 322 <span class="i">%NucleicAcidOtherCodeMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 323 <span class="i">%NucleicAcidNameMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 324 <span class="i">%NucleicAcidTypesMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 325 326 <span class="k">for</span> <span class="i">$Code</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%NucleicAcidDataMap</span><span class="s">)</span> <span class="s">{</span> 327 <span class="i">$NucleicAcidCodeMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$Code</span><span class="s">)</span>} = <span class="i">$Code</span><span class="sc">;</span> 328 329 <span class="i">$NucleicAcidName</span> = <span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}{<span class="w">Name</span>}<span class="sc">;</span> 330 <span class="i">$NucleicAcidNameMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$NucleicAcidName</span><span class="s">)</span>} = <span class="i">$Code</span><span class="sc">;</span> 331 332 <span class="i">$NucleicAcidType</span> = <span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}{<span class="w">Type</span>}<span class="sc">;</span> 333 <span class="k">if</span> <span class="s">(</span>! <span class="k">exists</span> <span class="i">$NucleicAcidTypesMap</span>{<span class="i">$NucleicAcidType</span>}<span class="s">)</span> <span class="s">{</span> 334 <span class="i">$NucleicAcidTypesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$NucleicAcidType</span><span class="s">)</span>} = <span class="i">$NucleicAcidType</span><span class="sc">;</span> 335 <span class="s">}</span> 336 337 <span class="i">@OtherCodes</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}{<span class="w">OtherCodes</span>}<span class="sc">;</span> 338 <span class="j">OTHERCODE:</span> <span class="k">for</span> <span class="i">$OtherCode</span> <span class="s">(</span><span class="i">@OtherCodes</span><span class="s">)</span> <span class="s">{</span> 339 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OtherCode</span><span class="s">)</span> <span class="s">{</span> 340 <span class="k">next</span> <span class="j">OTHERCODE</span><span class="sc">;</span> 341 <span class="s">}</span> 342 <span class="i">$OtherCode</span> = <span class="i">RemoveLeadingAndTrailingWhiteSpaces</span><span class="s">(</span><span class="i">$OtherCode</span><span class="s">)</span><span class="sc">;</span> 343 <span class="i">$NucleicAcidOtherCodeMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$OtherCode</span><span class="s">)</span>} = <span class="i">$Code</span><span class="sc">;</span> 344 <span class="s">}</span> 345 <span class="s">}</span> 346 <span class="s">}</span> 347 348 <span class="c"># Validate Nucleic acid ID...</span> <a name="_ValidateNucleicAcidID-"></a> 349 <span class="k">sub </span><span class="m">_ValidateNucleicAcidID</span> <span class="s">{</span> 350 <span class="k">my</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 351 <span class="k">my</span><span class="s">(</span><span class="i">$Code</span><span class="s">)</span> = <span class="k">undef</span><span class="sc">;</span> 352 353 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$NucleicAcidCodeMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span> 354 <span class="i">$Code</span> = <span class="i">$NucleicAcidCodeMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span>}<span class="sc">;</span> 355 <span class="s">}</span> 356 <span class="k">elsif</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$NucleicAcidOtherCodeMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span> 357 <span class="i">$Code</span> = <span class="i">$NucleicAcidOtherCodeMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span>}<span class="sc">;</span> 358 <span class="s">}</span> 359 <span class="k">elsif</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$NucleicAcidNameMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span> 360 <span class="i">$Code</span> = <span class="i">$NucleicAcidNameMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span>}<span class="sc">;</span> 361 <span class="s">}</span> 362 <span class="k">return</span> <span class="i">$Code</span><span class="sc">;</span> 363 <span class="s">}</span> 364 365 <a name="EOF-"></a></pre> <p> </p> <br /> <center> <img src="../../../images/h2o2.png"> </center> </body> </html>