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13 <pre>
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14 <a name="package-NucleicAcids-"></a> 1 <span class="k">package </span><span class="i">NucleicAcids</span><span class="sc">;</span>
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15 2 <span class="c">#</span>
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16 3 <span class="c"># $RCSfile: NucleicAcids.pm,v $</span>
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17 4 <span class="c"># $Date: 2015/02/28 20:47:18 $</span>
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18 5 <span class="c"># $Revision: 1.25 $</span>
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19 6 <span class="c">#</span>
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20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span>
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21 8 <span class="c">#</span>
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22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
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23 10 <span class="c">#</span>
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24 11 <span class="c"># This file is part of MayaChemTools.</span>
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25 12 <span class="c">#</span>
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26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
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27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
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28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
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29 16 <span class="c"># later version.</span>
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30 17 <span class="c">#</span>
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31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
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32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
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33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span>
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34 21 <span class="c"># details.</span>
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35 22 <span class="c">#</span>
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36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
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37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span>
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38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
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39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
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40 27 <span class="c">#</span>
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41 28
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42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
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43 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span>
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44 31 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span>
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45 32 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span>
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46 33 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span>
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47 34
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48 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>
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49 36
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50 37 <span class="i">@ISA</span> = <span class="q">qw(Exporter)</span><span class="sc">;</span>
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51 38 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span>
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52 39 <span class="i">@EXPORT_OK</span> = <span class="q">qw(GetNucleicAcids GetNucleicAcidsByType GetNucleicAcidPropertiesData GetNucleicAcidPropertiesNames IsNucleicAcid IsNucleicAcidProperty IsNucleicAcidType)</span><span class="sc">;</span>
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53 40
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54 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>
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55 42
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56 43 <span class="c">#</span>
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57 44 <span class="c"># Load nucleic acids data...</span>
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58 45 <span class="c">#</span>
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59 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>
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60 47 <span class="i">_LoadNucleicAcidsData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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61 48
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62 49 <span class="c">#</span>
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63 50 <span class="c"># Get a list of all known nucleic acids as one of these values:</span>
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64 51 <span class="c"># code or nucleic acid name...</span>
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65 52 <span class="c">#</span>
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66 <a name="GetNucleicAcids-"></a> 53 <span class="k">sub </span><span class="m">GetNucleicAcids</span> <span class="s">{</span>
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67 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>
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68 55
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69 56 <span class="i">$NameType</span> = <span class="q">'Code'</span><span class="sc">;</span>
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70 57 <span class="k">if</span> <span class="s">(</span><span class="i">@_</span> >= <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
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71 58 <span class="s">(</span><span class="i">$NameType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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72 59 <span class="s">}</span>
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73 60
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74 61 <span class="c"># Collect names...</span>
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75 62 <span class="i">@NucleicAcidNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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76 63 <span class="k">for</span> <span class="i">$Code</span> <span class="s">(</span><span class="i">@NucleicAcidCodes</span><span class="s">)</span> <span class="s">{</span>
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77 64 <span class="j">NAME :</span> <span class="s">{</span>
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78 65 <span class="k">if</span> <span class="s">(</span><span class="i">$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>
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79 66 <span class="i">$Name</span> = <span class="i">$Code</span><span class="sc">;</span>
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80 67 <span class="s">}</span>
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81 68 <span class="k">push</span> <span class="i">@NucleicAcidNames</span><span class="cm">,</span> <span class="i">$Name</span><span class="sc">;</span>
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82 69 <span class="s">}</span>
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83 70
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84 71 <span class="k">return</span> <span class="s">(</span><span class="k">wantarray</span> ? <span class="i">@NucleicAcidNames</span> <span class="co">:</span> \<span class="i">@NucleicAcidNames</span><span class="s">)</span><span class="sc">;</span>
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85 72 <span class="s">}</span>
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86 73
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87 74 <span class="c">#</span>
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88 75 <span class="c"># Get a list of all known nucleic acids by one of these specified types:</span>
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89 76 <span class="c"># Nucleobase, Nucleoside, Deoxynucleoside, Nucleotide, Deoxynucleotide. Default: Nucleoside</span>
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90 77 <span class="c">#</span>
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91 <a name="GetNucleicAcidsByType-"></a> 78 <span class="k">sub </span><span class="m">GetNucleicAcidsByType</span> <span class="s">{</span>
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92 79 <span class="k">my</span><span class="s">(</span><span class="i">$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">$Name</span><span class="cm">,</span> <span class="i">@NucleicAcidNames</span><span class="s">)</span><span class="sc">;</span>
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93 80
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94 81 <span class="i">$Type</span> = <span class="q">'Nucleoside'</span><span class="sc">;</span>
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95 82 <span class="i">$NameType</span> = <span class="q">'Code'</span><span class="sc">;</span>
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96 83 <span class="k">if</span> <span class="s">(</span><span class="i">@_</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
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97 84 <span class="s">(</span><span class="i">$Type</span><span class="cm">,</span> <span class="i">$NameType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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98 85 <span class="s">}</span>
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99 86 <span class="k">elsif</span> <span class="s">(</span><span class="i">@_</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
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100 87 <span class="s">(</span><span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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101 88 <span class="s">}</span>
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102 89
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103 90 <span class="c"># Collect names...</span>
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104 91 <span class="i">@NucleicAcidNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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105 92 <span class="j">CODE:</span> <span class="k">for</span> <span class="i">$Code</span> <span class="s">(</span><span class="i">@NucleicAcidCodes</span><span class="s">)</span> <span class="s">{</span>
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106 93 <span class="k">if</span> <span class="s">(</span><span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}{<span class="w">Type</span>} !~ <span class="q">/^$Type$/i</span> <span class="s">)</span> <span class="s">{</span>
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107 94 <span class="k">next</span> <span class="j">CODE</span><span class="sc">;</span>
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108 95 <span class="s">}</span>
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109 96 <span class="j">NAME :</span> <span class="s">{</span>
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110 97 <span class="k">if</span> <span class="s">(</span><span class="i">$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>
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111 98 <span class="i">$Name</span> = <span class="i">$Code</span><span class="sc">;</span>
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112 99 <span class="s">}</span>
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113 100 <span class="k">push</span> <span class="i">@NucleicAcidNames</span><span class="cm">,</span> <span class="i">$Name</span><span class="sc">;</span>
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114 101 <span class="s">}</span>
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115 102
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116 103 <span class="k">return</span> <span class="s">(</span><span class="k">wantarray</span> ? <span class="i">@NucleicAcidNames</span> <span class="co">:</span> \<span class="i">@NucleicAcidNames</span><span class="s">)</span><span class="sc">;</span>
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117 104 <span class="s">}</span>
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118 105
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119 106 <span class="c">#</span>
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120 107 <span class="c"># Get all available properties data for an nucleic acid using any of these symbols:</span>
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121 108 <span class="c"># code, other code or name.</span>
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122 109 <span class="c">#</span>
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123 110 <span class="c"># A reference to a hash array is returned with keys and values representing property</span>
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124 111 <span class="c"># name and its values respectively.</span>
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125 112 <span class="c">#</span>
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126 <a name="GetNucleicAcidPropertiesData-"></a> 113 <span class="k">sub </span><span class="m">GetNucleicAcidPropertiesData</span> <span class="s">{</span>
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127 114 <span class="k">my</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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128 115 <span class="k">my</span><span class="s">(</span><span class="i">$Code</span><span class="s">)</span><span class="sc">;</span>
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129 116
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130 117 <span class="k">if</span> <span class="s">(</span><span class="i">$Code</span> = <span class="i">_ValidateNucleicAcidID</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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131 118 <span class="k">return</span> \<span class="i">%</span>{<span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}}<span class="sc">;</span>
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132 119 <span class="s">}</span>
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133 120 <span class="k">else</span> <span class="s">{</span>
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134 121 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
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135 122 <span class="s">}</span>
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136 123 <span class="s">}</span>
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137 124
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138 125 <span class="c">#</span>
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139 126 <span class="c"># Get names of all available nucleic acid properties. A reference to an array containing</span>
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140 127 <span class="c"># names of all available properties is returned.</span>
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141 128 <span class="c">#</span>
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142 <a name="GetNucleicAcidPropertiesNames-"></a> 129 <span class="k">sub </span><span class="m">GetNucleicAcidPropertiesNames</span> <span class="s">{</span>
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143 130 <span class="k">my</span><span class="s">(</span><span class="i">$Mode</span><span class="s">)</span><span class="sc">;</span>
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144 131 <span class="k">my</span><span class="s">(</span><span class="i">$PropertyName</span><span class="cm">,</span> <span class="i">@PropertyNames</span><span class="s">)</span><span class="sc">;</span>
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145 132
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146 133 <span class="i">$Mode</span> = <span class="q">'ByGroup'</span><span class="sc">;</span>
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147 134 <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>
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148 135 <span class="s">(</span><span class="i">$Mode</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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149 136 <span class="s">}</span>
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150 137
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151 138 <span class="i">@PropertyNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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152 139 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^Alphabetical$/i</span><span class="s">)</span> <span class="s">{</span>
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153 140 <span class="k">my</span><span class="s">(</span><span class="i">$PropertyName</span><span class="s">)</span><span class="sc">;</span>
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154 141 <span class="c"># Code, OtherCodes and Name are always listed first...</span>
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155 142 <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>
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156 143 <span class="k">for</span> <span class="i">$PropertyName</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%NucleicAcidPropertyNamesMap</span><span class="s">)</span> <span class="s">{</span>
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157 144 <span class="k">if</span> <span class="s">(</span><span class="i">$PropertyName</span> !~ <span class="q">/^(Code|OtherCodes|Name)$/</span><span class="s">)</span> <span class="s">{</span>
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158 145 <span class="k">push</span> <span class="i">@PropertyNames</span><span class="cm">,</span> <span class="i">$PropertyName</span><span class="sc">;</span>
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159 146 <span class="s">}</span>
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160 147 <span class="s">}</span>
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161 148 <span class="s">}</span>
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162 149 <span class="k">else</span> <span class="s">{</span>
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163 150 <span class="k">push</span> <span class="i">@PropertyNames</span><span class="cm">,</span> <span class="i">@NucleicAcidPropertyNames</span><span class="sc">;</span>
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164 151 <span class="s">}</span>
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165 152 <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>
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166 153 <span class="s">}</span>
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167 154
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168 155 <span class="c">#</span>
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169 156 <span class="c"># Is it a known nucleic acid? Input is either a code or a name</span>
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170 157 <span class="c">#</span>
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171 <a name="IsNucleicAcid-"></a> 158 <span class="k">sub </span><span class="m">IsNucleicAcid</span> <span class="s">{</span>
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172 159 <span class="k">my</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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173 160 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="s">)</span><span class="sc">;</span>
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174 161
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175 162 <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>
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176 163
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177 164 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span>
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178 165 <span class="s">}</span>
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179 166
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180 167 <span class="c">#</span>
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181 168 <span class="c"># Is it an available nucleic acid property?</span>
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182 169 <span class="c">#</span>
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183 <a name="IsNucleicAcidProperty-"></a> 170 <span class="k">sub </span><span class="m">IsNucleicAcidProperty</span> <span class="s">{</span>
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184 171 <span class="k">my</span><span class="s">(</span><span class="i">$PropertyName</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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185 172 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="s">)</span><span class="sc">;</span>
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186 173
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187 174 <span class="i">$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>
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188 175
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189 176 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span>
|
|
|
190 177 <span class="s">}</span>
|
|
|
191 178
|
|
|
192 179 <span class="c">#</span>
|
|
|
193 180 <span class="c"># Is it an available nucleic acid type?</span>
|
|
|
194 181 <span class="c">#</span>
|
|
|
195 <a name="IsNucleicAcidType-"></a> 182 <span class="k">sub </span><span class="m">IsNucleicAcidType</span> <span class="s">{</span>
|
|
|
196 183 <span class="k">my</span><span class="s">(</span><span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
197 184 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="s">)</span><span class="sc">;</span>
|
|
|
198 185
|
|
|
199 186 <span class="i">$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>
|
|
|
200 187
|
|
|
201 188 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span>
|
|
|
202 189 <span class="s">}</span>
|
|
|
203 190
|
|
|
204 191 <span class="c">#</span>
|
|
|
205 192 <span class="c"># Implents GetNucleicAcid<PropertyName> for a valid proprty name.</span>
|
|
|
206 193 <span class="c">#</span>
|
|
|
207 <a name="AUTOLOAD-"></a> 194 <span class="k">sub </span><span class="m">AUTOLOAD</span> <span class="s">{</span>
|
|
|
208 195 <span class="k">my</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
209 196 <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>
|
|
|
210 197
|
|
|
211 198 <span class="i">$PropertyValue</span> = <span class="k">undef</span><span class="sc">;</span>
|
|
|
212 199
|
|
|
213 200 <span class="k">use</span> <span class="w">vars</span> <span class="q">qw($AUTOLOAD)</span><span class="sc">;</span>
|
|
|
214 201 <span class="i">$FunctionName</span> = <span class="i">$AUTOLOAD</span><span class="sc">;</span>
|
|
|
215 202 <span class="i">$FunctionName</span> =~ <span class="q">s/.*:://</span><span class="sc">;</span>
|
|
|
216 203
|
|
|
217 204 <span class="c"># Only Get<PropertyName> functions are supported...</span>
|
|
|
218 205 <span class="k">if</span> <span class="s">(</span><span class="i">$FunctionName</span> !~ <span class="q">/^Get/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
219 206 <span class="w">croak</span> <span class="q">"Error: Function, NucleicAcid::$FunctionName, is not supported by AUTOLOAD in NucleicAcid module: Only Get<PropertyName> functions are implemented..."</span><span class="sc">;</span>
|
|
|
220 207 <span class="s">}</span>
|
|
|
221 208
|
|
|
222 209 <span class="i">$PropertyName</span> = <span class="i">$FunctionName</span><span class="sc">;</span>
|
|
|
223 210 <span class="i">$PropertyName</span> =~ <span class="q">s/^GetNucleicAcid//</span><span class="sc">;</span>
|
|
|
224 211 <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>
|
|
|
225 212 <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, $PropertyName, specified..."</span><span class="sc">;</span>
|
|
|
226 213 <span class="s">}</span>
|
|
|
227 214
|
|
|
228 215 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$Code</span> = <span class="i">_ValidateNucleicAcidID</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
229 216 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
230 217 <span class="s">}</span>
|
|
|
231 218 <span class="i">$PropertyValue</span> = <span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}{<span class="i">$PropertyName</span>}<span class="sc">;</span>
|
|
|
232 219 <span class="k">return</span> <span class="i">$PropertyValue</span><span class="sc">;</span>
|
|
|
233 220 <span class="s">}</span>
|
|
|
234 221
|
|
|
235 222 <span class="c">#</span>
|
|
|
236 223 <span class="c"># Load NucleicAcidsData.csv files from <MayaChemTools>/lib directory...</span>
|
|
|
237 224 <span class="c">#</span>
|
|
|
238 <a name="_LoadNucleicAcidsData-"></a> 225 <span class="k">sub </span><span class="m">_LoadNucleicAcidsData</span> <span class="s">{</span>
|
|
|
239 226 <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>
|
|
|
240 227
|
|
|
241 228 <span class="i">$MayaChemToolsLibDir</span> = <span class="i">GetMayaChemToolsLibDirName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
242 229
|
|
|
243 230 <span class="i">$NucleicAcidsDataFile</span> = <span class="q">"$MayaChemToolsLibDir"</span> . <span class="q">"/data/NucleicAcidsData.csv"</span><span class="sc">;</span>
|
|
|
244 231
|
|
|
245 232 <span class="k">if</span> <span class="s">(</span>! <span class="k">-e</span> <span class="q">"$NucleicAcidsDataFile"</span><span class="s">)</span> <span class="s">{</span>
|
|
|
246 233 <span class="w">croak</span> <span class="q">"Error: MayaChemTools package file, $NucleicAcidsDataFile, is missing: Possible installation problems..."</span><span class="sc">;</span>
|
|
|
247 234 <span class="s">}</span>
|
|
|
248 235
|
|
|
249 236 <span class="i">_LoadData</span><span class="s">(</span><span class="i">$NucleicAcidsDataFile</span><span class="s">)</span><span class="sc">;</span>
|
|
|
250 237 <span class="s">}</span>
|
|
|
251 238
|
|
|
252 239 <span class="c">#</span>
|
|
|
253 240 <span class="c"># Load NucleicAcidsData.csv file from <MayaChemTools>/lib directory...</span>
|
|
|
254 241 <span class="c">#</span>
|
|
|
255 <a name="_LoadData-"></a> 242 <span class="k">sub </span><span class="m">_LoadData</span> <span class="s">{</span>
|
|
|
256 243 <span class="k">my</span><span class="s">(</span><span class="i">$NucleicAcidsDataFile</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
257 244
|
|
|
258 245 <span class="i">%NucleicAcidDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
259 246 <span class="i">@NucleicAcidCodes</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
260 247 <span class="i">@NucleicAcidPropertyNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
261 248 <span class="i">%NucleicAcidPropertyNamesMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
262 249 <span class="i">%NucleicAcidCodeMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
263 250 <span class="i">%NucleicAcidOtherCodeMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
264 251 <span class="i">%NucleicAcidNameMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
265 252 <span class="i">%NucleicAcidTypesMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
266 253
|
|
|
267 254 <span class="c"># Load property data for all nucleic acids...</span>
|
|
|
268 255 <span class="c">#</span>
|
|
|
269 256 <span class="c"># File Format:</span>
|
|
|
270 257 <span class="c"># "Code","OtherCodes","BasePair","Name","Type","ChemicalFormula","ChemicalFormulaAtpH7.5","MolecularWeight","ExactMass","ElementalComposition"</span>
|
|
|
271 258 <span class="c">#</span>
|
|
|
272 259 <span class="k">my</span><span class="s">(</span><span class="i">$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">$Units</span><span class="cm">,</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">@ColLabels</span><span class="s">)</span><span class="sc">;</span>
|
|
|
273 260
|
|
|
274 261 <span class="i">$InDelim</span> = <span class="q">"\,"</span><span class="sc">;</span>
|
|
|
275 262 <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: $! ..."</span><span class="sc">;</span>
|
|
|
276 263
|
|
|
277 264 <span class="c"># Skip lines up to column labels...</span>
|
|
|
278 265 <span class="j">LINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$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>
|
|
|
279 266 <span class="k">if</span> <span class="s">(</span><span class="i">$Line</span> !~ <span class="q">/^#/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
280 267 <span class="k">last</span> <span class="j">LINE</span><span class="sc">;</span>
|
|
|
281 268 <span class="s">}</span>
|
|
|
282 269 <span class="s">}</span>
|
|
|
283 270 <span class="i">@ColLabels</span>= <span class="i">quotewords</span><span class="s">(</span><span class="i">$InDelim</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="i">$Line</span><span class="s">)</span><span class="sc">;</span>
|
|
|
284 271 <span class="i">$NumOfCols</span> = <span class="i">@ColLabels</span><span class="sc">;</span>
|
|
|
285 272
|
|
|
286 273 <span class="c"># Extract property names from column labels...</span>
|
|
|
287 274 <span class="i">@NucleicAcidPropertyNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
288 275 <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>
|
|
|
289 276 <span class="i">$Name</span> = <span class="i">$ColLabels</span>[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
290 277 <span class="k">push</span> <span class="i">@NucleicAcidPropertyNames</span><span class="cm">,</span> <span class="i">$Name</span><span class="sc">;</span>
|
|
|
291 278
|
|
|
292 279 <span class="c"># Store property names...</span>
|
|
|
293 280 <span class="i">$NucleicAcidPropertyNamesMap</span>{<span class="i">$Name</span>} = <span class="i">$Name</span><span class="sc">;</span>
|
|
|
294 281 <span class="s">}</span>
|
|
|
295 282
|
|
|
296 283 <span class="c"># Process nucleic acid data...</span>
|
|
|
297 284 <span class="j">LINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$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>
|
|
|
298 285 <span class="k">if</span> <span class="s">(</span><span class="i">$Line</span> =~ <span class="q">/^#/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
299 286 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span>
|
|
|
300 287 <span class="s">}</span>
|
|
|
301 288 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
302 289 <span class="i">@LineWords</span> = <span class="i">quotewords</span><span class="s">(</span><span class="i">$InDelim</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="i">$Line</span><span class="s">)</span><span class="sc">;</span>
|
|
|
303 290 <span class="k">if</span> <span class="s">(</span><span class="i">@LineWords</span> != <span class="i">$NumOfCols</span><span class="s">)</span> <span class="s">{</span>
|
|
|
304 291 <span class="w">croak</span> <span class="q">"Error: The number of data fields, @LineWords, in $NucleicAcidsDataFile must be $NumOfCols.\nLine: $Line..."</span><span class="sc">;</span>
|
|
|
305 292 <span class="s">}</span>
|
|
|
306 293 <span class="i">$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">$LineWords</span>[<span class="n">3</span>]<span class="sc">;</span>
|
|
|
307 294 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
308 295 <span class="w">carp</span> <span class="q">"Warning: Ignoring data for nucleic acid $Code: It has already been loaded.\nLine: $Line...."</span><span class="sc">;</span>
|
|
|
309 296 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span>
|
|
|
310 297 <span class="s">}</span>
|
|
|
311 298
|
|
|
312 299 <span class="c"># Store all the values...</span>
|
|
|
313 300 <span class="k">push</span> <span class="i">@NucleicAcidCodes</span><span class="cm">,</span> <span class="i">$Code</span><span class="sc">;</span>
|
|
|
314 301 <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>
|
|
|
315 302 <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>
|
|
|
316 303 <span class="i">$Name</span> = <span class="i">$NucleicAcidPropertyNames</span>[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
317 304 <span class="i">$Value</span> = <span class="i">$LineWords</span>[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
318 305 <span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}{<span class="i">$Name</span>} = <span class="i">$Value</span><span class="sc">;</span>
|
|
|
319 306 <span class="s">}</span>
|
|
|
320 307 <span class="s">}</span>
|
|
|
321 308 <span class="k">close</span> <span class="w">NUCLEICACIDSDATAFILE</span><span class="sc">;</span>
|
|
|
322 309
|
|
|
323 310 <span class="c"># Setup one letter and nucleic acid name maps...</span>
|
|
|
324 311 <span class="i">_SetupNucleicAcidIDMap</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
325 312 <span class="s">}</span>
|
|
|
326 313
|
|
|
327 314 <span class="c">#</span>
|
|
|
328 315 <span class="c"># Setup lowercase other codes and name maps pointing</span>
|
|
|
329 316 <span class="c"># to code as show in data file.</span>
|
|
|
330 317 <span class="c">#</span>
|
|
|
331 <a name="_SetupNucleicAcidIDMap-"></a> 318 <span class="k">sub </span><span class="m">_SetupNucleicAcidIDMap</span> <span class="s">{</span>
|
|
|
332 319 <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>
|
|
|
333 320
|
|
|
334 321 <span class="i">%NucleicAcidCodeMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
335 322 <span class="i">%NucleicAcidOtherCodeMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
336 323 <span class="i">%NucleicAcidNameMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
337 324 <span class="i">%NucleicAcidTypesMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
338 325
|
|
|
339 326 <span class="k">for</span> <span class="i">$Code</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%NucleicAcidDataMap</span><span class="s">)</span> <span class="s">{</span>
|
|
|
340 327 <span class="i">$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>
|
|
|
341 328
|
|
|
342 329 <span class="i">$NucleicAcidName</span> = <span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}{<span class="w">Name</span>}<span class="sc">;</span>
|
|
|
343 330 <span class="i">$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>
|
|
|
344 331
|
|
|
345 332 <span class="i">$NucleicAcidType</span> = <span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}{<span class="w">Type</span>}<span class="sc">;</span>
|
|
|
346 333 <span class="k">if</span> <span class="s">(</span>! <span class="k">exists</span> <span class="i">$NucleicAcidTypesMap</span>{<span class="i">$NucleicAcidType</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
347 334 <span class="i">$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>
|
|
|
348 335 <span class="s">}</span>
|
|
|
349 336
|
|
|
350 337 <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>
|
|
|
351 338 <span class="j">OTHERCODE:</span> <span class="k">for</span> <span class="i">$OtherCode</span> <span class="s">(</span><span class="i">@OtherCodes</span><span class="s">)</span> <span class="s">{</span>
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352 339 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OtherCode</span><span class="s">)</span> <span class="s">{</span>
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353 340 <span class="k">next</span> <span class="j">OTHERCODE</span><span class="sc">;</span>
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354 341 <span class="s">}</span>
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355 342 <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>
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356 343 <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">$Code</span><span class="sc">;</span>
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357 344 <span class="s">}</span>
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358 345 <span class="s">}</span>
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359 346 <span class="s">}</span>
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360 347
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361 348 <span class="c"># Validate Nucleic acid ID...</span>
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362 <a name="_ValidateNucleicAcidID-"></a> 349 <span class="k">sub </span><span class="m">_ValidateNucleicAcidID</span> <span class="s">{</span>
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363 350 <span class="k">my</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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364 351 <span class="k">my</span><span class="s">(</span><span class="i">$Code</span><span class="s">)</span> = <span class="k">undef</span><span class="sc">;</span>
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365 352
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366 353 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$NucleicAcidCodeMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span>
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367 354 <span class="i">$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>
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368 355 <span class="s">}</span>
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369 356 <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>
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370 357 <span class="i">$Code</span> = <span class="i">$NucleicAcidOtherCodeMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span>}<span class="sc">;</span>
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371 358 <span class="s">}</span>
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372 359 <span class="k">elsif</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$NucleicAcidNameMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span>
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373 360 <span class="i">$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>
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374 361 <span class="s">}</span>
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375 362 <span class="k">return</span> <span class="i">$Code</span><span class="sc">;</span>
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376 363 <span class="s">}</span>
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377 364
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378 365
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379 <a name="EOF-"></a></pre>
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380 <p> </p>
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381 <br />
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382 <center>
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383 <img src="../../../images/h2o2.png">
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384 </center>
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385 </body>
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386 </html>
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