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1 <html>
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3 <title>MayaChemTools:Code:InfoNucleicAcids.pl</title>
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13 <pre>
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14 1 #!/usr/bin/perl -w
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15 2 <span class="c">#</span>
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16 3 <span class="c"># $RCSfile: InfoNucleicAcids.pl,v $</span>
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17 4 <span class="c"># $Date: 2015/02/28 20:46:20 $</span>
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18 5 <span class="c"># $Revision: 1.26 $</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">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">"$FindBin::Bin/../lib"</span><span class="sc">;</span>
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44 31 <span class="k">use</span> <span class="w">Getopt::Long</span><span class="sc">;</span>
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45 32 <span class="k">use</span> <span class="w">File::Basename</span><span class="sc">;</span>
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46 33 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span>
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47 34 <span class="k">use</span> <span class="w">Benchmark</span><span class="sc">;</span>
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48 35 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span>
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49 36 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span>
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50 37 <span class="k">use</span> <span class="w">NucleicAcids</span><span class="sc">;</span>
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51 38
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52 39 <span class="k">my</span><span class="s">(</span><span class="i">$ScriptName</span><span class="cm">,</span> <span class="i">%Options</span><span class="cm">,</span> <span class="i">$StartTime</span><span class="cm">,</span> <span class="i">$EndTime</span><span class="cm">,</span> <span class="i">$TotalTime</span><span class="s">)</span><span class="sc">;</span>
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53 40
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54 41 <span class="c"># Autoflush STDOUT</span>
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55 42 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span>
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56 43
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57 44 <span class="c"># Starting message...</span>
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58 45 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span>
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59 46 <span class="k">print</span> <span class="q">"\n$ScriptName: Starting...\n\n"</span><span class="sc">;</span>
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60 47 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
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61 48
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62 49 <span class="c"># Get the options and setup script...</span>
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63 50 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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64 51 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">help</span>}<span class="s">)</span> <span class="s">{</span>
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65 52 <span class="k">die</span> <span class="i">GetUsageFromPod</span><span class="s">(</span><span class="q">"$FindBin::Bin/$ScriptName"</span><span class="s">)</span><span class="sc">;</span>
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66 53 <span class="s">}</span>
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67 54
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68 55 <span class="k">print</span> <span class="q">"Processing options...\n"</span><span class="sc">;</span>
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69 56 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span>
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70 57 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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71 58
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72 59 <span class="i">ListNucleicAcidProperties</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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73 60 <span class="k">print</span> <span class="q">"\n$ScriptName:Done...\n\n"</span><span class="sc">;</span>
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74 61
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75 62 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
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76 63 <span class="i">$TotalTime</span> = <span class="w">timediff</span> <span class="s">(</span><span class="i">$EndTime</span><span class="cm">,</span> <span class="i">$StartTime</span><span class="s">)</span><span class="sc">;</span>
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77 64 <span class="k">print</span> <span class="q">"Total time: "</span><span class="cm">,</span> <span class="i">timestr</span><span class="s">(</span><span class="i">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
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78 65
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79 66 <span class="c">###############################################################################</span>
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80 67
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81 68 <span class="c"># List data for an nucleic acid...</span>
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82 <a name="ListNucleicAcidData-"></a> 69 <span class="k">sub </span><span class="m">ListNucleicAcidData</span> <span class="s">{</span>
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83 70 <span class="k">my</span><span class="s">(</span><span class="i">$DataLabelRef</span><span class="cm">,</span> <span class="i">$DataValueRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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84 71 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$Line</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
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85 72
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86 73 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">NucleicAcidRowsOutput</span>}<span class="s">)</span> <span class="s">{</span>
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87 74 <span class="i">$Line</span> = <span class="q">''</span><span class="sc">;</span>
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88 75 <span class="c"># Format data...</span>
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89 76 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>} || <span class="i">$Options</span>{<span class="w">outdelim</span>} !~ <span class="q">/^comma$/i</span><span class="s">)</span> <span class="s">{</span>
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90 77 <span class="i">$Line</span> = <span class="i">JoinWords</span><span class="s">(</span><span class="i">$DataValueRef</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>}<span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span>
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91 78 <span class="s">}</span>
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92 79 <span class="k">else</span> <span class="s">{</span>
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93 80 <span class="c"># Always quote values containing commas...</span>
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94 81 <span class="i">$Line</span> = <span class="s">(</span><span class="i">$DataValueRef</span>->[<span class="n">0</span>] =~ <span class="q">/\,/</span><span class="s">)</span> ? <span class="q">qq("$DataValueRef->[0]")</span> <span class="co">:</span> <span class="i">$DataValueRef</span>->[<span class="n">0</span>]<span class="sc">;</span>
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95 82 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">1</span> .. <span class="i">$#</span>{<span class="i">$DataValueRef</span>} <span class="s">)</span> <span class="s">{</span>
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96 83 <span class="i">$Value</span> = <span class="i">$DataValueRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span>
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97 84 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> =~ <span class="q">/\,/</span><span class="s">)</span> <span class="s">{</span>
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98 85 <span class="i">$Value</span> = <span class="q">qq("$Value")</span><span class="sc">;</span>
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99 86 <span class="s">}</span>
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100 87 <span class="i">$Line</span> .= <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>} . <span class="i">$Value</span><span class="sc">;</span>
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101 88 <span class="s">}</span>
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102 89 <span class="s">}</span>
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103 90 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span>
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104 91 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$Line\n"</span><span class="sc">;</span>
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105 92 <span class="s">}</span>
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106 93 <span class="k">else</span> <span class="s">{</span>
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107 94 <span class="k">print</span> <span class="q">"$Line\n"</span><span class="sc">;</span>
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108 95 <span class="s">}</span>
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109 96 <span class="s">}</span>
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110 97 <span class="k">else</span> <span class="s">{</span>
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111 98 <span class="c"># Format and list data...</span>
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112 99 <span class="i">$Line</span> = <span class="q">''</span><span class="sc">;</span>
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113 100 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$DataLabelRef</span>} <span class="s">)</span> <span class="s">{</span>
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114 101 <span class="i">$Line</span> = <span class="i">$DataLabelRef</span>->[<span class="i">$Index</span>] . <span class="q">' '</span> . <span class="i">$DataValueRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span>
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115 102 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span>
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116 103 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$Line\n"</span><span class="sc">;</span>
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117 104 <span class="s">}</span>
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118 105 <span class="k">else</span> <span class="s">{</span>
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119 106 <span class="k">print</span> <span class="q">"$Line\n"</span><span class="sc">;</span>
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120 107 <span class="s">}</span>
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121 108 <span class="s">}</span>
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122 109 <span class="s">}</span>
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123 110 <span class="s">}</span>
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124 111
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125 112 <span class="c"># List data for an nucleic acid...</span>
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126 <a name="ListHeaderRowData-"></a> 113 <span class="k">sub </span><span class="m">ListHeaderRowData</span> <span class="s">{</span>
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127 114 <span class="k">my</span><span class="s">(</span><span class="i">$DataLabelRef</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">$Line</span><span class="s">)</span><span class="sc">;</span>
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129 116
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130 117 <span class="c"># Format data...</span>
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131 118 <span class="i">$Line</span> = <span class="i">JoinWords</span><span class="s">(</span><span class="i">$DataLabelRef</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>}<span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span>
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132 119 <span class="i">$Line</span> =~ <span class="q">s/\://g</span><span class="sc">;</span>
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133 120 <span class="c"># List data...</span>
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134 121 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span>
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135 122 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$Line\n"</span><span class="sc">;</span>
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136 123 <span class="s">}</span>
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137 124 <span class="k">else</span> <span class="s">{</span>
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138 125 <span class="k">print</span> <span class="q">"$Line\n"</span><span class="sc">;</span>
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139 126 <span class="s">}</span>
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140 127 <span class="s">}</span>
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141 128
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142 129 <span class="c"># List properties for nucleic acids...</span>
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143 <a name="ListNucleicAcidProperties-"></a> 130 <span class="k">sub </span><span class="m">ListNucleicAcidProperties</span> <span class="s">{</span>
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144 131 <span class="k">my</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="cm">,</span> <span class="i">$NucleicAcidDataRef</span><span class="cm">,</span> <span class="i">$PropertyName</span><span class="cm">,</span> <span class="i">$PropertyValue</span><span class="cm">,</span> <span class="i">@PropertyLabels</span><span class="cm">,</span> <span class="i">@PropertyValues</span><span class="s">)</span><span class="sc">;</span>
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145 132
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146 133 <span class="k">print</span> <span class="q">"Listing information for nucleic acid(s)...\n"</span><span class="sc">;</span>
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147 134
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148 135 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span>
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149 136 <span class="k">print</span> <span class="q">"Generating file $OptionsInfo{OutFileName}...\n"</span><span class="sc">;</span>
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150 137 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">">$OptionsInfo{OutFileName}"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Couldn't open $OptionsInfo{OutFileName}: $!\n"</span><span class="sc">;</span>
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151 138 <span class="s">}</span>
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152 139
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153 140 <span class="c"># Setup property labels...</span>
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154 141 <span class="i">@PropertyLabels</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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155 142 <span class="k">for</span> <span class="i">$PropertyName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="s">)</span> <span class="s">{</span>
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156 143 <span class="k">push</span> <span class="i">@PropertyLabels</span><span class="cm">,</span> <span class="s">(</span><span class="q">"$PropertyName:"</span><span class="s">)</span><span class="sc">;</span>
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157 144 <span class="s">}</span>
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158 145
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159 146 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">NucleicAcidRowsOutput</span>}<span class="s">)</span> <span class="s">{</span>
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160 147 <span class="i">ListHeaderRowData</span><span class="s">(</span>\<span class="i">@PropertyLabels</span><span class="s">)</span><span class="sc">;</span>
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161 148 <span class="s">}</span>
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162 149
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163 150 <span class="c"># Go over specified properties...</span>
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164 151 <span class="k">for</span> <span class="i">$NucleicAcidID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedNucleicAcidIDs</span>}}<span class="s">)</span> <span class="s">{</span>
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165 152 <span class="i">$NucleicAcidDataRef</span> = <span class="i">NucleicAcids::GetNucleicAcidPropertiesData</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span><span class="sc">;</span>
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166 153
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167 154 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">NucleicAcidRowsOutput</span>}<span class="s">)</span> <span class="s">{</span>
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168 155 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span>
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169 156 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"\nListing properties for nucleic acid $NucleicAcidID...\n\n"</span><span class="sc">;</span>
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170 157 <span class="s">}</span>
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171 158 <span class="k">else</span> <span class="s">{</span>
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172 159 <span class="k">print</span> <span class="q">"\nListing properties for nucleic acid $NucleicAcidID...\n\n"</span><span class="sc">;</span>
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173 160 <span class="s">}</span>
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174 161 <span class="s">}</span>
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175 162
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176 163 <span class="c"># Collect data..</span>
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177 164 <span class="i">@PropertyValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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178 165 <span class="k">for</span> <span class="i">$PropertyName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="s">)</span> <span class="s">{</span>
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179 166 <span class="i">$PropertyValue</span> = <span class="i">$NucleicAcidDataRef</span>->{<span class="i">$PropertyName</span>}<span class="sc">;</span>
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180 167 <span class="k">if</span> <span class="s">(</span><span class="i">IsFloat</span><span class="s">(</span><span class="i">$PropertyValue</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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181 168 <span class="i">$PropertyValue</span> = <span class="k">sprintf</span><span class="s">(</span><span class="q">"%.$OptionsInfo{Precision}f"</span><span class="cm">,</span> <span class="i">$PropertyValue</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span>
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182 169 <span class="s">}</span>
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183 170 <span class="k">push</span> <span class="i">@PropertyValues</span><span class="cm">,</span> <span class="i">$PropertyValue</span><span class="sc">;</span>
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|
|
184 171 <span class="s">}</span>
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185 172 <span class="c"># List data...</span>
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|
186 173 <span class="i">ListNucleicAcidData</span><span class="s">(</span>\<span class="i">@PropertyLabels</span><span class="cm">,</span> \<span class="i">@PropertyValues</span><span class="s">)</span><span class="sc">;</span>
|
|
|
187 174 <span class="s">}</span>
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188 175 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span>
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|
189 176 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span>
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190 177 <span class="s">}</span>
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|
191 178 <span class="k">print</span> <span class="q">"\n"</span><span class="sc">;</span>
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|
192 179 <span class="s">}</span>
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193 180
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194 181 <span class="c"># Get propery names from categories...</span>
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195 <a name="GetPropertyNamesFromCategories-"></a> 182 <span class="k">sub </span><span class="m">GetPropertyNamesFromCategories</span> <span class="s">{</span>
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196 183 <span class="k">my</span><span class="s">(</span><span class="i">$CategoryName</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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197 184 <span class="k">my</span><span class="s">(</span><span class="i">@PropertyNames</span><span class="s">)</span><span class="sc">;</span>
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198 185
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199 186 <span class="i">@PropertyNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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200 187 <span class="k">if</span> <span class="s">(</span><span class="i">$CategoryName</span> =~ <span class="q">/^Basic$/i</span><span class="s">)</span> <span class="s">{</span>
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|
201 188 <span class="i">@PropertyNames</span> = <span class="s">(</span><span class="q">'Code'</span><span class="cm">,</span> <span class="q">'OtherCodes'</span><span class="cm">,</span> <span class="q">'Name'</span><span class="cm">,</span> <span class="q">'Type'</span><span class="cm">,</span> <span class="q">'MolecularFormula'</span><span class="cm">,</span> <span class="q">'MolecularWeight'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
202 189 <span class="s">}</span> <span class="k">elsif</span> <span class="s">(</span><span class="i">$CategoryName</span> =~ <span class="q">/^BasicPlus$/i</span><span class="s">)</span> <span class="s">{</span>
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|
203 190 <span class="i">@PropertyNames</span> = <span class="s">(</span><span class="q">'Code'</span><span class="cm">,</span> <span class="q">'OtherCodes'</span><span class="cm">,</span> <span class="q">'Name'</span><span class="cm">,</span> <span class="q">'Type'</span><span class="cm">,</span> <span class="q">'MolecularFormula'</span><span class="cm">,</span> <span class="q">'MolecularWeight'</span><span class="cm">,</span> <span class="q">'ExactMass'</span><span class="cm">,</span> <span class="q">'ElementalComposition'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
204 191 <span class="s">}</span>
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205 192
|
|
|
206 193 <span class="k">return</span> <span class="i">@PropertyNames</span><span class="sc">;</span>
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|
|
207 194 <span class="s">}</span>
|
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208 195
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|
|
209 196 <span class="c"># Process option values...</span>
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|
210 <a name="ProcessOptions-"></a> 197 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
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|
|
211 198 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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|
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212 199
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|
|
213 200 <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span>
|
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214 201
|
|
|
215 202 <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/^tab$/i</span> <span class="s">)</span> ? <span class="q">"\t"</span> <span class="co">:</span> <span class="s">(</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/^semicolon$/i</span><span class="s">)</span> ? <span class="q">"\;"</span> <span class="co">:</span> <span class="q">"\,"</span><span class="s">)</span><span class="sc">;</span>
|
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|
216 203 <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} =~ <span class="q">/^yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
217 204
|
|
|
218 205 <span class="i">$OptionsInfo</span>{<span class="w">Overwrite</span>} = <span class="k">defined</span> <span class="i">$Options</span>{<span class="w">overwrite</span>} ? <span class="i">$Options</span>{<span class="w">overwrite</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
219 206 <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} = <span class="k">defined</span> <span class="i">$Options</span>{<span class="w">root</span>} ? <span class="i">$Options</span>{<span class="w">root</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
220 207
|
|
|
221 208 <span class="i">$OptionsInfo</span>{<span class="w">Output</span>} = <span class="i">$Options</span>{<span class="w">output</span>}<span class="sc">;</span>
|
|
|
222 209 <span class="i">$OptionsInfo</span>{<span class="w">OutputStyle</span>} = <span class="i">$Options</span>{<span class="w">outputstyle</span>}<span class="sc">;</span>
|
|
|
223 210
|
|
|
224 211 <span class="i">$OptionsInfo</span>{<span class="w">NucleicAcidRowsOutput</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">outputstyle</span>} =~ <span class="q">/^NucleicAcidRows$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
225 212 <span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} =~ <span class="q">/^File$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
226 213
|
|
|
227 214 <span class="i">$OptionsInfo</span>{<span class="w">Precision</span>} = <span class="i">$Options</span>{<span class="w">precision</span>}<span class="sc">;</span>
|
|
|
228 215
|
|
|
229 216 <span class="k">my</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="cm">,</span> <span class="i">@NucleicAcidIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
230 217
|
|
|
231 218 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedNucleicAcidIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
232 219
|
|
|
233 220 <span class="c"># Set up Nucleic Acids IDs except for All mode...</span>
|
|
|
234 221 <span class="i">@NucleicAcidIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
235 222
|
|
|
236 223 <span class="k">if</span> <span class="s">(</span><span class="i">@ARGV</span> >= <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
|
|
|
237 224 <span class="k">push</span> <span class="i">@NucleicAcidIDs</span><span class="cm">,</span> <span class="i">@ARGV</span><span class="sc">;</span>
|
|
|
238 225 <span class="s">}</span>
|
|
|
239 226 <span class="k">else</span> <span class="s">{</span>
|
|
|
240 227 <span class="c"># Setup mode specified default values...</span>
|
|
|
241 228 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/NucleicAcidID/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
242 229 <span class="k">push</span> <span class="i">@NucleicAcidIDs</span><span class="cm">,</span> <span class="q">'A'</span><span class="sc">;</span>
|
|
|
243 230 <span class="s">}</span>
|
|
|
244 231 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/NucleicAcidType/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
245 232 <span class="k">push</span> <span class="i">@NucleicAcidIDs</span><span class="cm">,</span> <span class="q">'Nucleoside'</span><span class="sc">;</span>
|
|
|
246 233 <span class="s">}</span>
|
|
|
247 234 <span class="k">else</span> <span class="s">{</span>
|
|
|
248 235 <span class="k">push</span> <span class="i">@NucleicAcidIDs</span><span class="cm">,</span> <span class="q">'A'</span><span class="sc">;</span>
|
|
|
249 236 <span class="s">}</span>
|
|
|
250 237 <span class="s">}</span>
|
|
|
251 238
|
|
|
252 239 <span class="c"># Generate list of nucleic acids...</span>
|
|
|
253 240 <span class="k">if</span> <span class="s">(</span><span class="i">@ARGV</span> == <span class="n">1</span> && <span class="i">$ARGV</span>[<span class="n">0</span>] =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
254 241 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedNucleicAcidIDs</span>}}<span class="cm">,</span> <span class="i">NucleicAcids::GetNucleicAcids</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
255 242 <span class="s">}</span>
|
|
|
256 243 <span class="k">else</span> <span class="s">{</span>
|
|
|
257 244 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/NucleicAcidID/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
258 245 <span class="j">ID:</span> <span class="k">for</span> <span class="i">$NucleicAcidID</span> <span class="s">(</span><span class="i">@NucleicAcidIDs</span><span class="s">)</span> <span class="s">{</span>
|
|
|
259 246 <span class="k">if</span> <span class="s">(</span><span class="i">NucleicAcids::IsNucleicAcid</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
260 247 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedNucleicAcidIDs</span>}}<span class="cm">,</span> <span class="i">$NucleicAcidID</span><span class="sc">;</span>
|
|
|
261 248 <span class="s">}</span>
|
|
|
262 249 <span class="k">else</span> <span class="s">{</span>
|
|
|
263 250 <span class="k">warn</span> <span class="q">"Ignoring nucleic acid ID, $NucleicAcidID, specified using command line parameter option: Unknown nucleic acid ID...\n"</span><span class="sc">;</span>
|
|
|
264 251 <span class="k">next</span> <span class="j">ID</span><span class="sc">;</span>
|
|
|
265 252 <span class="s">}</span>
|
|
|
266 253 <span class="s">}</span>
|
|
|
267 254 <span class="s">}</span>
|
|
|
268 255 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/NucleicAcidType/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
269 256 <span class="j">ID:</span> <span class="k">for</span> <span class="i">$NucleicAcidID</span> <span class="s">(</span><span class="i">@NucleicAcidIDs</span><span class="s">)</span> <span class="s">{</span>
|
|
|
270 257 <span class="k">if</span> <span class="s">(</span>!<span class="i">NucleicAcids::IsNucleicAcidType</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
271 258 <span class="k">warn</span> <span class="q">"Ignoring nucleic acid type, $NucleicAcidID, specified using command line parameter option: Unknown nucleic acid type...\n"</span><span class="sc">;</span>
|
|
|
272 259 <span class="k">next</span> <span class="j">ID</span><span class="sc">;</span>
|
|
|
273 260 <span class="s">}</span>
|
|
|
274 261 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedNucleicAcidIDs</span>}}<span class="cm">,</span> <span class="i">NucleicAcids::GetNucleicAcidsByType</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span><span class="sc">;</span>
|
|
|
275 262 <span class="s">}</span>
|
|
|
276 263 <span class="s">}</span>
|
|
|
277 264 <span class="s">}</span>
|
|
|
278 265 <span class="i">SetupSpecifiedProperties</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
279 266
|
|
|
280 267 <span class="c"># Setup output file name...</span>
|
|
|
281 268 <span class="i">$OptionsInfo</span>{<span class="w">OutFileName</span>} = <span class="q">''</span><span class="sc">;</span>
|
|
|
282 269 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
283 270 <span class="k">my</span><span class="s">(</span><span class="i">$OutFileRoot</span><span class="cm">,</span> <span class="i">$OutFileExt</span><span class="s">)</span><span class="sc">;</span>
|
|
|
284 271
|
|
|
285 272 <span class="i">$OutFileRoot</span> = <span class="q">''</span><span class="sc">;</span>
|
|
|
286 273 <span class="i">$OutFileExt</span> = <span class="q">"csv"</span><span class="sc">;</span>
|
|
|
287 274 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/^tab$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
288 275 <span class="i">$OutFileExt</span> = <span class="q">"tsv"</span><span class="sc">;</span>
|
|
|
289 276 <span class="s">}</span>
|
|
|
290 277 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">root</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
291 278 <span class="k">my</span> <span class="s">(</span><span class="i">$RootFileDir</span><span class="cm">,</span> <span class="i">$RootFileName</span><span class="cm">,</span> <span class="i">$RootFileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">root</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
292 279 <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> && <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span>
|
|
|
293 280 <span class="i">$OutFileRoot</span> = <span class="i">$RootFileName</span><span class="sc">;</span>
|
|
|
294 281 <span class="s">}</span>
|
|
|
295 282 <span class="k">else</span> <span class="s">{</span>
|
|
|
296 283 <span class="i">$OutFileRoot</span> = <span class="i">$Options</span>{<span class="w">root</span>}<span class="sc">;</span>
|
|
|
297 284 <span class="s">}</span>
|
|
|
298 285 <span class="s">}</span>
|
|
|
299 286 <span class="k">else</span> <span class="s">{</span>
|
|
|
300 287 <span class="i">$OutFileRoot</span> = <span class="q">'NucleicAcidsInfo'</span><span class="sc">;</span>
|
|
|
301 288 <span class="s">}</span>
|
|
|
302 289 <span class="i">$OptionsInfo</span>{<span class="w">OutFileName</span>} = <span class="i">$OutFileRoot</span> . <span class="q">'.'</span> . <span class="i">$OutFileExt</span><span class="sc">;</span>
|
|
|
303 290 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">overwrite</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
304 291 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$OptionsInfo</span>{<span class="w">OutFileName</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
305 292 <span class="k">die</span> <span class="q">"Error: Output file, $OptionsInfo{OutFileName}, already exists.\nUse \-o --overwrite\ option or specify a different name using \"-r --root\" option.\n"</span><span class="sc">;</span>
|
|
|
306 293 <span class="s">}</span>
|
|
|
307 294 <span class="s">}</span>
|
|
|
308 295 <span class="s">}</span>
|
|
|
309 296 <span class="s">}</span>
|
|
|
310 297
|
|
|
311 298 <span class="c"># Setup properties to list...</span>
|
|
|
312 <a name="SetupSpecifiedProperties-"></a> 299 <span class="k">sub </span><span class="m">SetupSpecifiedProperties</span> <span class="s">{</span>
|
|
|
313 300
|
|
|
314 301 <span class="i">$OptionsInfo</span>{<span class="w">Properties</span>} = <span class="k">defined</span> <span class="i">$Options</span>{<span class="w">properties</span>} ? <span class="i">$Options</span>{<span class="w">properties</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
315 302
|
|
|
316 303 <span class="i">$OptionsInfo</span>{<span class="w">PropertiesMode</span>} = <span class="i">$Options</span>{<span class="w">propertiesmode</span>}<span class="sc">;</span>
|
|
|
317 304 <span class="i">$OptionsInfo</span>{<span class="w">PropertiesListing</span>} = <span class="i">$Options</span>{<span class="w">propertieslisting</span>}<span class="sc">;</span>
|
|
|
318 305
|
|
|
319 306 <span class="c"># Make sure appropriate properties/category names are specified...</span>
|
|
|
320 307 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
321 308 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">properties</span>} && <span class="s">(</span><span class="i">$Options</span>{<span class="w">propertiesmode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
322 309 <span class="k">warn</span> <span class="q">"Warning: Ignoring values specifed by \"-p --properties\" option: Not valid for All value of \"--propertiesmode\" option...\n"</span><span class="sc">;</span>
|
|
|
323 310 <span class="s">}</span>
|
|
|
324 311 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">propertiesmode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
325 312 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">propertieslisting</span>} =~ <span class="q">/^Alphabetical$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
326 313 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="cm">,</span> <span class="i">NucleicAcids::GetNucleicAcidPropertiesNames</span><span class="s">(</span><span class="q">'Alphabetical'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
327 314 <span class="s">}</span>
|
|
|
328 315 <span class="k">else</span> <span class="s">{</span>
|
|
|
329 316 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="cm">,</span> <span class="i">NucleicAcids::GetNucleicAcidPropertiesNames</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
330 317 <span class="s">}</span>
|
|
|
331 318 <span class="s">}</span>
|
|
|
332 319 <span class="k">else</span> <span class="s">{</span>
|
|
|
333 320 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">properties</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
334 321 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">propertiesmode</span>} =~ <span class="q">/^Categories$/i</span><span class="s">)</span> <span class="s">{</span>
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|
|
335 322 <span class="c"># Check category name...</span>
|
|
|
336 323 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">properties</span>} !~ <span class="q">/^(Basic|BasicPlus)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
337 324 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{properties}, for option \"-p --properties\" in conjunction with \"Categories\" value for option \"--propertiesmode\" is not valid. Allowed values: Basic and BasicPlus\n"</span><span class="sc">;</span>
|
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|
338 325 <span class="s">}</span>
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|
|
339 326 <span class="c"># Set propertynames...</span>
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|
340 327 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="cm">,</span> <span class="i">GetPropertyNamesFromCategories</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">properties</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
341 328 <span class="s">}</span>
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|
342 329 <span class="k">else</span> <span class="s">{</span>
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|
343 330 <span class="c"># Check property names..</span>
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|
344 331 <span class="k">my</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$PropertyName</span><span class="cm">,</span> <span class="i">@Names</span><span class="s">)</span><span class="sc">;</span>
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|
|
345 332 <span class="i">@Names</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">properties</span>}<span class="sc">;</span>
|
|
|
346 333 <span class="j">NAME:</span> <span class="k">for</span> <span class="i">$Name</span> <span class="s">(</span><span class="i">@Names</span><span class="s">)</span> <span class="s">{</span>
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|
|
347 334 <span class="i">$PropertyName</span> = <span class="i">RemoveLeadingAndTrailingWhiteSpaces</span><span class="s">(</span><span class="i">$Name</span><span class="s">)</span><span class="sc">;</span>
|
|
|
348 335 <span class="k">if</span> <span class="s">(</span><span class="i">NucleicAcids::IsNucleicAcidProperty</span><span class="s">(</span><span class="i">$PropertyName</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
349 336 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="cm">,</span> <span class="i">$PropertyName</span><span class="sc">;</span>
|
|
|
350 337 <span class="s">}</span>
|
|
|
351 338 <span class="k">else</span> <span class="s">{</span>
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|
352 339 <span class="k">warn</span> <span class="q">"Warning: Ignoring value, $Name, specifed by \"-p --properties\" option: Unknown property name...\n"</span><span class="sc">;</span>
|
|
|
353 340 <span class="s">}</span>
|
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|
354 341 <span class="s">}</span>
|
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|
355 342 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">propertieslisting</span>} =~ <span class="q">/^Alphabetical$/i</span><span class="s">)</span> <span class="s">{</span>
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|
356 343 <span class="c"># Code, OtherCodes and Name are always listed first...</span>
|
|
|
357 344 <span class="k">my</span><span class="s">(</span><span class="i">$CodePresent</span><span class="cm">,</span> <span class="i">$OtherCodesPresent</span><span class="cm">,</span> <span class="i">$NamePresent</span><span class="cm">,</span> <span class="i">@AlphabeticalProperties</span><span class="cm">,</span> <span class="i">%PropertiesMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
358 345 <span class="i">%PropertiesMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
359 346 <span class="i">@AlphabeticalProperties</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
360 347 <span class="i">$CodePresent</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$OtherCodesPresent</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$NamePresent</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
361 348 <span class="j">NAME:</span> <span class="k">for</span> <span class="i">$Name</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
362 349 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^Code$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
363 350 <span class="i">$CodePresent</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
364 351 <span class="k">next</span> <span class="j">NAME</span><span class="sc">;</span>
|
|
|
365 352 <span class="s">}</span>
|
|
|
366 353 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^OtherCodes$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
367 354 <span class="i">$OtherCodesPresent</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
368 355 <span class="k">next</span> <span class="j">NAME</span><span class="sc">;</span>
|
|
|
369 356 <span class="s">}</span>
|
|
|
370 357 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^Name$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
371 358 <span class="i">$NamePresent</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
372 359 <span class="k">next</span> <span class="j">NAME</span><span class="sc">;</span>
|
|
|
373 360 <span class="s">}</span>
|
|
|
374 361 <span class="i">$PropertiesMap</span>{<span class="i">$Name</span>} = <span class="i">$Name</span><span class="sc">;</span>
|
|
|
375 362 <span class="s">}</span>
|
|
|
376 363 <span class="c"># Setup the alphabetical list...</span>
|
|
|
377 364 <span class="k">if</span> <span class="s">(</span><span class="i">$CodePresent</span><span class="s">)</span> <span class="s">{</span>
|
|
|
378 365 <span class="k">push</span> <span class="i">@AlphabeticalProperties</span><span class="cm">,</span> <span class="q">'Code'</span><span class="sc">;</span>
|
|
|
379 366 <span class="s">}</span>
|
|
|
380 367 <span class="k">if</span> <span class="s">(</span><span class="i">$OtherCodesPresent</span><span class="s">)</span> <span class="s">{</span>
|
|
|
381 368 <span class="k">push</span> <span class="i">@AlphabeticalProperties</span><span class="cm">,</span> <span class="q">'OtherCodesPresent'</span><span class="sc">;</span>
|
|
|
382 369 <span class="s">}</span>
|
|
|
383 370 <span class="k">if</span> <span class="s">(</span><span class="i">$NamePresent</span><span class="s">)</span> <span class="s">{</span>
|
|
|
384 371 <span class="k">push</span> <span class="i">@AlphabeticalProperties</span><span class="cm">,</span> <span class="q">'Name'</span><span class="sc">;</span>
|
|
|
385 372 <span class="s">}</span>
|
|
|
386 373 <span class="k">for</span> <span class="i">$Name</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%PropertiesMap</span><span class="s">)</span> <span class="s">{</span>
|
|
|
387 374 <span class="k">push</span> <span class="i">@AlphabeticalProperties</span><span class="cm">,</span> <span class="i">$Name</span><span class="sc">;</span>
|
|
|
388 375 <span class="s">}</span>
|
|
|
389 376 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
390 377 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="cm">,</span> <span class="i">@AlphabeticalProperties</span><span class="sc">;</span>
|
|
|
391 378 <span class="s">}</span>
|
|
|
392 379 <span class="s">}</span>
|
|
|
393 380 <span class="s">}</span>
|
|
|
394 381 <span class="k">else</span> <span class="s">{</span>
|
|
|
395 382 <span class="c"># Set default value...</span>
|
|
|
396 383 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="cm">,</span> <span class="i">GetPropertyNamesFromCategories</span><span class="s">(</span><span class="q">'Basic'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
397 384 <span class="s">}</span>
|
|
|
398 385 <span class="s">}</span>
|
|
|
399 386 <span class="s">}</span>
|
|
|
400 387
|
|
|
401 388 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span>
|
|
|
402 <a name="SetupScriptUsage-"></a> 389 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
|
|
|
403 390
|
|
|
404 391 <span class="c"># Retrieve all the options...</span>
|
|
|
405 392 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
406 393 <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">"NucleicAcidID"</span><span class="sc">;</span>
|
|
|
407 394 <span class="i">$Options</span>{<span class="w">outdelim</span>} = <span class="q">"comma"</span><span class="sc">;</span>
|
|
|
408 395 <span class="i">$Options</span>{<span class="w">output</span>} = <span class="q">"STDOUT"</span><span class="sc">;</span>
|
|
|
409 396 <span class="i">$Options</span>{<span class="w">outputstyle</span>} = <span class="q">"NucleicAcidBlock"</span><span class="sc">;</span>
|
|
|
410 397 <span class="i">$Options</span>{<span class="w">precision</span>} = <span class="n">4</span><span class="sc">;</span>
|
|
|
411 398 <span class="i">$Options</span>{<span class="w">propertiesmode</span>} = <span class="q">"Categories"</span><span class="sc">;</span>
|
|
|
412 399 <span class="i">$Options</span>{<span class="w">propertieslisting</span>} = <span class="q">"ByGroup"</span><span class="sc">;</span>
|
|
|
413 400 <span class="i">$Options</span>{<span class="w">quote</span>} = <span class="q">"yes"</span><span class="sc">;</span>
|
|
|
414 401
|
|
|
415 402 <span class="k">if</span> <span class="s">(</span>!<span class="i">GetOptions</span><span class="s">(</span>\<span class="i">%Options</span><span class="cm">,</span> <span class="q">"help|h"</span><span class="cm">,</span> <span class="q">"mode|m=s"</span><span class="cm">,</span> <span class="q">"outdelim=s"</span><span class="cm">,</span> <span class="q">"output=s"</span><span class="cm">,</span> <span class="q">"outputstyle=s"</span><span class="cm">,</span> <span class="q">"overwrite|o"</span><span class="cm">,</span> <span class="q">"precision=i"</span><span class="cm">,</span> <span class="q">"properties|p=s"</span><span class="cm">,</span> <span class="q">"propertieslisting=s"</span><span class="cm">,</span> <span class="q">"propertiesmode=s"</span><span class="cm">,</span> <span class="q">"quote|q=s"</span><span class="cm">,</span> <span class="q">"root|r=s"</span><span class="cm">,</span> <span class="q">"workingdir|w=s"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
416 403 <span class="k">die</span> <span class="q">"\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"</span><span class="sc">;</span>
|
|
|
417 404 <span class="s">}</span>
|
|
|
418 405 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
419 406 <span class="k">if</span> <span class="s">(</span>! <span class="k">-d</span> <span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
420 407 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"</span><span class="sc">;</span>
|
|
|
421 408 <span class="s">}</span>
|
|
|
422 409 <span class="k">chdir</span> <span class="i">$Options</span>{<span class="w">workingdir</span>} <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't chdir $Options{workingdir}: $! \n"</span><span class="sc">;</span>
|
|
|
423 410 <span class="s">}</span>
|
|
|
424 411 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} !~ <span class="q">/^(NucleicAcidID|NucleicAcidType)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
425 412 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{mode}, for option \"--mode\" is not valid. Allowed values: NucleicAcidID or NucleicAcidType\n"</span><span class="sc">;</span>
|
|
|
426 413 <span class="s">}</span>
|
|
|
427 414 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} !~ <span class="q">/^(comma|semicolon|tab)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
428 415 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n"</span><span class="sc">;</span>
|
|
|
429 416 <span class="s">}</span>
|
|
|
430 417 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} !~ <span class="q">/^(STDOUT|File)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
431 418 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: STDOUT or File\n"</span><span class="sc">;</span>
|
|
|
432 419 <span class="s">}</span>
|
|
|
433 420 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outputstyle</span>} !~ <span class="q">/^(NucleicAcidBlock|NucleicAcidRows)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
434 421 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{outputstyle}, for option \"--outputstyle\" is not valid. Allowed values: NucleicAcidBlock or NucleicAcidRows\n"</span><span class="sc">;</span>
|
|
|
435 422 <span class="s">}</span>
|
|
|
436 423 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">precision</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
437 424 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{precision}, for option \"-p --precision\" is not valid. Allowed values: > 0 \n"</span><span class="sc">;</span>
|
|
|
438 425 <span class="s">}</span>
|
|
|
439 426 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">propertiesmode</span>} !~ <span class="q">/^(Categories|Names|All)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
440 427 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{propertiesmode}, for option \"--propertiesmode\" is not valid. Allowed values: Categories, Names, or All\n"</span><span class="sc">;</span>
|
|
|
441 428 <span class="s">}</span>
|
|
|
442 429 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">propertieslisting</span>} !~ <span class="q">/^(ByGroup|Alphabetical)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
443 430 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{propertieslisting}, for option \"--propertieslisting\" is not valid. Allowed values: ByGroup, or Alphabetical\n"</span><span class="sc">;</span>
|
|
|
444 431 <span class="s">}</span>
|
|
|
445 432 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
446 433 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: yes or no\n"</span><span class="sc">;</span>
|
|
|
447 434 <span class="s">}</span>
|
|
|
448 435 <span class="s">}</span>
|
|
|
449 436
|
|
|
450 <a name="EOF-"></a></pre>
|
|
|
451 <p> </p>
|
|
|
452 <br />
|
|
|
453 <center>
|
|
|
454 <img src="../../../images/h2o2.png">
|
|
|
455 </center>
|
|
|
456 </body>
|
|
|
457 </html>
|
