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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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<html> <head> <title>MayaChemTools:Code:InfoAminoAcids.pl</title> <meta http-equiv="content-type" content="text/html;charset=utf-8"> <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> </head> <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> <br/> <center> <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> </center> <br/> <pre> 1 #!/usr/bin/perl -w 2 <span class="c">#</span> 3 <span class="c"># $RCSfile: InfoAminoAcids.pl,v $</span> 4 <span class="c"># $Date: 2015/02/28 20:46:20 $</span> 5 <span class="c"># $Revision: 1.26 $</span> 6 <span class="c">#</span> 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> 8 <span class="c">#</span> 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> 10 <span class="c">#</span> 11 <span class="c"># This file is part of MayaChemTools.</span> 12 <span class="c">#</span> 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> 16 <span class="c"># later version.</span> 17 <span class="c">#</span> 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> 21 <span class="c"># details.</span> 22 <span class="c">#</span> 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> 27 <span class="c">#</span> 28 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> 30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">"$FindBin::Bin/../lib"</span><span class="sc">;</span> 31 <span class="k">use</span> <span class="w">Getopt::Long</span><span class="sc">;</span> 32 <span class="k">use</span> <span class="w">File::Basename</span><span class="sc">;</span> 33 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span> 34 <span class="k">use</span> <span class="w">Benchmark</span><span class="sc">;</span> 35 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span> 36 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span> 37 <span class="k">use</span> <span class="w">AminoAcids</span><span class="sc">;</span> 38 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> 40 41 <span class="c"># Autoflush STDOUT</span> 42 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span> 43 44 <span class="c"># Starting message...</span> 45 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span> 46 <span class="k">print</span> <span class="q">"\n$ScriptName: Starting...\n\n"</span><span class="sc">;</span> 47 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span> 48 49 <span class="c"># Get the options and setup script...</span> 50 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 51 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">help</span>}<span class="s">)</span> <span class="s">{</span> 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> 53 <span class="s">}</span> 54 55 <span class="k">print</span> <span class="q">"Processing options...\n"</span><span class="sc">;</span> 56 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span> 57 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 58 59 <span class="i">ListAminoAcidProperties</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 60 <span class="k">print</span> <span class="q">"\n$ScriptName:Done...\n\n"</span><span class="sc">;</span> 61 62 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span> 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">$StartTime</span><span class="s">)</span><span class="sc">;</span> 64 <span class="k">print</span> <span class="q">"Total time: "</span><span class="cm">,</span> <span class="i">timestr</span><span class="s">(</span><span class="i">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> 65 66 <span class="c">###############################################################################</span> 67 68 <span class="c"># List data for an amino acid...</span> <a name="ListAminoAcidData-"></a> 69 <span class="k">sub </span><span class="m">ListAminoAcidData</span> <span class="s">{</span> 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> 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">$Value</span><span class="s">)</span><span class="sc">;</span> 72 73 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">AminoAcidRowsOutput</span>}<span class="s">)</span> <span class="s">{</span> 74 <span class="i">$Line</span> = <span class="q">''</span><span class="sc">;</span> 75 <span class="c"># Format data...</span> 76 <span class="k">if</span> <span class="s">(</span><span class="i">$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> 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> 78 <span class="s">}</span> 79 <span class="k">else</span> <span class="s">{</span> 80 <span class="c"># Always quote values containing commas...</span> 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> 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">$DataValueRef</span>} <span class="s">)</span> <span class="s">{</span> 83 <span class="i">$Value</span> = <span class="i">$DataValueRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> 84 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> =~ <span class="q">/\,/</span><span class="s">)</span> <span class="s">{</span> 85 <span class="i">$Value</span> = <span class="q">qq("$Value")</span><span class="sc">;</span> 86 <span class="s">}</span> 87 <span class="i">$Line</span> .= <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>} . <span class="i">$Value</span><span class="sc">;</span> 88 <span class="s">}</span> 89 <span class="s">}</span> 90 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span> 91 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$Line\n"</span><span class="sc">;</span> 92 <span class="s">}</span> 93 <span class="k">else</span> <span class="s">{</span> 94 <span class="k">print</span> <span class="q">"$Line\n"</span><span class="sc">;</span> 95 <span class="s">}</span> 96 <span class="s">}</span> 97 <span class="k">else</span> <span class="s">{</span> 98 <span class="c"># Format and list data...</span> 99 <span class="i">$Line</span> = <span class="q">''</span><span class="sc">;</span> 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">$DataLabelRef</span>} <span class="s">)</span> <span class="s">{</span> 101 <span class="i">$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> 102 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span> 103 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$Line\n"</span><span class="sc">;</span> 104 <span class="s">}</span> 105 <span class="k">else</span> <span class="s">{</span> 106 <span class="k">print</span> <span class="q">"$Line\n"</span><span class="sc">;</span> 107 <span class="s">}</span> 108 <span class="s">}</span> 109 <span class="s">}</span> 110 <span class="s">}</span> 111 112 <span class="c"># List data for an amino acid...</span> <a name="ListHeaderRowData-"></a> 113 <span class="k">sub </span><span class="m">ListHeaderRowData</span> <span class="s">{</span> 114 <span class="k">my</span><span class="s">(</span><span class="i">$DataLabelRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 115 <span class="k">my</span><span class="s">(</span><span class="i">$Line</span><span class="s">)</span><span class="sc">;</span> 116 117 <span class="c"># Format data...</span> 118 <span class="i">$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">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span> 119 <span class="i">$Line</span> =~ <span class="q">s/\://g</span><span class="sc">;</span> 120 <span class="c"># List data...</span> 121 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span> 122 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$Line\n"</span><span class="sc">;</span> 123 <span class="s">}</span> 124 <span class="k">else</span> <span class="s">{</span> 125 <span class="k">print</span> <span class="q">"$Line\n"</span><span class="sc">;</span> 126 <span class="s">}</span> 127 <span class="s">}</span> 128 129 <span class="c"># List properties for amino acids...</span> <a name="ListAminoAcidProperties-"></a> 130 <span class="k">sub </span><span class="m">ListAminoAcidProperties</span> <span class="s">{</span> 131 <span class="k">my</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="cm">,</span> <span class="i">$AminoAcidDataRef</span><span class="cm">,</span> <span class="i">$PropertyName</span><span class="cm">,</span> <span class="i">$PropertyValue</span><span class="cm">,</span> <span class="i">@PropertyLabels</span><span class="cm">,</span> <span class="i">@PropertyValues</span><span class="s">)</span><span class="sc">;</span> 132 133 <span class="k">print</span> <span class="q">"Listing information for amino acid(s)...\n"</span><span class="sc">;</span> 134 135 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span> 136 <span class="k">print</span> <span class="q">"Generating file $OptionsInfo{OutFileName}...\n"</span><span class="sc">;</span> 137 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">">$OptionsInfo{OutFileName}"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Couldn't open $OptionsInfo{OutFileName}: $!\n"</span><span class="sc">;</span> 138 <span class="s">}</span> 139 140 <span class="c"># Setup property labels...</span> 141 <span class="i">@PropertyLabels</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 142 <span class="k">for</span> <span class="i">$PropertyName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="s">)</span> <span class="s">{</span> 143 <span class="k">push</span> <span class="i">@PropertyLabels</span><span class="cm">,</span> <span class="s">(</span><span class="q">"$PropertyName:"</span><span class="s">)</span><span class="sc">;</span> 144 <span class="s">}</span> 145 146 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">AminoAcidRowsOutput</span>}<span class="s">)</span> <span class="s">{</span> 147 <span class="i">ListHeaderRowData</span><span class="s">(</span>\<span class="i">@PropertyLabels</span><span class="s">)</span><span class="sc">;</span> 148 <span class="s">}</span> 149 150 <span class="c"># Go over specified properties...</span> 151 <span class="k">for</span> <span class="i">$AminoAcidID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAminoAcidIDs</span>}}<span class="s">)</span> <span class="s">{</span> 152 <span class="i">$AminoAcidDataRef</span> = <span class="i">AminoAcids::GetAminoAcidPropertiesData</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="s">)</span><span class="sc">;</span> 153 154 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">AminoAcidRowsOutput</span>}<span class="s">)</span> <span class="s">{</span> 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> 156 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"\nListing properties for amino acid $AminoAcidID...\n\n"</span><span class="sc">;</span> 157 <span class="s">}</span> 158 <span class="k">else</span> <span class="s">{</span> 159 <span class="k">print</span> <span class="q">"\nListing properties for amino acid $AminoAcidID...\n\n"</span><span class="sc">;</span> 160 <span class="s">}</span> 161 <span class="s">}</span> 162 163 <span class="c"># Collect data..</span> 164 <span class="i">@PropertyValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 165 <span class="k">for</span> <span class="i">$PropertyName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="s">)</span> <span class="s">{</span> 166 <span class="i">$PropertyValue</span> = <span class="i">$AminoAcidDataRef</span>->{<span class="i">$PropertyName</span>}<span class="sc">;</span> 167 <span class="k">if</span> <span class="s">(</span><span class="i">IsFloat</span><span class="s">(</span><span class="i">$PropertyValue</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 168 <span class="i">$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> 169 <span class="s">}</span> 170 <span class="k">push</span> <span class="i">@PropertyValues</span><span class="cm">,</span> <span class="i">$PropertyValue</span><span class="sc">;</span> 171 <span class="s">}</span> 172 <span class="c"># List data...</span> 173 <span class="i">ListAminoAcidData</span><span class="s">(</span>\<span class="i">@PropertyLabels</span><span class="cm">,</span> \<span class="i">@PropertyValues</span><span class="s">)</span><span class="sc">;</span> 174 <span class="s">}</span> 175 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span> 176 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span> 177 <span class="s">}</span> 178 <span class="k">print</span> <span class="q">"\n"</span><span class="sc">;</span> 179 <span class="s">}</span> 180 181 <span class="c"># Get propery names from categories...</span> <a name="GetPropertyNamesFromCategories-"></a> 182 <span class="k">sub </span><span class="m">GetPropertyNamesFromCategories</span> <span class="s">{</span> 183 <span class="k">my</span><span class="s">(</span><span class="i">$CategoryName</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 184 <span class="k">my</span><span class="s">(</span><span class="i">@PropertyNames</span><span class="s">)</span><span class="sc">;</span> 185 186 <span class="i">@PropertyNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 187 <span class="k">if</span> <span class="s">(</span><span class="i">$CategoryName</span> =~ <span class="q">/^Basic$/i</span><span class="s">)</span> <span class="s">{</span> 188 <span class="i">@PropertyNames</span> = <span class="s">(</span><span class="q">'ThreeLetterCode'</span><span class="cm">,</span> <span class="q">'OneLetterCode'</span><span class="cm">,</span> <span class="q">'AminoAcid'</span><span class="cm">,</span> <span class="q">'DNACodons'</span><span class="cm">,</span> <span class="q">'RNACodons'</span><span class="cm">,</span> <span class="q">'ChemicalFormula'</span><span class="cm">,</span><span class="q">'MolecularWeight'</span><span class="cm">,</span> <span class="q">'LinearStructure'</span><span class="cm">,</span> <span class="q">'LinearStructureAtpH7.4'</span><span class="s">)</span><span class="sc">;</span> 189 <span class="s">}</span> <span class="k">elsif</span> <span class="s">(</span><span class="i">$CategoryName</span> =~ <span class="q">/^BasicPlus$/i</span><span class="s">)</span> <span class="s">{</span> 190 <span class="i">@PropertyNames</span> = <span class="s">(</span><span class="q">'ThreeLetterCode'</span><span class="cm">,</span> <span class="q">'OneLetterCode'</span><span class="cm">,</span> <span class="q">'AminoAcid'</span><span class="cm">,</span> <span class="q">'DNACodons'</span><span class="cm">,</span> <span class="q">'RNACodons'</span><span class="cm">,</span> <span class="q">'AcidicBasic'</span><span class="cm">,</span> <span class="q">'PolarNonpolar'</span><span class="cm">,</span> <span class="q">'Charged'</span><span class="cm">,</span> <span class="q">'Aromatic'</span><span class="cm">,</span> <span class="q">'HydrophobicHydophilic'</span><span class="cm">,</span> <span class="q">'IsoelectricPoint'</span><span class="cm">,</span> <span class="q">'pKCOOH'</span><span class="cm">,</span> <span class="q">'pKNH3+'</span><span class="cm">,</span> <span class="q">'ChemicalFormula'</span><span class="cm">,</span> <span class="q">'MolecularWeight'</span><span class="cm">,</span> <span class="q">'ExactMass'</span><span class="cm">,</span> <span class="q">'ChemicalFormulaMinusH2O'</span><span class="cm">,</span> <span class="q">'MolecularWeightMinusH2O(18.01524)'</span><span class="cm">,</span> <span class="q">'ExactMassMinusH2O(18.01056)'</span><span class="cm">,</span><span class="q">'LinearStructure'</span><span class="cm">,</span> <span class="q">'LinearStructureAtpH7.4'</span><span class="s">)</span><span class="sc">;</span> 191 <span class="s">}</span> <span class="k">elsif</span> <span class="s">(</span><span class="i">$CategoryName</span> =~ <span class="q">/^BasicAndHydrophobicity$/i</span><span class="s">)</span> <span class="s">{</span> 192 <span class="i">@PropertyNames</span> = <span class="s">(</span><span class="q">'ThreeLetterCode'</span><span class="cm">,</span> <span class="q">'OneLetterCode'</span><span class="cm">,</span> <span class="q">'AminoAcid'</span><span class="cm">,</span> <span class="q">'DNACodons'</span><span class="cm">,</span> <span class="q">'RNACodons'</span><span class="cm">,</span> <span class="q">'ChemicalFormula'</span><span class="cm">,</span> <span class="q">'MolecularWeight'</span><span class="cm">,</span> <span class="q">'LinearStructure'</span><span class="cm">,</span> <span class="q">'LinearStructureAtpH7.4'</span><span class="cm">,</span> <span class="q">'HydrophobicityEisenbergAndOthers'</span><span class="cm">,</span> <span class="q">'HydrophobicityHoppAndWoods'</span><span class="cm">,</span> <span class="q">'HydrophobicityJanin'</span><span class="cm">,</span> <span class="q">'HydrophobicityKyteAndDoolittle'</span><span class="cm">,</span> <span class="q">'HydrophobicityRoseAndOthers'</span><span class="cm">,</span> <span class="q">'HydrophobicityWolfendenAndOthers'</span><span class="s">)</span><span class="sc">;</span> 193 <span class="s">}</span> <span class="k">elsif</span> <span class="s">(</span><span class="i">$CategoryName</span> =~ <span class="q">/^BasicAndHydrophobicityPlus$/i</span><span class="s">)</span> <span class="s">{</span> 194 <span class="i">@PropertyNames</span> = <span class="s">(</span><span class="q">'ThreeLetterCode'</span><span class="cm">,</span> <span class="q">'OneLetterCode'</span><span class="cm">,</span> <span class="q">'AminoAcid'</span><span class="cm">,</span> <span class="q">'DNACodons'</span><span class="cm">,</span> <span class="q">'RNACodons'</span><span class="cm">,</span> <span class="q">'ChemicalFormula'</span><span class="cm">,</span> <span class="q">'MolecularWeight'</span><span class="cm">,</span> <span class="q">'LinearStructure'</span><span class="cm">,</span> <span class="q">'LinearStructureAtpH7.4'</span><span class="cm">,</span> <span class="q">'HydrophobicityAbrahamAndLeo'</span><span class="cm">,</span> <span class="q">'HydrophobicityBlack'</span><span class="cm">,</span> <span class="q">'HydrophobicityBullAndBreese'</span><span class="cm">,</span> <span class="q">'HydrophobicityChothia'</span><span class="cm">,</span> <span class="q">'HydrophobicityEisenbergAndOthers'</span><span class="cm">,</span> <span class="q">'HydrophobicityFauchereAndOthers'</span><span class="cm">,</span> <span class="q">'HydrophobicityGuy'</span><span class="cm">,</span> <span class="q">'HydrophobicityHPLCAtpH3.4Cowan'</span><span class="cm">,</span> <span class="q">'HydrophobicityHPLCAtpH7.5Cowan'</span><span class="cm">,</span> <span class="q">'HydrophobicityHPLCParkerAndOthers'</span><span class="cm">,</span> <span class="q">'HydrophobicityHPLCWilsonAndOthers'</span><span class="cm">,</span> <span class="q">'HydrophobicityHoppAndWoods'</span><span class="cm">,</span> <span class="q">'HydrophobicityJanin'</span><span class="cm">,</span> <span class="q">'HydrophobicityKyteAndDoolittle'</span><span class="cm">,</span> <span class="q">'HydrophobicityManavalanAndOthers'</span><span class="cm">,</span> <span class="q">'HydrophobicityMiyazawaAndOthers'</span><span class="cm">,</span> <span class="q">'HydrophobicityOMHSweetAndOthers'</span><span class="cm">,</span> <span class="q">'HydrophobicityRaoAndArgos'</span><span class="cm">,</span> <span class="q">'HydrophobicityRfMobility'</span><span class="cm">,</span> <span class="q">'HydrophobicityRoseAndOthers'</span><span class="cm">,</span> <span class="q">'HydrophobicityRoseman'</span><span class="cm">,</span> <span class="q">'HydrophobicityWellingAndOthers'</span><span class="cm">,</span> <span class="q">'HydrophobicityWolfendenAndOthers'</span><span class="s">)</span><span class="sc">;</span> 195 <span class="s">}</span> 196 197 <span class="k">return</span> <span class="i">@PropertyNames</span><span class="sc">;</span> 198 <span class="s">}</span> 199 200 <span class="c"># Process option values...</span> <a name="ProcessOptions-"></a> 201 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span> 202 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 203 204 <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> 205 <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$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 206 207 <span class="i">$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> 208 <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">$Options</span>{<span class="w">root</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span> 209 210 <span class="i">$OptionsInfo</span>{<span class="w">OutputStyle</span>} = <span class="i">$Options</span>{<span class="w">outputstyle</span>}<span class="sc">;</span> 211 212 <span class="i">$OptionsInfo</span>{<span class="w">AminoAcidRowsOutput</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">outputstyle</span>} =~ <span class="q">/^AminoAcidRows$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 213 <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$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 214 215 <span class="i">$OptionsInfo</span>{<span class="w">Precision</span>} = <span class="i">$Options</span>{<span class="w">precision</span>}<span class="sc">;</span> 216 217 <span class="k">my</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="cm">,</span> <span class="i">@AminoAcidIDs</span><span class="s">)</span><span class="sc">;</span> 218 219 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAminoAcidIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 220 221 <span class="c"># Set up Amino Acids IDs except for All mode...</span> 222 <span class="i">@AminoAcidIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 223 224 <span class="k">if</span> <span class="s">(</span><span class="i">@ARGV</span> >= <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 225 <span class="k">push</span> <span class="i">@AminoAcidIDs</span><span class="cm">,</span> <span class="i">@ARGV</span><span class="sc">;</span> 226 <span class="s">}</span> 227 <span class="k">else</span> <span class="s">{</span> 228 <span class="c"># Setup mode specified default values...</span> 229 <span class="k">push</span> <span class="i">@AminoAcidIDs</span><span class="cm">,</span> <span class="q">'Ala'</span><span class="sc">;</span> 230 <span class="s">}</span> 231 232 <span class="c"># Generate list of amino acids...</span> 233 <span class="k">if</span> <span class="s">(</span><span class="i">@ARGV</span> == <span class="n">1</span> && <span class="i">$ARGV</span>[<span class="n">0</span>] =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span> 234 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAminoAcidIDs</span>}}<span class="cm">,</span> <span class="i">AminoAcids::GetAminoAcids</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 235 <span class="s">}</span> 236 <span class="k">else</span> <span class="s">{</span> 237 <span class="j">ID:</span> <span class="k">for</span> <span class="i">$AminoAcidID</span> <span class="s">(</span><span class="i">@AminoAcidIDs</span><span class="s">)</span> <span class="s">{</span> 238 <span class="k">if</span> <span class="s">(</span><span class="i">AminoAcids::IsAminoAcid</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 239 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAminoAcidIDs</span>}}<span class="cm">,</span> <span class="i">$AminoAcidID</span><span class="sc">;</span> 240 <span class="s">}</span> 241 <span class="k">else</span> <span class="s">{</span> 242 <span class="k">warn</span> <span class="q">"Ignoring amino acid ID, $AminoAcidID, specified using command line parameter option: Unknown amino acid ID...\n"</span><span class="sc">;</span> 243 <span class="k">next</span> <span class="j">ID</span><span class="sc">;</span> 244 <span class="s">}</span> 245 <span class="s">}</span> 246 <span class="s">}</span> 247 <span class="i">SetupSpecifiedProperties</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 248 249 <span class="c"># Setup output file name...</span> 250 <span class="i">$OptionsInfo</span>{<span class="w">OutFileName</span>} = <span class="q">''</span><span class="sc">;</span> 251 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span> 252 <span class="k">my</span><span class="s">(</span><span class="i">$OutFileRoot</span><span class="cm">,</span> <span class="i">$OutFileExt</span><span class="s">)</span><span class="sc">;</span> 253 254 <span class="i">$OutFileRoot</span> = <span class="q">''</span><span class="sc">;</span> 255 <span class="i">$OutFileExt</span> = <span class="q">"csv"</span><span class="sc">;</span> 256 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/^tab$/i</span><span class="s">)</span> <span class="s">{</span> 257 <span class="i">$OutFileExt</span> = <span class="q">"tsv"</span><span class="sc">;</span> 258 <span class="s">}</span> 259 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">root</span>}<span class="s">)</span> <span class="s">{</span> 260 <span class="k">my</span> <span class="s">(</span><span class="i">$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">$Options</span>{<span class="w">root</span>}<span class="s">)</span><span class="sc">;</span> 261 <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> && <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span> 262 <span class="i">$OutFileRoot</span> = <span class="i">$RootFileName</span><span class="sc">;</span> 263 <span class="s">}</span> 264 <span class="k">else</span> <span class="s">{</span> 265 <span class="i">$OutFileRoot</span> = <span class="i">$Options</span>{<span class="w">root</span>}<span class="sc">;</span> 266 <span class="s">}</span> 267 <span class="s">}</span> 268 <span class="k">else</span> <span class="s">{</span> 269 <span class="i">$OutFileRoot</span> = <span class="q">'AminoAcidsInfo'</span><span class="sc">;</span> 270 <span class="s">}</span> 271 <span class="i">$OptionsInfo</span>{<span class="w">OutFileName</span>} = <span class="i">$OutFileRoot</span> . <span class="q">'.'</span> . <span class="i">$OutFileExt</span><span class="sc">;</span> 272 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">overwrite</span>}<span class="s">)</span> <span class="s">{</span> 273 <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> 274 <span class="k">die</span> <span class="q">"Error: Output file, $OptionsInfo{OutFileName}, already exists.\nUse \-o --overwrite\ option or specify a different name using \"-r --root\" option.\n"</span><span class="sc">;</span> 275 <span class="s">}</span> 276 <span class="s">}</span> 277 <span class="s">}</span> 278 <span class="s">}</span> 279 280 <span class="c"># Setup properties to list...</span> <a name="SetupSpecifiedProperties-"></a> 281 <span class="k">sub </span><span class="m">SetupSpecifiedProperties</span> <span class="s">{</span> 282 283 <span class="i">$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> 284 285 <span class="i">$OptionsInfo</span>{<span class="w">PropertiesMode</span>} = <span class="i">$Options</span>{<span class="w">propertiesmode</span>}<span class="sc">;</span> 286 <span class="i">$OptionsInfo</span>{<span class="w">PropertiesListing</span>} = <span class="i">$Options</span>{<span class="w">propertieslisting</span>}<span class="sc">;</span> 287 288 <span class="c"># Make sure appropriate properties/category names are specified...</span> 289 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 290 <span class="k">if</span> <span class="s">(</span><span class="i">$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> 291 <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> 292 <span class="s">}</span> 293 <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> 294 <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> 295 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="cm">,</span> <span class="i">AminoAcids::GetAminoAcidPropertiesNames</span><span class="s">(</span><span class="q">'Alphabetical'</span><span class="s">)</span><span class="sc">;</span> 296 <span class="s">}</span> 297 <span class="k">else</span> <span class="s">{</span> 298 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="cm">,</span> <span class="i">AminoAcids::GetAminoAcidPropertiesNames</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 299 <span class="s">}</span> 300 <span class="s">}</span> 301 <span class="k">else</span> <span class="s">{</span> 302 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">properties</span>}<span class="s">)</span> <span class="s">{</span> 303 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">propertiesmode</span>} =~ <span class="q">/^Categories$/i</span><span class="s">)</span> <span class="s">{</span> 304 <span class="c"># Check category name...</span> 305 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">properties</span>} !~ <span class="q">/^(Basic|BasicPlus|BasicAndHydrophobicity|BasicAndHydrophobicityPlus)$/i</span><span class="s">)</span> <span class="s">{</span> 306 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{properties}, for option \"-p --properties\" in conjunction with \"Categories\" value for option \"--propertiesmode\" is not valid. Allowed values: Basic, BasicPlus, BasicAndHydrophobicity, and BasicAndHydrophobicityPlus\n"</span><span class="sc">;</span> 307 <span class="s">}</span> 308 <span class="c"># Set propertynames...</span> 309 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="cm">,</span> <span class="i">GetPropertyNamesFromCategories</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">properties</span>}<span class="s">)</span><span class="sc">;</span> 310 <span class="s">}</span> 311 <span class="k">else</span> <span class="s">{</span> 312 <span class="c"># Check property names..</span> 313 <span class="k">my</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$PropertyName</span><span class="cm">,</span> <span class="i">@Names</span><span class="s">)</span><span class="sc">;</span> 314 <span class="i">@Names</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">properties</span>}<span class="sc">;</span> 315 <span class="j">NAME:</span> <span class="k">for</span> <span class="i">$Name</span> <span class="s">(</span><span class="i">@Names</span><span class="s">)</span> <span class="s">{</span> 316 <span class="i">$PropertyName</span> = <span class="i">RemoveLeadingAndTrailingWhiteSpaces</span><span class="s">(</span><span class="i">$Name</span><span class="s">)</span><span class="sc">;</span> 317 <span class="k">if</span> <span class="s">(</span><span class="i">AminoAcids::IsAminoAcidProperty</span><span class="s">(</span><span class="i">$PropertyName</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 318 <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> 319 <span class="s">}</span> 320 <span class="k">else</span> <span class="s">{</span> 321 <span class="k">warn</span> <span class="q">"Warning: Ignoring value, $Name, specifed by \"-p --properties\" option: Unknown property name...\n"</span><span class="sc">;</span> 322 <span class="s">}</span> 323 <span class="s">}</span> 324 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">propertieslisting</span>} =~ <span class="q">/^Alphabetical$/i</span><span class="s">)</span> <span class="s">{</span> 325 <span class="c"># ThreeLetterCode, OneLetterCode and AminoAcid are always listed first...</span> 326 <span class="c"># NaturalIsotopeData in the end...</span> 327 <span class="k">my</span><span class="s">(</span><span class="i">$OneLetterCodePresent</span><span class="cm">,</span> <span class="i">$ThreeLetterCodePresent</span><span class="cm">,</span> <span class="i">$AminoAcidPresent</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> 328 <span class="i">%PropertiesMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 329 <span class="i">@AlphabeticalProperties</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 330 <span class="i">$OneLetterCodePresent</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$ThreeLetterCodePresent</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$AminoAcidPresent</span> = <span class="n">0</span><span class="sc">;</span> 331 <span class="j">NAME:</span> <span class="k">for</span> <span class="i">$Name</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="s">)</span> <span class="s">{</span> 332 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^OneLetterCode$/i</span><span class="s">)</span> <span class="s">{</span> 333 <span class="i">$OneLetterCodePresent</span> = <span class="n">1</span><span class="sc">;</span> 334 <span class="k">next</span> <span class="j">NAME</span><span class="sc">;</span> 335 <span class="s">}</span> 336 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^ThreeLetterCode$/i</span><span class="s">)</span> <span class="s">{</span> 337 <span class="i">$ThreeLetterCodePresent</span> = <span class="n">1</span><span class="sc">;</span> 338 <span class="k">next</span> <span class="j">NAME</span><span class="sc">;</span> 339 <span class="s">}</span> 340 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^AminoAcid$/i</span><span class="s">)</span> <span class="s">{</span> 341 <span class="i">$AminoAcidPresent</span> = <span class="n">1</span><span class="sc">;</span> 342 <span class="k">next</span> <span class="j">NAME</span><span class="sc">;</span> 343 <span class="s">}</span> 344 <span class="i">$PropertiesMap</span>{<span class="i">$Name</span>} = <span class="i">$Name</span><span class="sc">;</span> 345 <span class="s">}</span> 346 <span class="c"># Setup the alphabetical list...</span> 347 <span class="k">if</span> <span class="s">(</span><span class="i">$ThreeLetterCodePresent</span><span class="s">)</span> <span class="s">{</span> 348 <span class="k">push</span> <span class="i">@AlphabeticalProperties</span><span class="cm">,</span> <span class="q">'ThreeLetterCode'</span><span class="sc">;</span> 349 <span class="s">}</span> 350 <span class="k">if</span> <span class="s">(</span><span class="i">$OneLetterCodePresent</span><span class="s">)</span> <span class="s">{</span> 351 <span class="k">push</span> <span class="i">@AlphabeticalProperties</span><span class="cm">,</span> <span class="q">'OneLetterCode'</span><span class="sc">;</span> 352 <span class="s">}</span> 353 <span class="k">if</span> <span class="s">(</span><span class="i">$AminoAcidPresent</span><span class="s">)</span> <span class="s">{</span> 354 <span class="k">push</span> <span class="i">@AlphabeticalProperties</span><span class="cm">,</span> <span class="q">'AminoAcid'</span><span class="sc">;</span> 355 <span class="s">}</span> 356 <span class="k">for</span> <span class="i">$Name</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%PropertiesMap</span><span class="s">)</span> <span class="s">{</span> 357 <span class="k">push</span> <span class="i">@AlphabeticalProperties</span><span class="cm">,</span> <span class="i">$Name</span><span class="sc">;</span> 358 <span class="s">}</span> 359 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 360 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="cm">,</span> <span class="i">@AlphabeticalProperties</span><span class="sc">;</span> 361 <span class="s">}</span> 362 <span class="s">}</span> 363 <span class="s">}</span> 364 <span class="k">else</span> <span class="s">{</span> 365 <span class="c"># Set default value...</span> 366 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="cm">,</span> <span class="i">GetPropertyNamesFromCategories</span><span class="s">(</span><span class="q">'Basic'</span><span class="s">)</span><span class="sc">;</span> 367 <span class="s">}</span> 368 <span class="s">}</span> 369 <span class="s">}</span> 370 371 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span> <a name="SetupScriptUsage-"></a> 372 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span> 373 374 <span class="c"># Retrieve all the options...</span> 375 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 376 <span class="i">$Options</span>{<span class="w">outdelim</span>} = <span class="q">"comma"</span><span class="sc">;</span> 377 <span class="i">$Options</span>{<span class="w">output</span>} = <span class="q">"STDOUT"</span><span class="sc">;</span> 378 <span class="i">$Options</span>{<span class="w">outputstyle</span>} = <span class="q">"AminoAcidBlock"</span><span class="sc">;</span> 379 <span class="i">$Options</span>{<span class="w">precision</span>} = <span class="n">4</span><span class="sc">;</span> 380 <span class="i">$Options</span>{<span class="w">propertiesmode</span>} = <span class="q">"Categories"</span><span class="sc">;</span> 381 <span class="i">$Options</span>{<span class="w">propertieslisting</span>} = <span class="q">"ByGroup"</span><span class="sc">;</span> 382 <span class="i">$Options</span>{<span class="w">quote</span>} = <span class="q">"yes"</span><span class="sc">;</span> 383 384 <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">"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> 385 <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 $ScriptName -h\" command and try again...\n"</span><span class="sc">;</span> 386 <span class="s">}</span> 387 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span> 388 <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> 389 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"</span><span class="sc">;</span> 390 <span class="s">}</span> 391 <span class="k">chdir</span> <span class="i">$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}: $! \n"</span><span class="sc">;</span> 392 <span class="s">}</span> 393 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} !~ <span class="q">/^(comma|semicolon|tab)$/i</span><span class="s">)</span> <span class="s">{</span> 394 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n"</span><span class="sc">;</span> 395 <span class="s">}</span> 396 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} !~ <span class="q">/^(STDOUT|File)$/i</span><span class="s">)</span> <span class="s">{</span> 397 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: STDOUT or File\n"</span><span class="sc">;</span> 398 <span class="s">}</span> 399 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outputstyle</span>} !~ <span class="q">/^(AminoAcidBlock|AminoAcidRows)$/i</span><span class="s">)</span> <span class="s">{</span> 400 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{outputstyle}, for option \"--outputstyle\" is not valid. Allowed values: AminoAcidBlock or AminoAcidRows\n"</span><span class="sc">;</span> 401 <span class="s">}</span> 402 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">precision</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> 403 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{precision}, for option \"-p --precision\" is not valid. Allowed values: > 0 \n"</span><span class="sc">;</span> 404 <span class="s">}</span> 405 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">propertiesmode</span>} !~ <span class="q">/^(Categories|Names|All)$/i</span><span class="s">)</span> <span class="s">{</span> 406 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{propertiesmode}, for option \"--propertiesmode\" is not valid. Allowed values: Categories, Names, or All\n"</span><span class="sc">;</span> 407 <span class="s">}</span> 408 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">propertieslisting</span>} !~ <span class="q">/^(ByGroup|Alphabetical)$/i</span><span class="s">)</span> <span class="s">{</span> 409 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{propertieslisting}, for option \"--propertieslisting\" is not valid. Allowed values: ByGroup, or Alphabetical\n"</span><span class="sc">;</span> 410 <span class="s">}</span> 411 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span> 412 <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> 413 <span class="s">}</span> 414 <span class="s">}</span> 415 <a name="EOF-"></a></pre> <p> </p> <br /> <center> <img src="../../../images/h2o2.png"> </center> </body> </html>