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comparison docs/scripts/html/code/InfoAminoAcids.html @ 0:4816e4a8ae95 draft default tip
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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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| -1:000000000000 | 0:4816e4a8ae95 |
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| 1 <html> | |
| 2 <head> | |
| 3 <title>MayaChemTools:Code:InfoAminoAcids.pl</title> | |
| 4 <meta http-equiv="content-type" content="text/html;charset=utf-8"> | |
| 5 <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> | |
| 6 </head> | |
| 7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> | |
| 8 <br/> | |
| 9 <center> | |
| 10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> | |
| 11 </center> | |
| 12 <br/> | |
| 13 <pre> | |
| 14 1 #!/usr/bin/perl -w | |
| 15 2 <span class="c">#</span> | |
| 16 3 <span class="c"># $RCSfile: InfoAminoAcids.pl,v $</span> | |
| 17 4 <span class="c"># $Date: 2015/02/28 20:46:20 $</span> | |
| 18 5 <span class="c"># $Revision: 1.26 $</span> | |
| 19 6 <span class="c">#</span> | |
| 20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> | |
| 21 8 <span class="c">#</span> | |
| 22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> | |
| 23 10 <span class="c">#</span> | |
| 24 11 <span class="c"># This file is part of MayaChemTools.</span> | |
| 25 12 <span class="c">#</span> | |
| 26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> | |
| 27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> | |
| 28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> | |
| 29 16 <span class="c"># later version.</span> | |
| 30 17 <span class="c">#</span> | |
| 31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> | |
| 32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> | |
| 33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> | |
| 34 21 <span class="c"># details.</span> | |
| 35 22 <span class="c">#</span> | |
| 36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> | |
| 37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> | |
| 38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> | |
| 39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> | |
| 40 27 <span class="c">#</span> | |
| 41 28 | |
| 42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> | |
| 43 30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">"$FindBin::Bin/../lib"</span><span class="sc">;</span> | |
| 44 31 <span class="k">use</span> <span class="w">Getopt::Long</span><span class="sc">;</span> | |
| 45 32 <span class="k">use</span> <span class="w">File::Basename</span><span class="sc">;</span> | |
| 46 33 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span> | |
| 47 34 <span class="k">use</span> <span class="w">Benchmark</span><span class="sc">;</span> | |
| 48 35 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span> | |
| 49 36 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span> | |
| 50 37 <span class="k">use</span> <span class="w">AminoAcids</span><span class="sc">;</span> | |
| 51 38 | |
| 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> | |
| 53 40 | |
| 54 41 <span class="c"># Autoflush STDOUT</span> | |
| 55 42 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span> | |
| 56 43 | |
| 57 44 <span class="c"># Starting message...</span> | |
| 58 45 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span> | |
| 59 46 <span class="k">print</span> <span class="q">"\n$ScriptName: Starting...\n\n"</span><span class="sc">;</span> | |
| 60 47 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span> | |
| 61 48 | |
| 62 49 <span class="c"># Get the options and setup script...</span> | |
| 63 50 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 64 51 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">help</span>}<span class="s">)</span> <span class="s">{</span> | |
| 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> | |
| 66 53 <span class="s">}</span> | |
| 67 54 | |
| 68 55 <span class="k">print</span> <span class="q">"Processing options...\n"</span><span class="sc">;</span> | |
| 69 56 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span> | |
| 70 57 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 71 58 | |
| 72 59 <span class="i">ListAminoAcidProperties</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 73 60 <span class="k">print</span> <span class="q">"\n$ScriptName:Done...\n\n"</span><span class="sc">;</span> | |
| 74 61 | |
| 75 62 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span> | |
| 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">$StartTime</span><span class="s">)</span><span class="sc">;</span> | |
| 77 64 <span class="k">print</span> <span class="q">"Total time: "</span><span class="cm">,</span> <span class="i">timestr</span><span class="s">(</span><span class="i">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> | |
| 78 65 | |
| 79 66 <span class="c">###############################################################################</span> | |
| 80 67 | |
| 81 68 <span class="c"># List data for an amino acid...</span> | |
| 82 <a name="ListAminoAcidData-"></a> 69 <span class="k">sub </span><span class="m">ListAminoAcidData</span> <span class="s">{</span> | |
| 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> | |
| 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">$Value</span><span class="s">)</span><span class="sc">;</span> | |
| 85 72 | |
| 86 73 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">AminoAcidRowsOutput</span>}<span class="s">)</span> <span class="s">{</span> | |
| 87 74 <span class="i">$Line</span> = <span class="q">''</span><span class="sc">;</span> | |
| 88 75 <span class="c"># Format data...</span> | |
| 89 76 <span class="k">if</span> <span class="s">(</span><span class="i">$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> | |
| 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> | |
| 91 78 <span class="s">}</span> | |
| 92 79 <span class="k">else</span> <span class="s">{</span> | |
| 93 80 <span class="c"># Always quote values containing commas...</span> | |
| 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> | |
| 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">$DataValueRef</span>} <span class="s">)</span> <span class="s">{</span> | |
| 96 83 <span class="i">$Value</span> = <span class="i">$DataValueRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 97 84 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> =~ <span class="q">/\,/</span><span class="s">)</span> <span class="s">{</span> | |
| 98 85 <span class="i">$Value</span> = <span class="q">qq("$Value")</span><span class="sc">;</span> | |
| 99 86 <span class="s">}</span> | |
| 100 87 <span class="i">$Line</span> .= <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>} . <span class="i">$Value</span><span class="sc">;</span> | |
| 101 88 <span class="s">}</span> | |
| 102 89 <span class="s">}</span> | |
| 103 90 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span> | |
| 104 91 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$Line\n"</span><span class="sc">;</span> | |
| 105 92 <span class="s">}</span> | |
| 106 93 <span class="k">else</span> <span class="s">{</span> | |
| 107 94 <span class="k">print</span> <span class="q">"$Line\n"</span><span class="sc">;</span> | |
| 108 95 <span class="s">}</span> | |
| 109 96 <span class="s">}</span> | |
| 110 97 <span class="k">else</span> <span class="s">{</span> | |
| 111 98 <span class="c"># Format and list data...</span> | |
| 112 99 <span class="i">$Line</span> = <span class="q">''</span><span class="sc">;</span> | |
| 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">$DataLabelRef</span>} <span class="s">)</span> <span class="s">{</span> | |
| 114 101 <span class="i">$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> | |
| 115 102 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span> | |
| 116 103 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$Line\n"</span><span class="sc">;</span> | |
| 117 104 <span class="s">}</span> | |
| 118 105 <span class="k">else</span> <span class="s">{</span> | |
| 119 106 <span class="k">print</span> <span class="q">"$Line\n"</span><span class="sc">;</span> | |
| 120 107 <span class="s">}</span> | |
| 121 108 <span class="s">}</span> | |
| 122 109 <span class="s">}</span> | |
| 123 110 <span class="s">}</span> | |
| 124 111 | |
| 125 112 <span class="c"># List data for an amino acid...</span> | |
| 126 <a name="ListHeaderRowData-"></a> 113 <span class="k">sub </span><span class="m">ListHeaderRowData</span> <span class="s">{</span> | |
| 127 114 <span class="k">my</span><span class="s">(</span><span class="i">$DataLabelRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 128 115 <span class="k">my</span><span class="s">(</span><span class="i">$Line</span><span class="s">)</span><span class="sc">;</span> | |
| 129 116 | |
| 130 117 <span class="c"># Format data...</span> | |
| 131 118 <span class="i">$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">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span> | |
| 132 119 <span class="i">$Line</span> =~ <span class="q">s/\://g</span><span class="sc">;</span> | |
| 133 120 <span class="c"># List data...</span> | |
| 134 121 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span> | |
| 135 122 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$Line\n"</span><span class="sc">;</span> | |
| 136 123 <span class="s">}</span> | |
| 137 124 <span class="k">else</span> <span class="s">{</span> | |
| 138 125 <span class="k">print</span> <span class="q">"$Line\n"</span><span class="sc">;</span> | |
| 139 126 <span class="s">}</span> | |
| 140 127 <span class="s">}</span> | |
| 141 128 | |
| 142 129 <span class="c"># List properties for amino acids...</span> | |
| 143 <a name="ListAminoAcidProperties-"></a> 130 <span class="k">sub </span><span class="m">ListAminoAcidProperties</span> <span class="s">{</span> | |
| 144 131 <span class="k">my</span><span class="s">(</span><span class="i">$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">$PropertyValue</span><span class="cm">,</span> <span class="i">@PropertyLabels</span><span class="cm">,</span> <span class="i">@PropertyValues</span><span class="s">)</span><span class="sc">;</span> | |
| 145 132 | |
| 146 133 <span class="k">print</span> <span class="q">"Listing information for amino acid(s)...\n"</span><span class="sc">;</span> | |
| 147 134 | |
| 148 135 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span> | |
| 149 136 <span class="k">print</span> <span class="q">"Generating file $OptionsInfo{OutFileName}...\n"</span><span class="sc">;</span> | |
| 150 137 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">">$OptionsInfo{OutFileName}"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Couldn't open $OptionsInfo{OutFileName}: $!\n"</span><span class="sc">;</span> | |
| 151 138 <span class="s">}</span> | |
| 152 139 | |
| 153 140 <span class="c"># Setup property labels...</span> | |
| 154 141 <span class="i">@PropertyLabels</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 155 142 <span class="k">for</span> <span class="i">$PropertyName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 156 143 <span class="k">push</span> <span class="i">@PropertyLabels</span><span class="cm">,</span> <span class="s">(</span><span class="q">"$PropertyName:"</span><span class="s">)</span><span class="sc">;</span> | |
| 157 144 <span class="s">}</span> | |
| 158 145 | |
| 159 146 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">AminoAcidRowsOutput</span>}<span class="s">)</span> <span class="s">{</span> | |
| 160 147 <span class="i">ListHeaderRowData</span><span class="s">(</span>\<span class="i">@PropertyLabels</span><span class="s">)</span><span class="sc">;</span> | |
| 161 148 <span class="s">}</span> | |
| 162 149 | |
| 163 150 <span class="c"># Go over specified properties...</span> | |
| 164 151 <span class="k">for</span> <span class="i">$AminoAcidID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAminoAcidIDs</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 165 152 <span class="i">$AminoAcidDataRef</span> = <span class="i">AminoAcids::GetAminoAcidPropertiesData</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="s">)</span><span class="sc">;</span> | |
| 166 153 | |
| 167 154 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">AminoAcidRowsOutput</span>}<span class="s">)</span> <span class="s">{</span> | |
| 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> | |
| 169 156 <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> | |
| 170 157 <span class="s">}</span> | |
| 171 158 <span class="k">else</span> <span class="s">{</span> | |
| 172 159 <span class="k">print</span> <span class="q">"\nListing properties for amino acid $AminoAcidID...\n\n"</span><span class="sc">;</span> | |
| 173 160 <span class="s">}</span> | |
| 174 161 <span class="s">}</span> | |
| 175 162 | |
| 176 163 <span class="c"># Collect data..</span> | |
| 177 164 <span class="i">@PropertyValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 178 165 <span class="k">for</span> <span class="i">$PropertyName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 179 166 <span class="i">$PropertyValue</span> = <span class="i">$AminoAcidDataRef</span>->{<span class="i">$PropertyName</span>}<span class="sc">;</span> | |
| 180 167 <span class="k">if</span> <span class="s">(</span><span class="i">IsFloat</span><span class="s">(</span><span class="i">$PropertyValue</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 181 168 <span class="i">$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> | |
| 182 169 <span class="s">}</span> | |
| 183 170 <span class="k">push</span> <span class="i">@PropertyValues</span><span class="cm">,</span> <span class="i">$PropertyValue</span><span class="sc">;</span> | |
| 184 171 <span class="s">}</span> | |
| 185 172 <span class="c"># List data...</span> | |
| 186 173 <span class="i">ListAminoAcidData</span><span class="s">(</span>\<span class="i">@PropertyLabels</span><span class="cm">,</span> \<span class="i">@PropertyValues</span><span class="s">)</span><span class="sc">;</span> | |
| 187 174 <span class="s">}</span> | |
| 188 175 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span> | |
| 189 176 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span> | |
| 190 177 <span class="s">}</span> | |
| 191 178 <span class="k">print</span> <span class="q">"\n"</span><span class="sc">;</span> | |
| 192 179 <span class="s">}</span> | |
| 193 180 | |
| 194 181 <span class="c"># Get propery names from categories...</span> | |
| 195 <a name="GetPropertyNamesFromCategories-"></a> 182 <span class="k">sub </span><span class="m">GetPropertyNamesFromCategories</span> <span class="s">{</span> | |
| 196 183 <span class="k">my</span><span class="s">(</span><span class="i">$CategoryName</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 197 184 <span class="k">my</span><span class="s">(</span><span class="i">@PropertyNames</span><span class="s">)</span><span class="sc">;</span> | |
| 198 185 | |
| 199 186 <span class="i">@PropertyNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 200 187 <span class="k">if</span> <span class="s">(</span><span class="i">$CategoryName</span> =~ <span class="q">/^Basic$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 201 188 <span class="i">@PropertyNames</span> = <span class="s">(</span><span class="q">'ThreeLetterCode'</span><span class="cm">,</span> <span class="q">'OneLetterCode'</span><span class="cm">,</span> <span class="q">'AminoAcid'</span><span class="cm">,</span> <span class="q">'DNACodons'</span><span class="cm">,</span> <span class="q">'RNACodons'</span><span class="cm">,</span> <span class="q">'ChemicalFormula'</span><span class="cm">,</span><span class="q">'MolecularWeight'</span><span class="cm">,</span> <span class="q">'LinearStructure'</span><span class="cm">,</span> <span class="q">'LinearStructureAtpH7.4'</span><span class="s">)</span><span class="sc">;</span> | |
| 202 189 <span class="s">}</span> <span class="k">elsif</span> <span class="s">(</span><span class="i">$CategoryName</span> =~ <span class="q">/^BasicPlus$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 203 190 <span class="i">@PropertyNames</span> = <span class="s">(</span><span class="q">'ThreeLetterCode'</span><span class="cm">,</span> <span class="q">'OneLetterCode'</span><span class="cm">,</span> <span class="q">'AminoAcid'</span><span class="cm">,</span> <span class="q">'DNACodons'</span><span class="cm">,</span> <span class="q">'RNACodons'</span><span class="cm">,</span> <span class="q">'AcidicBasic'</span><span class="cm">,</span> <span class="q">'PolarNonpolar'</span><span class="cm">,</span> <span class="q">'Charged'</span><span class="cm">,</span> <span class="q">'Aromatic'</span><span class="cm">,</span> <span class="q">'HydrophobicHydophilic'</span><span class="cm">,</span> <span class="q">'IsoelectricPoint'</span><span class="cm">,</span> <span class="q">'pKCOOH'</span><span class="cm">,</span> <span class="q">'pKNH3+'</span><span class="cm">,</span> <span class="q">'ChemicalFormula'</span><span class="cm">,</span> <span class="q">'MolecularWeight'</span><span class="cm">,</span> <span class="q">'ExactMass'</span><span class="cm">,</span> <span class="q">'ChemicalFormulaMinusH2O'</span><span class="cm">,</span> <span class="q">'MolecularWeightMinusH2O(18.01524)'</span><span class="cm">,</span> <span class="q">'ExactMassMinusH2O(18.01056)'</span><span class="cm">,</span><span class="q">'LinearStructure'</span><span class="cm">,</span> <span class="q">'LinearStructureAtpH7.4'</span><span class="s">)</span><span class="sc">;</span> | |
| 204 191 <span class="s">}</span> <span class="k">elsif</span> <span class="s">(</span><span class="i">$CategoryName</span> =~ <span class="q">/^BasicAndHydrophobicity$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 205 192 <span class="i">@PropertyNames</span> = <span class="s">(</span><span class="q">'ThreeLetterCode'</span><span class="cm">,</span> <span class="q">'OneLetterCode'</span><span class="cm">,</span> <span class="q">'AminoAcid'</span><span class="cm">,</span> <span class="q">'DNACodons'</span><span class="cm">,</span> <span class="q">'RNACodons'</span><span class="cm">,</span> <span class="q">'ChemicalFormula'</span><span class="cm">,</span> <span class="q">'MolecularWeight'</span><span class="cm">,</span> <span class="q">'LinearStructure'</span><span class="cm">,</span> <span class="q">'LinearStructureAtpH7.4'</span><span class="cm">,</span> <span class="q">'HydrophobicityEisenbergAndOthers'</span><span class="cm">,</span> <span class="q">'HydrophobicityHoppAndWoods'</span><span class="cm">,</span> <span class="q">'HydrophobicityJanin'</span><span class="cm">,</span> <span class="q">'HydrophobicityKyteAndDoolittle'</span><span class="cm">,</span> <span class="q">'HydrophobicityRoseAndOthers'</span><span class="cm">,</span> <span class="q">'HydrophobicityWolfendenAndOthers'</span><span class="s">)</span><span class="sc">;</span> | |
| 206 193 <span class="s">}</span> <span class="k">elsif</span> <span class="s">(</span><span class="i">$CategoryName</span> =~ <span class="q">/^BasicAndHydrophobicityPlus$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 207 194 <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> | |
| 208 195 <span class="s">}</span> | |
| 209 196 | |
| 210 197 <span class="k">return</span> <span class="i">@PropertyNames</span><span class="sc">;</span> | |
| 211 198 <span class="s">}</span> | |
| 212 199 | |
| 213 200 <span class="c"># Process option values...</span> | |
| 214 <a name="ProcessOptions-"></a> 201 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span> | |
| 215 202 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 216 203 | |
| 217 204 <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> | |
| 218 205 <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$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 219 206 | |
| 220 207 <span class="i">$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> | |
| 221 208 <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">$Options</span>{<span class="w">root</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span> | |
| 222 209 | |
| 223 210 <span class="i">$OptionsInfo</span>{<span class="w">OutputStyle</span>} = <span class="i">$Options</span>{<span class="w">outputstyle</span>}<span class="sc">;</span> | |
| 224 211 | |
| 225 212 <span class="i">$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> | |
| 226 213 <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$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 227 214 | |
| 228 215 <span class="i">$OptionsInfo</span>{<span class="w">Precision</span>} = <span class="i">$Options</span>{<span class="w">precision</span>}<span class="sc">;</span> | |
| 229 216 | |
| 230 217 <span class="k">my</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="cm">,</span> <span class="i">@AminoAcidIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 231 218 | |
| 232 219 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAminoAcidIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 233 220 | |
| 234 221 <span class="c"># Set up Amino Acids IDs except for All mode...</span> | |
| 235 222 <span class="i">@AminoAcidIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 236 223 | |
| 237 224 <span class="k">if</span> <span class="s">(</span><span class="i">@ARGV</span> >= <span class="n">1</span><span class="s">)</span> <span class="s">{</span> | |
| 238 225 <span class="k">push</span> <span class="i">@AminoAcidIDs</span><span class="cm">,</span> <span class="i">@ARGV</span><span class="sc">;</span> | |
| 239 226 <span class="s">}</span> | |
| 240 227 <span class="k">else</span> <span class="s">{</span> | |
| 241 228 <span class="c"># Setup mode specified default values...</span> | |
| 242 229 <span class="k">push</span> <span class="i">@AminoAcidIDs</span><span class="cm">,</span> <span class="q">'Ala'</span><span class="sc">;</span> | |
| 243 230 <span class="s">}</span> | |
| 244 231 | |
| 245 232 <span class="c"># Generate list of amino acids...</span> | |
| 246 233 <span class="k">if</span> <span class="s">(</span><span class="i">@ARGV</span> == <span class="n">1</span> && <span class="i">$ARGV</span>[<span class="n">0</span>] =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 247 234 <span class="k">push</span> <span class="i">@</span>{<span class="i">$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> | |
| 248 235 <span class="s">}</span> | |
| 249 236 <span class="k">else</span> <span class="s">{</span> | |
| 250 237 <span class="j">ID:</span> <span class="k">for</span> <span class="i">$AminoAcidID</span> <span class="s">(</span><span class="i">@AminoAcidIDs</span><span class="s">)</span> <span class="s">{</span> | |
| 251 238 <span class="k">if</span> <span class="s">(</span><span class="i">AminoAcids::IsAminoAcid</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 252 239 <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> | |
| 253 240 <span class="s">}</span> | |
| 254 241 <span class="k">else</span> <span class="s">{</span> | |
| 255 242 <span class="k">warn</span> <span class="q">"Ignoring amino acid ID, $AminoAcidID, specified using command line parameter option: Unknown amino acid ID...\n"</span><span class="sc">;</span> | |
| 256 243 <span class="k">next</span> <span class="j">ID</span><span class="sc">;</span> | |
| 257 244 <span class="s">}</span> | |
| 258 245 <span class="s">}</span> | |
| 259 246 <span class="s">}</span> | |
| 260 247 <span class="i">SetupSpecifiedProperties</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 261 248 | |
| 262 249 <span class="c"># Setup output file name...</span> | |
| 263 250 <span class="i">$OptionsInfo</span>{<span class="w">OutFileName</span>} = <span class="q">''</span><span class="sc">;</span> | |
| 264 251 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span> | |
| 265 252 <span class="k">my</span><span class="s">(</span><span class="i">$OutFileRoot</span><span class="cm">,</span> <span class="i">$OutFileExt</span><span class="s">)</span><span class="sc">;</span> | |
| 266 253 | |
| 267 254 <span class="i">$OutFileRoot</span> = <span class="q">''</span><span class="sc">;</span> | |
| 268 255 <span class="i">$OutFileExt</span> = <span class="q">"csv"</span><span class="sc">;</span> | |
| 269 256 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/^tab$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 270 257 <span class="i">$OutFileExt</span> = <span class="q">"tsv"</span><span class="sc">;</span> | |
| 271 258 <span class="s">}</span> | |
| 272 259 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">root</span>}<span class="s">)</span> <span class="s">{</span> | |
| 273 260 <span class="k">my</span> <span class="s">(</span><span class="i">$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">$Options</span>{<span class="w">root</span>}<span class="s">)</span><span class="sc">;</span> | |
| 274 261 <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> && <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span> | |
| 275 262 <span class="i">$OutFileRoot</span> = <span class="i">$RootFileName</span><span class="sc">;</span> | |
| 276 263 <span class="s">}</span> | |
| 277 264 <span class="k">else</span> <span class="s">{</span> | |
| 278 265 <span class="i">$OutFileRoot</span> = <span class="i">$Options</span>{<span class="w">root</span>}<span class="sc">;</span> | |
| 279 266 <span class="s">}</span> | |
| 280 267 <span class="s">}</span> | |
| 281 268 <span class="k">else</span> <span class="s">{</span> | |
| 282 269 <span class="i">$OutFileRoot</span> = <span class="q">'AminoAcidsInfo'</span><span class="sc">;</span> | |
| 283 270 <span class="s">}</span> | |
| 284 271 <span class="i">$OptionsInfo</span>{<span class="w">OutFileName</span>} = <span class="i">$OutFileRoot</span> . <span class="q">'.'</span> . <span class="i">$OutFileExt</span><span class="sc">;</span> | |
| 285 272 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">overwrite</span>}<span class="s">)</span> <span class="s">{</span> | |
| 286 273 <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> | |
| 287 274 <span class="k">die</span> <span class="q">"Error: Output file, $OptionsInfo{OutFileName}, already exists.\nUse \-o --overwrite\ option or specify a different name using \"-r --root\" option.\n"</span><span class="sc">;</span> | |
| 288 275 <span class="s">}</span> | |
| 289 276 <span class="s">}</span> | |
| 290 277 <span class="s">}</span> | |
| 291 278 <span class="s">}</span> | |
| 292 279 | |
| 293 280 <span class="c"># Setup properties to list...</span> | |
| 294 <a name="SetupSpecifiedProperties-"></a> 281 <span class="k">sub </span><span class="m">SetupSpecifiedProperties</span> <span class="s">{</span> | |
| 295 282 | |
| 296 283 <span class="i">$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> | |
| 297 284 | |
| 298 285 <span class="i">$OptionsInfo</span>{<span class="w">PropertiesMode</span>} = <span class="i">$Options</span>{<span class="w">propertiesmode</span>}<span class="sc">;</span> | |
| 299 286 <span class="i">$OptionsInfo</span>{<span class="w">PropertiesListing</span>} = <span class="i">$Options</span>{<span class="w">propertieslisting</span>}<span class="sc">;</span> | |
| 300 287 | |
| 301 288 <span class="c"># Make sure appropriate properties/category names are specified...</span> | |
| 302 289 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 303 290 <span class="k">if</span> <span class="s">(</span><span class="i">$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> | |
| 304 291 <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> | |
| 305 292 <span class="s">}</span> | |
| 306 293 <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> | |
| 307 294 <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> | |
| 308 295 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="cm">,</span> <span class="i">AminoAcids::GetAminoAcidPropertiesNames</span><span class="s">(</span><span class="q">'Alphabetical'</span><span class="s">)</span><span class="sc">;</span> | |
| 309 296 <span class="s">}</span> | |
| 310 297 <span class="k">else</span> <span class="s">{</span> | |
| 311 298 <span class="k">push</span> <span class="i">@</span>{<span class="i">$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> | |
| 312 299 <span class="s">}</span> | |
| 313 300 <span class="s">}</span> | |
| 314 301 <span class="k">else</span> <span class="s">{</span> | |
| 315 302 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">properties</span>}<span class="s">)</span> <span class="s">{</span> | |
| 316 303 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">propertiesmode</span>} =~ <span class="q">/^Categories$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 317 304 <span class="c"># Check category name...</span> | |
| 318 305 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">properties</span>} !~ <span class="q">/^(Basic|BasicPlus|BasicAndHydrophobicity|BasicAndHydrophobicityPlus)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 319 306 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{properties}, for option \"-p --properties\" in conjunction with \"Categories\" value for option \"--propertiesmode\" is not valid. Allowed values: Basic, BasicPlus, BasicAndHydrophobicity, and BasicAndHydrophobicityPlus\n"</span><span class="sc">;</span> | |
| 320 307 <span class="s">}</span> | |
| 321 308 <span class="c"># Set propertynames...</span> | |
| 322 309 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="cm">,</span> <span class="i">GetPropertyNamesFromCategories</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">properties</span>}<span class="s">)</span><span class="sc">;</span> | |
| 323 310 <span class="s">}</span> | |
| 324 311 <span class="k">else</span> <span class="s">{</span> | |
| 325 312 <span class="c"># Check property names..</span> | |
| 326 313 <span class="k">my</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$PropertyName</span><span class="cm">,</span> <span class="i">@Names</span><span class="s">)</span><span class="sc">;</span> | |
| 327 314 <span class="i">@Names</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">properties</span>}<span class="sc">;</span> | |
| 328 315 <span class="j">NAME:</span> <span class="k">for</span> <span class="i">$Name</span> <span class="s">(</span><span class="i">@Names</span><span class="s">)</span> <span class="s">{</span> | |
| 329 316 <span class="i">$PropertyName</span> = <span class="i">RemoveLeadingAndTrailingWhiteSpaces</span><span class="s">(</span><span class="i">$Name</span><span class="s">)</span><span class="sc">;</span> | |
| 330 317 <span class="k">if</span> <span class="s">(</span><span class="i">AminoAcids::IsAminoAcidProperty</span><span class="s">(</span><span class="i">$PropertyName</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 331 318 <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> | |
| 332 319 <span class="s">}</span> | |
| 333 320 <span class="k">else</span> <span class="s">{</span> | |
| 334 321 <span class="k">warn</span> <span class="q">"Warning: Ignoring value, $Name, specifed by \"-p --properties\" option: Unknown property name...\n"</span><span class="sc">;</span> | |
| 335 322 <span class="s">}</span> | |
| 336 323 <span class="s">}</span> | |
| 337 324 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">propertieslisting</span>} =~ <span class="q">/^Alphabetical$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 338 325 <span class="c"># ThreeLetterCode, OneLetterCode and AminoAcid are always listed first...</span> | |
| 339 326 <span class="c"># NaturalIsotopeData in the end...</span> | |
| 340 327 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 341 328 <span class="i">%PropertiesMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 342 329 <span class="i">@AlphabeticalProperties</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 343 330 <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">$AminoAcidPresent</span> = <span class="n">0</span><span class="sc">;</span> | |
| 344 331 <span class="j">NAME:</span> <span class="k">for</span> <span class="i">$Name</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 345 332 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^OneLetterCode$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 346 333 <span class="i">$OneLetterCodePresent</span> = <span class="n">1</span><span class="sc">;</span> | |
| 347 334 <span class="k">next</span> <span class="j">NAME</span><span class="sc">;</span> | |
| 348 335 <span class="s">}</span> | |
| 349 336 <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> | |
| 350 337 <span class="i">$ThreeLetterCodePresent</span> = <span class="n">1</span><span class="sc">;</span> | |
| 351 338 <span class="k">next</span> <span class="j">NAME</span><span class="sc">;</span> | |
| 352 339 <span class="s">}</span> | |
| 353 340 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^AminoAcid$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 354 341 <span class="i">$AminoAcidPresent</span> = <span class="n">1</span><span class="sc">;</span> | |
| 355 342 <span class="k">next</span> <span class="j">NAME</span><span class="sc">;</span> | |
| 356 343 <span class="s">}</span> | |
| 357 344 <span class="i">$PropertiesMap</span>{<span class="i">$Name</span>} = <span class="i">$Name</span><span class="sc">;</span> | |
| 358 345 <span class="s">}</span> | |
| 359 346 <span class="c"># Setup the alphabetical list...</span> | |
| 360 347 <span class="k">if</span> <span class="s">(</span><span class="i">$ThreeLetterCodePresent</span><span class="s">)</span> <span class="s">{</span> | |
| 361 348 <span class="k">push</span> <span class="i">@AlphabeticalProperties</span><span class="cm">,</span> <span class="q">'ThreeLetterCode'</span><span class="sc">;</span> | |
| 362 349 <span class="s">}</span> | |
| 363 350 <span class="k">if</span> <span class="s">(</span><span class="i">$OneLetterCodePresent</span><span class="s">)</span> <span class="s">{</span> | |
| 364 351 <span class="k">push</span> <span class="i">@AlphabeticalProperties</span><span class="cm">,</span> <span class="q">'OneLetterCode'</span><span class="sc">;</span> | |
| 365 352 <span class="s">}</span> | |
| 366 353 <span class="k">if</span> <span class="s">(</span><span class="i">$AminoAcidPresent</span><span class="s">)</span> <span class="s">{</span> | |
| 367 354 <span class="k">push</span> <span class="i">@AlphabeticalProperties</span><span class="cm">,</span> <span class="q">'AminoAcid'</span><span class="sc">;</span> | |
| 368 355 <span class="s">}</span> | |
| 369 356 <span class="k">for</span> <span class="i">$Name</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%PropertiesMap</span><span class="s">)</span> <span class="s">{</span> | |
| 370 357 <span class="k">push</span> <span class="i">@AlphabeticalProperties</span><span class="cm">,</span> <span class="i">$Name</span><span class="sc">;</span> | |
| 371 358 <span class="s">}</span> | |
| 372 359 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 373 360 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="cm">,</span> <span class="i">@AlphabeticalProperties</span><span class="sc">;</span> | |
| 374 361 <span class="s">}</span> | |
| 375 362 <span class="s">}</span> | |
| 376 363 <span class="s">}</span> | |
| 377 364 <span class="k">else</span> <span class="s">{</span> | |
| 378 365 <span class="c"># Set default value...</span> | |
| 379 366 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="cm">,</span> <span class="i">GetPropertyNamesFromCategories</span><span class="s">(</span><span class="q">'Basic'</span><span class="s">)</span><span class="sc">;</span> | |
| 380 367 <span class="s">}</span> | |
| 381 368 <span class="s">}</span> | |
| 382 369 <span class="s">}</span> | |
| 383 370 | |
| 384 371 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span> | |
| 385 <a name="SetupScriptUsage-"></a> 372 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span> | |
| 386 373 | |
| 387 374 <span class="c"># Retrieve all the options...</span> | |
| 388 375 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 389 376 <span class="i">$Options</span>{<span class="w">outdelim</span>} = <span class="q">"comma"</span><span class="sc">;</span> | |
| 390 377 <span class="i">$Options</span>{<span class="w">output</span>} = <span class="q">"STDOUT"</span><span class="sc">;</span> | |
| 391 378 <span class="i">$Options</span>{<span class="w">outputstyle</span>} = <span class="q">"AminoAcidBlock"</span><span class="sc">;</span> | |
| 392 379 <span class="i">$Options</span>{<span class="w">precision</span>} = <span class="n">4</span><span class="sc">;</span> | |
| 393 380 <span class="i">$Options</span>{<span class="w">propertiesmode</span>} = <span class="q">"Categories"</span><span class="sc">;</span> | |
| 394 381 <span class="i">$Options</span>{<span class="w">propertieslisting</span>} = <span class="q">"ByGroup"</span><span class="sc">;</span> | |
| 395 382 <span class="i">$Options</span>{<span class="w">quote</span>} = <span class="q">"yes"</span><span class="sc">;</span> | |
| 396 383 | |
| 397 384 <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> | |
| 398 385 <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 $ScriptName -h\" command and try again...\n"</span><span class="sc">;</span> | |
| 399 386 <span class="s">}</span> | |
| 400 387 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span> | |
| 401 388 <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> | |
| 402 389 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"</span><span class="sc">;</span> | |
| 403 390 <span class="s">}</span> | |
| 404 391 <span class="k">chdir</span> <span class="i">$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}: $! \n"</span><span class="sc">;</span> | |
| 405 392 <span class="s">}</span> | |
| 406 393 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} !~ <span class="q">/^(comma|semicolon|tab)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 407 394 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n"</span><span class="sc">;</span> | |
| 408 395 <span class="s">}</span> | |
| 409 396 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} !~ <span class="q">/^(STDOUT|File)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 410 397 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: STDOUT or File\n"</span><span class="sc">;</span> | |
| 411 398 <span class="s">}</span> | |
| 412 399 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outputstyle</span>} !~ <span class="q">/^(AminoAcidBlock|AminoAcidRows)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 413 400 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{outputstyle}, for option \"--outputstyle\" is not valid. Allowed values: AminoAcidBlock or AminoAcidRows\n"</span><span class="sc">;</span> | |
| 414 401 <span class="s">}</span> | |
| 415 402 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">precision</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 416 403 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{precision}, for option \"-p --precision\" is not valid. Allowed values: > 0 \n"</span><span class="sc">;</span> | |
| 417 404 <span class="s">}</span> | |
| 418 405 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">propertiesmode</span>} !~ <span class="q">/^(Categories|Names|All)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 419 406 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{propertiesmode}, for option \"--propertiesmode\" is not valid. Allowed values: Categories, Names, or All\n"</span><span class="sc">;</span> | |
| 420 407 <span class="s">}</span> | |
| 421 408 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">propertieslisting</span>} !~ <span class="q">/^(ByGroup|Alphabetical)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 422 409 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{propertieslisting}, for option \"--propertieslisting\" is not valid. Allowed values: ByGroup, or Alphabetical\n"</span><span class="sc">;</span> | |
| 423 410 <span class="s">}</span> | |
| 424 411 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} !~ <span class="q">/^(yes|no)$/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{quote}, for option \"-q --quote\" is not valid. Allowed values: yes or no\n"</span><span class="sc">;</span> | |
| 426 413 <span class="s">}</span> | |
| 427 414 <span class="s">}</span> | |
| 428 415 | |
| 429 <a name="EOF-"></a></pre> | |
| 430 <p> </p> | |
| 431 <br /> | |
| 432 <center> | |
| 433 <img src="../../../images/h2o2.png"> | |
| 434 </center> | |
| 435 </body> | |
| 436 </html> |