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1 <html>
2 <head>
3 <title>MayaChemTools:Code:InfoNucleicAcids.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: InfoNucleicAcids.pl,v $</span>
17 4 <span class="c"># $Date: 2015/02/28 20:46:20 $</span>
18 5 <span class="c"># $Revision: 1.26 $</span>
19 6 <span class="c">#</span>
20 7 <span class="c"># Author: Manish Sud &lt;msud@san.rr.com&gt;</span>
21 8 <span class="c">#</span>
22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
23 10 <span class="c">#</span>
24 11 <span class="c"># This file is part of MayaChemTools.</span>
25 12 <span class="c">#</span>
26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
29 16 <span class="c"># later version.</span>
30 17 <span class="c">#</span>
31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span>
34 21 <span class="c"># details.</span>
35 22 <span class="c">#</span>
36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
37 24 <span class="c"># along with MayaChemTools; if not, see &lt;http://www.gnu.org/licenses/&gt; or</span>
38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
40 27 <span class="c">#</span>
41 28
42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
43 30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">&quot;$FindBin::Bin/../lib&quot;</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">NucleicAcids</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">$0</span><span class="s">)</span><span class="sc">;</span>
59 46 <span class="k">print</span> <span class="q">&quot;\n$ScriptName: Starting...\n\n&quot;</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">&quot;$FindBin::Bin/$ScriptName&quot;</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">&quot;Processing options...\n&quot;</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">ListNucleicAcidProperties</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73 60 <span class="k">print</span> <span class="q">&quot;\n$ScriptName:Done...\n\n&quot;</span><span class="sc">;</span>
74 61
75 62 <span class="i">$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">$StartTime</span><span class="s">)</span><span class="sc">;</span>
77 64 <span class="k">print</span> <span class="q">&quot;Total time: &quot;</span><span class="cm">,</span> <span class="i">timestr</span><span class="s">(</span><span class="i">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
78 65
79 66 <span class="c">###############################################################################</span>
80 67
81 68 <span class="c"># List data for an nucleic acid...</span>
82 <a name="ListNucleicAcidData-"></a> 69 <span class="k">sub </span><span class="m">ListNucleicAcidData</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">NucleicAcidRowsOutput</span>}<span class="s">)</span> <span class="s">{</span>
87 74 <span class="i">$Line</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
88 75 <span class="c"># Format data...</span>
89 76 <span class="k">if</span> <span class="s">(</span><span class="i">$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>-&gt;[<span class="n">0</span>] =~ <span class="q">/\,/</span><span class="s">)</span> ? <span class="q">qq(&quot;$DataValueRef-&gt;[0]&quot;)</span> <span class="co">:</span> <span class="i">$DataValueRef</span>-&gt;[<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">$DataValueRef</span>-&gt;[<span class="i">$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(&quot;$Value&quot;)</span><span class="sc">;</span>
99 86 <span class="s">}</span>
100 87 <span class="i">$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">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span>
104 91 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$Line\n&quot;</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">&quot;$Line\n&quot;</span><span class="sc">;</span>
108 95 <span class="s">}</span>
109 96 <span class="s">}</span>
110 97 <span class="k">else</span> <span class="s">{</span>
111 98 <span class="c"># Format and list data...</span>
112 99 <span class="i">$Line</span> = <span class="q">&#39;&#39;</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">$DataLabelRef</span>-&gt;[<span class="i">$Index</span>] . <span class="q">&#39; &#39;</span> . <span class="i">$DataValueRef</span>-&gt;[<span class="i">$Index</span>]<span class="sc">;</span>
115 102 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span>
116 103 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$Line\n&quot;</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">&quot;$Line\n&quot;</span><span class="sc">;</span>
120 107 <span class="s">}</span>
121 108 <span class="s">}</span>
122 109 <span class="s">}</span>
123 110 <span class="s">}</span>
124 111
125 112 <span class="c"># List data for an nucleic acid...</span>
126 <a name="ListHeaderRowData-"></a> 113 <span class="k">sub </span><span class="m">ListHeaderRowData</span> <span class="s">{</span>
127 114 <span class="k">my</span><span class="s">(</span><span class="i">$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">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span>
135 122 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$Line\n&quot;</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">&quot;$Line\n&quot;</span><span class="sc">;</span>
139 126 <span class="s">}</span>
140 127 <span class="s">}</span>
141 128
142 129 <span class="c"># List properties for nucleic acids...</span>
143 <a name="ListNucleicAcidProperties-"></a> 130 <span class="k">sub </span><span class="m">ListNucleicAcidProperties</span> <span class="s">{</span>
144 131 <span class="k">my</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="cm">,</span> <span class="i">$NucleicAcidDataRef</span><span class="cm">,</span> <span class="i">$PropertyName</span><span class="cm">,</span> <span class="i">$PropertyValue</span><span class="cm">,</span> <span class="i">@PropertyLabels</span><span class="cm">,</span> <span class="i">@PropertyValues</span><span class="s">)</span><span class="sc">;</span>
145 132
146 133 <span class="k">print</span> <span class="q">&quot;Listing information for nucleic acid(s)...\n&quot;</span><span class="sc">;</span>
147 134
148 135 <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Generating file $OptionsInfo{OutFileName}...\n&quot;</span><span class="sc">;</span>
150 137 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">&quot;&gt;$OptionsInfo{OutFileName}&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Couldn&#39;t open $OptionsInfo{OutFileName}: $!\n&quot;</span><span class="sc">;</span>
151 138 <span class="s">}</span>
152 139
153 140 <span class="c"># Setup property labels...</span>
154 141 <span class="i">@PropertyLabels</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
155 142 <span class="k">for</span> <span class="i">$PropertyName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="s">)</span> <span class="s">{</span>
156 143 <span class="k">push</span> <span class="i">@PropertyLabels</span><span class="cm">,</span> <span class="s">(</span><span class="q">&quot;$PropertyName:&quot;</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">$OptionsInfo</span>{<span class="w">NucleicAcidRowsOutput</span>}<span class="s">)</span> <span class="s">{</span>
160 147 <span class="i">ListHeaderRowData</span><span class="s">(</span>\<span class="i">@PropertyLabels</span><span class="s">)</span><span class="sc">;</span>
161 148 <span class="s">}</span>
162 149
163 150 <span class="c"># Go over specified properties...</span>
164 151 <span class="k">for</span> <span class="i">$NucleicAcidID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedNucleicAcidIDs</span>}}<span class="s">)</span> <span class="s">{</span>
165 152 <span class="i">$NucleicAcidDataRef</span> = <span class="i">NucleicAcids::GetNucleicAcidPropertiesData</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span><span class="sc">;</span>
166 153
167 154 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">NucleicAcidRowsOutput</span>}<span class="s">)</span> <span class="s">{</span>
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">&quot;\nListing properties for nucleic acid $NucleicAcidID...\n\n&quot;</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">&quot;\nListing properties for nucleic acid $NucleicAcidID...\n\n&quot;</span><span class="sc">;</span>
173 160 <span class="s">}</span>
174 161 <span class="s">}</span>
175 162
176 163 <span class="c"># Collect data..</span>
177 164 <span class="i">@PropertyValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
178 165 <span class="k">for</span> <span class="i">$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">$NucleicAcidDataRef</span>-&gt;{<span class="i">$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">&quot;%.$OptionsInfo{Precision}f&quot;</span><span class="cm">,</span> <span class="i">$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">$PropertyValue</span><span class="sc">;</span>
184 171 <span class="s">}</span>
185 172 <span class="c"># List data...</span>
186 173 <span class="i">ListNucleicAcidData</span><span class="s">(</span>\<span class="i">@PropertyLabels</span><span class="cm">,</span> \<span class="i">@PropertyValues</span><span class="s">)</span><span class="sc">;</span>
187 174 <span class="s">}</span>
188 175 <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;\n&quot;</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$/i</span><span class="s">)</span> <span class="s">{</span>
201 188 <span class="i">@PropertyNames</span> = <span class="s">(</span><span class="q">&#39;Code&#39;</span><span class="cm">,</span> <span class="q">&#39;OtherCodes&#39;</span><span class="cm">,</span> <span class="q">&#39;Name&#39;</span><span class="cm">,</span> <span class="q">&#39;Type&#39;</span><span class="cm">,</span> <span class="q">&#39;MolecularFormula&#39;</span><span class="cm">,</span> <span class="q">&#39;MolecularWeight&#39;</span><span class="s">)</span><span class="sc">;</span>
202 189 <span class="s">}</span> <span class="k">elsif</span> <span class="s">(</span><span class="i">$CategoryName</span> =~ <span class="q">/^BasicPlus$/i</span><span class="s">)</span> <span class="s">{</span>
203 190 <span class="i">@PropertyNames</span> = <span class="s">(</span><span class="q">&#39;Code&#39;</span><span class="cm">,</span> <span class="q">&#39;OtherCodes&#39;</span><span class="cm">,</span> <span class="q">&#39;Name&#39;</span><span class="cm">,</span> <span class="q">&#39;Type&#39;</span><span class="cm">,</span> <span class="q">&#39;MolecularFormula&#39;</span><span class="cm">,</span> <span class="q">&#39;MolecularWeight&#39;</span><span class="cm">,</span> <span class="q">&#39;ExactMass&#39;</span><span class="cm">,</span> <span class="q">&#39;ElementalComposition&#39;</span><span class="s">)</span><span class="sc">;</span>
204 191 <span class="s">}</span>
205 192
206 193 <span class="k">return</span> <span class="i">@PropertyNames</span><span class="sc">;</span>
207 194 <span class="s">}</span>
208 195
209 196 <span class="c"># Process option values...</span>
210 <a name="ProcessOptions-"></a> 197 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
211 198 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
212 199
213 200 <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span>
214 201
215 202 <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/^tab$/i</span> <span class="s">)</span> ? <span class="q">&quot;\t&quot;</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">&quot;\;&quot;</span> <span class="co">:</span> <span class="q">&quot;\,&quot;</span><span class="s">)</span><span class="sc">;</span>
216 203 <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} =~ <span class="q">/^yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
217 204
218 205 <span class="i">$OptionsInfo</span>{<span class="w">Overwrite</span>} = <span class="k">defined</span> <span class="i">$Options</span>{<span class="w">overwrite</span>} ? <span class="i">$Options</span>{<span class="w">overwrite</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
219 206 <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} = <span class="k">defined</span> <span class="i">$Options</span>{<span class="w">root</span>} ? <span class="i">$Options</span>{<span class="w">root</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
220 207
221 208 <span class="i">$OptionsInfo</span>{<span class="w">Output</span>} = <span class="i">$Options</span>{<span class="w">output</span>}<span class="sc">;</span>
222 209 <span class="i">$OptionsInfo</span>{<span class="w">OutputStyle</span>} = <span class="i">$Options</span>{<span class="w">outputstyle</span>}<span class="sc">;</span>
223 210
224 211 <span class="i">$OptionsInfo</span>{<span class="w">NucleicAcidRowsOutput</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">outputstyle</span>} =~ <span class="q">/^NucleicAcidRows$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
225 212 <span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} =~ <span class="q">/^File$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
226 213
227 214 <span class="i">$OptionsInfo</span>{<span class="w">Precision</span>} = <span class="i">$Options</span>{<span class="w">precision</span>}<span class="sc">;</span>
228 215
229 216 <span class="k">my</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="cm">,</span> <span class="i">@NucleicAcidIDs</span><span class="s">)</span><span class="sc">;</span>
230 217
231 218 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedNucleicAcidIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
232 219
233 220 <span class="c"># Set up Nucleic Acids IDs except for All mode...</span>
234 221 <span class="i">@NucleicAcidIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
235 222
236 223 <span class="k">if</span> <span class="s">(</span><span class="i">@ARGV</span> &gt;= <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
237 224 <span class="k">push</span> <span class="i">@NucleicAcidIDs</span><span class="cm">,</span> <span class="i">@ARGV</span><span class="sc">;</span>
238 225 <span class="s">}</span>
239 226 <span class="k">else</span> <span class="s">{</span>
240 227 <span class="c"># Setup mode specified default values...</span>
241 228 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/NucleicAcidID/i</span><span class="s">)</span> <span class="s">{</span>
242 229 <span class="k">push</span> <span class="i">@NucleicAcidIDs</span><span class="cm">,</span> <span class="q">&#39;A&#39;</span><span class="sc">;</span>
243 230 <span class="s">}</span>
244 231 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/NucleicAcidType/i</span><span class="s">)</span> <span class="s">{</span>
245 232 <span class="k">push</span> <span class="i">@NucleicAcidIDs</span><span class="cm">,</span> <span class="q">&#39;Nucleoside&#39;</span><span class="sc">;</span>
246 233 <span class="s">}</span>
247 234 <span class="k">else</span> <span class="s">{</span>
248 235 <span class="k">push</span> <span class="i">@NucleicAcidIDs</span><span class="cm">,</span> <span class="q">&#39;A&#39;</span><span class="sc">;</span>
249 236 <span class="s">}</span>
250 237 <span class="s">}</span>
251 238
252 239 <span class="c"># Generate list of nucleic acids...</span>
253 240 <span class="k">if</span> <span class="s">(</span><span class="i">@ARGV</span> == <span class="n">1</span> &amp;&amp; <span class="i">$ARGV</span>[<span class="n">0</span>] =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
254 241 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedNucleicAcidIDs</span>}}<span class="cm">,</span> <span class="i">NucleicAcids::GetNucleicAcids</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
255 242 <span class="s">}</span>
256 243 <span class="k">else</span> <span class="s">{</span>
257 244 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/NucleicAcidID/i</span><span class="s">)</span> <span class="s">{</span>
258 245 <span class="j">ID:</span> <span class="k">for</span> <span class="i">$NucleicAcidID</span> <span class="s">(</span><span class="i">@NucleicAcidIDs</span><span class="s">)</span> <span class="s">{</span>
259 246 <span class="k">if</span> <span class="s">(</span><span class="i">NucleicAcids::IsNucleicAcid</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
260 247 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedNucleicAcidIDs</span>}}<span class="cm">,</span> <span class="i">$NucleicAcidID</span><span class="sc">;</span>
261 248 <span class="s">}</span>
262 249 <span class="k">else</span> <span class="s">{</span>
263 250 <span class="k">warn</span> <span class="q">&quot;Ignoring nucleic acid ID, $NucleicAcidID, specified using command line parameter option: Unknown nucleic acid ID...\n&quot;</span><span class="sc">;</span>
264 251 <span class="k">next</span> <span class="j">ID</span><span class="sc">;</span>
265 252 <span class="s">}</span>
266 253 <span class="s">}</span>
267 254 <span class="s">}</span>
268 255 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/NucleicAcidType/i</span><span class="s">)</span> <span class="s">{</span>
269 256 <span class="j">ID:</span> <span class="k">for</span> <span class="i">$NucleicAcidID</span> <span class="s">(</span><span class="i">@NucleicAcidIDs</span><span class="s">)</span> <span class="s">{</span>
270 257 <span class="k">if</span> <span class="s">(</span>!<span class="i">NucleicAcids::IsNucleicAcidType</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
271 258 <span class="k">warn</span> <span class="q">&quot;Ignoring nucleic acid type, $NucleicAcidID, specified using command line parameter option: Unknown nucleic acid type...\n&quot;</span><span class="sc">;</span>
272 259 <span class="k">next</span> <span class="j">ID</span><span class="sc">;</span>
273 260 <span class="s">}</span>
274 261 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedNucleicAcidIDs</span>}}<span class="cm">,</span> <span class="i">NucleicAcids::GetNucleicAcidsByType</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span><span class="sc">;</span>
275 262 <span class="s">}</span>
276 263 <span class="s">}</span>
277 264 <span class="s">}</span>
278 265 <span class="i">SetupSpecifiedProperties</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
279 266
280 267 <span class="c"># Setup output file name...</span>
281 268 <span class="i">$OptionsInfo</span>{<span class="w">OutFileName</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
282 269 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span>
283 270 <span class="k">my</span><span class="s">(</span><span class="i">$OutFileRoot</span><span class="cm">,</span> <span class="i">$OutFileExt</span><span class="s">)</span><span class="sc">;</span>
284 271
285 272 <span class="i">$OutFileRoot</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
286 273 <span class="i">$OutFileExt</span> = <span class="q">&quot;csv&quot;</span><span class="sc">;</span>
287 274 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/^tab$/i</span><span class="s">)</span> <span class="s">{</span>
288 275 <span class="i">$OutFileExt</span> = <span class="q">&quot;tsv&quot;</span><span class="sc">;</span>
289 276 <span class="s">}</span>
290 277 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">root</span>}<span class="s">)</span> <span class="s">{</span>
291 278 <span class="k">my</span> <span class="s">(</span><span class="i">$RootFileDir</span><span class="cm">,</span> <span class="i">$RootFileName</span><span class="cm">,</span> <span class="i">$RootFileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">root</span>}<span class="s">)</span><span class="sc">;</span>
292 279 <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> &amp;&amp; <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span>
293 280 <span class="i">$OutFileRoot</span> = <span class="i">$RootFileName</span><span class="sc">;</span>
294 281 <span class="s">}</span>
295 282 <span class="k">else</span> <span class="s">{</span>
296 283 <span class="i">$OutFileRoot</span> = <span class="i">$Options</span>{<span class="w">root</span>}<span class="sc">;</span>
297 284 <span class="s">}</span>
298 285 <span class="s">}</span>
299 286 <span class="k">else</span> <span class="s">{</span>
300 287 <span class="i">$OutFileRoot</span> = <span class="q">&#39;NucleicAcidsInfo&#39;</span><span class="sc">;</span>
301 288 <span class="s">}</span>
302 289 <span class="i">$OptionsInfo</span>{<span class="w">OutFileName</span>} = <span class="i">$OutFileRoot</span> . <span class="q">&#39;.&#39;</span> . <span class="i">$OutFileExt</span><span class="sc">;</span>
303 290 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">overwrite</span>}<span class="s">)</span> <span class="s">{</span>
304 291 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$OptionsInfo</span>{<span class="w">OutFileName</span>}<span class="s">)</span> <span class="s">{</span>
305 292 <span class="k">die</span> <span class="q">&quot;Error: Output file, $OptionsInfo{OutFileName}, already exists.\nUse \-o --overwrite\ option or specify a different name using \&quot;-r --root\&quot; option.\n&quot;</span><span class="sc">;</span>
306 293 <span class="s">}</span>
307 294 <span class="s">}</span>
308 295 <span class="s">}</span>
309 296 <span class="s">}</span>
310 297
311 298 <span class="c"># Setup properties to list...</span>
312 <a name="SetupSpecifiedProperties-"></a> 299 <span class="k">sub </span><span class="m">SetupSpecifiedProperties</span> <span class="s">{</span>
313 300
314 301 <span class="i">$OptionsInfo</span>{<span class="w">Properties</span>} = <span class="k">defined</span> <span class="i">$Options</span>{<span class="w">properties</span>} ? <span class="i">$Options</span>{<span class="w">properties</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
315 302
316 303 <span class="i">$OptionsInfo</span>{<span class="w">PropertiesMode</span>} = <span class="i">$Options</span>{<span class="w">propertiesmode</span>}<span class="sc">;</span>
317 304 <span class="i">$OptionsInfo</span>{<span class="w">PropertiesListing</span>} = <span class="i">$Options</span>{<span class="w">propertieslisting</span>}<span class="sc">;</span>
318 305
319 306 <span class="c"># Make sure appropriate properties/category names are specified...</span>
320 307 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
321 308 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">properties</span>} &amp;&amp; <span class="s">(</span><span class="i">$Options</span>{<span class="w">propertiesmode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
322 309 <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring values specifed by \&quot;-p --properties\&quot; option: Not valid for All value of \&quot;--propertiesmode\&quot; option...\n&quot;</span><span class="sc">;</span>
323 310 <span class="s">}</span>
324 311 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">propertiesmode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
325 312 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">propertieslisting</span>} =~ <span class="q">/^Alphabetical$/i</span><span class="s">)</span> <span class="s">{</span>
326 313 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="cm">,</span> <span class="i">NucleicAcids::GetNucleicAcidPropertiesNames</span><span class="s">(</span><span class="q">&#39;Alphabetical&#39;</span><span class="s">)</span><span class="sc">;</span>
327 314 <span class="s">}</span>
328 315 <span class="k">else</span> <span class="s">{</span>
329 316 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="cm">,</span> <span class="i">NucleicAcids::GetNucleicAcidPropertiesNames</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
330 317 <span class="s">}</span>
331 318 <span class="s">}</span>
332 319 <span class="k">else</span> <span class="s">{</span>
333 320 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">properties</span>}<span class="s">)</span> <span class="s">{</span>
334 321 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">propertiesmode</span>} =~ <span class="q">/^Categories$/i</span><span class="s">)</span> <span class="s">{</span>
335 322 <span class="c"># Check category name...</span>
336 323 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">properties</span>} !~ <span class="q">/^(Basic|BasicPlus)$/i</span><span class="s">)</span> <span class="s">{</span>
337 324 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{properties}, for option \&quot;-p --properties\&quot; in conjunction with \&quot;Categories\&quot; value for option \&quot;--propertiesmode\&quot; is not valid. Allowed values: Basic and BasicPlus\n&quot;</span><span class="sc">;</span>
338 325 <span class="s">}</span>
339 326 <span class="c"># Set propertynames...</span>
340 327 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="cm">,</span> <span class="i">GetPropertyNamesFromCategories</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">properties</span>}<span class="s">)</span><span class="sc">;</span>
341 328 <span class="s">}</span>
342 329 <span class="k">else</span> <span class="s">{</span>
343 330 <span class="c"># Check property names..</span>
344 331 <span class="k">my</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$PropertyName</span><span class="cm">,</span> <span class="i">@Names</span><span class="s">)</span><span class="sc">;</span>
345 332 <span class="i">@Names</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">properties</span>}<span class="sc">;</span>
346 333 <span class="j">NAME:</span> <span class="k">for</span> <span class="i">$Name</span> <span class="s">(</span><span class="i">@Names</span><span class="s">)</span> <span class="s">{</span>
347 334 <span class="i">$PropertyName</span> = <span class="i">RemoveLeadingAndTrailingWhiteSpaces</span><span class="s">(</span><span class="i">$Name</span><span class="s">)</span><span class="sc">;</span>
348 335 <span class="k">if</span> <span class="s">(</span><span class="i">NucleicAcids::IsNucleicAcidProperty</span><span class="s">(</span><span class="i">$PropertyName</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
349 336 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="cm">,</span> <span class="i">$PropertyName</span><span class="sc">;</span>
350 337 <span class="s">}</span>
351 338 <span class="k">else</span> <span class="s">{</span>
352 339 <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring value, $Name, specifed by \&quot;-p --properties\&quot; option: Unknown property name...\n&quot;</span><span class="sc">;</span>
353 340 <span class="s">}</span>
354 341 <span class="s">}</span>
355 342 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">propertieslisting</span>} =~ <span class="q">/^Alphabetical$/i</span><span class="s">)</span> <span class="s">{</span>
356 343 <span class="c"># Code, OtherCodes and Name are always listed first...</span>
357 344 <span class="k">my</span><span class="s">(</span><span class="i">$CodePresent</span><span class="cm">,</span> <span class="i">$OtherCodesPresent</span><span class="cm">,</span> <span class="i">$NamePresent</span><span class="cm">,</span> <span class="i">@AlphabeticalProperties</span><span class="cm">,</span> <span class="i">%PropertiesMap</span><span class="s">)</span><span class="sc">;</span>
358 345 <span class="i">%PropertiesMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
359 346 <span class="i">@AlphabeticalProperties</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
360 347 <span class="i">$CodePresent</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$OtherCodesPresent</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$NamePresent</span> = <span class="n">0</span><span class="sc">;</span>
361 348 <span class="j">NAME:</span> <span class="k">for</span> <span class="i">$Name</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="s">)</span> <span class="s">{</span>
362 349 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^Code$/i</span><span class="s">)</span> <span class="s">{</span>
363 350 <span class="i">$CodePresent</span> = <span class="n">1</span><span class="sc">;</span>
364 351 <span class="k">next</span> <span class="j">NAME</span><span class="sc">;</span>
365 352 <span class="s">}</span>
366 353 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^OtherCodes$/i</span><span class="s">)</span> <span class="s">{</span>
367 354 <span class="i">$OtherCodesPresent</span> = <span class="n">1</span><span class="sc">;</span>
368 355 <span class="k">next</span> <span class="j">NAME</span><span class="sc">;</span>
369 356 <span class="s">}</span>
370 357 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^Name$/i</span><span class="s">)</span> <span class="s">{</span>
371 358 <span class="i">$NamePresent</span> = <span class="n">1</span><span class="sc">;</span>
372 359 <span class="k">next</span> <span class="j">NAME</span><span class="sc">;</span>
373 360 <span class="s">}</span>
374 361 <span class="i">$PropertiesMap</span>{<span class="i">$Name</span>} = <span class="i">$Name</span><span class="sc">;</span>
375 362 <span class="s">}</span>
376 363 <span class="c"># Setup the alphabetical list...</span>
377 364 <span class="k">if</span> <span class="s">(</span><span class="i">$CodePresent</span><span class="s">)</span> <span class="s">{</span>
378 365 <span class="k">push</span> <span class="i">@AlphabeticalProperties</span><span class="cm">,</span> <span class="q">&#39;Code&#39;</span><span class="sc">;</span>
379 366 <span class="s">}</span>
380 367 <span class="k">if</span> <span class="s">(</span><span class="i">$OtherCodesPresent</span><span class="s">)</span> <span class="s">{</span>
381 368 <span class="k">push</span> <span class="i">@AlphabeticalProperties</span><span class="cm">,</span> <span class="q">&#39;OtherCodesPresent&#39;</span><span class="sc">;</span>
382 369 <span class="s">}</span>
383 370 <span class="k">if</span> <span class="s">(</span><span class="i">$NamePresent</span><span class="s">)</span> <span class="s">{</span>
384 371 <span class="k">push</span> <span class="i">@AlphabeticalProperties</span><span class="cm">,</span> <span class="q">&#39;Name&#39;</span><span class="sc">;</span>
385 372 <span class="s">}</span>
386 373 <span class="k">for</span> <span class="i">$Name</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%PropertiesMap</span><span class="s">)</span> <span class="s">{</span>
387 374 <span class="k">push</span> <span class="i">@AlphabeticalProperties</span><span class="cm">,</span> <span class="i">$Name</span><span class="sc">;</span>
388 375 <span class="s">}</span>
389 376 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
390 377 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="cm">,</span> <span class="i">@AlphabeticalProperties</span><span class="sc">;</span>
391 378 <span class="s">}</span>
392 379 <span class="s">}</span>
393 380 <span class="s">}</span>
394 381 <span class="k">else</span> <span class="s">{</span>
395 382 <span class="c"># Set default value...</span>
396 383 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="cm">,</span> <span class="i">GetPropertyNamesFromCategories</span><span class="s">(</span><span class="q">&#39;Basic&#39;</span><span class="s">)</span><span class="sc">;</span>
397 384 <span class="s">}</span>
398 385 <span class="s">}</span>
399 386 <span class="s">}</span>
400 387
401 388 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span>
402 <a name="SetupScriptUsage-"></a> 389 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
403 390
404 391 <span class="c"># Retrieve all the options...</span>
405 392 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
406 393 <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">&quot;NucleicAcidID&quot;</span><span class="sc">;</span>
407 394 <span class="i">$Options</span>{<span class="w">outdelim</span>} = <span class="q">&quot;comma&quot;</span><span class="sc">;</span>
408 395 <span class="i">$Options</span>{<span class="w">output</span>} = <span class="q">&quot;STDOUT&quot;</span><span class="sc">;</span>
409 396 <span class="i">$Options</span>{<span class="w">outputstyle</span>} = <span class="q">&quot;NucleicAcidBlock&quot;</span><span class="sc">;</span>
410 397 <span class="i">$Options</span>{<span class="w">precision</span>} = <span class="n">4</span><span class="sc">;</span>
411 398 <span class="i">$Options</span>{<span class="w">propertiesmode</span>} = <span class="q">&quot;Categories&quot;</span><span class="sc">;</span>
412 399 <span class="i">$Options</span>{<span class="w">propertieslisting</span>} = <span class="q">&quot;ByGroup&quot;</span><span class="sc">;</span>
413 400 <span class="i">$Options</span>{<span class="w">quote</span>} = <span class="q">&quot;yes&quot;</span><span class="sc">;</span>
414 401
415 402 <span class="k">if</span> <span class="s">(</span>!<span class="i">GetOptions</span><span class="s">(</span>\<span class="i">%Options</span><span class="cm">,</span> <span class="q">&quot;help|h&quot;</span><span class="cm">,</span> <span class="q">&quot;mode|m=s&quot;</span><span class="cm">,</span> <span class="q">&quot;outdelim=s&quot;</span><span class="cm">,</span> <span class="q">&quot;output=s&quot;</span><span class="cm">,</span> <span class="q">&quot;outputstyle=s&quot;</span><span class="cm">,</span> <span class="q">&quot;overwrite|o&quot;</span><span class="cm">,</span> <span class="q">&quot;precision=i&quot;</span><span class="cm">,</span> <span class="q">&quot;properties|p=s&quot;</span><span class="cm">,</span> <span class="q">&quot;propertieslisting=s&quot;</span><span class="cm">,</span> <span class="q">&quot;propertiesmode=s&quot;</span><span class="cm">,</span> <span class="q">&quot;quote|q=s&quot;</span><span class="cm">,</span> <span class="q">&quot;root|r=s&quot;</span><span class="cm">,</span> <span class="q">&quot;workingdir|w=s&quot;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
416 403 <span class="k">die</span> <span class="q">&quot;\nTo get a list of valid options and their values, use \&quot;$ScriptName -h\&quot; or\n\&quot;perl -S $ScriptName -h\&quot; command and try again...\n&quot;</span><span class="sc">;</span>
417 404 <span class="s">}</span>
418 405 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
419 406 <span class="k">if</span> <span class="s">(</span>! <span class="k">-d</span> <span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
420 407 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{workingdir}, for option \&quot;-w --workingdir\&quot; is not a directory name.\n&quot;</span><span class="sc">;</span>
421 408 <span class="s">}</span>
422 409 <span class="k">chdir</span> <span class="i">$Options</span>{<span class="w">workingdir</span>} <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Couldn&#39;t chdir $Options{workingdir}: $! \n&quot;</span><span class="sc">;</span>
423 410 <span class="s">}</span>
424 411 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} !~ <span class="q">/^(NucleicAcidID|NucleicAcidType)$/i</span><span class="s">)</span> <span class="s">{</span>
425 412 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{mode}, for option \&quot;--mode\&quot; is not valid. Allowed values: NucleicAcidID or NucleicAcidType\n&quot;</span><span class="sc">;</span>
426 413 <span class="s">}</span>
427 414 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} !~ <span class="q">/^(comma|semicolon|tab)$/i</span><span class="s">)</span> <span class="s">{</span>
428 415 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{outdelim}, for option \&quot;--outdelim\&quot; is not valid. Allowed values: comma, tab, or semicolon\n&quot;</span><span class="sc">;</span>
429 416 <span class="s">}</span>
430 417 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} !~ <span class="q">/^(STDOUT|File)$/i</span><span class="s">)</span> <span class="s">{</span>
431 418 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{output}, for option \&quot;--output\&quot; is not valid. Allowed values: STDOUT or File\n&quot;</span><span class="sc">;</span>
432 419 <span class="s">}</span>
433 420 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outputstyle</span>} !~ <span class="q">/^(NucleicAcidBlock|NucleicAcidRows)$/i</span><span class="s">)</span> <span class="s">{</span>
434 421 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{outputstyle}, for option \&quot;--outputstyle\&quot; is not valid. Allowed values: NucleicAcidBlock or NucleicAcidRows\n&quot;</span><span class="sc">;</span>
435 422 <span class="s">}</span>
436 423 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">precision</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
437 424 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{precision}, for option \&quot;-p --precision\&quot; is not valid. Allowed values: &gt; 0 \n&quot;</span><span class="sc">;</span>
438 425 <span class="s">}</span>
439 426 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">propertiesmode</span>} !~ <span class="q">/^(Categories|Names|All)$/i</span><span class="s">)</span> <span class="s">{</span>
440 427 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{propertiesmode}, for option \&quot;--propertiesmode\&quot; is not valid. Allowed values: Categories, Names, or All\n&quot;</span><span class="sc">;</span>
441 428 <span class="s">}</span>
442 429 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">propertieslisting</span>} !~ <span class="q">/^(ByGroup|Alphabetical)$/i</span><span class="s">)</span> <span class="s">{</span>
443 430 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{propertieslisting}, for option \&quot;--propertieslisting\&quot; is not valid. Allowed values: ByGroup, or Alphabetical\n&quot;</span><span class="sc">;</span>
444 431 <span class="s">}</span>
445 432 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span>
446 433 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{quote}, for option \&quot;-q --quote\&quot; is not valid. Allowed values: yes or no\n&quot;</span><span class="sc">;</span>
447 434 <span class="s">}</span>
448 435 <span class="s">}</span>
449 436
450 <a name="EOF-"></a></pre>
451 <p>&nbsp;</p>
452 <br />
453 <center>
454 <img src="../../../images/h2o2.png">
455 </center>
456 </body>
457 </html>