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1 <html>
2 <head>
3 <title>MayaChemTools:Code:ExtractFromSequenceFiles.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">
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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>
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12 <br/>
13 <pre>
14 1 #!/usr/bin/perl -w
15 2 <span class="c">#</span>
16 3 <span class="c"># $RCSfile: ExtractFromSequenceFiles.pl,v $</span>
17 4 <span class="c"># $Date: 2015/02/28 20:46:19 $</span>
18 5 <span class="c"># $Revision: 1.23 $</span>
19 6 <span class="c">#</span>
20 7 <span class="c"># Author: Manish Sud &lt;msud@san.rr.com&gt;</span>
21 8 <span class="c">#</span>
22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
23 10 <span class="c">#</span>
24 11 <span class="c"># This file is part of MayaChemTools.</span>
25 12 <span class="c">#</span>
26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
29 16 <span class="c"># later version.</span>
30 17 <span class="c">#</span>
31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span>
34 21 <span class="c"># details.</span>
35 22 <span class="c">#</span>
36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
37 24 <span class="c"># along with MayaChemTools; if not, see &lt;http://www.gnu.org/licenses/&gt; or</span>
38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
40 27 <span class="c">#</span>
41 28
42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
43 30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">&quot;$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">SequenceFileUtil</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">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
61 48
62 49 <span class="c"># Setup script usage message...</span>
63 50 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
64 51 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">help</span>} || <span class="i">@ARGV</span> &lt; <span class="n">1</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="c"># Expand wild card file names...</span>
69 56 <span class="k">my</span><span class="s">(</span><span class="i">@SequenceFilesList</span><span class="s">)</span><span class="sc">;</span>
70 57 <span class="i">@SequenceFilesList</span> = <span class="i">ExpandFileNames</span><span class="s">(</span>\<span class="i">@ARGV</span><span class="cm">,</span> <span class="q">&quot;aln msf fasta fta pir&quot;</span><span class="s">)</span><span class="sc">;</span>
71 58
72 59 <span class="c"># Process options...</span>
73 60 <span class="k">print</span> <span class="q">&quot;Processing options...\n&quot;</span><span class="sc">;</span>
74 61 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span>
75 62 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
76 63
77 64 <span class="c"># Set up information about input files...</span>
78 65 <span class="k">print</span> <span class="q">&quot;Checking input sequence file(s)...\n&quot;</span><span class="sc">;</span>
79 66 <span class="k">my</span><span class="s">(</span><span class="i">%SequenceFilesInfo</span><span class="s">)</span><span class="sc">;</span>
80 67 <span class="i">RetrieveSequenceFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
81 68
82 69 <span class="c"># Process input files..</span>
83 70 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
84 71 <span class="k">if</span> <span class="s">(</span><span class="i">@SequenceFilesList</span> &gt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
85 72 <span class="k">print</span> <span class="q">&quot;\nProcessing sequence files...\n&quot;</span><span class="sc">;</span>
86 73 <span class="s">}</span>
87 74 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SequenceFilesList</span><span class="s">)</span> <span class="s">{</span>
88 75 <span class="k">if</span> <span class="s">(</span><span class="i">$SequenceFilesInfo</span>{<span class="w">FilesOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span>
89 76 <span class="k">print</span> <span class="q">&quot;\nProcessing file $SequenceFilesList[$FileIndex]...\n&quot;</span><span class="sc">;</span>
90 77 <span class="i">ExtractFromSequenceFiles</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
91 78 <span class="s">}</span>
92 79 <span class="s">}</span>
93 80 <span class="k">print</span> <span class="q">&quot;\n$ScriptName:Done...\n\n&quot;</span><span class="sc">;</span>
94 81
95 82 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
96 83 <span class="i">$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>
97 84 <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">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
98 85
99 86 <span class="c">###############################################################################</span>
100 87
101 88 <span class="c"># Extract from sequence files...</span>
102 <a name="ExtractFromSequenceFiles-"></a> 89 <span class="k">sub </span><span class="m">ExtractFromSequenceFiles</span> <span class="s">{</span>
103 90 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
104 91 <span class="k">my</span><span class="s">(</span><span class="i">$OutSequenceFile</span><span class="cm">,</span> <span class="i">$SequenceFile</span><span class="cm">,</span> <span class="i">$SequenceDataRef</span><span class="cm">,</span> <span class="i">$SpecifiedSequenceDataRef</span><span class="s">)</span><span class="sc">;</span>
105 92
106 93 <span class="c"># Read sequence file...</span>
107 94 <span class="i">$SequenceFile</span> = <span class="i">$SequenceFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span>
108 95 <span class="k">open</span> <span class="w">SEQUENCEFILE</span><span class="cm">,</span> <span class="q">&quot;$SequenceFile&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Can&#39;t open $SequenceFile: $! \n&quot;</span><span class="sc">;</span>
109 96 <span class="i">$SequenceDataRef</span> = <span class="i">ReadSequenceFile</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="sc">;</span>
110 97 <span class="k">close</span> <span class="w">SEQUENCEFILE</span><span class="sc">;</span>
111 98
112 99 <span class="i">$OutSequenceFile</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFile</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
113 100 <span class="k">print</span> <span class="q">&quot;Generating sequence file $OutSequenceFile...\n&quot;</span><span class="sc">;</span>
114 101
115 102 <span class="c"># Retrieve sequence data for specified sequences...</span>
116 103 <span class="i">$SpecifiedSequenceDataRef</span> = <span class="i">GetSpecifiedSequenceData</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="s">)</span><span class="sc">;</span>
117 104
118 105 <span class="c"># Handle gaps...</span>
119 106 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">IgnoreGaps</span>}<span class="s">)</span> <span class="s">{</span>
120 107 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SpecifiedSequenceDataRef</span>-&gt;{<span class="w">IDs</span>}} &gt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
121 108 <span class="k">if</span> <span class="s">(</span><span class="i">AreSequenceLengthsIdentical</span><span class="s">(</span><span class="i">$SpecifiedSequenceDataRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
122 109 <span class="i">$SpecifiedSequenceDataRef</span> = <span class="i">RemoveSequenceAlignmentGapColumns</span><span class="s">(</span><span class="i">$SpecifiedSequenceDataRef</span><span class="s">)</span><span class="sc">;</span>
123 110 <span class="s">}</span>
124 111 <span class="s">}</span>
125 112 <span class="k">else</span> <span class="s">{</span>
126 113 <span class="c"># Remove the gaps from the sequence...</span>
127 114 <span class="k">my</span><span class="s">(</span><span class="i">$ID</span><span class="cm">,</span> <span class="i">$Sequence</span><span class="s">)</span><span class="sc">;</span>
128 115 <span class="i">$ID</span> = <span class="i">$SpecifiedSequenceDataRef</span>-&gt;{<span class="w">IDs</span>}[<span class="n">0</span>]<span class="sc">;</span>
129 116 <span class="i">$Sequence</span> = <span class="i">$SpecifiedSequenceDataRef</span>-&gt;{<span class="w">Sequence</span>}{<span class="i">$ID</span>}<span class="sc">;</span>
130 117 <span class="i">$SpecifiedSequenceDataRef</span>-&gt;{<span class="w">Sequence</span>}{<span class="i">$ID</span>} = <span class="i">RemoveSequenceGaps</span><span class="s">(</span><span class="i">$Sequence</span><span class="s">)</span><span class="sc">;</span>
131 118 <span class="s">}</span>
132 119 <span class="s">}</span>
133 120
134 121 <span class="c"># Write out the file...</span>
135 122 <span class="i">WritePearsonFastaSequenceFile</span><span class="s">(</span><span class="i">$OutSequenceFile</span><span class="cm">,</span> <span class="i">$SpecifiedSequenceDataRef</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">MaxSequenceLength</span>}<span class="s">)</span><span class="sc">;</span>
136 123 <span class="s">}</span>
137 124
138 125 <span class="c"># Get specified sequence data...</span>
139 <a name="GetSpecifiedSequenceData-"></a> 126 <span class="k">sub </span><span class="m">GetSpecifiedSequenceData</span> <span class="s">{</span>
140 127 <span class="k">my</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
141 128
142 129 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^SequenceID$/i</span><span class="s">)</span> <span class="s">{</span>
143 130 <span class="k">return</span> <span class="i">GetDataBySequenceIDs</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="s">)</span><span class="sc">;</span>
144 131 <span class="s">}</span>
145 132 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^SequenceNum$/i</span><span class="s">)</span> <span class="s">{</span>
146 133 <span class="k">return</span> <span class="i">GetDataBySequenceNums</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="s">)</span><span class="sc">;</span>
147 134 <span class="s">}</span>
148 135 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^SequenceNumRange$/i</span><span class="s">)</span> <span class="s">{</span>
149 136 <span class="k">return</span> <span class="i">GetDataBySequenceNumRange</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="s">)</span><span class="sc">;</span>
150 137 <span class="s">}</span>
151 138 <span class="k">else</span> <span class="s">{</span>
152 139 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
153 140 <span class="s">}</span>
154 141 <span class="s">}</span>
155 142
156 143 <span class="c"># Get specified sequence data...</span>
157 <a name="GetDataBySequenceIDs-"></a> 144 <span class="k">sub </span><span class="m">GetDataBySequenceIDs</span> <span class="s">{</span>
158 145 <span class="k">my</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
159 146 <span class="k">my</span><span class="s">(</span><span class="i">$ID</span><span class="cm">,</span> <span class="i">$SequenceCount</span><span class="cm">,</span> <span class="i">$IDMatched</span><span class="cm">,</span> <span class="i">$SpecifiedID</span><span class="cm">,</span> <span class="i">%SpecifiedSequenceDataMap</span><span class="s">)</span><span class="sc">;</span>
160 147
161 148 <span class="c"># Go over sequences and collect sequences for writing out a new sequence file...</span>
162 149 <span class="i">%SpecifiedSequenceDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
163 150 <span class="i">@</span>{<span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">IDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
164 151 <span class="i">%</span>{<span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">Description</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
165 152 <span class="i">%</span>{<span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">Sequence</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
166 153
167 154 <span class="i">$SequenceCount</span> = <span class="n">0</span><span class="sc">;</span>
168 155 <span class="j">ID:</span> <span class="k">for</span> <span class="i">$ID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SequenceDataRef</span>-&gt;{<span class="w">IDs</span>}}<span class="s">)</span> <span class="s">{</span>
169 156 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">MatchExactSequenceIDs</span>}<span class="s">)</span> <span class="s">{</span>
170 157 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDsMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="i">$ID</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span>
171 158 <span class="k">next</span> <span class="j">ID</span><span class="sc">;</span>
172 159 <span class="s">}</span>
173 160 <span class="k">if</span> <span class="s">(</span><span class="i">$SequenceCount</span> &gt;= <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDs</span>}}<span class="s">)</span> <span class="s">{</span>
174 161 <span class="k">last</span> <span class="j">ID</span><span class="sc">;</span>
175 162 <span class="s">}</span>
176 163 <span class="i">$SequenceCount</span>++<span class="sc">;</span>
177 164 <span class="s">}</span>
178 165 <span class="k">else</span> <span class="s">{</span>
179 166 <span class="c"># Does this ID contains specified ID as substring...</span>
180 167 <span class="i">$IDMatched</span> = <span class="n">0</span><span class="sc">;</span>
181 168 <span class="j">SPECIFIEDID:</span> <span class="k">for</span> <span class="i">$SpecifiedID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDs</span>}}<span class="s">)</span> <span class="s">{</span>
182 169 <span class="k">if</span> <span class="s">(</span><span class="i">$ID</span> =~ <span class="q">/$SpecifiedID/i</span><span class="s">)</span> <span class="s">{</span>
183 170 <span class="i">$IDMatched</span> = <span class="n">1</span><span class="sc">;</span>
184 171 <span class="k">last</span> <span class="j">SPECIFIEDID</span><span class="sc">;</span>
185 172 <span class="s">}</span>
186 173 <span class="s">}</span>
187 174 <span class="k">if</span> <span class="s">(</span>!<span class="i">$IDMatched</span><span class="s">)</span> <span class="s">{</span>
188 175 <span class="k">next</span> <span class="j">ID</span><span class="sc">;</span>
189 176 <span class="s">}</span>
190 177 <span class="i">$SequenceCount</span>++<span class="sc">;</span>
191 178 <span class="s">}</span>
192 179 <span class="c"># Collect sequence data...</span>
193 180 <span class="k">push</span> <span class="i">@</span>{<span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">IDs</span>}}<span class="cm">,</span> <span class="i">$ID</span><span class="sc">;</span>
194 181 <span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">Description</span>}{<span class="i">$ID</span>} = <span class="i">$SequenceDataRef</span>-&gt;{<span class="w">Description</span>}{<span class="i">$ID</span>}<span class="sc">;</span>
195 182 <span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$ID</span>} = <span class="i">$SequenceDataRef</span>-&gt;{<span class="w">Sequence</span>}{<span class="i">$ID</span>}<span class="sc">;</span>
196 183 <span class="s">}</span>
197 184
198 185 <span class="k">return</span> \<span class="i">%SpecifiedSequenceDataMap</span><span class="sc">;</span>
199 186 <span class="s">}</span>
200 187
201 188 <span class="c"># Get specified sequence data...</span>
202 <a name="GetDataBySequenceNums-"></a> 189 <span class="k">sub </span><span class="m">GetDataBySequenceNums</span> <span class="s">{</span>
203 190 <span class="k">my</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
204 191 <span class="k">my</span><span class="s">(</span><span class="i">$ID</span><span class="cm">,</span> <span class="i">$SequenceNum</span><span class="cm">,</span> <span class="i">$SequenceCount</span><span class="cm">,</span> <span class="i">%SpecifiedSequenceDataMap</span><span class="s">)</span><span class="sc">;</span>
205 192
206 193 <span class="c"># Go over sequences and collect sequences for writing out a new sequence file...</span>
207 194 <span class="i">%SpecifiedSequenceDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
208 195 <span class="i">@</span>{<span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">IDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
209 196 <span class="i">%</span>{<span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">Description</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
210 197 <span class="i">%</span>{<span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">Sequence</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
211 198
212 199 <span class="i">$SequenceNum</span> = <span class="n">0</span><span class="sc">;</span>
213 200 <span class="i">$SequenceCount</span> = <span class="n">0</span><span class="sc">;</span>
214 201 <span class="j">ID:</span> <span class="k">for</span> <span class="i">$ID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SequenceDataRef</span>-&gt;{<span class="w">IDs</span>}}<span class="s">)</span> <span class="s">{</span>
215 202 <span class="i">$SequenceNum</span>++<span class="sc">;</span>
216 203 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDsMap</span>}{<span class="i">$SequenceNum</span>}<span class="s">)</span> <span class="s">{</span>
217 204 <span class="k">next</span> <span class="j">ID</span><span class="sc">;</span>
218 205 <span class="s">}</span>
219 206 <span class="k">if</span> <span class="s">(</span><span class="i">$SequenceCount</span> &gt;= <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDs</span>}}<span class="s">)</span> <span class="s">{</span>
220 207 <span class="k">last</span> <span class="j">ID</span><span class="sc">;</span>
221 208 <span class="s">}</span>
222 209 <span class="i">$SequenceCount</span>++<span class="sc">;</span>
223 210
224 211 <span class="c"># Collect sequence data...</span>
225 212 <span class="k">push</span> <span class="i">@</span>{<span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">IDs</span>}}<span class="cm">,</span> <span class="i">$ID</span><span class="sc">;</span>
226 213 <span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">Description</span>}{<span class="i">$ID</span>} = <span class="i">$SequenceDataRef</span>-&gt;{<span class="w">Description</span>}{<span class="i">$ID</span>}<span class="sc">;</span>
227 214 <span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$ID</span>} = <span class="i">$SequenceDataRef</span>-&gt;{<span class="w">Sequence</span>}{<span class="i">$ID</span>}<span class="sc">;</span>
228 215 <span class="s">}</span>
229 216
230 217 <span class="k">return</span> \<span class="i">%SpecifiedSequenceDataMap</span><span class="sc">;</span>
231 218 <span class="s">}</span>
232 219
233 220 <span class="c"># Get specified sequence data...</span>
234 <a name="GetDataBySequenceNumRange-"></a> 221 <span class="k">sub </span><span class="m">GetDataBySequenceNumRange</span> <span class="s">{</span>
235 222 <span class="k">my</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
236 223 <span class="k">my</span><span class="s">(</span><span class="i">$ID</span><span class="cm">,</span> <span class="i">$SequenceNum</span><span class="cm">,</span> <span class="i">$SequenceCount</span><span class="cm">,</span> <span class="i">%SpecifiedSequenceDataMap</span><span class="s">)</span><span class="sc">;</span>
237 224
238 225 <span class="c"># Go over sequences and collect sequences for writing out a new sequence file...</span>
239 226 <span class="i">%SpecifiedSequenceDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
240 227 <span class="i">@</span>{<span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">IDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
241 228 <span class="i">%</span>{<span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">Description</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
242 229 <span class="i">%</span>{<span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">Sequence</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
243 230
244 231 <span class="i">$SequenceNum</span> = <span class="n">0</span><span class="sc">;</span>
245 232 <span class="i">$SequenceCount</span> = <span class="n">0</span><span class="sc">;</span>
246 233 <span class="j">ID:</span> <span class="k">for</span> <span class="i">$ID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SequenceDataRef</span>-&gt;{<span class="w">IDs</span>}}<span class="s">)</span> <span class="s">{</span>
247 234 <span class="i">$SequenceNum</span>++<span class="sc">;</span>
248 235
249 236 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$SequenceNum</span> &gt;= <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDs</span>}[<span class="n">0</span>] &amp;&amp; <span class="i">$SequenceNum</span> &lt;= <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDs</span>}[<span class="n">1</span>]<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
250 237 <span class="k">next</span> <span class="j">ID</span><span class="sc">;</span>
251 238 <span class="s">}</span>
252 239 <span class="k">if</span> <span class="s">(</span><span class="i">$SequenceNum</span> &gt; <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDs</span>}[<span class="n">1</span>]<span class="s">)</span> <span class="s">{</span>
253 240 <span class="k">last</span> <span class="j">ID</span><span class="sc">;</span>
254 241 <span class="s">}</span>
255 242 <span class="i">$SequenceCount</span>++<span class="sc">;</span>
256 243 <span class="c"># Collect sequence data...</span>
257 244 <span class="k">push</span> <span class="i">@</span>{<span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">IDs</span>}}<span class="cm">,</span> <span class="i">$ID</span><span class="sc">;</span>
258 245 <span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">Description</span>}{<span class="i">$ID</span>} = <span class="i">$SequenceDataRef</span>-&gt;{<span class="w">Description</span>}{<span class="i">$ID</span>}<span class="sc">;</span>
259 246 <span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$ID</span>} = <span class="i">$SequenceDataRef</span>-&gt;{<span class="w">Sequence</span>}{<span class="i">$ID</span>}<span class="sc">;</span>
260 247 <span class="s">}</span>
261 248
262 249 <span class="k">return</span> \<span class="i">%SpecifiedSequenceDataMap</span><span class="sc">;</span>
263 250 <span class="s">}</span>
264 251
265 252
266 253 <span class="c"># Process option values...</span>
267 <a name="ProcessOptions-"></a> 254 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
268 255 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
269 256
270 257 <span class="c"># Miscellaneous options...</span>
271 258 <span class="i">$OptionsInfo</span>{<span class="w">IgnoreGaps</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">ignoregaps</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>
272 259
273 260 <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span>
274 261 <span class="i">$OptionsInfo</span>{<span class="w">MatchExactSequenceIDs</span>} = <span class="i">$Options</span>{<span class="w">sequenceidmatch</span>} =~ <span class="q">/Exact/i</span> ? <span class="n">1</span> <span class="co">:</span><span class="n">0</span><span class="sc">;</span>
275 262
276 263 <span class="c"># Check specified sequences value...</span>
277 264 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequences</span>} = <span class="i">$Options</span>{<span class="w">sequences</span>}<span class="sc">;</span>
278 265 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
279 266 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDsMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
280 267
281 268 <span class="k">my</span><span class="s">(</span><span class="i">@SpecifiedSequenceIDs</span><span class="s">)</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
282 269 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^SequenceID$/i</span><span class="s">)</span> <span class="s">{</span>
283 270 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">sequences</span>}<span class="s">)</span> <span class="s">{</span>
284 271 <span class="k">die</span> <span class="q">&quot;Error: No value specified for option \&quot;-s, --Sequences\&quot; during \&quot;SequenceID\&quot; of \&quot;-m, --mode\&quot; option\n&quot;</span><span class="sc">;</span>
285 272 <span class="s">}</span>
286 273 <span class="i">@SpecifiedSequenceIDs</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">sequences</span>}<span class="sc">;</span>
287 274 <span class="s">}</span>
288 275 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^SequenceNum$/i</span><span class="s">)</span> <span class="s">{</span>
289 276 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">sequences</span>}<span class="s">)</span> <span class="s">{</span>
290 277 <span class="i">@SpecifiedSequenceIDs</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">sequences</span>}<span class="sc">;</span>
291 278 <span class="k">my</span><span class="s">(</span><span class="i">$SequenceNum</span><span class="s">)</span><span class="sc">;</span>
292 279 <span class="k">for</span> <span class="i">$SequenceNum</span> <span class="s">(</span><span class="i">@SpecifiedSequenceIDs</span><span class="s">)</span> <span class="s">{</span>
293 280 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$SequenceNum</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
294 281 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $SequenceNum, in \&quot;$Options{sequences}\&quot; for option \&quot;-s, --Sequences\&quot; is not valid: Valid values: &gt; 0\n&quot;</span><span class="sc">;</span>
295 282 <span class="s">}</span>
296 283 <span class="s">}</span>
297 284 <span class="s">}</span>
298 285 <span class="k">else</span> <span class="s">{</span>
299 286 <span class="k">push</span> <span class="i">@SpecifiedSequenceIDs</span><span class="cm">,</span> <span class="q">&quot;1&quot;</span><span class="sc">;</span>
300 287 <span class="s">}</span>
301 288 <span class="s">}</span>
302 289 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^SequenceNumRange$/i</span><span class="s">)</span> <span class="s">{</span>
303 290 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">sequences</span>}<span class="s">)</span> <span class="s">{</span>
304 291 <span class="k">die</span> <span class="q">&quot;Error: No value specified for option \&quot;-s, --Sequences\&quot; during \&quot;SequenceNumRange\&quot; of \&quot;-m, --mode\&quot; option\n&quot;</span><span class="sc">;</span>
305 292 <span class="s">}</span>
306 293 <span class="i">@SpecifiedSequenceIDs</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">sequences</span>}<span class="sc">;</span>
307 294 <span class="k">if</span> <span class="s">(</span><span class="i">@SpecifiedSequenceIDs</span> != <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
308 295 <span class="k">die</span> <span class="q">&quot;Error: The number of values&quot;</span><span class="cm">,</span> <span class="k">scalar</span> <span class="i">@SpecifiedSequenceIDs</span><span class="cm">,</span> <span class="q">&quot; specified, $Options{sequences}, for option \&quot;-s, --Sequences\&quot; are not valid. Number of values must be 2 to indicate starting and ending sequence number.\n&quot;</span><span class="sc">;</span>
309 296 <span class="s">}</span>
310 297 <span class="k">my</span><span class="s">(</span><span class="i">$SequenceNum</span><span class="s">)</span><span class="sc">;</span>
311 298 <span class="k">for</span> <span class="i">$SequenceNum</span> <span class="s">(</span><span class="i">@SpecifiedSequenceIDs</span><span class="s">)</span> <span class="s">{</span>
312 299 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$SequenceNum</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
313 300 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $SequenceNum, in \&quot;$Options{sequences}\&quot; for option \&quot;-s, --Sequences\&quot; is not valid: Valid values: &gt; 0\n&quot;</span><span class="sc">;</span>
314 301 <span class="s">}</span>
315 302 <span class="s">}</span>
316 303 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedSequenceIDs</span>[<span class="n">0</span>] &gt; <span class="i">$SpecifiedSequenceIDs</span>[<span class="n">1</span>]<span class="s">)</span> <span class="s">{</span>
317 304 <span class="k">die</span> <span class="q">&quot;Error: The value specified \&quot;$Options{sequences}\&quot; for option \&quot;-s, --Sequences\&quot; are not valid: Starting sequence number $SpecifiedSequenceIDs[0] must be smaller than ending sequence number $SpecifiedSequenceIDs[1]\n&quot;</span><span class="sc">;</span>
318 305 <span class="s">}</span>
319 306 <span class="s">}</span>
320 307 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDs</span>}}<span class="cm">,</span> <span class="i">@SpecifiedSequenceIDs</span><span class="sc">;</span>
321 308 <span class="k">my</span><span class="s">(</span><span class="i">$SequenceID</span><span class="s">)</span><span class="sc">;</span>
322 309 <span class="k">for</span> <span class="i">$SequenceID</span> <span class="s">(</span><span class="i">@SpecifiedSequenceIDs</span><span class="s">)</span> <span class="s">{</span>
323 310 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^SequenceID$/i</span><span class="s">)</span> <span class="s">{</span>
324 311 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDsMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="i">$SequenceID</span><span class="s">)</span>} = <span class="i">$SequenceID</span><span class="sc">;</span>
325 312 <span class="s">}</span>
326 313 <span class="k">else</span> <span class="s">{</span>
327 314 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDsMap</span>}{<span class="i">$SequenceID</span>} = <span class="i">$SequenceID</span><span class="sc">;</span>
328 315 <span class="s">}</span>
329 316 <span class="s">}</span>
330 317
331 318 <span class="i">$OptionsInfo</span>{<span class="w">MaxSequenceLength</span>} = <span class="i">$Options</span>{<span class="w">sequencelength</span>}<span class="sc">;</span>
332 319 <span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>} = <span class="i">$Options</span>{<span class="w">overwrite</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
333 320 <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} = <span class="i">$Options</span>{<span class="w">root</span>} ? <span class="i">$Options</span>{<span class="w">root</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
334 321 <span class="s">}</span>
335 322
336 323 <span class="c"># Retrieve information about sequence files...</span>
337 <a name="RetrieveSequenceFilesInfo-"></a> 324 <span class="k">sub </span><span class="m">RetrieveSequenceFilesInfo</span> <span class="s">{</span>
338 325 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$SequenceFile</span><span class="cm">,</span> <span class="i">$FileSupported</span><span class="cm">,</span> <span class="i">$FileFormat</span><span class="cm">,</span> <span class="i">$SequenceCount</span><span class="cm">,</span> <span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="cm">,</span> <span class="i">$OutFileRoot</span><span class="cm">,</span> <span class="i">$OutFileExt</span><span class="cm">,</span> <span class="i">$OutFileMode</span><span class="cm">,</span> <span class="i">$SequenceDataRef</span><span class="s">)</span><span class="sc">;</span>
339 326
340 327 <span class="i">%SequenceFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
341 328 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">FilesOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
342 329 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileRoot</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
343 330 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileExt</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
344 331 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">OutFile</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
345 332 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">Format</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
346 333 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">SequenceCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
347 334
348 335 <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SequenceFilesList</span><span class="s">)</span> <span class="s">{</span>
349 336 <span class="i">$SequenceFile</span> = <span class="i">$SequenceFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
350 337 <span class="i">$SequenceFilesInfo</span>{<span class="w">FilesOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
351 338 <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="q">&#39;&#39;</span><span class="sc">;</span>
352 339 <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileExt</span>}[<span class="i">$Index</span>] = <span class="q">&#39;&#39;</span><span class="sc">;</span>
353 340 <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFile</span>}[<span class="i">$Index</span>] = <span class="q">&#39;&#39;</span><span class="sc">;</span>
354 341 <span class="i">$SequenceFilesInfo</span>{<span class="w">Format</span>}[<span class="i">$Index</span>] = <span class="q">&#39;NotSupported&#39;</span><span class="sc">;</span>
355 342 <span class="i">$SequenceFilesInfo</span>{<span class="w">SequenceCount</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
356 343
357 344 <span class="k">if</span> <span class="s">(</span>! <span class="k">open</span> <span class="w">SEQUENCEFILE</span><span class="cm">,</span> <span class="q">&quot;$SequenceFile&quot;</span><span class="s">)</span> <span class="s">{</span>
358 345 <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SequenceFile: Couldn&#39;t open it: $! \n&quot;</span><span class="sc">;</span>
359 346 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
360 347 <span class="s">}</span>
361 348 <span class="k">close</span> <span class="w">SEQUENCEFILE</span><span class="sc">;</span>
362 349
363 350 <span class="s">(</span><span class="i">$FileSupported</span><span class="cm">,</span> <span class="i">$FileFormat</span><span class="s">)</span> = <span class="i">IsSupportedSequenceFile</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="sc">;</span>
364 351 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FileSupported</span><span class="s">)</span> <span class="s">{</span>
365 352 <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SequenceFile: Sequence file format is not supported.\n&quot;</span><span class="sc">;</span>
366 353 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
367 354 <span class="s">}</span>
368 355 <span class="i">$SequenceDataRef</span> = <span class="i">ReadSequenceFile</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="sc">;</span>
369 356
370 357 <span class="i">$SequenceCount</span> = <span class="i">$SequenceDataRef</span>-&gt;{<span class="w">Count</span>}<span class="sc">;</span>
371 358 <span class="k">if</span> <span class="s">(</span>!<span class="i">$SequenceCount</span><span class="s">)</span> <span class="s">{</span>
372 359 <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SequenceFile: Sequence data is missing.\n&quot;</span><span class="sc">;</span>
373 360 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
374 361 <span class="s">}</span>
375 362
376 363 <span class="c"># Setup output file names...</span>
377 364 <span class="i">$FileDir</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span> <span class="i">$FileName</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span> <span class="i">$FileExt</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span>
378 365 <span class="s">(</span><span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="sc">;</span>
379 366 <span class="i">$OutFileExt</span> = <span class="q">&#39;fasta&#39;</span><span class="sc">;</span>
380 367 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} &amp;&amp; <span class="s">(</span><span class="i">@SequenceFilesList</span> == <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
381 368 <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">$RootFileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="s">)</span><span class="sc">;</span>
382 369 <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>
383 370 <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span>
384 371 <span class="s">}</span>
385 372 <span class="k">else</span> <span class="s">{</span>
386 373 <span class="i">$FileName</span> = <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="sc">;</span>
387 374 <span class="s">}</span>
388 375 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span>
389 376 <span class="s">}</span>
390 377 <span class="k">else</span> <span class="s">{</span>
391 378 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span>
392 379 <span class="s">}</span>
393 380 <span class="j">MODE:</span> <span class="s">{</span>
394 381 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^SequenceID$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$OutFileMode</span> = <span class="q">&#39;SequenceID&#39;</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span><span class="s">}</span>
395 382 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^SequenceNum$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$OutFileMode</span> = <span class="q">&#39;SequenceNum&#39;</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span><span class="s">}</span>
396 383 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^SequenceNumRange$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$OutFileMode</span> = <span class="q">&#39;SequenceNumRange&#39;</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span><span class="s">}</span>
397 384 <span class="i">$OutFileMode</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
398 385 <span class="s">}</span>
399 386 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>}<span class="s">)</span> <span class="s">{</span>
400 387 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="q">&quot;${OutFileRoot}${OutFileMode}.${OutFileExt}&quot;</span><span class="s">)</span> <span class="s">{</span>
401 388 <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SequenceFile: The file ${OutFileRoot}${OutFileMode}.${OutFileExt} already exists\n&quot;</span><span class="sc">;</span>
402 389 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
403 390 <span class="s">}</span>
404 391 <span class="s">}</span>
405 392
406 393 <span class="i">$SequenceFilesInfo</span>{<span class="w">FilesOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span>
407 394 <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileRoot</span><span class="sc">;</span>
408 395 <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileExt</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileExt</span><span class="sc">;</span>
409 396 <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFile</span>}[<span class="i">$Index</span>] = <span class="q">&quot;${OutFileRoot}${OutFileMode}.${OutFileExt}&quot;</span><span class="sc">;</span>
410 397
411 398 <span class="i">$SequenceFilesInfo</span>{<span class="w">Format</span>}[<span class="i">$Index</span>] = <span class="i">$FileFormat</span><span class="sc">;</span>
412 399 <span class="i">$SequenceFilesInfo</span>{<span class="w">SequenceCount</span>}[<span class="i">$Index</span>] = <span class="i">$SequenceCount</span><span class="sc">;</span>
413 400 <span class="s">}</span>
414 401 <span class="s">}</span>
415 402
416 403 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span>
417 <a name="SetupScriptUsage-"></a> 404 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
418 405
419 406 <span class="c"># Retrieve all the options...</span>
420 407 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
421 408 <span class="i">$Options</span>{<span class="w">ignoregaps</span>} = <span class="q">&#39;Yes&#39;</span><span class="sc">;</span>
422 409 <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">&#39;SequenceNum&#39;</span><span class="sc">;</span>
423 410 <span class="i">$Options</span>{<span class="w">sequenceidmatch</span>} = <span class="q">&#39;Relaxed&#39;</span><span class="sc">;</span>
424 411 <span class="i">$Options</span>{<span class="w">sequencelength</span>} = <span class="n">80</span><span class="sc">;</span>
425 412
426 413 <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;ignoregaps|i=s&quot;</span><span class="cm">,</span> <span class="q">&quot;mode|m=s&quot;</span><span class="cm">,</span> <span class="q">&quot;overwrite|o&quot;</span><span class="cm">,</span> <span class="q">&quot;root|r=s&quot;</span><span class="cm">,</span> <span class="q">&quot;sequences|s=s&quot;</span><span class="cm">,</span> <span class="q">&quot;sequenceidmatch=s&quot;</span><span class="cm">,</span> <span class="q">&quot;sequencelength=i&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>
427 414 <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 $ScriptName -h\&quot; command and try again...\n&quot;</span><span class="sc">;</span>
428 415 <span class="s">}</span>
429 416 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
430 417 <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>
431 418 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{workingdir}, for option \&quot;-w --workingdir\&quot; is not a directory name.\n&quot;</span><span class="sc">;</span>
432 419 <span class="s">}</span>
433 420 <span class="k">chdir</span> <span class="i">$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}: $! \n&quot;</span><span class="sc">;</span>
434 421 <span class="s">}</span>
435 422 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">ignoregaps</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span>
436 423 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{ignoregaps}, for option \&quot;-q --quote\&quot; is not valid. Allowed values: yes or no\n&quot;</span><span class="sc">;</span>
437 424 <span class="s">}</span>
438 425 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} !~ <span class="q">/^(SequenceID|SequenceNum|SequenceNumRange)$/i</span><span class="s">)</span> <span class="s">{</span>
439 426 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{mode}, for option \&quot;-m --mode\&quot; is not valid. Allowed values: SequenceID, SequenceNum, or SequenceNumRange\n&quot;</span><span class="sc">;</span>
440 427 <span class="s">}</span>
441 428 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">sequenceidmatch</span>} !~ <span class="q">/^(Exact|Relaxed)$/i</span><span class="s">)</span> <span class="s">{</span>
442 429 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{sequenceidmatch}, for option \&quot;--SequenceIDMatch\&quot; is not valid. Allowed values: Exact or Relaxed\n&quot;</span><span class="sc">;</span>
443 430 <span class="s">}</span>
444 431 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">sequencelength</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
445 432 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{sequencelength}, for option \&quot;--SequenceLength\&quot; is not valid. Allowed values: &gt;0\n&quot;</span><span class="sc">;</span>
446 433 <span class="s">}</span>
447 434 <span class="s">}</span>
448 435
449 <a name="EOF-"></a></pre>
450 <p>&nbsp;</p>
451 <br />
452 <center>
453 <img src="../../../images/h2o2.png">
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