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1 <html> | |
2 <head> | |
3 <title>MayaChemTools:Code:Fingerprints::FingerprintsFileUtil.pm</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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13 <pre> | |
14 <a name="package-Fingerprints::FingerprintsFileUtil-"></a> 1 <span class="k">package </span><span class="i">Fingerprints::FingerprintsFileUtil</span><span class="sc">;</span> | |
15 2 <span class="c">#</span> | |
16 3 <span class="c"># $RCSfile: FingerprintsFileUtil.pm,v $</span> | |
17 4 <span class="c"># $Date: 2015/02/28 20:48:54 $</span> | |
18 5 <span class="c"># $Revision: 1.14 $</span> | |
19 6 <span class="c">#</span> | |
20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> | |
21 8 <span class="c">#</span> | |
22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> | |
23 10 <span class="c">#</span> | |
24 11 <span class="c"># This file is part of MayaChemTools.</span> | |
25 12 <span class="c">#</span> | |
26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> | |
27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> | |
28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> | |
29 16 <span class="c"># later version.</span> | |
30 17 <span class="c">#</span> | |
31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> | |
32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> | |
33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> | |
34 21 <span class="c"># details.</span> | |
35 22 <span class="c">#</span> | |
36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> | |
37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> | |
38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> | |
39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> | |
40 27 <span class="c">#</span> | |
41 28 | |
42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> | |
43 30 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span> | |
44 31 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span> | |
45 32 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
46 33 <span class="k">use</span> <span class="w">FileUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
47 34 <span class="k">use</span> <span class="w">FileIO::FingerprintsSDFileIO</span><span class="sc">;</span> | |
48 35 <span class="k">use</span> <span class="w">FileIO::FingerprintsTextFileIO</span><span class="sc">;</span> | |
49 36 <span class="k">use</span> <span class="w">FileIO::FingerprintsFPFileIO</span><span class="sc">;</span> | |
50 37 | |
51 38 <span class="k">use</span> <span class="w">vars</span> <span class="q">qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS)</span><span class="sc">;</span> | |
52 39 | |
53 40 <span class="i">@ISA</span> = <span class="q">qw(Exporter)</span><span class="sc">;</span> | |
54 41 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> | |
55 42 <span class="i">@EXPORT_OK</span> = <span class="q">qw(GetFingerprintsFileType ReadAndProcessFingerpritsData NewFingerprintsFileIO)</span><span class="sc">;</span> | |
56 43 | |
57 44 <span class="i">%EXPORT_TAGS</span> = <span class="s">(</span><span class="w">all</span> <span class="cm">=></span> <span class="s">[</span><span class="i">@EXPORT</span><span class="cm">,</span> <span class="i">@EXPORT_OK</span><span class="s">]</span><span class="s">)</span><span class="sc">;</span> | |
58 45 | |
59 46 <span class="c"># Generate new FingerprintsFileIO object for a SD, FP or Text fingerprints file specified using file name</span> | |
60 47 <span class="c"># along other appropriate parameters...</span> | |
61 48 <span class="c">#</span> | |
62 <a name="NewFingerprintsFileIO-"></a> 49 <span class="k">sub </span><span class="m">NewFingerprintsFileIO</span> <span class="s">{</span> | |
63 50 <span class="k">my</span><span class="s">(</span><span class="i">%FingerprintsFileIOParams</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
64 51 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsFileIO</span><span class="cm">,</span> <span class="i">$FileType</span><span class="s">)</span><span class="sc">;</span> | |
65 52 | |
66 53 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$FingerprintsFileIOParams</span>{<span class="w">Name</span>}<span class="s">)</span> && <span class="i">TextUtil::IsNotEmpty</span><span class="s">(</span><span class="i">$FingerprintsFileIOParams</span>{<span class="w">Name</span>}<span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
67 54 <span class="w">carp</span> <span class="q">"Warning: Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO: Can't create new FingerprintsFileIO object: File name is not specified...\n"</span><span class="sc">;</span> | |
68 55 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
69 56 <span class="s">}</span> | |
70 57 | |
71 58 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$FingerprintsFileIOParams</span>{<span class="w">Mode</span>}<span class="s">)</span> && <span class="i">TextUtil::IsNotEmpty</span><span class="s">(</span><span class="i">$FingerprintsFileIOParams</span>{<span class="w">Mode</span>}<span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
72 59 <span class="w">carp</span> <span class="q">"Warning: Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO: Can't create new FingerprintsFileIO object: File mode is not specified...\n"</span><span class="sc">;</span> | |
73 60 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
74 61 <span class="s">}</span> | |
75 62 | |
76 63 <span class="i">$FileType</span> = <span class="i">GetFingerprintsFileType</span><span class="s">(</span><span class="i">$FingerprintsFileIOParams</span>{<span class="w">Name</span>}<span class="s">)</span><span class="sc">;</span> | |
77 64 <span class="k">if</span> <span class="s">(</span><span class="i">TextUtil::IsEmpty</span><span class="s">(</span><span class="i">$FileType</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
78 65 <span class="w">carp</span> <span class="q">"Warning: Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO: Can't create new FingerprintsFileIO object: File type is not specified...\n"</span><span class="sc">;</span> | |
79 66 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
80 67 <span class="s">}</span> | |
81 68 | |
82 69 <span class="c"># Generate fingerprints IO object...</span> | |
83 70 <span class="j">FILETYPE:</span> <span class="s">{</span> | |
84 71 <span class="k">if</span> <span class="s">(</span><span class="i">$FileType</span> =~ <span class="q">/^SD$/i</span><span class="s">)</span> <span class="s">{</span> | |
85 72 <span class="i">$FingerprintsFileIO</span> = <span class="w">new</span> <span class="i">FileIO::FingerprintsSDFileIO</span><span class="s">(</span><span class="i">%FingerprintsFileIOParams</span><span class="s">)</span><span class="sc">;</span> | |
86 73 <span class="k">last</span> <span class="j">FILETYPE</span><span class="sc">;</span> | |
87 74 <span class="s">}</span> | |
88 75 <span class="k">if</span> <span class="s">(</span><span class="i">$FileType</span> =~ <span class="q">/^FP$/i</span><span class="s">)</span> <span class="s">{</span> | |
89 76 <span class="i">$FingerprintsFileIO</span> = <span class="w">new</span> <span class="i">FileIO::FingerprintsFPFileIO</span><span class="s">(</span><span class="i">%FingerprintsFileIOParams</span><span class="s">)</span><span class="sc">;</span> | |
90 77 <span class="k">last</span> <span class="j">FILETYPE</span><span class="sc">;</span> | |
91 78 <span class="s">}</span> | |
92 79 <span class="k">if</span> <span class="s">(</span><span class="i">$FileType</span> =~ <span class="q">/^Text$/i</span><span class="s">)</span> <span class="s">{</span> | |
93 80 <span class="i">$FingerprintsFileIO</span> = <span class="w">new</span> <span class="i">FileIO::FingerprintsTextFileIO</span><span class="s">(</span><span class="i">%FingerprintsFileIOParams</span><span class="s">)</span><span class="sc">;</span> | |
94 81 <span class="k">last</span> <span class="j">FILETYPE</span><span class="sc">;</span> | |
95 82 <span class="s">}</span> | |
96 83 <span class="i">$FingerprintsFileIO</span> = <span class="k">undef</span><span class="sc">;</span> | |
97 84 <span class="w">carp</span> <span class="q">"Warning: Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO: Fingerprints file type, $FileType, is not valid. Supported file types: SD, FP or Text\n"</span><span class="sc">;</span> | |
98 85 <span class="s">}</span> | |
99 86 | |
100 87 <span class="k">return</span> <span class="i">$FingerprintsFileIO</span><span class="sc">;</span> | |
101 88 <span class="s">}</span> | |
102 89 | |
103 90 <span class="c"># Get fingerpritns file type from fingerprints file name...</span> | |
104 91 <span class="c">#</span> | |
105 <a name="GetFingerprintsFileType-"></a> 92 <span class="k">sub </span><span class="m">GetFingerprintsFileType</span> <span class="s">{</span> | |
106 93 <span class="k">my</span><span class="s">(</span><span class="i">$FileName</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
107 94 <span class="k">my</span><span class="s">(</span><span class="i">$FileType</span><span class="s">)</span><span class="sc">;</span> | |
108 95 | |
109 96 <span class="i">$FileType</span> = <span class="q">''</span><span class="sc">;</span> | |
110 97 <span class="j">FILETYPE:</span> <span class="s">{</span> | |
111 98 <span class="k">if</span> <span class="s">(</span><span class="i">FileUtil::CheckFileType</span><span class="s">(</span><span class="i">$FileName</span><span class="cm">,</span> <span class="q">"sdf sd"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
112 99 <span class="i">$FileType</span> = <span class="q">'SD'</span><span class="sc">;</span> | |
113 100 <span class="k">last</span> <span class="j">FILETYPE</span><span class="sc">;</span> | |
114 101 <span class="s">}</span> | |
115 102 <span class="k">if</span> <span class="s">(</span><span class="i">FileUtil::CheckFileType</span><span class="s">(</span><span class="i">$FileName</span><span class="cm">,</span> <span class="q">"fpf fp"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
116 103 <span class="i">$FileType</span> = <span class="q">'FP'</span><span class="sc">;</span> | |
117 104 <span class="k">last</span> <span class="j">FILETYPE</span><span class="sc">;</span> | |
118 105 <span class="s">}</span> | |
119 106 <span class="k">if</span> <span class="s">(</span><span class="i">FileUtil::CheckFileType</span><span class="s">(</span><span class="i">$FileName</span><span class="cm">,</span> <span class="q">"csv tsv"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
120 107 <span class="i">$FileType</span> = <span class="q">'Text'</span><span class="sc">;</span> | |
121 108 <span class="k">last</span> <span class="j">FILETYPE</span><span class="sc">;</span> | |
122 109 <span class="s">}</span> | |
123 110 <span class="i">$FileType</span> = <span class="q">''</span><span class="sc">;</span> | |
124 111 <span class="w">carp</span> <span class="q">"Warning: Fingerprints::FingerprintsFileUtil::GetFingerprintsFileType: Can't determine fingerprints file type for $FileName: It's not a fingerprints file...\n"</span><span class="sc">;</span> | |
125 112 <span class="s">}</span> | |
126 113 | |
127 114 <span class="k">return</span> <span class="i">$FileType</span><span class="sc">;</span> | |
128 115 <span class="s">}</span> | |
129 116 | |
130 117 | |
131 118 <span class="c"># Process fingerprints bit-vector and vector string data in a file using FingerprintsFileIO</span> | |
132 119 <span class="c"># object and return a references to arrays of CompoundIDs and FingerprintsObjects...</span> | |
133 120 <span class="c">#</span> | |
134 121 <span class="c"># Note:</span> | |
135 122 <span class="c"># . The file open and close is automatically performed during processing.</span> | |
136 123 <span class="c">#</span> | |
137 <a name="ReadAndProcessFingerpritsData-"></a> 124 <span class="k">sub </span><span class="m">ReadAndProcessFingerpritsData</span> <span class="s">{</span> | |
138 125 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsFileIO</span><span class="cm">,</span> <span class="i">$CheckCompoundIDs</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
139 126 <span class="k">my</span><span class="s">(</span><span class="i">$CompoundID</span><span class="cm">,</span> <span class="i">$FingerprintsCount</span><span class="cm">,</span> <span class="i">$IgnoredFingerprintsCount</span><span class="cm">,</span> <span class="i">@CompundIDs</span><span class="cm">,</span> <span class="i">@FingerprintsObjects</span><span class="cm">,</span> <span class="i">%UniqueCompoundIDs</span><span class="s">)</span><span class="sc">;</span> | |
140 127 | |
141 128 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FingerprintsFileIO</span><span class="s">)</span> <span class="s">{</span> | |
142 129 <span class="k">return</span> <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span> | |
143 130 <span class="s">}</span> | |
144 131 <span class="i">$CheckCompoundIDs</span> = <span class="k">defined</span> <span class="i">$CheckCompoundIDs</span> ? <span class="i">$CheckCompoundIDs</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
145 132 | |
146 133 <span class="k">print</span> <span class="q">"\nReading and processing fingerprints data...\n"</span><span class="sc">;</span> | |
147 134 | |
148 135 <span class="s">(</span><span class="i">$FingerprintsCount</span><span class="cm">,</span> <span class="i">$IgnoredFingerprintsCount</span><span class="s">)</span> = <span class="s">(</span><span class="n">0</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span> | |
149 136 | |
150 137 <span class="i">@CompundIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
151 138 <span class="i">@FingerprintsObjects</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
152 139 | |
153 140 <span class="i">%UniqueCompoundIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
154 141 | |
155 142 <span class="c"># Check and open file for reading...</span> | |
156 143 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FingerprintsFileIO</span><span class="i">->GetStatus</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
157 144 <span class="i">$FingerprintsFileIO</span><span class="i">->Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
158 145 <span class="s">}</span> | |
159 146 | |
160 147 <span class="j">FINGERPRINTS:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$FingerprintsFileIO</span><span class="i">->Read</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
161 148 <span class="i">$FingerprintsCount</span>++<span class="sc">;</span> | |
162 149 | |
163 150 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FingerprintsFileIO</span><span class="i">->IsFingerprintsDataValid</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
164 151 <span class="i">$IgnoredFingerprintsCount</span>++<span class="sc">;</span> | |
165 152 <span class="k">next</span> <span class="j">FINGERPRINTS</span><span class="sc">;</span> | |
166 153 <span class="s">}</span> | |
167 154 | |
168 155 <span class="k">if</span> <span class="s">(</span><span class="i">$CheckCompoundIDs</span><span class="s">)</span> <span class="s">{</span> | |
169 156 <span class="i">$CompoundID</span> = <span class="i">$FingerprintsFileIO</span><span class="i">->GetCompoundID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
170 157 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$UniqueCompoundIDs</span>{<span class="i">$CompoundID</span>}<span class="s">)</span> <span class="s">{</span> | |
171 158 <span class="k">warn</span> <span class="q">"Warning: Ignoring fingerprints data for compound ID $CompoundID: Multiple entries for compound ID in fingerprints file.\n"</span><span class="sc">;</span> | |
172 159 <span class="i">$IgnoredFingerprintsCount</span>++<span class="sc">;</span> | |
173 160 <span class="k">next</span> <span class="j">FINGERPRINTS</span><span class="sc">;</span> | |
174 161 <span class="s">}</span> | |
175 162 <span class="i">$UniqueCompoundIDs</span>{<span class="i">$CompoundID</span>} = <span class="i">$CompoundID</span><span class="sc">;</span> | |
176 163 <span class="s">}</span> | |
177 164 | |
178 165 <span class="k">push</span> <span class="i">@FingerprintsObjects</span><span class="cm">,</span> <span class="i">$FingerprintsFileIO</span><span class="i">->GetFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
179 166 <span class="k">push</span> <span class="i">@CompundIDs</span><span class="cm">,</span> <span class="i">$FingerprintsFileIO</span><span class="i">->GetCompoundID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
180 167 <span class="s">}</span> | |
181 168 <span class="i">$FingerprintsFileIO</span><span class="i">->Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
182 169 | |
183 170 <span class="k">print</span> <span class="q">"Number of fingerprints data entries: $FingerprintsCount\n"</span><span class="sc">;</span> | |
184 171 <span class="k">print</span> <span class="q">"Number of fingerprints date entries processed successfully: "</span><span class="cm">,</span> <span class="s">(</span><span class="i">$FingerprintsCount</span> - <span class="i">$IgnoredFingerprintsCount</span><span class="s">)</span> <span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> | |
185 172 <span class="k">print</span> <span class="q">"Number of fingerprints data entries ignored due to missing/invalid data: $IgnoredFingerprintsCount\n\n"</span><span class="sc">;</span> | |
186 173 | |
187 174 <span class="k">return</span> <span class="s">(</span>\<span class="i">@CompundIDs</span><span class="cm">,</span> \<span class="i">@FingerprintsObjects</span><span class="s">)</span><span class="sc">;</span> | |
188 175 <span class="s">}</span> | |
189 176 | |
190 177 | |
191 <a name="EOF-"></a></pre> | |
192 <p> </p> | |
193 <br /> | |
194 <center> | |
195 <img src="../../../images/h2o2.png"> | |
196 </center> | |
197 </body> | |
198 </html> |