Mercurial > repos > deepakjadmin > mayatool3_test3
diff mayachemtools/docs/modules/html/code/FingerprintsFileUtil.html @ 0:73ae111cf86f draft
Uploaded
| author | deepakjadmin |
|---|---|
| date | Wed, 20 Jan 2016 11:55:01 -0500 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/modules/html/code/FingerprintsFileUtil.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,198 @@ +<html> +<head> +<title>MayaChemTools:Code:Fingerprints::FingerprintsFileUtil.pm</title> +<meta http-equiv="content-type" content="text/html;charset=utf-8"> +<link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> +</head> +<body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> +<br/> +<center> +<a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> +</center> +<br/> +<pre> +<a name="package-Fingerprints::FingerprintsFileUtil-"></a> 1 <span class="k">package </span><span class="i">Fingerprints::FingerprintsFileUtil</span><span class="sc">;</span> + 2 <span class="c">#</span> + 3 <span class="c"># $RCSfile: FingerprintsFileUtil.pm,v $</span> + 4 <span class="c"># $Date: 2015/02/28 20:48:54 $</span> + 5 <span class="c"># $Revision: 1.14 $</span> + 6 <span class="c">#</span> + 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> + 8 <span class="c">#</span> + 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> + 10 <span class="c">#</span> + 11 <span class="c"># This file is part of MayaChemTools.</span> + 12 <span class="c">#</span> + 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> + 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> + 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> + 16 <span class="c"># later version.</span> + 17 <span class="c">#</span> + 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> + 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> + 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> + 21 <span class="c"># details.</span> + 22 <span class="c">#</span> + 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> + 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> + 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> + 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> + 27 <span class="c">#</span> + 28 + 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> + 30 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span> + 31 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span> + 32 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 33 <span class="k">use</span> <span class="w">FileUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 34 <span class="k">use</span> <span class="w">FileIO::FingerprintsSDFileIO</span><span class="sc">;</span> + 35 <span class="k">use</span> <span class="w">FileIO::FingerprintsTextFileIO</span><span class="sc">;</span> + 36 <span class="k">use</span> <span class="w">FileIO::FingerprintsFPFileIO</span><span class="sc">;</span> + 37 + 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> + 39 + 40 <span class="i">@ISA</span> = <span class="q">qw(Exporter)</span><span class="sc">;</span> + 41 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> + 42 <span class="i">@EXPORT_OK</span> = <span class="q">qw(GetFingerprintsFileType ReadAndProcessFingerpritsData NewFingerprintsFileIO)</span><span class="sc">;</span> + 43 + 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> + 45 + 46 <span class="c"># Generate new FingerprintsFileIO object for a SD, FP or Text fingerprints file specified using file name</span> + 47 <span class="c"># along other appropriate parameters...</span> + 48 <span class="c">#</span> +<a name="NewFingerprintsFileIO-"></a> 49 <span class="k">sub </span><span class="m">NewFingerprintsFileIO</span> <span class="s">{</span> + 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> + 51 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsFileIO</span><span class="cm">,</span> <span class="i">$FileType</span><span class="s">)</span><span class="sc">;</span> + 52 + 53 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$FingerprintsFileIOParams</span>{<span class="w">Name</span>}<span class="s">)</span> && <span class="i">TextUtil::IsNotEmpty</span><span class="s">(</span><span class="i">$FingerprintsFileIOParams</span>{<span class="w">Name</span>}<span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 54 <span class="w">carp</span> <span class="q">"Warning: Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO: Can't create new FingerprintsFileIO object: File name is not specified...\n"</span><span class="sc">;</span> + 55 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> + 56 <span class="s">}</span> + 57 + 58 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$FingerprintsFileIOParams</span>{<span class="w">Mode</span>}<span class="s">)</span> && <span class="i">TextUtil::IsNotEmpty</span><span class="s">(</span><span class="i">$FingerprintsFileIOParams</span>{<span class="w">Mode</span>}<span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 59 <span class="w">carp</span> <span class="q">"Warning: Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO: Can't create new FingerprintsFileIO object: File mode is not specified...\n"</span><span class="sc">;</span> + 60 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> + 61 <span class="s">}</span> + 62 + 63 <span class="i">$FileType</span> = <span class="i">GetFingerprintsFileType</span><span class="s">(</span><span class="i">$FingerprintsFileIOParams</span>{<span class="w">Name</span>}<span class="s">)</span><span class="sc">;</span> + 64 <span class="k">if</span> <span class="s">(</span><span class="i">TextUtil::IsEmpty</span><span class="s">(</span><span class="i">$FileType</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 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> + 66 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> + 67 <span class="s">}</span> + 68 + 69 <span class="c"># Generate fingerprints IO object...</span> + 70 <span class="j">FILETYPE:</span> <span class="s">{</span> + 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> + 72 <span class="i">$FingerprintsFileIO</span> = <span class="w">new</span> <span class="i">FileIO::FingerprintsSDFileIO</span><span class="s">(</span><span class="i">%FingerprintsFileIOParams</span><span class="s">)</span><span class="sc">;</span> + 73 <span class="k">last</span> <span class="j">FILETYPE</span><span class="sc">;</span> + 74 <span class="s">}</span> + 75 <span class="k">if</span> <span class="s">(</span><span class="i">$FileType</span> =~ <span class="q">/^FP$/i</span><span class="s">)</span> <span class="s">{</span> + 76 <span class="i">$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> + 77 <span class="k">last</span> <span class="j">FILETYPE</span><span class="sc">;</span> + 78 <span class="s">}</span> + 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> + 80 <span class="i">$FingerprintsFileIO</span> = <span class="w">new</span> <span class="i">FileIO::FingerprintsTextFileIO</span><span class="s">(</span><span class="i">%FingerprintsFileIOParams</span><span class="s">)</span><span class="sc">;</span> + 81 <span class="k">last</span> <span class="j">FILETYPE</span><span class="sc">;</span> + 82 <span class="s">}</span> + 83 <span class="i">$FingerprintsFileIO</span> = <span class="k">undef</span><span class="sc">;</span> + 84 <span class="w">carp</span> <span class="q">"Warning: Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO: Fingerprints file type, $FileType, is not valid. Supported file types: SD, FP or Text\n"</span><span class="sc">;</span> + 85 <span class="s">}</span> + 86 + 87 <span class="k">return</span> <span class="i">$FingerprintsFileIO</span><span class="sc">;</span> + 88 <span class="s">}</span> + 89 + 90 <span class="c"># Get fingerpritns file type from fingerprints file name...</span> + 91 <span class="c">#</span> +<a name="GetFingerprintsFileType-"></a> 92 <span class="k">sub </span><span class="m">GetFingerprintsFileType</span> <span class="s">{</span> + 93 <span class="k">my</span><span class="s">(</span><span class="i">$FileName</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 94 <span class="k">my</span><span class="s">(</span><span class="i">$FileType</span><span class="s">)</span><span class="sc">;</span> + 95 + 96 <span class="i">$FileType</span> = <span class="q">''</span><span class="sc">;</span> + 97 <span class="j">FILETYPE:</span> <span class="s">{</span> + 98 <span class="k">if</span> <span class="s">(</span><span class="i">FileUtil::CheckFileType</span><span class="s">(</span><span class="i">$FileName</span><span class="cm">,</span> <span class="q">"sdf sd"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 99 <span class="i">$FileType</span> = <span class="q">'SD'</span><span class="sc">;</span> + 100 <span class="k">last</span> <span class="j">FILETYPE</span><span class="sc">;</span> + 101 <span class="s">}</span> + 102 <span class="k">if</span> <span class="s">(</span><span class="i">FileUtil::CheckFileType</span><span class="s">(</span><span class="i">$FileName</span><span class="cm">,</span> <span class="q">"fpf fp"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 103 <span class="i">$FileType</span> = <span class="q">'FP'</span><span class="sc">;</span> + 104 <span class="k">last</span> <span class="j">FILETYPE</span><span class="sc">;</span> + 105 <span class="s">}</span> + 106 <span class="k">if</span> <span class="s">(</span><span class="i">FileUtil::CheckFileType</span><span class="s">(</span><span class="i">$FileName</span><span class="cm">,</span> <span class="q">"csv tsv"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 107 <span class="i">$FileType</span> = <span class="q">'Text'</span><span class="sc">;</span> + 108 <span class="k">last</span> <span class="j">FILETYPE</span><span class="sc">;</span> + 109 <span class="s">}</span> + 110 <span class="i">$FileType</span> = <span class="q">''</span><span class="sc">;</span> + 111 <span class="w">carp</span> <span class="q">"Warning: Fingerprints::FingerprintsFileUtil::GetFingerprintsFileType: Can't determine fingerprints file type for $FileName: It's not a fingerprints file...\n"</span><span class="sc">;</span> + 112 <span class="s">}</span> + 113 + 114 <span class="k">return</span> <span class="i">$FileType</span><span class="sc">;</span> + 115 <span class="s">}</span> + 116 + 117 + 118 <span class="c"># Process fingerprints bit-vector and vector string data in a file using FingerprintsFileIO</span> + 119 <span class="c"># object and return a references to arrays of CompoundIDs and FingerprintsObjects...</span> + 120 <span class="c">#</span> + 121 <span class="c"># Note:</span> + 122 <span class="c"># . The file open and close is automatically performed during processing.</span> + 123 <span class="c">#</span> +<a name="ReadAndProcessFingerpritsData-"></a> 124 <span class="k">sub </span><span class="m">ReadAndProcessFingerpritsData</span> <span class="s">{</span> + 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> + 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">$IgnoredFingerprintsCount</span><span class="cm">,</span> <span class="i">@CompundIDs</span><span class="cm">,</span> <span class="i">@FingerprintsObjects</span><span class="cm">,</span> <span class="i">%UniqueCompoundIDs</span><span class="s">)</span><span class="sc">;</span> + 127 + 128 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FingerprintsFileIO</span><span class="s">)</span> <span class="s">{</span> + 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> + 130 <span class="s">}</span> + 131 <span class="i">$CheckCompoundIDs</span> = <span class="k">defined</span> <span class="i">$CheckCompoundIDs</span> ? <span class="i">$CheckCompoundIDs</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 132 + 133 <span class="k">print</span> <span class="q">"\nReading and processing fingerprints data...\n"</span><span class="sc">;</span> + 134 + 135 <span class="s">(</span><span class="i">$FingerprintsCount</span><span class="cm">,</span> <span class="i">$IgnoredFingerprintsCount</span><span class="s">)</span> = <span class="s">(</span><span class="n">0</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span> + 136 + 137 <span class="i">@CompundIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 138 <span class="i">@FingerprintsObjects</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 139 + 140 <span class="i">%UniqueCompoundIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 141 + 142 <span class="c"># Check and open file for reading...</span> + 143 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FingerprintsFileIO</span><span class="i">->GetStatus</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 144 <span class="i">$FingerprintsFileIO</span><span class="i">->Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 145 <span class="s">}</span> + 146 + 147 <span class="j">FINGERPRINTS:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$FingerprintsFileIO</span><span class="i">->Read</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 148 <span class="i">$FingerprintsCount</span>++<span class="sc">;</span> + 149 + 150 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FingerprintsFileIO</span><span class="i">->IsFingerprintsDataValid</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 151 <span class="i">$IgnoredFingerprintsCount</span>++<span class="sc">;</span> + 152 <span class="k">next</span> <span class="j">FINGERPRINTS</span><span class="sc">;</span> + 153 <span class="s">}</span> + 154 + 155 <span class="k">if</span> <span class="s">(</span><span class="i">$CheckCompoundIDs</span><span class="s">)</span> <span class="s">{</span> + 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> + 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> + 158 <span class="k">warn</span> <span class="q">"Warning: Ignoring fingerprints data for compound ID $CompoundID: Multiple entries for compound ID in fingerprints file.\n"</span><span class="sc">;</span> + 159 <span class="i">$IgnoredFingerprintsCount</span>++<span class="sc">;</span> + 160 <span class="k">next</span> <span class="j">FINGERPRINTS</span><span class="sc">;</span> + 161 <span class="s">}</span> + 162 <span class="i">$UniqueCompoundIDs</span>{<span class="i">$CompoundID</span>} = <span class="i">$CompoundID</span><span class="sc">;</span> + 163 <span class="s">}</span> + 164 + 165 <span class="k">push</span> <span class="i">@FingerprintsObjects</span><span class="cm">,</span> <span class="i">$FingerprintsFileIO</span><span class="i">->GetFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 166 <span class="k">push</span> <span class="i">@CompundIDs</span><span class="cm">,</span> <span class="i">$FingerprintsFileIO</span><span class="i">->GetCompoundID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 167 <span class="s">}</span> + 168 <span class="i">$FingerprintsFileIO</span><span class="i">->Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 169 + 170 <span class="k">print</span> <span class="q">"Number of fingerprints data entries: $FingerprintsCount\n"</span><span class="sc">;</span> + 171 <span class="k">print</span> <span class="q">"Number of fingerprints date entries processed successfully: "</span><span class="cm">,</span> <span class="s">(</span><span class="i">$FingerprintsCount</span> - <span class="i">$IgnoredFingerprintsCount</span><span class="s">)</span> <span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 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> + 173 + 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> + 175 <span class="s">}</span> + 176 + 177 +<a name="EOF-"></a></pre> +<p> </p> +<br /> +<center> +<img src="../../../images/h2o2.png"> +</center> +</body> +</html>