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3 <title>MayaChemTools:Documentation:MergeTextFilesWithSD.pl</title>
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14 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./MergeTextFiles.html" title="MergeTextFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./ModifyNewLineChar.html" title="ModifyNewLineChar.html">Next</a></td><td width="34%" align="middle"><strong>MergeTextFilesWithSD.pl</strong></td><td width="33%" align="right"><a href="././code/MergeTextFilesWithSD.html" title="View source code">Code</a> | <a href="./../pdf/MergeTextFilesWithSD.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/MergeTextFilesWithSD.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/MergeTextFilesWithSD.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/MergeTextFilesWithSD.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
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16 </table>
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17 </div>
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18 <p>
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19 </p>
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20 <h2>NAME</h2>
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21 <p>MergeTextFilesWithSD.pl - Merge CSV or TSV TextFile(s) into SDFile</p>
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22 <p>
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23 </p>
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24 <h2>SYNOPSIS</h2>
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25 <p>MergeTextFilesWithSD.pl SDFile TextFile(s)...</p>
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26 <p>MergeTextFilesWithSD.pl [<strong>-h, --help</strong>] [<strong>--indelim</strong> comma | semicolon]
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27 [<strong>-c, --columns</strong> colnum,...;... | collabel,...;...] [<strong>-k, --keys</strong> colkeynum;... | colkeylabel;...]
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28 [<strong>-m, --mode</strong> colnum | collabel] [<strong>-o, --overwrite</strong>] [<strong>-r, --root</strong> rootname]
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29 [<strong>-s, --sdkey</strong> sdfieldname] [<strong>-w, --workingdir</strong> dirname] SDFile TextFile(s)...</p>
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30 <p>
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31 </p>
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32 <h2>DESCRIPTION</h2>
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33 <p>Merge multiple CSV or TSV <em>TextFile(s)</em> into <em>SDFile</em>. Unless <strong>-k --keys</strong>
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34 option is used, data rows from all <em>TextFile(s)</em> are added to <em>SDFile</em> in a
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35 sequential order, and the number of compounds in <em>SDFile</em> is used to determine
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36 how many rows of data are added from <em>TextFile(s)</em>.</p>
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37 <p>Multiple <em>TextFile(s)</em> names are separated by spaces. The valid file extensions are <em>.csv</em> and
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38 <em>.tsv</em> for comma/semicolon and tab delimited text files respectively. All other file names
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39 are ignored. All the text files in a current directory can be specified by <em>*.csv</em>,
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40 <em>*.tsv</em>, or the current directory name. The <strong>--indelim</strong> option determines the
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41 format of <em>TextFile(s)</em>. Any file which doesn't correspond to the format indicated
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42 by <strong>--indelim</strong> option is ignored.</p>
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43 <p>
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44 </p>
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45 <h2>OPTIONS</h2>
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46 <dl>
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47 <dt><strong><strong>-h, --help</strong></strong></dt>
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48 <dd>
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49 <p>Print this help message.</p>
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50 </dd>
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51 <dt><strong><strong>--indelim</strong> <em>comma | semicolon</em></strong></dt>
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52 <dd>
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53 <p>Input delimiter for CSV <em>TextFile(s)</em>. Possible values: <em>comma or semicolon</em>.
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54 Default value: <em>comma</em>. For TSV files, this option is ignored and <em>tab</em> is used as a
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55 delimiter.</p>
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56 </dd>
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57 <dt><strong><strong>-c, --columns</strong> <em>colnum,...;... | collabel,...;...</em></strong></dt>
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58 <dd>
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59 <p>This value is mode specific. It is a list of columns to merge into <em>SDFile</em>
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60 specified by column numbers or labels for each text file delimited by ";".
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61 All <em>TextFile(s)</em> are merged into <em>SDFile</em>.</p>
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62 <p>Default value: <em>all;all;...</em>. By default, all columns from TextFile(s) are
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63 merged into <em>SDFile</em>.</p>
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64 <p>For <em>colnum</em> mode, input value format is: <em>colnum,...;colnum,...;...</em>. Example:</p>
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65 <div class="OptionsBox">
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66 "1,2;1,3,4;7,8,9"</div>
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67 <p>For <em>collabel</em> mode, input value format is: <em>collabel,...;collabel,...;...</em>. Example:</p>
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68 <div class="OptionsBox">
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69 "MW,SumNO;SumNHOH,ClogP,PSA;MolName,Mol_Id,Extreg"</div>
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70 </dd>
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71 <dt><strong><strong>-k, --keys</strong> <em>colkeynum;... | colkeylabel;...</em></strong></dt>
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72 <dd>
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73 <p>This value is mode specific. It specifies column keys to use for merging
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74 <em>TextFile(s)</em> into <em>SDFile</em>. The column keys, delimited by ";", are specified by column
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75 numbers or labels for <em>TextFile(s)</em>.</p>
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76 <p>By default, data rows from <em>TextFile(s)</em> are merged into <em>SDFile</em> in the order they appear.</p>
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77 <p>For <em>colnum</em> mode, input value format is:<em>colkeynum, colkeynum;...</em>. Example:</p>
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78 <div class="OptionsBox">
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79 "1;3;7"</div>
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80 <p>For <em>collabel</em> mode, input value format is:<em>colkeylabel, colkeylabel;...</em>. Example:</p>
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81 <div class="OptionsBox">
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82 "Mol_Id;Mol_Id;Cmpd_Id"</div>
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83 </dd>
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84 <dt><strong><strong>-m, --mode</strong> <em>colnum | collabel</em></strong></dt>
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85 <dd>
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86 <p>Specify how to merge <em>TextFile(s)</em> into <em>SDFile</em>: using column numbers or column labels.
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87 Possible values: <em>colnum or collabel</em>. Default value: <em>colnum</em>.</p>
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88 </dd>
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89 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
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90 <dd>
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91 <p>Overwrite existing files.</p>
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92 </dd>
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93 <dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt>
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94 <dd>
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95 <p>New SD file name is generated using the root: <Root>.sdf. Default file name:
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96 <InitialSDFileName>MergedWith<FirstTextFileName>1To<Count>.sdf.</p>
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97 </dd>
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98 <dt><strong><strong>-s, --sdkey</strong> <em>sdfieldname</em></strong></dt>
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99 <dd>
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100 <p><em>SDFile</em> data field name used as a key to merge data from TextFile(s). By default,
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101 data rows from <em>TextFile(s)</em> are merged into <em>SDFile</em> in the order they appear.</p>
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102 </dd>
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103 <dt><strong><strong>-w, --workingdir</strong> <em>dirname</em></strong></dt>
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104 <dd>
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105 <p>Location of working directory. Default: current directory.</p>
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106 </dd>
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107 </dl>
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108 <p>
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109 </p>
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110 <h2>EXAMPLES</h2>
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111 <p>To merge Sample1.csv and Sample2.csv into Sample.sdf and generate
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112 NewSample.sdf, type:</p>
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113 <div class="ExampleBox">
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114 % MergeTextFileswithSD.pl -r NewSample -o Sample.sdf
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115 Sample1.csv Sample2.csv</div>
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116 <p>To merge all Sample*.tsv into Sample.sdf and generate NewSample.sdf file, type:</p>
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117 <div class="ExampleBox">
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118 % MergeTextFilesWithSD.pl -r NewSample -o Sample.sdf
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119 Sample*.tsv</div>
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120 <p>To merge column numbers "1,2" and "3,4,5" from Sample2.csv and Sample3.csv
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121 into Sample.sdf and to generate NewSample.sdf, type:</p>
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122 <div class="ExampleBox">
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123 % MergeTextFilesWithSD.pl -r NewSample -m colnum -c "1,2;3,4,5"
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124 -o Sample.sdf Sample1.csv Sample2.csv</div>
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125 <p>To merge column "Mol_ID,Formula,MolWeight" and "Mol_ID,ChemBankID,NAME"
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126 from Sample1.csv and Sample2.csv into Sample.sdf using "Mol_ID" as SD and column keys
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127 to generate NewSample.sdf, type:</p>
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128 <div class="ExampleBox">
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129 % MergeTextFilesWithSD.pl -r NewSample -s Mol_ID -k "Mol_ID;Mol_ID"
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130 -m collabel -c "Mol_ID,Formula,MolWeight;Mol_ID,ChemBankID,NAME"
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131 -o Sample1.sdf Sample1.csv Sample2.csv</div>
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132 <p>
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133 </p>
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134 <h2>AUTHOR</h2>
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135 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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136 <p>
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137 </p>
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138 <h2>SEE ALSO</h2>
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139 <p><a href="./ExtractFromSDFiles.html">ExtractFromSDFiles.pl</a>, <a href="./FilterSDFiles.html">FilterSDFiles.pl</a>, <a href="./InfoSDFiles.html">InfoSDFiles.pl</a>, <a href="./JoinSDFiles.html">JoinSDFiles.pl</a>, <a href="./JoinTextFiles.html">JoinTextFiles.pl</a>, 
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140 <a href="./MergeTextFiles.html">MergeTextFiles.pl</a>, <a href="./ModifyTextFilesFormat.html">ModifyTextFilesFormat.pl</a>, <a href="./SplitSDFiles.html">SplitSDFiles.pl</a>, <a href="./SplitTextFiles.html">SplitTextFiles.pl</a>
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141 </p>
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142 <p>
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143 </p>
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144 <h2>COPYRIGHT</h2>
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145 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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146 <p>This file is part of MayaChemTools.</p>
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147 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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148 the terms of the GNU Lesser General Public License as published by the Free
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149 Software Foundation; either version 3 of the License, or (at your option)
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150 any later version.</p>
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151 <p> </p><p> </p><div class="DocNav">
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152 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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153 <tr align="left" valign="top"><td width="33%" align="left"><a href="./MergeTextFiles.html" title="MergeTextFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./ModifyNewLineChar.html" title="ModifyNewLineChar.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>MergeTextFilesWithSD.pl</strong></td></tr>
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154 </table>
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155 </div>
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156 <br />
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157 <center>
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