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