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3 <title>MayaChemTools:Documentation:ExtractFromTextFiles.pl</title>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./ExtractFromSequenceFiles.html" title="ExtractFromSequenceFiles.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./FilterSDFiles.html" title="FilterSDFiles.html">Next</a></td><td width="34%" align="middle"><strong>ExtractFromTextFiles.pl</strong></td><td width="33%" align="right"><a href="././code/ExtractFromTextFiles.html" title="View source code">Code</a>&nbsp;|&nbsp;<a href="./../pdf/ExtractFromTextFiles.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/ExtractFromTextFiles.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/ExtractFromTextFiles.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/ExtractFromTextFiles.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>ExtractFromTextFiles.pl - Extract specific data from TextFile(s)</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>ExtractFromTextFiles.pl TextFile(s)...</p>
26 <p>ExtractFromTextFiles.pl [<strong>-c, --colmode</strong> colnum | collabel] [<strong>--categorycol </strong> number | string]
27 [<strong>--columns</strong> &quot;colnum,[colnum]...&quot; | &quot;collabel,[collabel]...&quot;] [<strong>-h, --help</strong>]
28 [<strong>--indelim</strong> <em>comma | semicolon</em>] [<strong>-m, --mode </strong> <em>columns | rows | categories</em>]
29 [<strong>-o, --overwrite</strong>] [<strong>--outdelim</strong> <em>comma | tab | semicolon</em>] [<strong>-q, --quote</strong> <em>yes | no</em>]
30 [<strong>--rows</strong> &quot;colid,value,criteria...&quot; | &quot;colid,value...&quot; | &quot;colid,mincolvalue,maxcolvalue&quot; | &quot;rownum,rownum,...&quot; | colid | &quot;minrownum,maxrownum&quot;]
31 [ <strong>--rowsmode</strong> rowsbycolvalue | rowsbycolvaluelist | rowsbycolvaluerange | rowbymincolvalue | rowbymaxcolvalue | rownums | rownumrange]
32 [<strong>-r, --root</strong> <em>rootname</em>] [<strong>-w, --workingdir</strong> <em>dirname</em>] TextFile(s)...</p>
33 <p>
34 </p>
35 <h2>DESCRIPTION</h2>
36 <p>Extract column(s)/row(s) data from <em>TextFile(s)</em> identified by column numbers or labels. Or categorize
37 data using a specified column category. During categorization, a summary text file is
38 generated containing category name and count; an additional text file, containing data for
39 for each category, is also generated. The file names are separated by space. The
40 valid file extensions are <em>.csv</em> and <em>.tsv</em> for comma/semicolon and tab delimited
41 text files respectively. All other file names are ignored. All the text files in a
42 current directory can be specified by <em>*.csv</em>, <em>*.tsv</em>, or the current directory
43 name. The <strong>--indelim</strong> option determines the format of <em>TextFile(s)</em>. Any file
44 which doesn't correspond to the format indicated by <strong>--indelim</strong> option is ignored.</p>
45 <p>
46 </p>
47 <h2>OPTIONS</h2>
48 <dl>
49 <dt><strong><strong>-c, --colmode</strong> <em>colnum | collabel</em></strong></dt>
50 <dd>
51 <p>Specify how columns are identified in <em>TextFile(s)</em>: using column number or column
52 label. Possible values: <em>colnum or collabel</em>. Default value: <em>colnum</em>.</p>
53 </dd>
54 <dt><strong><strong>--categorycol </strong> <em>number | string</em></strong></dt>
55 <dd>
56 <p>Column used to categorize data. Default value: First column.</p>
57 <p>For <em>colnum</em> value of <strong>-c, --colmode</strong> option, input value is a column number.
58 Example: <em>1</em>.</p>
59 <p>For <em>collabel</em> value of <strong>-c, --colmode</strong> option, input value is a column label.
60 Example: <em>Mol_ID</em>.</p>
61 </dd>
62 <dt><strong><strong>--columns</strong> <em>&quot;colnum,[colnum]...&quot; | &quot;collabel,[collabel]...&quot;</em></strong></dt>
63 <dd>
64 <p>List of comma delimited columns to extract. Default value: First column.</p>
65 <p>For <em>colnum</em> value of <strong>-c, --colmode</strong> option, input values format is:
66 <em>colnum,colnum,...</em>. Example: <em>1,3,5</em></p>
67 <p>For <em>collabel</em> value of <strong>-c, --colmode</strong> option, input values format is:
68 <em>collabel,collabel,..</em>. Example: <em>Mol_ID,MolWeight</em></p>
69 </dd>
70 <dt><strong><strong>-h, --help</strong></strong></dt>
71 <dd>
72 <p>Print this help message.</p>
73 </dd>
74 <dt><strong><strong>--indelim</strong> <em>comma | semicolon</em></strong></dt>
75 <dd>
76 <p>Input delimiter for CSV <em>TextFile(s)</em>. Possible values: <em>comma or semicolon</em>.
77 Default value: <em>comma</em>. For TSV files, this option is ignored and <em>tab</em> is used as a
78 delimiter.</p>
79 </dd>
80 <dt><strong><strong>-m, --mode </strong> <em>columns | rows | categories</em></strong></dt>
81 <dd>
82 <p>Specify what to extract from <em>TextFile(s)</em>. Possible values: <em>columns, rows,
83 or categories</em>. Default value: <em>columns</em>.</p>
84 <p>For <em>columns</em> mode, data for appropriate columns specified by <strong>--columns</strong> option
85 is extracted from <em>TextFile(s)</em> and placed into new text files.</p>
86 <p>For <em>rows</em> mode, appropriate rows specified in conjuction with <strong>--rowsmode</strong> and
87 <strong>rows</strong> options are extracted from <em>TextFile(s)</em> and placed into new text files.</p>
88 <p>For <em>categories</em> mode, coulmn specified by <strong>--categorycol</strong> is
89 used to categorize data, and a summary text file is generated
90 containing category name and count; an additional text file, containing data for
91 for each category, is also generated.</p>
92 </dd>
93 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
94 <dd>
95 <p>Overwrite existing files.</p>
96 </dd>
97 <dt><strong><strong>--outdelim</strong> <em>comma | tab | semicolon</em>.</strong></dt>
98 <dd>
99 <p>Output text file delimiter. Possible values: <em>comma, tab, or semicolon</em>.
100 Default value: <em>comma</em></p>
101 </dd>
102 <dt><strong><strong>-q, --quote</strong> <em>yes | no</em></strong></dt>
103 <dd>
104 <p>Put quotes around column values in output text file. Possible values: <em>yes or
105 no</em>. Default value: <em>yes</em>.</p>
106 </dd>
107 <dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt>
108 <dd>
109 <p>New file name is generated using the root: &lt;Root&gt;.&lt;Ext&gt;. Default for new file
110 names: &lt;TextFile&gt;CategoriesSummary.&lt;Ext&gt;, &lt;TextFile&gt;ExtractedColumns.&lt;Ext&gt;, and
111 &lt;TextFile&gt;ExtractedRows.&lt;Ext&gt; for <em>categories</em>, <em>columns</em>, and <em>rows</em> mode
112 respectively. And &lt;TextFile&gt;Category&lt;CategoryName&gt;.&lt;Ext&gt;
113 for each category retrieved from each text file. The output file type determines &lt;Ext&gt;
114 value: csv and tsv for CSV, and TSV files respectively.</p>
115 <p>This option is ignored for multiple input files.</p>
116 </dd>
117 <dt><strong><strong>--rows</strong> <em>&quot;colid,value,criteria...&quot; | &quot;colid,value...&quot; | &quot;colid,mincolvalue,maxcolvalue&quot; | &quot;rownum,rownum,...&quot; | colid | &quot;minrownum,maxrownum&quot;</em></strong></dt>
118 <dd>
119 <p>This value is <strong>--rowsmode</strong> specific. In general, it's a list of comma separated column ids and
120 associated mode specific value. Based on Column ids specification, column label or number, is
121 controlled by <strong>-c, --colmode</strong> option.</p>
122 <p>First line containing column labels is always written out. And value comparisons assume
123 numerical column data.</p>
124 <p>For <em>rowsbycolvalue</em> mode, input value format contains these triplets:
125 <em>colid,value, criteria...</em>. Possible values for criteria: <em>le, ge or eq</em>.
126 Examples:</p>
127 <div class="OptionsBox">
128 MolWt,450,le
129 <br/> MolWt,450,le,LogP,5,le,SumNumNO,10,le,SumNHOH,5,le</div>
130 <p>For <em>rowsbycolvaluelist</em> mode, input value format is: <em>colid,value...</em>. Examples:</p>
131 <div class="OptionsBox">
132 Mol_ID,20
133 <br/> Mol_ID,20,1002,1115</div>
134 <p>For <em>rowsbycolvaluerange</em> mode, input value format is: <em>colid,mincolvalue,maxcolvalue</em>. Examples:</p>
135 <div class="OptionsBox">
136 MolWt,100,450</div>
137 <p>For <em>rowbymincolvalue, rowbymaxcolvalue</em> modes, input value format is: <em>colid</em>.</p>
138 <p>For <em>rownum</em> mode, input value format is: <em>rownum</em>. Default value: <em>2</em>.</p>
139 <p>For <em>rownumrange</em> mode, input value format is: <em>minrownum, maxrownum</em>. Examples:</p>
140 <div class="OptionsBox">
141 10,40</div>
142 </dd>
143 <dt><strong><strong>--rowsmode</strong> <em>rowsbycolvalue | rowsbycolvaluelist | rowsbycolvaluerange | rowbymincolvalue | rowbymaxcolvalue | rownums | rownumrange</em></strong></dt>
144 <dd>
145 <p>Specify how to extract rows from <em>TextFile(s)</em>. Possible values: <em>rowsbycolvalue, rowsbycolvaluelist, rowsbycolvaluerange,
146 rowbymincolvalue, rowbymaxcolvalue, rownum, rownumrange</em>. Default value: <em>rownum</em>.</p>
147 <p>Use <strong>--rows</strong> option to list rows criterion used for extraction of rows from
148 <em>TextFile(s)</em>.</p>
149 </dd>
150 <dt><strong><strong>-w, --workingdir</strong> <em>dirname</em></strong></dt>
151 <dd>
152 <p>Location of working directory. Default: current directory.</p>
153 </dd>
154 </dl>
155 <p>
156 </p>
157 <h2>EXAMPLES</h2>
158 <p>To extract first column from a text file and generate a new CSV text file NewSample1.csv,
159 type:</p>
160 <div class="ExampleBox">
161 % ExtractFromTextFiles.pl -r NewSample1 -o Sample1.csv</div>
162 <p>To extract columns Mol_ID, MolWeight, and NAME from Sample1.csv and generate a new
163 textfile NewSample1.tsv with no quotes, type:</p>
164 <div class="ExampleBox">
165 % ExtractFromTextFiles.pl -m columns -c collabel --columns &quot;Mol_ID,
166 MolWeight,NAME&quot; --outdelim tab --quote no -r NewSample1
167 -o Sample1.csv</div>
168 <p>To extract rows containing values for MolWeight column of less than 450 from
169 Sample1.csv and generate a new textfile NewSample1.csv, type:</p>
170 <div class="ExampleBox">
171 % ExtractFromTextFiles.pl -m rows --rowsmode rowsbycolvalue
172 -c collabel --rows MolWeight,450,le -r NewSample1
173 -o Sample1.csv</div>
174 <p>To extract rows containing values for MolWeight column between 400 and 500 from
175 Sample1.csv and generate a new textfile NewSample1.csv, type:</p>
176 <div class="ExampleBox">
177 % ExtractFromTextFiles.pl -m rows --rowsmode rowsbycolvaluerange
178 -c collabel --rows MolWeight,450,500 -r NewSample1
179 -o Sample1.csv</div>
180 <p>To extract a row containing minimum value for column MolWeight from Sample1.csv and generate
181 a new textfile NewSample1.csv, type:</p>
182 <div class="ExampleBox">
183 % ExtractFromTextFiles.pl -m rows --rowsmode rowbymincolvalue
184 -c collabel --rows MolWeight -r NewSample1
185 -o Sample1.csv</div>
186 <p>
187 </p>
188 <h2>AUTHOR</h2>
189 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
190 <p>
191 </p>
192 <h2>SEE ALSO</h2>
193 <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>
194 </p>
195 <p>
196 </p>
197 <h2>COPYRIGHT</h2>
198 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
199 <p>This file is part of MayaChemTools.</p>
200 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
201 the terms of the GNU Lesser General Public License as published by the Free
202 Software Foundation; either version 3 of the License, or (at your option)
203 any later version.</p>
204 <p>&nbsp</p><p>&nbsp</p><div class="DocNav">
205 <table width="100%" border=0 cellpadding=0 cellspacing=2>
206 <tr align="left" valign="top"><td width="33%" align="left"><a href="./ExtractFromSequenceFiles.html" title="ExtractFromSequenceFiles.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./FilterSDFiles.html" title="FilterSDFiles.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>ExtractFromTextFiles.pl</strong></td></tr>
207 </table>
208 </div>
209 <br />
210 <center>
211 <img src="../../images/h2o2.png">
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