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<section id="content" class="body">
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<header>
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<h1>
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Basic operations with SED
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</h1>
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<ol class="breadcrumb">
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<li>
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<time class="published" datetime="2018-12-24T15:03:00+01:00">
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24 décembre 2018
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</time>
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</li>
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<li>Linux</li>
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<li>Bash</li>
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</ol>
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</header>
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<div class='article_content'>
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<p>In this article we will learn about some of the main uses we can use <code>sed</code> for :
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<em> replacing
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</em> deleting
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* printing </p>
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<p>For this example we will learn how to remove the comments starting with the '#' sign and the blank lines for the following file :</p>
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<div class="highlight"><pre><span></span>## Header of input.csv
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#this file contains information I want to parse with a simple program.
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#The header, the footer or any comment starting with a "#" will be removed
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#The blank lines will also be removed
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#img,processed,defaut
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#bloc 1
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0,a0000.tif,,
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1,a0001.tif,True,"(139, 63)(145, 91)"
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2,a0002.tif,True,"(93, 72)(24, 162)(31, 64)"
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3,a0003.tif,,
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4,a0004.tif,,
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5,a0005.tif,,
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6,a0006.tif,,
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7,a0007.tif,,
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8,a0008.tif,,
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9,a0009.tif,True,"(127, 80)(104, 60)(87, 63)(53, 78)(17, 126)"
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10,a0010.tif,,
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11,a0011.tif,True,"(39, 78)(84, 110)" # a random comment passing by
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#end of bloc 1
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#bloc 2
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12,a0012.tif,,
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13,a0013.tif,,
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14,a0014.tif,,
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15,a0015.tif,True,"(146, 65)(146, 89)(139, 146)(16, 68)"
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16,a0016.tif,True,"(51, 59)(77, 69)(145, 78)(139, 112)(97, 123)(17, 148)"
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17,a0017.tif,,
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#end of bloc 2
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#bloc 3
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18,a0018.tif,,
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19,a0019.tif,,
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20,a0020.tif,True,"(57, 99)(12, 113)(27, 139)(16, 158)"
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21,a0021.tif,,
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22,a0022.tif,,
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23,a0023.tif,,
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24,a0024.tif,,
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25,a0025.tif,,
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26,a0026.tif,,
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#end of bloc 3
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27,a0027.tif,True,"(11, 86)(29, 74)(92, 68)(109, 129)(132, 104)"
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28,a0028.tif,,
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29,a0029.tif,True,"(128, 58)"
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30,a0030.tif,True,"(133, 59)(99, 77)(111, 100)(115, 153)"
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31,a0031.tif,True,"(43, 154)(27, 177)"
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## footer : end of file
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</pre></div>
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<h2>Anatomy of a SED command</h2>
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<p>If we run the command : </p>
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<div class="highlight"><pre><span></span>sed <span class="s2">""</span> input.csv
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</pre></div>
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<p>Everything inside the brackets will be interpreted as a sed command. In our case, there is nothing hence the file will be printed to the consol without any modification.</p>
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<p>You can put in the quotation mark one of sed's many commands for instance <code>s</code> that stands for substitude and is one of the most commonly used.</p>
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<p>In our csv we use the comma separator, let's say that we want to change it to a semicolon. We would do :</p>
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<div class="highlight"><pre><span></span>sed <span class="s2">"s/,/;/"</span> input.csv
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</pre></div>
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<p>so we have <code>s</code> meaning that we want to use the replace command followed by a <code>/</code> and the caracter(s) we want to replace followed by a <code>/</code> and the caracter(s) we want to replace it with and finally a <code>/</code>.</p>
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<p>The result is the following :</p>
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<div class="highlight"><pre><span></span>## Header
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#this file contains information I want to parse with a simple program.
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#The header; the footer or any comment starting with a "#" will be removed
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#The blank lines will also be removed
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#img;processed,defaut
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#bloc 1
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0;a0000.tif,,
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1;a0001.tif,True,"(139, 63)(145, 91)"
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2;a0002.tif,True,"(93, 72)(24, 162)(31, 64)"
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3;a0003.tif,,
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4;a0004.tif,,
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5;a0005.tif,,
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6;a0006.tif,,
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7;a0007.tif,,
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8;a0008.tif,,
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9;a0009.tif,True,"(127, 80)(104, 60)(87, 63)(53, 78)(17, 126)"
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10;a0010.tif,,
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11;a0011.tif,True,"(39, 78)(84, 110)" # a random comment passing by
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#end of bloc 1
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#bloc 2
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12;a0012.tif,,
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13;a0013.tif,,
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14;a0014.tif,,
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15;a0015.tif,True,"(146, 65)(146, 89)(139, 146)(16, 68)"
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16;a0016.tif,True,"(51, 59)(77, 69)(145, 78)(139, 112)(97, 123)(17, 148)"
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17;a0017.tif,,
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#end of bloc 2
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#bloc 3
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18;a0018.tif,,
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19;a0019.tif,,
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20;a0020.tif,True,"(57, 99)(12, 113)(27, 139)(16, 158)"
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21;a0021.tif,,
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22;a0022.tif,,
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23;a0023.tif,,
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24;a0024.tif,,
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25;a0025.tif,,
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26;a0026.tif,,
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#end of bloc 3
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27;a0027.tif,True,"(11, 86)(29, 74)(92, 68)(109, 129)(132, 104)"
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28;a0028.tif,,
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29;a0029.tif,True,"(128, 58)"
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30;a0030.tif,True,"(133, 59)(99, 77)(111, 100)(115, 153)"
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31;a0031.tif,True,"(43, 154)(27, 177)"
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## footer : end of file
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</pre></div>
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<p>As you can see, only the first comma has been replaced, in order to repeat the command multiple times per line we need to specify the <code>g</code> option</p>
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<div class="highlight"><pre><span></span>sed <span class="s2">"s/,/;/g"</span> input.csv
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</pre></div>
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<div class="highlight"><pre><span></span>## Header
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#this file contains information I want to parse with a simple program.
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#The header; the footer or any comment starting with a "#" will be removed
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#The blank lines will also be removed
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#img;processed;defaut
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#bloc 1
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0;a0000.tif;;
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1;a0001.tif;True;"(139; 63)(145; 91)"
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2;a0002.tif;True;"(93; 72)(24; 162)(31; 64)"
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3;a0003.tif;;
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4;a0004.tif;;
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5;a0005.tif;;
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6;a0006.tif;;
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7;a0007.tif;;
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8;a0008.tif;;
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9;a0009.tif;True;"(127; 80)(104; 60)(87; 63)(53; 78)(17; 126)"
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10;a0010.tif;;
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11;a0011.tif;True;"(39; 78)(84; 110)" # a random comment passing by
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#end of bloc 1
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#bloc 2
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12;a0012.tif;;
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13;a0013.tif;;
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14;a0014.tif;;
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15;a0015.tif;True;"(146; 65)(146; 89)(139; 146)(16; 68)"
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16;a0016.tif;True;"(51; 59)(77; 69)(145; 78)(139; 112)(97; 123)(17; 148)"
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17;a0017.tif;;
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#end of bloc 2
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#bloc 3
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18;a0018.tif;;
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19;a0019.tif;;
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20;a0020.tif;True;"(57; 99)(12; 113)(27; 139)(16; 158)"
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21;a0021.tif;;
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22;a0022.tif;;
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23;a0023.tif;;
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24;a0024.tif;;
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25;a0025.tif;;
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26;a0026.tif;;
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#end of bloc 3
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27;a0027.tif;True;"(11; 86)(29; 74)(92; 68)(109; 129)(132; 104)"
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28;a0028.tif;;
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29;a0029.tif;True;"(128; 58)"
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30;a0030.tif;True;"(133; 59)(99; 77)(111; 100)(115; 153)"
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31;a0031.tif;True;"(43; 154)(27; 177)"
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## footer : end of file
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</pre></div>
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<h2>Removing comments</h2>
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<p>In order to remove comments, we can replace the pattern of a comment by nothing. A commant starts with a # sign and is followed by an arbitrarly long chain of characters. In order to match this pattern, we will use a regular expression.</p>
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<div class="highlight"><pre><span></span>sed <span class="s2">"s/#.*//g"</span> input.csv
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</pre></div>
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<p><code>#.*</code> means : find strings that start with a <code>#</code>, the <code>.</code> stands for any character, finally, the <code>*</code> means that the <code>.</code> can be repeated any number of times. That means that <code>sed</code> will look for a string starting with a # followed by any characters that come after in the line.</p>
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<p>If we want to do something a bit cleaner, we can try to remove any whitespace before the comments as well. In order to do so, we will use the <code>\s</code> regular expression that represents a whitespace. If we want to make sure that we removed any whitespace before the comments, we will do <code>\s*</code></p>
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<p>The final regular expression is then <code>\s*#.*</code> and it will then be replaced by nothing. </p>
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<p>Finally, the command becomes </p>
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<div class="highlight"><pre><span></span>sed <span class="s2">"s/\s*#.*//g"</span> input.csv
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</pre></div>
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<p>If we run that command, all our comments have disappeared </p>
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<div class="highlight"><pre><span></span>0,a0000.tif,,
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1,a0001.tif,True,"(139, 63)(145, 91)"
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2,a0002.tif,True,"(93, 72)(24, 162)(31, 64)"
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3,a0003.tif,,
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4,a0004.tif,,
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5,a0005.tif,,
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6,a0006.tif,,
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7,a0007.tif,,
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8,a0008.tif,,
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9,a0009.tif,True,"(127, 80)(104, 60)(87, 63)(53, 78)(17, 126)"
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10,a0010.tif,,
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11,a0011.tif,True,"(39, 78)(84, 110)"
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|
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|
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12,a0012.tif,,
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13,a0013.tif,,
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14,a0014.tif,,
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15,a0015.tif,True,"(146, 65)(146, 89)(139, 146)(16, 68)"
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16,a0016.tif,True,"(51, 59)(77, 69)(145, 78)(139, 112)(97, 123)(17, 148)"
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17,a0017.tif,,
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|
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18,a0018.tif,,
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19,a0019.tif,,
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20,a0020.tif,True,"(57, 99)(12, 113)(27, 139)(16, 158)"
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21,a0021.tif,,
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22,a0022.tif,,
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23,a0023.tif,,
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24,a0024.tif,,
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25,a0025.tif,,
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26,a0026.tif,,
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27,a0027.tif,True,"(11, 86)(29, 74)(92, 68)(109, 129)(132, 104)"
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28,a0028.tif,,
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29,a0029.tif,True,"(128, 58)"
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30,a0030.tif,True,"(133, 59)(99, 77)(111, 100)(115, 153)"
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31,a0031.tif,True,"(43, 154)(27, 177)"
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</pre></div>
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<h2>Removing blank lines</h2>
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<p>In order to remove the blank lines, we need to specify to <code>sed</code> a pattern corresponding to a blank line and use the <code>d</code> command where the <code>d</code> stands for delete. The delete command expects the pattern to the between /</p>
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<p>Now let's define what pattern a blank line corresponds to. Since there is no symbol for blankness, we can do the following <code>^$</code>. <code>^</code> means the begining of a line and <code>$</code> corresponds to the end of a line.</p>
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<p>So whenever we find a blank line we delete it. </p>
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<div class="highlight"><pre><span></span>sed <span class="s2">"/^</span>$<span class="s2">/ d"</span> input.csv
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</pre></div>
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<div class="highlight"><pre><span></span>## Header
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#this file contains information I want to parse with a simple program.
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#The header, the footer or any comment starting with a "#" will be removed
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#The blank lines will also be removed
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#img,processed,defaut
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#bloc 1
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|
0,a0000.tif,,
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1,a0001.tif,True,"(139, 63)(145, 91)"
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2,a0002.tif,True,"(93, 72)(24, 162)(31, 64)"
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3,a0003.tif,,
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4,a0004.tif,,
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5,a0005.tif,,
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6,a0006.tif,,
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7,a0007.tif,,
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8,a0008.tif,,
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9,a0009.tif,True,"(127, 80)(104, 60)(87, 63)(53, 78)(17, 126)"
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10,a0010.tif,,
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11,a0011.tif,True,"(39, 78)(84, 110)" # a random comment passing by
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#end of bloc 1
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#bloc 2
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12,a0012.tif,,
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13,a0013.tif,,
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14,a0014.tif,,
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15,a0015.tif,True,"(146, 65)(146, 89)(139, 146)(16, 68)"
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16,a0016.tif,True,"(51, 59)(77, 69)(145, 78)(139, 112)(97, 123)(17, 148)"
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17,a0017.tif,,
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#end of bloc 2
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#bloc 3
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18,a0018.tif,,
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19,a0019.tif,,
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20,a0020.tif,True,"(57, 99)(12, 113)(27, 139)(16, 158)"
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21,a0021.tif,,
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22,a0022.tif,,
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23,a0023.tif,,
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24,a0024.tif,,
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25,a0025.tif,,
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26,a0026.tif,,
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#end of bloc 3
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27,a0027.tif,True,"(11, 86)(29, 74)(92, 68)(109, 129)(132, 104)"
|
|
28,a0028.tif,,
|
|
29,a0029.tif,True,"(128, 58)"
|
|
30,a0030.tif,True,"(133, 59)(99, 77)(111, 100)(115, 153)"
|
|
31,a0031.tif,True,"(43, 154)(27, 177)"
|
|
## footer : end of file
|
|
</pre></div>
|
|
|
|
|
|
<h3>combining the sed commands</h3>
|
|
<p>We can concatenate sed commands by separating them with a semicolon. Hence the final <code>sed</code> command will be :</p>
|
|
<div class="highlight"><pre><span></span>sed <span class="s2">"s/\s*#.*//g;/^</span>$<span class="s2">/ d"</span> input.csv
|
|
</pre></div>
|
|
|
|
|
|
<p>and the final output is </p>
|
|
<div class="highlight"><pre><span></span>0,a0000.tif,,
|
|
1,a0001.tif,True,"(139, 63)(145, 91)"
|
|
2,a0002.tif,True,"(93, 72)(24, 162)(31, 64)"
|
|
3,a0003.tif,,
|
|
4,a0004.tif,,
|
|
5,a0005.tif,,
|
|
6,a0006.tif,,
|
|
7,a0007.tif,,
|
|
8,a0008.tif,,
|
|
9,a0009.tif,True,"(127, 80)(104, 60)(87, 63)(53, 78)(17, 126)"
|
|
10,a0010.tif,,
|
|
11,a0011.tif,True,"(39, 78)(84, 110)"
|
|
12,a0012.tif,,
|
|
13,a0013.tif,,
|
|
14,a0014.tif,,
|
|
15,a0015.tif,True,"(146, 65)(146, 89)(139, 146)(16, 68)"
|
|
16,a0016.tif,True,"(51, 59)(77, 69)(145, 78)(139, 112)(97, 123)(17, 148)"
|
|
17,a0017.tif,,
|
|
18,a0018.tif,,
|
|
19,a0019.tif,,
|
|
20,a0020.tif,True,"(57, 99)(12, 113)(27, 139)(16, 158)"
|
|
21,a0021.tif,,
|
|
22,a0022.tif,,
|
|
23,a0023.tif,,
|
|
24,a0024.tif,,
|
|
25,a0025.tif,,
|
|
26,a0026.tif,,
|
|
27,a0027.tif,True,"(11, 86)(29, 74)(92, 68)(109, 129)(132, 104)"
|
|
28,a0028.tif,,
|
|
29,a0029.tif,True,"(128, 58)"
|
|
30,a0030.tif,True,"(133, 59)(99, 77)(111, 100)(115, 153)"
|
|
31,a0031.tif,True,"(43, 154)(27, 177)"
|
|
</pre></div>
|
|
|
|
|
|
<h3>Overwritting the file</h3>
|
|
<p>If we want to overwrite the result of <code>sed</code> on the input file, we need to add the option <code>-i</code>. So if you are running <code>sed</code> without <code>-i</code>, it is safe and won't alter your files.</p>
|
|
<div class="highlight"><pre><span></span>sed -i <span class="s2">"s/\s*#.*//g;/^</span>$<span class="s2">/ d"</span> input.csv
|
|
</pre></div>
|
|
</div>
|
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<aside>
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<div class="bug-reporting__panel">
|
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<h3>Find an error or bug? Have a suggestion?</h3>
|
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<p>Everything on this site is avaliable on GitHub. Head on over and <a href='https://github.com/redoules/redoules.github.io/issues/new'>submit an issue.</a> You can also message me directly by <a href='mailto:guillaume.redoules@gadz.org'>email</a>.</p>
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<center>This project contains 81 pages and is available on <a href="https://github.com/redoules/redoules.github.io">GitHub</a>.
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<br/>
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Copyright © Guillaume Redoulès,
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<time datetime="2018">2018</time>.
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