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<!DOCTYPE html>
<!-- START: inst/pkgdown/templates/layout.html --><!-- Generated by pkgdown: do not edit by hand --><html lang="en" data-bs-theme="auto"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><title>The Unix Shell: Loops</title><meta name="viewport" content="width=device-width, initial-scale=1"><script src="assets/themetoggle.js"></script><link rel="stylesheet" type="text/css" href="assets/styles.css"><script src="assets/scripts.js" type="text/javascript"></script><!-- mathjax --><script type="text/x-mathjax-config">
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<h1>Loops</h1>
<p>Last updated on 2023-11-10 |
<a href="https://github.com/swcarpentry/shell-novice/edit/main/episodes/05-loop.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
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<div class="overview card">
<h2 class="card-header">Overview</h2>
<div class="row g-0">
<div class="col-md-4">
<div class="card-body">
<div class="inner">
<h3 class="card-title">Questions</h3>
<ul><li>How can I perform the same actions on many different files?</li>
</ul></div>
</div>
</div>
<div class="col-md-8">
<div class="card-body">
<div class="inner bordered">
<h3 class="card-title">Objectives</h3>
<ul><li>Write a loop that applies one or more commands separately to each
file in a set of files.</li>
<li>Trace the values taken on by a loop variable during execution of the
loop.</li>
<li>Explain the difference between a variable’s name and its value.</li>
<li>Explain why spaces and some punctuation characters shouldn’t be used
in file names.</li>
<li>Demonstrate how to see what commands have recently been
executed.</li>
<li>Re-run recently executed commands without retyping them.</li>
</ul></div>
</div>
</div>
</div>
</div>
<p><strong>Loops</strong> are a programming construct which allow us to
repeat a command or set of commands for each item in a list. As such
they are key to productivity improvements through automation. Similar to
wildcards and tab completion, using loops also reduces the amount of
typing required (and hence reduces the number of typing mistakes).</p>
<p>Suppose we have several hundred genome data files named
<code>basilisk.dat</code>, <code>minotaur.dat</code>, and
<code>unicorn.dat</code>. For this example, we’ll use the
<code>exercise-data/creatures</code> directory which only has three
example files, but the principles can be applied to many many more files
at once.</p>
<p>The structure of these files is the same: the common name,
classification, and updated date are presented on the first three lines,
with DNA sequences on the following lines. Let’s look at the files:</p>
<div class="codewrapper sourceCode" id="cb1">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="ex">$</span> head <span class="at">-n</span> 5 basilisk.dat minotaur.dat unicorn.dat</span></code></pre>
</div>
<p>We would like to print out the classification for each species, which
is given on the second line of each file. For each file, we would need
to execute the command <code>head -n 2</code> and pipe this to
<code>tail -n 1</code>. We’ll use a loop to solve this problem, but
first let’s look at the general form of a loop, using the pseudo-code
below:</p>
<div class="codewrapper sourceCode" id="cb2">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a><span class="co"># The word "for" indicates the start of a "For-loop" command</span></span>
<span id="cb2-2"><a href="#cb2-2" tabindex="-1"></a><span class="cf">for</span> thing <span class="kw">in</span> list_of_things </span>
<span id="cb2-3"><a href="#cb2-3" tabindex="-1"></a><span class="co">#The word "do" indicates the start of job execution list</span></span>
<span id="cb2-4"><a href="#cb2-4" tabindex="-1"></a><span class="cf">do</span> </span>
<span id="cb2-5"><a href="#cb2-5" tabindex="-1"></a> <span class="co"># Indentation within the loop is not required, but aids legibility</span></span>
<span id="cb2-6"><a href="#cb2-6" tabindex="-1"></a> <span class="ex">operation_using/command</span> <span class="va">$thing</span> </span>
<span id="cb2-7"><a href="#cb2-7" tabindex="-1"></a><span class="co"># The word "done" indicates the end of a loop</span></span>
<span id="cb2-8"><a href="#cb2-8" tabindex="-1"></a><span class="cf">done</span> </span></code></pre>
</div>
<p>and we can apply this to our example like this:</p>
<div class="codewrapper sourceCode" id="cb3">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a><span class="ex">$</span> for filename in basilisk.dat minotaur.dat unicorn.dat</span>
<span id="cb3-2"><a href="#cb3-2" tabindex="-1"></a><span class="op">></span> do</span>
<span id="cb3-3"><a href="#cb3-3" tabindex="-1"></a><span class="op">></span> echo <span class="va">$filename</span></span>
<span id="cb3-4"><a href="#cb3-4" tabindex="-1"></a><span class="op">></span> head <span class="ex">-n</span> 2 <span class="va">$filename</span> <span class="kw">|</span> <span class="fu">tail</span> <span class="at">-n</span> 1</span>
<span id="cb3-5"><a href="#cb3-5" tabindex="-1"></a><span class="op">></span> done</span></code></pre>
</div>
<div class="codewrapper">
<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="output" tabindex="0"><code>basilisk.dat
CLASSIFICATION: basiliscus vulgaris
minotaur.dat
CLASSIFICATION: bos hominus
unicorn.dat
CLASSIFICATION: equus monoceros</code></pre>
</div>
<div id="follow-the-prompt" class="callout">
<div class="callout-square">
<i class="callout-icon" data-feather="bell"></i>
</div>
<div id="follow-the-prompt" class="callout-inner">
<h3 class="callout-title">Follow the Prompt</h3>
<div class="callout-content">
<p>The shell prompt changes from <code>$</code> to <code>></code> and
back again as we were typing in our loop. The second prompt,
<code>></code>, is different to remind us that we haven’t finished
typing a complete command yet. A semicolon, <code>;</code>, can be used
to separate two commands written on a single line.</p>
</div>
</div>
</div>
<p>When the shell sees the keyword <code>for</code>, it knows to repeat
a command (or group of commands) once for each item in a list. Each time
the loop runs (called an iteration), an item in the list is assigned in
sequence to the <strong>variable</strong>, and the commands inside the
loop are executed, before moving on to the next item in the list. Inside
the loop, we call for the variable’s value by putting <code>$</code> in
front of it. The <code>$</code> tells the shell interpreter to treat the
variable as a variable name and substitute its value in its place,
rather than treat it as text or an external command.</p>
<p>In this example, the list is three filenames:
<code>basilisk.dat</code>, <code>minotaur.dat</code>, and
<code>unicorn.dat</code>. Each time the loop iterates, we first use
<code>echo</code> to print the value that the variable
<code>$filename</code> currently holds. This is not necessary for the
result, but beneficial for us here to have an easier time to follow
along. Next, we will run the <code>head</code> command on the file
currently referred to by <code>$filename</code>. The first time through
the loop, <code>$filename</code> is <code>basilisk.dat</code>. The
interpreter runs the command <code>head</code> on
<code>basilisk.dat</code> and pipes the first two lines to the
<code>tail</code> command, which then prints the second line of
<code>basilisk.dat</code>. For the second iteration,
<code>$filename</code> becomes <code>minotaur.dat</code>. This time, the
shell runs <code>head</code> on <code>minotaur.dat</code> and pipes the
first two lines to the <code>tail</code> command, which then prints the
second line of <code>minotaur.dat</code>. For the third iteration,
<code>$filename</code> becomes <code>unicorn.dat</code>, so the shell
runs the <code>head</code> command on that file, and <code>tail</code>
on the output of that. Since the list was only three items, the shell
exits the <code>for</code> loop.</p>
<div id="same-symbols-different-meanings" class="callout">
<div class="callout-square">
<i class="callout-icon" data-feather="bell"></i>
</div>
<div id="same-symbols-different-meanings" class="callout-inner">
<h3 class="callout-title">Same Symbols, Different Meanings</h3>
<div class="callout-content">
<p>Here we see <code>></code> being used as a shell prompt, whereas
<code>></code> is also used to redirect output. Similarly,
<code>$</code> is used as a shell prompt, but, as we saw earlier, it is
also used to ask the shell to get the value of a variable.</p>
<p>If the <em>shell</em> prints <code>></code> or <code>$</code> then
it expects you to type something, and the symbol is a prompt.</p>
<p>If <em>you</em> type <code>></code> or <code>$</code> yourself, it
is an instruction from you that the shell should redirect output or get
the value of a variable.</p>
</div>
</div>
</div>
<p>When using variables it is also possible to put the names into curly
braces to clearly delimit the variable name: <code>$filename</code> is
equivalent to <code>${filename}</code>, but is different from
<code>${file}name</code>. You may find this notation in other people’s
programs.</p>
<p>We have called the variable in this loop <code>filename</code> in
order to make its purpose clearer to human readers. The shell itself
doesn’t care what the variable is called; if we wrote this loop as:</p>
<div class="codewrapper sourceCode" id="cb5">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a><span class="ex">$</span> for x in basilisk.dat minotaur.dat unicorn.dat</span>
<span id="cb5-2"><a href="#cb5-2" tabindex="-1"></a><span class="op">></span> do</span>
<span id="cb5-3"><a href="#cb5-3" tabindex="-1"></a><span class="op">></span> head <span class="ex">-n</span> 2 <span class="va">$x</span> <span class="kw">|</span> <span class="fu">tail</span> <span class="at">-n</span> 1</span>
<span id="cb5-4"><a href="#cb5-4" tabindex="-1"></a><span class="op">></span> done</span></code></pre>
</div>
<p>or:</p>
<div class="codewrapper sourceCode" id="cb6">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb6-1"><a href="#cb6-1" tabindex="-1"></a><span class="ex">$</span> for temperature in basilisk.dat minotaur.dat unicorn.dat</span>
<span id="cb6-2"><a href="#cb6-2" tabindex="-1"></a><span class="op">></span> do</span>
<span id="cb6-3"><a href="#cb6-3" tabindex="-1"></a><span class="op">></span> head <span class="ex">-n</span> 2 <span class="va">$temperature</span> <span class="kw">|</span> <span class="fu">tail</span> <span class="at">-n</span> 1</span>
<span id="cb6-4"><a href="#cb6-4" tabindex="-1"></a><span class="op">></span> done</span></code></pre>
</div>
<p>it would work exactly the same way. <em>Don’t do this.</em> Programs
are only useful if people can understand them, so meaningless names
(like <code>x</code>) or misleading names (like
<code>temperature</code>) increase the odds that the program won’t do
what its readers think it does.</p>
<p>In the above examples, the variables (<code>thing</code>,
<code>filename</code>, <code>x</code> and <code>temperature</code>)
could have been given any other name, as long as it is meaningful to
both the person writing the code and the person reading it.</p>
<p>Note also that loops can be used for other things than filenames,
like a list of numbers or a subset of data.</p>
<div id="write-your-own-loop" class="callout challenge">
<div class="callout-square">
<i class="callout-icon" data-feather="zap"></i>
</div>
<div id="write-your-own-loop" class="callout-inner">
<h3 class="callout-title">Write your own loop</h3>
<div class="callout-content">
<p>How would you write a loop that echoes all 10 numbers from 0 to
9?</p>
</div>
</div>
</div>
<div id="accordionSolution1" class="accordion challenge-accordion accordion-flush">
<div class="accordion-item">
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</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb7-1"><a href="#cb7-1" tabindex="-1"></a><span class="ex">$</span> for loop_variable in 0 1 2 3 4 5 6 7 8 9</span>
<span id="cb7-2"><a href="#cb7-2" tabindex="-1"></a><span class="op">></span> do</span>
<span id="cb7-3"><a href="#cb7-3" tabindex="-1"></a><span class="op">></span> echo <span class="va">$loop_variable</span></span>
<span id="cb7-4"><a href="#cb7-4" tabindex="-1"></a><span class="op">></span> done</span></code></pre>
</div>
<div class="codewrapper">
<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="output" tabindex="0"><code><span><span class="fl">0</span></span>
<span><span class="fl">1</span></span>
<span><span class="fl">2</span></span>
<span><span class="fl">3</span></span>
<span><span class="fl">4</span></span>
<span><span class="fl">5</span></span>
<span><span class="fl">6</span></span>
<span><span class="fl">7</span></span>
<span><span class="fl">8</span></span>
<span><span class="fl">9</span></span></code></pre>
</div>
</div>
</div>
</div>
</div>
<div id="variables-in-loops" class="callout challenge">
<div class="callout-square">
<i class="callout-icon" data-feather="zap"></i>
</div>
<div id="variables-in-loops" class="callout-inner">
<h3 class="callout-title">Variables in Loops</h3>
<div class="callout-content">
<p>This exercise refers to the
<code>shell-lesson-data/exercise-data/alkanes</code> directory.
<code>ls *.pdb</code> gives the following output:</p>
<div class="codewrapper">
<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="output" tabindex="0"><code>cubane.pdb ethane.pdb methane.pdb octane.pdb pentane.pdb propane.pdb</code></pre>
</div>
<p>What is the output of the following code?</p>
<div class="codewrapper sourceCode" id="cb10">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb10-1"><a href="#cb10-1" tabindex="-1"></a><span class="ex">$</span> for datafile in <span class="pp">*</span>.pdb</span>
<span id="cb10-2"><a href="#cb10-2" tabindex="-1"></a><span class="op">></span> do</span>
<span id="cb10-3"><a href="#cb10-3" tabindex="-1"></a><span class="op">></span> ls <span class="ex">*.pdb</span></span>
<span id="cb10-4"><a href="#cb10-4" tabindex="-1"></a><span class="op">></span> done</span></code></pre>
</div>
<p>Now, what is the output of the following code?</p>
<div class="codewrapper sourceCode" id="cb11">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb11-1"><a href="#cb11-1" tabindex="-1"></a><span class="ex">$</span> for datafile in <span class="pp">*</span>.pdb</span>
<span id="cb11-2"><a href="#cb11-2" tabindex="-1"></a><span class="op">></span> do</span>
<span id="cb11-3"><a href="#cb11-3" tabindex="-1"></a><span class="op">></span> ls <span class="va">$datafile</span></span>
<span id="cb11-4"><a href="#cb11-4" tabindex="-1"></a><span class="op">></span> done</span></code></pre>
</div>
<p>Why do these two loops give different outputs?</p>
</div>
</div>
</div>
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</button>
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<div class="accordion-body">
<p>The first code block gives the same output on each iteration through
the loop. Bash expands the wildcard <code>*.pdb</code> within the loop
body (as well as before the loop starts) to match all files ending in
<code>.pdb</code> and then lists them using <code>ls</code>. The
expanded loop would look like this:</p>
<div class="codewrapper sourceCode" id="cb12">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb12-1"><a href="#cb12-1" tabindex="-1"></a><span class="ex">$</span> for datafile in cubane.pdb ethane.pdb methane.pdb octane.pdb pentane.pdb propane.pdb</span>
<span id="cb12-2"><a href="#cb12-2" tabindex="-1"></a><span class="op">></span> do</span>
<span id="cb12-3"><a href="#cb12-3" tabindex="-1"></a><span class="op">></span> ls <span class="ex">cubane.pdb</span> ethane.pdb methane.pdb octane.pdb pentane.pdb propane.pdb</span>
<span id="cb12-4"><a href="#cb12-4" tabindex="-1"></a><span class="op">></span> done</span></code></pre>
</div>
<div class="codewrapper">
<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="output" tabindex="0"><code>cubane.pdb ethane.pdb methane.pdb octane.pdb pentane.pdb propane.pdb
cubane.pdb ethane.pdb methane.pdb octane.pdb pentane.pdb propane.pdb
cubane.pdb ethane.pdb methane.pdb octane.pdb pentane.pdb propane.pdb
cubane.pdb ethane.pdb methane.pdb octane.pdb pentane.pdb propane.pdb
cubane.pdb ethane.pdb methane.pdb octane.pdb pentane.pdb propane.pdb
cubane.pdb ethane.pdb methane.pdb octane.pdb pentane.pdb propane.pdb</code></pre>
</div>
<p>The second code block lists a different file on each loop iteration.
The value of the <code>datafile</code> variable is evaluated using
<code>$datafile</code>, and then listed using <code>ls</code>.</p>
<div class="codewrapper">
<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="output" tabindex="0"><code><span><span class="va">cubane.pdb</span></span>
<span><span class="va">ethane.pdb</span></span>
<span><span class="va">methane.pdb</span></span>
<span><span class="va">octane.pdb</span></span>
<span><span class="va">pentane.pdb</span></span>
<span><span class="va">propane.pdb</span></span></code></pre>
</div>
</div>
</div>
</div>
</div>
<div id="limiting-sets-of-files" class="callout challenge">
<div class="callout-square">
<i class="callout-icon" data-feather="zap"></i>
</div>
<div id="limiting-sets-of-files" class="callout-inner">
<h3 class="callout-title">Limiting Sets of Files</h3>
<div class="callout-content">
<p>What would be the output of running the following loop in the
<code>shell-lesson-data/exercise-data/alkanes</code> directory?</p>
<div class="codewrapper sourceCode" id="cb15">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb15-1"><a href="#cb15-1" tabindex="-1"></a><span class="ex">$</span> for filename in c<span class="pp">*</span></span>
<span id="cb15-2"><a href="#cb15-2" tabindex="-1"></a><span class="op">></span> do</span>
<span id="cb15-3"><a href="#cb15-3" tabindex="-1"></a><span class="op">></span> ls <span class="va">$filename</span></span>
<span id="cb15-4"><a href="#cb15-4" tabindex="-1"></a><span class="op">></span> done</span></code></pre>
</div>
<ol style="list-style-type: decimal"><li>No files are listed.</li>
<li>All files are listed.</li>
<li>Only <code>cubane.pdb</code>, <code>octane.pdb</code> and
<code>pentane.pdb</code> are listed.</li>
<li>Only <code>cubane.pdb</code> is listed.</li>
</ol></div>
</div>
</div>
<div id="accordionSolution3" class="accordion challenge-accordion accordion-flush">
<div class="accordion-item">
<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
<h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
</button>
<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
<div class="accordion-body">
<p>4 is the correct answer. <code>*</code> matches zero or more
characters, so any file name starting with the letter c, followed by
zero or more other characters will be matched.</p>
</div>
</div>
</div>
</div>
<div id="limiting-sets-of-files" class="callout challenge">
<div class="callout-square">
<i class="callout-icon" data-feather="zap"></i>
</div>
<div id="limiting-sets-of-files" class="callout-inner">
<h3 class="callout-title">Limiting Sets of Files<em>
(continued)</em>
</h3>
<div class="callout-content">
<p>How would the output differ from using this command instead?</p>
<div class="codewrapper sourceCode" id="cb16">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb16-1"><a href="#cb16-1" tabindex="-1"></a><span class="ex">$</span> for filename in <span class="pp">*</span>c<span class="pp">*</span></span>
<span id="cb16-2"><a href="#cb16-2" tabindex="-1"></a><span class="op">></span> do</span>
<span id="cb16-3"><a href="#cb16-3" tabindex="-1"></a><span class="op">></span> ls <span class="va">$filename</span></span>
<span id="cb16-4"><a href="#cb16-4" tabindex="-1"></a><span class="op">></span> done</span></code></pre>
</div>
<ol style="list-style-type: decimal"><li>The same files would be listed.</li>
<li>All the files are listed this time.</li>
<li>No files are listed this time.</li>
<li>The files <code>cubane.pdb</code> and <code>octane.pdb</code> will
be listed.</li>
<li>Only the file <code>octane.pdb</code> will be listed.</li>
</ol></div>
</div>
</div>
<div id="accordionSolution4" class="accordion challenge-accordion accordion-flush">
<div class="accordion-item">
<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
<h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
</button>
<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
<div class="accordion-body">
<p>4 is the correct answer. <code>*</code> matches zero or more
characters, so a file name with zero or more characters before a letter
c and zero or more characters after the letter c will be matched.</p>
</div>
</div>
</div>
</div>
<div id="saving-to-a-file-in-a-loop---part-one" class="callout challenge">
<div class="callout-square">
<i class="callout-icon" data-feather="zap"></i>
</div>
<div id="saving-to-a-file-in-a-loop---part-one" class="callout-inner">
<h3 class="callout-title">Saving to a File in a Loop - Part One</h3>
<div class="callout-content">
<p>In the <code>shell-lesson-data/exercise-data/alkanes</code>
directory, what is the effect of this loop?</p>
<div class="codewrapper sourceCode" id="cb17">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb17-1"><a href="#cb17-1" tabindex="-1"></a><span class="cf">for</span> alkanes <span class="kw">in</span> <span class="pp">*</span>.pdb</span>
<span id="cb17-2"><a href="#cb17-2" tabindex="-1"></a><span class="cf">do</span></span>
<span id="cb17-3"><a href="#cb17-3" tabindex="-1"></a> <span class="bu">echo</span> <span class="va">$alkanes</span></span>
<span id="cb17-4"><a href="#cb17-4" tabindex="-1"></a> <span class="fu">cat</span> <span class="va">$alkanes</span> <span class="op">></span> alkanes.pdb</span>
<span id="cb17-5"><a href="#cb17-5" tabindex="-1"></a><span class="cf">done</span></span></code></pre>
</div>
<ol style="list-style-type: decimal"><li>Prints <code>cubane.pdb</code>, <code>ethane.pdb</code>,
<code>methane.pdb</code>, <code>octane.pdb</code>,
<code>pentane.pdb</code> and <code>propane.pdb</code>, and the text from
<code>propane.pdb</code> will be saved to a file called
<code>alkanes.pdb</code>.</li>
<li>Prints <code>cubane.pdb</code>, <code>ethane.pdb</code>, and
<code>methane.pdb</code>, and the text from all three files would be
concatenated and saved to a file called <code>alkanes.pdb</code>.</li>
<li>Prints <code>cubane.pdb</code>, <code>ethane.pdb</code>,
<code>methane.pdb</code>, <code>octane.pdb</code>, and
<code>pentane.pdb</code>, and the text from <code>propane.pdb</code>
will be saved to a file called <code>alkanes.pdb</code>.</li>
<li>None of the above.</li>
</ol></div>
</div>
</div>
<div id="accordionSolution5" class="accordion challenge-accordion accordion-flush">
<div class="accordion-item">
<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
<h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
</button>
<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
<div class="accordion-body">
<ol style="list-style-type: decimal"><li>The text from each file in turn gets written to the
<code>alkanes.pdb</code> file. However, the file gets overwritten on
each loop iteration, so the final content of <code>alkanes.pdb</code> is
the text from the <code>propane.pdb</code> file.</li>
</ol></div>
</div>
</div>
</div>
<div id="saving-to-a-file-in-a-loop---part-two" class="callout challenge">
<div class="callout-square">
<i class="callout-icon" data-feather="zap"></i>
</div>
<div id="saving-to-a-file-in-a-loop---part-two" class="callout-inner">
<h3 class="callout-title">Saving to a File in a Loop - Part Two</h3>
<div class="callout-content">
<p>Also in the <code>shell-lesson-data/exercise-data/alkanes</code>
directory, what would be the output of the following loop?</p>
<div class="codewrapper sourceCode" id="cb18">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb18-1"><a href="#cb18-1" tabindex="-1"></a><span class="cf">for</span> datafile <span class="kw">in</span> <span class="pp">*</span>.pdb</span>
<span id="cb18-2"><a href="#cb18-2" tabindex="-1"></a><span class="cf">do</span></span>
<span id="cb18-3"><a href="#cb18-3" tabindex="-1"></a> <span class="fu">cat</span> <span class="va">$datafile</span> <span class="op">>></span> all.pdb</span>
<span id="cb18-4"><a href="#cb18-4" tabindex="-1"></a><span class="cf">done</span></span></code></pre>
</div>
<ol style="list-style-type: decimal"><li>All of the text from <code>cubane.pdb</code>,
<code>ethane.pdb</code>, <code>methane.pdb</code>,
<code>octane.pdb</code>, and <code>pentane.pdb</code> would be
concatenated and saved to a file called <code>all.pdb</code>.</li>
<li>The text from <code>ethane.pdb</code> will be saved to a file called
<code>all.pdb</code>.</li>
<li>All of the text from <code>cubane.pdb</code>,
<code>ethane.pdb</code>, <code>methane.pdb</code>,
<code>octane.pdb</code>, <code>pentane.pdb</code> and
<code>propane.pdb</code> would be concatenated and saved to a file
called <code>all.pdb</code>.</li>
<li>All of the text from <code>cubane.pdb</code>,
<code>ethane.pdb</code>, <code>methane.pdb</code>,
<code>octane.pdb</code>, <code>pentane.pdb</code> and
<code>propane.pdb</code> would be printed to the screen and saved to a
file called <code>all.pdb</code>.</li>
</ol></div>
</div>
</div>
<div id="accordionSolution6" class="accordion challenge-accordion accordion-flush">
<div class="accordion-item">
<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
<h4 class="accordion-header" id="headingSolution6"> Show me the solution </h4>
</button>
<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
<div class="accordion-body">
<p>3 is the correct answer. <code>>></code> appends to a file,
rather than overwriting it with the redirected output from a command.
Given the output from the <code>cat</code> command has been redirected,
nothing is printed to the screen.</p>
</div>
</div>
</div>
</div>
<p>Let’s continue with our example in the
<code>shell-lesson-data/exercise-data/creatures</code> directory. Here’s
a slightly more complicated loop:</p>
<div class="codewrapper sourceCode" id="cb19">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb19-1"><a href="#cb19-1" tabindex="-1"></a><span class="ex">$</span> for filename in <span class="pp">*</span>.dat</span>
<span id="cb19-2"><a href="#cb19-2" tabindex="-1"></a><span class="op">></span> do</span>
<span id="cb19-3"><a href="#cb19-3" tabindex="-1"></a><span class="op">></span> echo <span class="va">$filename</span></span>
<span id="cb19-4"><a href="#cb19-4" tabindex="-1"></a><span class="op">></span> head <span class="ex">-n</span> 100 <span class="va">$filename</span> <span class="kw">|</span> <span class="fu">tail</span> <span class="at">-n</span> 20</span>
<span id="cb19-5"><a href="#cb19-5" tabindex="-1"></a><span class="op">></span> done</span></code></pre>
</div>
<p>The shell starts by expanding <code>*.dat</code> to create the list
of files it will process. The <strong>loop body</strong> then executes
two commands for each of those files. The first command,
<code>echo</code>, prints its command-line arguments to standard output.
For example:</p>
<div class="codewrapper sourceCode" id="cb20">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb20-1"><a href="#cb20-1" tabindex="-1"></a><span class="ex">$</span> echo hello there</span></code></pre>
</div>
<p>prints:</p>
<div class="codewrapper">
<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="output" tabindex="0"><code>hello there</code></pre>
</div>
<p>In this case, since the shell expands <code>$filename</code> to be
the name of a file, <code>echo $filename</code> prints the name of the
file. Note that we can’t write this as:</p>
<div class="codewrapper sourceCode" id="cb22">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb22-1"><a href="#cb22-1" tabindex="-1"></a><span class="ex">$</span> for filename in <span class="pp">*</span>.dat</span>
<span id="cb22-2"><a href="#cb22-2" tabindex="-1"></a><span class="op">></span> do</span>
<span id="cb22-3"><a href="#cb22-3" tabindex="-1"></a><span class="op">></span> <span class="va">$filename</span></span>
<span id="cb22-4"><a href="#cb22-4" tabindex="-1"></a><span class="op">></span> head <span class="ex">-n</span> 100 <span class="va">$filename</span> <span class="kw">|</span> <span class="fu">tail</span> <span class="at">-n</span> 20</span>
<span id="cb22-5"><a href="#cb22-5" tabindex="-1"></a><span class="op">></span> done</span></code></pre>
</div>
<p>because then the first time through the loop, when
<code>$filename</code> expanded to <code>basilisk.dat</code>, the shell
would try to run <code>basilisk.dat</code> as a program. Finally, the
<code>head</code> and <code>tail</code> combination selects lines 81-100
from whatever file is being processed (assuming the file has at least
100 lines).</p>
<div id="spaces-in-names" class="callout">
<div class="callout-square">
<i class="callout-icon" data-feather="bell"></i>
</div>
<div id="spaces-in-names" class="callout-inner">
<h3 class="callout-title">Spaces in Names</h3>
<div class="callout-content">
<p>Spaces are used to separate the elements of the list that we are
going to loop over. If one of those elements contains a space character,
we need to surround it with quotes, and do the same thing to our loop
variable. Suppose our data files are named:</p>
<pre class="source"><code>red dragon.dat
purple unicorn.dat</code></pre>
<p>To loop over these files, we would need to add double quotes like
so:</p>
<div class="codewrapper sourceCode" id="cb24">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb24-1"><a href="#cb24-1" tabindex="-1"></a><span class="ex">$</span> for filename in <span class="st">"red dragon.dat"</span> <span class="st">"purple unicorn.dat"</span></span>
<span id="cb24-2"><a href="#cb24-2" tabindex="-1"></a><span class="op">></span> do</span>
<span id="cb24-3"><a href="#cb24-3" tabindex="-1"></a><span class="op">></span> head <span class="ex">-n</span> 100 <span class="st">"</span><span class="va">$filename</span><span class="st">"</span> <span class="kw">|</span> <span class="fu">tail</span> <span class="at">-n</span> 20</span>
<span id="cb24-4"><a href="#cb24-4" tabindex="-1"></a><span class="op">></span> done</span></code></pre>
</div>
<p>It is simpler to avoid using spaces (or other special characters) in
filenames.</p>
<p>The files above don’t exist, so if we run the above code, the
<code>head</code> command will be unable to find them; however, the
error message returned will show the name of the files it is
expecting:</p>
<div class="codewrapper">
<h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="error" tabindex="0"><code>head: cannot open ‘red dragon.dat' for reading: No such file or directory
head: cannot open ‘purple unicorn.dat' for reading: No such file or directory</code></pre>
</div>
<p>Try removing the quotes around <code>$filename</code> in the loop
above to see the effect of the quote marks on spaces. Note that we get a
result from the loop command for unicorn.dat when we run this code in
the <code>creatures</code> directory:</p>
<div class="codewrapper">
<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="output" tabindex="0"><code>head: cannot open ‘red' for reading: No such file or directory
head: cannot open ‘dragon.dat' for reading: No such file or directory
head: cannot open ‘purple' for reading: No such file or directory
CGGTACCGAA
AAGGGTCGCG
CAAGTGTTCC
...</code></pre>
</div>
</div>
</div>
</div>
<p>We would like to modify each of the files in
<code>shell-lesson-data/exercise-data/creatures</code>, but also save a
version of the original files. We want to copy the original files to new
files named <code>original-basilisk.dat</code> and
<code>original-unicorn.dat</code>, for example. We can’t use:</p>
<div class="codewrapper sourceCode" id="cb27">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb27-1"><a href="#cb27-1" tabindex="-1"></a><span class="ex">$</span> cp <span class="pp">*</span>.dat original-<span class="pp">*</span>.dat</span></code></pre>
</div>
<p>because that would expand to:</p>
<div class="codewrapper sourceCode" id="cb28">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb28-1"><a href="#cb28-1" tabindex="-1"></a><span class="ex">$</span> cp basilisk.dat minotaur.dat unicorn.dat original-<span class="pp">*</span>.dat</span></code></pre>
</div>
<p>This wouldn’t back up our files, instead we get an error:</p>
<div class="codewrapper">
<h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="error" tabindex="0"><code>cp: target `original-*.dat' is not a directory</code></pre>
</div>
<p>This problem arises when <code>cp</code> receives more than two
inputs. When this happens, it expects the last input to be a directory
where it can copy all the files it was passed. Since there is no
directory named <code>original-*.dat</code> in the
<code>creatures</code> directory, we get an error.</p>
<p>Instead, we can use a loop:</p>
<div class="codewrapper sourceCode" id="cb30">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb30-1"><a href="#cb30-1" tabindex="-1"></a><span class="ex">$</span> for filename in <span class="pp">*</span>.dat</span>
<span id="cb30-2"><a href="#cb30-2" tabindex="-1"></a><span class="op">></span> do</span>
<span id="cb30-3"><a href="#cb30-3" tabindex="-1"></a><span class="op">></span> cp <span class="va">$filename</span> original-<span class="va">$filename</span></span>
<span id="cb30-4"><a href="#cb30-4" tabindex="-1"></a><span class="op">></span> done</span></code></pre>
</div>
<p>This loop runs the <code>cp</code> command once for each filename.
The first time, when <code>$filename</code> expands to
<code>basilisk.dat</code>, the shell executes:</p>
<div class="codewrapper sourceCode" id="cb31">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb31-1"><a href="#cb31-1" tabindex="-1"></a><span class="fu">cp</span> basilisk.dat original-basilisk.dat</span></code></pre>
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<p>The second time, the command is:</p>
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<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb32-1"><a href="#cb32-1" tabindex="-1"></a><span class="fu">cp</span> minotaur.dat original-minotaur.dat</span></code></pre>
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<p>The third and last time, the command is:</p>
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<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb33-1"><a href="#cb33-1" tabindex="-1"></a><span class="fu">cp</span> unicorn.dat original-unicorn.dat</span></code></pre>
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<p>Since the <code>cp</code> command does not normally produce any
output, it’s hard to check that the loop is working correctly. However,
we learned earlier how to print strings using <code>echo</code>, and we
can modify the loop to use <code>echo</code> to print our commands
without actually executing them. As such we can check what commands
<em>would be</em> run in the unmodified loop.</p>
<p>The following diagram shows what happens when the modified loop is
executed and demonstrates how the judicious use of <code>echo</code> is
a good debugging technique.</p>
<figure><img src="fig/shell_script_for_loop_flow_chart.svg" alt='The for loop "for filename in .dat; do echo cp $filename original-$filename;done" will successively assign the names of all ".dat" files in your currentdirectory to the variable "$filename" and then execute the command. With thefiles "basilisk.dat", "minotaur.dat" and "unicorn.dat" in the current directorythe loop will successively call the echo command three times and print threelines: "cp basislisk.dat original-basilisk.dat", then "cp minotaur.datoriginal-minotaur.dat" and finally "cp unicorn.datoriginal-unicorn.dat"' class="figure mx-auto d-block"></figure><section><h2 class="section-heading" id="nelles-pipeline-processing-files">Nelle’s Pipeline: Processing Files<a class="anchor" aria-label="anchor" href="#nelles-pipeline-processing-files"></a></h2>