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<!DOCTYPE html>
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<h1>Glossary</h1>
<p> Last updated on 2023-05-08 |
<a href="https://github.com/datacarpentry/shell-genomics/edit/main/learners/reference.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
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<section id="glossary"><h2 class="section-heading">Glossary<a class="anchor" aria-label="anchor" href="#glossary"></a>
</h2>
<hr class="half-width"><dl><dt><span id="absolute-path">absolute path</span></dt>
<dd>
A <a href="#path">path</a> that refers to a particular location in a
file system. Absolute paths are usually written with respect to the file
system’s <a href="#root-directory">root directory</a>, and begin with
either “/” (on Unix) or “\” (on Microsoft Windows). See also: <a href="#relative-path">relative path</a>.
</dd>
<dt><span id="argument">argument</span></dt>
<dd>
A value given to a function or program when it runs. The term is often
used interchangeably (and inconsistently) with <a href="#parameter">parameter</a>.
</dd>
<dt><span id="command-shell">command shell</span></dt>
<dd>
See <a href="#shell">shell</a>
</dd>
<dt><span id="command-line-interface">command-line interface</span></dt>
<dd>
A user interface based on typing commands, usually at a <a href="#read-evaluate-print-loop">REPL</a>. See also: <a href="#graphical-user-interface">graphical user interface</a>.
</dd>
<dt><span id="comment">comment</span></dt>
<dd>
A remark in a program that is intended to help human readers understand
what is going on, but is ignored by the computer. Comments in Python, R,
and the Unix shell start with a <code>#</code> character and run to the
end of the line; comments in SQL start with <code>--</code>, and other
languages have other conventions.
</dd>
<dt><span id="current-working-directory">current working
directory</span></dt>
<dd>
The directory that <a href="#relative-path">relative paths</a> are
calculated from; equivalently, the place where files referenced by name
only are searched for. Every <a href="#process">process</a> has a
current working directory. The current working directory is usually
referred to using the shorthand notation <code>.</code> (pronounced
“dot”).
</dd>
<dt><span id="file-system">file system</span></dt>
<dd>
A set of files, directories, and I/O devices (such as keyboards and
screens). A file system may be spread across many physical devices, or
many file systems may be stored on a single physical device; the <a href="#operating-system">operating system</a> manages access.
</dd>
<dt><span id="filename-extension">filename extension</span></dt>
<dd>
The portion of a file’s name that comes after the final “.” character.
By convention this identifies the file’s type: <code>.txt</code> means
“text file”, <code>.png</code> means “Portable Network Graphics file”,
and so on. These conventions are not enforced by most operating systems:
it is perfectly possible (but confusing!) to name an MP3 sound file
<code>homepage.html</code>. Since many applications use filename
extensions to identify the <a href="#mime-type">MIME type</a> of the
file, misnaming files may cause those applications to fail.
</dd>
<dt><span id="filter">filter</span></dt>
<dd>
A program that transforms a stream of data. Many Unix command-line tools
are written as filters: they read data from <a href="#standard-input">standard input</a>, process it, and write the
result to <a href="#standard-output">standard output</a>.
</dd>
<dt><span id="flag">flag</span></dt>
<dd>
A terse way to specify an option or setting to a command-line program.
By convention Unix applications use a dash followed by a single letter,
such as <code>-v</code>, or two dashes followed by a word, such as
<code>--verbose</code>, while DOS applications use a slash, such as
<code>/V</code>. Depending on the application, a flag may be followed by
a single argument, as in <code>-o /tmp/output.txt</code>.
</dd>
<dt><span id="for-loop">for loop</span></dt>
<dd>
A loop that is executed once for each value in some kind of set, list,
or range. See also: <a href="#while-loop">while loop</a>.
</dd>
<dt><span id="graphical-user-interface">graphical user
interface</span></dt>
<dd>
A user interface based on selecting items and actions from a graphical
display, usually controlled by using a mouse. See also: <a href="#command-line-interface">command-line interface</a>.
</dd>
<dt><span id="home-directory">home directory</span></dt>
<dd>
The default directory associated with an account on a computer system.
By convention, all of a user’s files are stored in or below her home
directory.
</dd>
<dt><span id="loop">loop</span></dt>
<dd>
A set of instructions to be executed multiple times. Consists of a <a href="#loop-body">loop body</a> and (usually) a condition for exiting
the loop. See also <a href="#for-loop">for loop</a> and <a href="#while-loop">while loop</a>.
</dd>
<dt><span id="loop-body">loop body</span></dt>
<dd>
The set of statements or commands that are repeated inside a <a href="#for-loop">for loop</a> or <a href="#while-loop">while loop</a>.
</dd>
<dt><span id="mime-type">MIME type</span></dt>
<dd>
MIME (Multi-Purpose Internet Mail Extensions) types describe different
file types for exchange on the Internet, for example images, audio, and
documents.
</dd>
<dt><span id="operating-system">operating system</span></dt>
<dd>
Software that manages interactions between users, hardware, and software
<a href="#process">processes</a>. Common examples are Linux, OS X, and
Windows.
</dd>
<dt><span id="parameter">parameter</span></dt>
<dd>
A variable named in a function’s declaration that is used to hold a
value passed into the call. The term is often used interchangeably (and
inconsistently) with <a href="#argument">argument</a>.
</dd>
<dt><span id="parent-directory">parent directory</span></dt>
<dd>
The directory that “contains” the one in question. Every directory in a
file system except the <a href="#root-directory">root directory</a> has
a parent. A directory’s parent is usually referred to using the
shorthand notation <code>..</code> (pronounced “dot dot”).
</dd>
<dt><span id="path">path</span></dt>
<dd>
A description that specifies the location of a file or directory within
a <a href="#file-system">file system</a>. See also: <a href="#absolute-path">absolute path</a>, <a href="#relative-path">relative path</a>.
</dd>
<dt><span id="pipe">pipe</span></dt>
<dd>
A connection from the output of one program to the input of another.
When two or more programs are connected in this way, they are called a
“pipeline”.
</dd>
<dt><span id="process">process</span></dt>
<dd>
A running instance of a program, containing code, variable values, open
files and network connections, and so on. Processes are the “actors”
that the <a href="#operating-system">operating system</a> manages; it
typically runs each process for a few milliseconds at a time to give the
impression that they are executing simultaneously.
</dd>
<dt><span id="prompt">prompt</span></dt>
<dd>
A character or characters display by a <a href="#read-evaluate-print-loop">REPL</a> to show that it is waiting for
its next command.
</dd>
<dt><span id="quoting">quoting</span></dt>
<dd>
(in the shell): Using quotation marks of various kinds to prevent the
shell from interpreting special characters. For example, to pass the
string <code>*.txt</code> to a program, it is usually necessary to write
it as <code>'*.txt'</code> (with single quotes) so that the shell will
not try to expand the <code>*</code> wildcard.
</dd>
<dt><span id="read-evaluate-print-loop">read-evaluate-print
loop</span></dt>
<dd>
(REPL): A <a href="#command-line-interface">command-line interface</a>
that reads a command from the user, executes it, prints the result, and
waits for another command.
</dd>
<dt><span id="redirect">redirect</span></dt>
<dd>
To send a command’s output to a file rather than to the screen or
another command, or equivalently to read a command’s input from a file.
</dd>
<dt><span id="regular-expression">regular expression</span></dt>
<dd>
A pattern that specifies a set of character strings. REs are most often
used to find sequences of characters in strings.
</dd>
<dt><span id="relative-path">relative path</span></dt>
<dd>
A <a href="#path">path</a> that specifies the location of a file or
directory with respect to the <a href="#current-working-directory">current working directory</a>. Any
path that does not begin with a separator character (“/” or “\”) is a
relative path. See also: <a href="#absolute-path">absolute path</a>.
</dd>
<dt><span id="root-directory">root directory</span></dt>
<dd>
The top-most directory in a <a href="#file-system">file system</a>. Its
name is “/” on Unix (including Linux and Mac OS X) and “\” on Microsoft
Windows.
</dd>
<dt><span id="shell">shell</span></dt>
<dd>
A <a href="#command-line%20interface">command-line interface</a> such as
Bash (the Bourne-Again Shell) or the Microsoft Windows DOS shell that
allows a user to interact with the <a href="#operating-system">operating
system</a>.
</dd>
<dt><span id="shell-script">shell script</span></dt>
<dd>
A set of <a href="#shell">shell</a> commands stored in a file for
re-use. A shell script is a program executed by the shell; the name
“script” is used for historical reasons.
</dd>
<dt><span id="standard-input">standard input</span></dt>
<dd>
A process’s default input stream. In interactive command-line
applications, it is typically connected to the keyboard; in a <a href="#pipe">pipe</a>, it receives data from the <a href="#standard-output">standard output</a> of the preceding process.
</dd>
<dt><span id="standard-output">standard output</span></dt>
<dd>
A process’s default output stream. In interactive command-line
applications, data sent to standard output is displayed on the screen;
in a <a href="#pipe">pipe</a>, it is passed to the <a href="#standard-input">standard input</a> of the next process.
</dd>
<dt><span id="sub-directory">sub-directory</span></dt>
<dd>
A directory contained within another directory.
</dd>
<dt><span id="tab-completion">tab completion</span></dt>
<dd>
A feature provided by many interactive systems in which pressing the Tab
key triggers automatic completion of the current word or command.
</dd>
<dt><span id="variable">variable</span></dt>
<dd>
A name in a program that is associated with a value or a collection of
values.
</dd>
<dt><span id="while-loop">while loop</span></dt>
<dd>
A loop that keeps executing as long as some condition is true. See also:
<a href="#for-loop">for loop</a>.
</dd>
<dt><span id="wildcard">wildcard</span></dt>
<dd>
A character used in pattern matching. In the Unix shell, the wildcard
<code>*</code> matches zero or more characters, so that
<code>*.txt</code> matches all files whose names end in
<code>.txt</code>.
</dd>
</dl></section><section id="external-references"><h2 class="section-heading">External references<a class="anchor" aria-label="anchor" href="#external-references"></a>
</h2>
<hr class="half-width"><div class="section level3">
<h3 id="opening-a-terminal">Opening a terminal<a class="anchor" aria-label="anchor" href="#opening-a-terminal"></a></h3>
<ul><li><a href="https://www.macworld.co.uk/feature/mac-software/how-use-terminal-on-mac-3608274/" class="external-link">How
to Use Terminal on a Mac</a></li>
<li><a href="https://git-for-windows.github.io/" class="external-link">Git for
Windows</a></li>
<li><a href="https://www.windowscentral.com/how-install-bash-shell-command-line-windows-10" class="external-link">How
to Install Bash shell command-line tool on Windows 10</a></li>
<li><a href="https://www.howtogeek.com/249966/how-to-install-and-use-the-linux-bash-shell-on-windows-10/" class="external-link">Install
and Use the Linux Bash Shell on Windows 10</a></li>
<li><a href="https://www.howtogeek.com/265900/everything-you-can-do-with-windows-10s-new-bash-shell/" class="external-link">Using
the Windows 10 Bash Shell</a></li>
<li><a href="https://faculty.smu.edu/reynolds/unixtut/windows.html" class="external-link">Using a
UNIX/Linux emulator (Cygwin) or Secure Shell (SSH) client
(Putty)</a></li>
<li><a href="https://www.biorxiv.org/content/early/2017/04/07/122424.full.pdf+html" class="external-link">Addressing
the digital divide in contemporary biology: Lessons from teaching
UNIX</a></li>
<li><a href="https://files.fosswire.com/2007/08/fwunixref.pdf" class="external-link">Unix
cheat sheet</a></li>
</ul></div>
<div class="section level3">
<h3 id="manuals">Manuals<a class="anchor" aria-label="anchor" href="#manuals"></a></h3>
<ul><li><a href="https://www.gnu.org/software/bash/manual/html_node/index.html" class="external-link">GNU
BASH reference</a></li>
<li><a href="https://www.gnu.org/manual/manual.html" class="external-link">GNU manual</a></li>
<li><a href="https://www.gnu.org/software/coreutils/manual/coreutils.html" class="external-link">Core
GNU utilities</a></li>
</ul></div>
<div class="section level3">
<h3 id="fastq-files">FASTQ files<a class="anchor" aria-label="anchor" href="#fastq-files"></a></h3>
<ul><li><a href="https://en.wikipedia.org/wiki/Phred_quality_score" class="external-link">Phred
quality score</a></li>
<li><a href="https://en.wikipedia.org/wiki/FASTQ_format" class="external-link">FASTQ
format</a></li>
</ul></div>
<div class="section level3">
<h3 id="high-throughput-sequencing">High-throughput sequencing<a class="anchor" aria-label="anchor" href="#high-throughput-sequencing"></a></h3>
<ul><li>Illumina Sequencing Technology <a href="https://www.youtube.com/watch?v=womKfikWlxM" class="external-link">YouTube
video</a>
</li>
</ul></div>
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