Using the Command Line: Glossary

Key Points

Navigating Files and Directories

  • The /, ~, and .. characters represent important navigational shortcuts.

  • Relative paths specify a location starting from the current location, while absolute paths specify a location from the root of the file system.
Working with Files and Directories

  • You can view file contents using less, cat, head or tail.

  • The commands cp, mv, and mkdir are useful for manipulating existing files and creating new directories.

  • The history command and the up arrow on your keyboard can be used to repeat recently used commands.
Redirection

  • grep is a powerful search tool with many options for customization.

  • >, >>, and | are different ways of redirecting output.

  • command > file redirects a command’s output to a file.

  • command >> file redirects a command’s output to a file without overwriting the existing contents of the file.

  • command_1 | command_2 redirects the output of the first command as input to the second command.

Glossary

absolute path
A path that refers to a particular location in a file system. Absolute paths are usually written with respect to the file system’s root directory, and begin with either “/” (on Unix) or “\” (on Microsoft Windows). See also: relative path.
accession
a unique identifier assigned to each sequence or set of sequences
argument
A value given to a function or program when it runs. The term is often used interchangeably (and inconsistently) with parameter.
command shell
See shell
command-line interface
A user interface based on typing commands, usually at a REPL. See also: graphical user interface.
current working directory
The directory that relative paths are calculated from; equivalently, the place where files referenced by name only are searched for. Every process has a current working directory. The current working directory is usually referred to using the shorthand notation . (pronounced “dot”).
file system
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 operating system manages access.
filename extension
The portion of a file’s name that comes after the final “.” character. By convention this identifies the file’s type: .txt means “text file”, .png 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 homepage.html. Since many applications use filename extensions to identify the MIME type of the file, misnaming files may cause those applications to fail.
flag
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 -v, or two dashes followed by a word, such as --verbose, while DOS applications use a slash, such as /V. Depending on the application, a flag may be followed by a single argument, as in -o /tmp/output.txt.
graphical user interface
A user interface based on selecting items and actions from a graphical display, usually controlled by using a mouse. See also: command-line interface.
home directory
The default directory associated with an account on a computer system. By convention, all of a user’s files are stored in or below their home directory.
NGS
common acronym for “Next Generation Sequencing” currently being replaced by “High Throughput Sequencing”
operating system
Software that manages interactions between users, hardware, and software processes. Common examples are Linux, OS X, and Windows.
parent directory
The directory that “contains” the one in question. Every directory in a file system except the root directory has a parent. A directory’s parent is usually referred to using the shorthand notation .. (pronounced “dot dot”).
path
A description that specifies the location of a file or directory within a file system. See also: absolute path, relative path.
pipe
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”.
process
A running instance of a program, containing code, variable values, open files and network connections, and so on. Processes are the “actors” that the operating system manages; it typically runs each process for a few milliseconds at a time to give the impression that they are executing simultaneously.
prompt
A character or characters display by a REPL to show that it is waiting for its next command.
read-evaluate-print loop
(REPL): A command-line interface that reads a command from the user, executes it, prints the result, and waits for another command.
redirect
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.
regular expression
A pattern that specifies a set of character strings. REs are most often used to find sequences of characters in strings.
relative path
A path that specifies the location of a file or directory with respect to the current working directory. Any path that does not begin with a separator character (“/” or “\”) is a relative path. See also: absolute path.
root directory
The top-most directory in a file system. Its name is “/” on Unix (including Linux and Mac OS X) and “\” on Microsoft Windows.
shell
A command-line interface such as Bash (the Bourne-Again Shell) or the Microsoft Windows DOS shell that allows a user to interact with the operating system.
shell script
A set of shell 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.
standard input
A process’s default input stream. In interactive command-line applications, it is typically connected to the keyboard; in a pipe, it receives data from the standard output of the preceding process.
standard output
A process’s default output stream. In interactive command-line applications, data sent to standard output is displayed on the screen; in a pipe, it is passed to the standard input of the next process.
sub-directory
A directory contained within another directory.
tab completion
A feature provided by many interactive systems in which pressing the Tab key triggers automatic completion of the current word or command.
variable
A name in a program that is associated with a value or a collection of values.
wildcard
A character used in pattern matching. In the Unix shell, the wildcard * matches zero or more characters, so that *.txt matches all files whose names end in .txt.

External references

Opening a terminal

Manuals

FASTQ files

High-throughput sequencing