Standard I/O and Command Redirection

Unix commands communicate via the command line interface. They can print information out to the terminal for you to see, and accept input from the keyboard (that is, from you!)

Every Unix program starts out with three connections to the outside world. These connections are called "streams" because they act like a stream of information (metaphorically speaking):

standard input

This is a communications stream initially attached to the keyboard. When the program reads from standard input, it reads whatever text you type in.

standard output

This stream is initially attached to the command window. Anything the program prints to this channel appears in your terminal window.

standard error

This stream is also initially attached to the command window. It is a separate channel intended for printing error messages.

The word "initially" might lead you to think that standard input, output and error can somehow be detached from their starting places and reattached somewhere else. And you'd be right. You can attach one or more of these three streams to a file, a device, or even to another program. This sounds esoteric, but it is actually very useful.

A Simple Example

The wc program counts lines, characters and words in data sent to its standard input. You can use it interactively like this:

(~) 62% wc
Mary had a little lamb,
little lamb,
little lamb.

Mary had a little lamb,
whose fleece was white as snow.
^D
      6      20     107

In this example, I ran the wc program. It waited for me to type in a little poem. When I was done, I typed the END-OF-FILE character, control-D (^D for short). wc then printed out three numbers indicating the number of lines, words and characters in the input.

More often, you'll want to count the number of lines in a big file; say a file filled with DNA sequences. You can do this by redirecting wc's standard input from a file. This uses the < metacharacter:

(~) 63% wc <big_file.fasta
      2943    2998     419272

If you wanted to record these counts for posterity, you could redirect standard output as well using the > metacharacter:

(~) 64% wc <big_file.fasta >count.txt

Now if you cat the file count.txt, you'll see that the data has been recorded. cat works by taking its standard input and copying it to standard output. We redirect standard input from the count.txt file, and leave standard output at its default, attached to the terminal:

(~) 65% cat <count.txt
      2943    2998     419272

Redirection Meta-Characters

Here's the complete list of redirection commands for tcsh:

<filename	Redirect standard input to file
>filename	Redirect standard output to file
>&filename	Redirect standard error to file

These can be combined. For example, this command redirects standard input from the file named /etc/passwd, writes its results into the file search.out, and writes its error messages (if any) into a file named search.err. What does it do? It searches the password file for a user named "root" and returns all lines that refer to that user.

(~) 66% grep root </etc/passwd >search.out >&search.err

Filters, Filenames and Standard Input

Many Unix commands act as filters, taking data from a file or standard input, transforming the data, and writing the results to standard output. Most filters are designed so that if they are called with one or more filenames on the command line, they will use those files as input. Otherwise they will act on standard input. For example, these two commands are equivalent:

(~) 66% grep 'gatttgc' <big_file.fasta
(~) 67% grep 'gatttgc' big_file.fasta

Both commands use the grep command to search for the string "gatttgc" in the file big_file.fasta. The first one searches standard input, which happens to be redirected from the file. The second command is explicitly given the name of the file on the command line.

Sometimes you want a filter to act on a series of files, one of which happens to be standard input. Many filters let you use "-" on the command line as an alias for standard input. Example:

(~) 68% grep 'gatttgc' big_file.fasta bigger_file.fasta -

This example searches for "gatttgc" in three places. First it looks in big_file.fasta, then in bigger_file.fasta, and lastly in standard input (which, since it isn't redirected, will come from the keyboard).

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