AWK(1)

awk

NAME
awk - pattern-directed scanning and processing language

SYNOPSIS
awk [ -F fs ] [ -v var=value ] [ 'prog' | -f progfile ] [ file ... ]

DESCRIPTION
Awk scans each input file for lines that match any of a set of patterns specified literally in prog or in one or more files specified as -f progfile. With each pattern there can be an associated action that will be performed when a line of a file matches the pattern. Each line is matched against the pattern portion of every pattern-action statement; the associated action is performed for each matched pattern. The file name - means the standard input. Any file of the form var=value is treated as an assignment, not a filename, and is executed at the time it would have been opened if it were a filename. The option -v followed by var=value is an assignment to be done before prog is executed; any number of -v options may be present. The -F fs option defines the input field separator to be the regular expression fs.

An input line is normally made up of fields separated by white space, or by regular expression FS. The fields are denoted $1, $2, ..., while $0 refers to the entire line. If FS is null, the input line is split into one field per character.

A pattern-action statement has the form

    pattern { action }

A missing { action } means print the line; a missing pattern always matches. Pattern-action statements are separated by newlines or semicolons.

An action is a sequence of statements. A statement can be one of the following:

    if( expression ) statement [ else statement ]
    while( expression ) statement
    for( expression ; expression ; expression ) statement
    for( var in array ) statement
    do statement while( expression )
    break
    continue
    { [ statement ... ] }
    expression	# commonly var = expression
    print [ expression-list ] [ > expression ]
    printf format [ , expression-list ] [ > expression ]
    return [ expression ]
    next	# skip remaining patterns on this input line
    nextfile	# skip rest of this file, open next, start at top
    delete array[ expression ]	# delete an array element
    delete array	# delete all elements of array
    exit [ expression ]	# exit immediately; status is expression

Statements are terminated by semicolons, newlines or right braces. An empty expression-list stands for $0. String constants are quoted " ", with the usual C escapes recognized within. Expressions take on string or numeric values as appropriate, and are built using the operators + - * / % ^ (exponentiation), and concatenation (indicated by white space). The operators ! ++ -- += -= *= /= %= ^= > >= < <= == != ?: are also available in expressions. Variables may be scalars, array elements (denoted x[i]) or fields. Variables are initialized to the null string. Array subscripts may be any string, not necessarily numeric; this allows for a form of associative memory. Multiple subscripts such as [i,j,k] are permitted; the constituents are concatenated, separated by the value of SUBSEP.

The print statement prints its arguments on the standard output (or on a file if >file or >>file is present or on a pipe if |cmd is present), separated by the current output field separator, and terminated by the output record separator. file and cmd may be literal names or parenthesized expressions; identical string values in different statements denote the same open file. The printf statement formats its expression list according to the format (see printf(3)). The built-in function close(expr) closes the file or pipe expr. The built-in function fflush(expr) flushes any buffered output for the file or pipe expr.

The mathematical functions exp, log, sqrt, sin, cos, and atan2 are built in. Other built-in functions:

length
    the length of its argument taken as a string, or of $0 if no argument.

rand
    random number on (0,1)

srand
    sets seed for rand and returns the previous seed.

int truncates to an integer value

substr(s, m, n)
    the n-character substring of s that begins at position m counted from 1.

index(s, t)
    the position in s where the string t occurs, or 0 if it does not.

match(s, r)
    the position in s where the regular expression r occurs, or 0 if it does not. The variables RSTART and RLENGTH are set to the position and length of the matched string.

split(s, a, fs)
    splits the string s into array elements a[1], a[2], ..., a[n], and returns n. The separation is done with the regular expression fs or with the field separator FS if fs is not given. An empty string as field separator splits the string into one array element per character.

sub(r, t, s)
    substitutes t for the first occurrence of the regular expression r in the string s. If s is not given, $0 is used.

gsub
    same as sub except that all occurrences of the regular expression are replaced; sub and gsub return the number of replacements.

sprintf(fmt, expr, ... )
    the string resulting from formatting expr ... according to the printf(3) format fmt

system(cmd)
    executes cmd and returns its exit status

tolower(str)
    returns a copy of str with all upper-case characters translated to their corresponding lower-case equivalents.

toupper(str)
    returns a copy of str with all lower-case characters translated to their corresponding upper-case equivalents.

The ``function'' getline sets $0 to the next input record from the current input file; getline <file sets $0 to the next record from file. getline x sets variable x instead. Finally, cmd | getline pipes the output of cmd into getline; each call of getline returns the next line of output from cmd. In all cases, getline returns 1 for a successful input, 0 for end of file, and -1 for an error.

Patterns are arbitrary Boolean combinations (with ! || &&) of regular expressions and relational expressions. Regular expressions are as in egrep; see grep(1). Isolated regular expressions in a pattern apply to the entire line. Regular expressions may also occur in relational expressions, using the operators ~ and !~. /re/ is a constant regular expression; any string (constant or variable) may be used as a regular expression, except in the position of an isolated regular expression in a pattern.

A pattern may consist of two patterns separated by a comma; in this case, the action is performed for all lines from an occurrence of the first pattern though an occurrence of the second.

A relational expression is one of the following:

    expression matchop regular-expression
    expression relop expression
    expression in array-name
    (expr,expr,...) in array-name

where a relop is any of the six relational operators in C, and a matchop is either ~ (matches) or !~ (does not match). A conditional is an arithmetic expression, a relational expression, or a Boolean combination of these.

The special patterns BEGIN and END may be used to capture control before the first input line is read and after the last. BEGIN and END do not combine with other patterns.

Variable names with special meanings:

CONVFMT
    conversion format used when converting numbers (default %.6g)

FS  regular expression used to separate fields; also settable by option -Ffs.

NF  number of fields in the current record

NR  ordinal number of the current record

FNR ordinal number of the current record in the current file

FILENAME
    the name of the current input file

RS  input record separator (default newline)

OFS output field separator (default blank)

ORS output record separator (default newline)

OFMT
    output format for numbers (default %.6g)

SUBSEP
    separates multiple subscripts (default 034)

ARGC
    argument count, assignable

ARGV
    argument array, assignable; non-null members are taken as filenames

ENVIRON
    array of environment variables; subscripts are names.

Functions may be defined (at the position of a pattern-action statement) thus:

    function foo(a, b, c) { ...; return x }

Parameters are passed by value if scalar and by reference if array name; functions may be called recursively. Parameters are local to the function; all other variables are global. Thus local variables may be created by providing excess parameters in the function definition.

EXAMPLES

length($0) > 72
Print lines longer than 72 characters.

{ print $2, $1 }
Print first two fields in opposite order.

    BEGIN { FS = ",[ \t]*|[ \t]+" }
          { print $2, $1 }

    Same, with input fields separated by comma and/or blanks and tabs.

    	{ s += $1 }
    END	{ print "sum is", s, " average is", s/NR }

    Add up first column, print sum and average.

/start/, /stop/
Print all lines between start/stop pairs.

    BEGIN	{	# Simulate echo(1)
    	for (i = 1; i < ARGC; i++) printf "%s ", ARGV[i]
    	printf "\n"
    	exit }

BIOAWK EXTENSIONS

Bioawk adds a new -c fmt option that specifies the input format. The behavior of bioawk may vary depending on the value of fmt. When fmt is header or hdr, bioawk parses named columns. It automatically adds variables whose names are taken from the first line and values from the column index. Special characters are converted to a underscore. When fmt is sam, vcf, bed or gff, it sets predefined column names. Users may check out the predefined column names by -c help. When fmt is fastx, bioawk will parse the input FASTA or FASTQ file into a TAB-delimited format first with each line consisting of sequence name, sequence, quality and comments, and then sets column names. Note that when -c fmt is in use, the input file can be optionally gzip'ed.

Bioawk also adds more built-in functions:

reverse(s)
    reverse string s

revcomp(s)
    reverse complement a nucleotide string s in the IUB encoding.

trimq(qual, beg, end, param)
    trim quality string qual in the Sanger scale using Richard Mott's algorithm (used in Phred). The 0-based beginning and ending positions are written to beg and end, respectively. The last arguement param is the single parameter used in the algorithm, which is optional and defaults 0.05.

and(x, y)
    bit AND operation (& in C)

or(x, y)
    bit OR operation (| in C)

xor(x, y)
    bit XOR operation (^ in C)

SEE ALSO
lex(1), sed(1)
A. V. Aho, B. W. Kernighan, P. J. Weinberger, The AWK Programming Language, Addison-Wesley, 1988. ISBN 0-201-07981-X

BUGS
There are no explicit conversions between numbers and strings. To force an expression to be treated as a number add 0 to it; to force it to be treated as a string concatenate "" to it.
The scope rules for variables in functions are a botch; the syntax is worse.