AWK

Awk is an powerful command language that allows the user to manipulate files containing columns of data and strings. Awk is extremely useful, both for general operation of Unix commands, and for data reduction (e.g. IRAF). You might also learn how to use the stream editor sed. Many applications of awk resemble those done on PC spreadsheets.

This file contains a number of examples of how to use awk. I have compiled this table gradually over a couple of years as I've learned to do new things. Everyone who reduces data with IRAF should learn the fundamentals of AWK Learning to do even simple things will save you a lot of time in the long run. It should take you less than an hour to read through this file and learn the basics.

There are two ways to run awk. A simple awk command can be run from a single command line. More complex awk scripts should be written to a command file. I present examples of both types of input below.

Awk takes each line of input and tries to match the 'pattern' (see below), and if it succeeds it will do whatever you tell it to do within the {} (called the action). Awk works best on files that have columns of numbers or strings that are separated by whitespace (tabs or spaces), though on most machines you can use the -F option if your columns are set apart by another character. Awk refers to the first column as $1, the second column as $2, etc., and the whole line as $0. If you have a file (such as a catalog) that always has numbers in specific columns, you may also want to run the command 'colrm' and combine it with awk. There is a manual page on colrm. There is also a very incomplete man page on awk.

I'll lead you through two examples. First, suppose you have a file called 'file1' that has 2 columns of numbers, and you want to make a new file called 'file2' that has columns 1 and 2 as before, but also adds a third column which is the ratio of the numbers in columns 1 and 2. Suppose you want the new 3-column file (file2) to contain only those lines with column 1 smaller than column 2. Either of the following two commands does what you want:

awk '$1 < $2 {print $0, $1/$2}' file1 > file2

-- or --

cat file1 | awk '$1 < $2 {print $0, $1/$2}' > file2

Let's look at the second one. You all know that 'cat file1' prints the contents of file1 to your screen. The | (called a pipe) directs the output of 'cat file1', which normally goes to your screen, to the command awk. Awk considers the input from 'cat file1' one line at a time, and tries to match the 'pattern'. The pattern is whatever is between the first ' and the {, in this case the pattern is $1 < $2. If the pattern is false, awk goes on to the next line. If the pattern is true, awk does whatever is in the {}. In this case we have asked awk to check if the first column is less than the second. If there is no pattern, awk assumes the pattern is true, and goes onto the action contained in the {}.

What is the action? Almost always it is a print statement of some sort. In this case we want awk to print the entire line, i.e. $0, and then print the ratio of columns 1 and 2, i.e. $1/$2. We close the action with a }, and close the awk command with a '. Finally, to store the final 3-column output into file2 (otherwise it prints to the screen), we add a '> file2'.

As a second example, suppose you have several thousand files you want to move into a new directory and rename by appending a .dat to the filenames. You could do this one by one (several hours), or use vi to make a decent command file to do it (several minutes), or use awk (several seconds). Suppose the files are named junk* (* is wildcard for any sequence of characters), and need to be moved to ../iraf and have a '.dat' appended to the name. To do this type

ls junk* | awk '{print "mv "$0" ../iraf/"$0".dat"}' | csh

ls junk* lists the filenames, and this output is piped into awk instead of going to your screen. There is no pattern (nothing between the ' and the {), so awk proceeds to print something for each line. For example, if the first two lines from 'ls junk*' produced junk1 and junk2, respectively, then awk would print:

mv junk1 ../iraf/junk1.dat
mv junk2 ../iraf/junk2.dat

At this point the mv commands are simply printed to the screen. To execute the command we take the output of awk and pipe it back into the operating system (the C-shell). Hence, to finish the statement we add a ' | csh'.

More complex awk scripts need to be run from a file. The syntax for such cases is:

cat file1 | awk -f a.awk > file2

where file1 is the input file, file2 is the output file, and a.awk is a file containing awk commands. Examples below that contain more than one line of awk need to be run from files.

Some useful awk variables defined for you are NF (number of columns), NR (the current line that awk is working on), END (true if awk reaches the EOF), BEGIN (true before awk reads anything), and length (number of characters in a line or a string). There is also looping capability, a search (/) command, a substring command (extremely useful), and formatted printing available. There are logical variables || (or) and && (and) that can be used in 'pattern'. You can define and manipulate your own user defined variables. Examples are outlined below. The only bug I know of is that Sun's version of awk won't do trig functions, though it does do logs. There is something called gawk (a Gnu product), which does a few more things than Sun's awk, but they are basically the same. Note the use of the 'yes' command below. Coupled with 'head' and 'awk' you save an hour of typing if you have a lot of files to analyze or rename.

Good luck!

EXAMPLES      # is the comment character for awk.  'field' means 'column'

# Print first two fields in opposite order:
  awk '{ print $2, $1 }' file


# Print lines longer than 72 characters:
  awk 'length > 72' file
    

# Print length of string in 2nd column
  awk '{print length($2)}' file


# Add up first column, print sum and average:
       { s += $1 }
  END  { print "sum is", s, " average is", s/NR }


# Print fields in reverse order:
  awk '{ for (i = NF; i > 0; --i) print $i }' file


# Print the last line
      {line = $0}
  END {print line}


# Print the total number of lines that contain the word Pat
  /Pat/ {nlines = nlines + 1}
  END {print nlines}


# Print all lines between start/stop pairs:
  awk '/start/, /stop/' file


# Print all lines whose first field is different from previous one:
  awk '$1 != prev { print; prev = $1 }' file


# Print column 3 if column 1 > column 2:
  awk '$1 > $2 {print $3}' file
     

# Print line if column 3 > column 2:
  awk '$3 > $2' file


# Count number of lines where col 3 > col 1
  awk '$3 > $1 {print i + "1"; i++}' file


# Print sequence number and then column 1 of file:
  awk '{print NR, $1}' file


# Print every line after erasing the 2nd field
  awk '{$2 = ""; print}' file


# Print hi 28 times
  yes | head -28 | awk '{ print "hi" }'


# Print hi.0010 to hi.0099 (NOTE IRAF USERS!)
  yes | head -90 | awk '{printf("hi00%2.0f \n", NR+9)}'

# Print out 4 random numbers between 0 and 1
yes | head -4 | awk '{print rand()}'

# Print out 40 random integers modulo 5
yes | head -40 | awk '{print int(100*rand()) % 5}'


# Replace every field by its absolute value
  { for (i = 1; i <= NF; i=i+1) if ($i < 0) $i = -$i print}

# If you have another character that delimits fields, use the -F option
# For example, to print out the phone number for Jones in the following file,
# 000902|Beavis|Theodore|333-242-2222|149092
# 000901|Jones|Bill|532-382-0342|234023
# ...
# type
  awk -F"|" '$2=="Jones"{print $4}' filename



# Some looping commands
# Remove a bunch of print jobs from the queue
  BEGIN{
 for (i=875;i>833;i--){
  printf "lprm -Plw %d\n", i
 } exit
       }


 Formatted printouts are of the form printf( "format\n", value1, value2, ... valueN)
  e.g. printf("howdy %-8s What it is bro. %.2f\n", $1, $2*$3)
 %s = string
 %-8s = 8 character string left justified
  %.2f = number with 2 places after .
 %6.2f = field 6 chars with 2 chars after .
 \n is newline
 \t is a tab


# Print frequency histogram of column of numbers
$2 <= 0.1 {na=na+1}
($2 > 0.1) && ($2 <= 0.2) {nb = nb+1}
($2 > 0.2) && ($2 <= 0.3) {nc = nc+1}
($2 > 0.3) && ($2 <= 0.4) {nd = nd+1}
($2 > 0.4) && ($2 <= 0.5) {ne = ne+1}
($2 > 0.5) && ($2 <= 0.6) {nf = nf+1}
($2 > 0.6) && ($2 <= 0.7) {ng = ng+1}
($2 > 0.7) && ($2 <= 0.8) {nh = nh+1}
($2 > 0.8) && ($2 <= 0.9) {ni = ni+1}
($2 > 0.9) {nj = nj+1}
END {print na, nb, nc, nd, ne, nf, ng, nh, ni, nj, NR}


# Find maximum and minimum values present in column 1
NR == 1 {m=$1 ; p=$1}
$1 >= m {m = $1}
$1 <= p {p = $1}
END { print "Max = " m, "   Min = " p }

# Example of defining variables, multiple commands on one line
NR == 1 {prev=$4; preva = $1; prevb = $2; n=0; sum=0}
$4 != prev {print preva, prevb, prev, sum/n; n=0; sum=0; prev = $4; preva = $1; prevb = $2}
$4 == prev {n++; sum=sum+$5/$6}
END {print preva, prevb, prev, sum/n}

# Example of defining and using a function, inserting values into an array
# and doing integer arithmetic mod(n). This script finds the number of days
# elapsed since Jan 1, 1901. (from http://www.netlib.org/research/awkbookcode/ch3)
function daynum(y, m, d,    days, i, n)
{   # 1 == Jan 1, 1901
    split("31 28 31 30 31 30 31 31 30 31 30 31", days)
    # 365 days a year, plus one for each leap year
    n = (y-1901) * 365 + int((y-1901)/4)
    if (y % 4 == 0) # leap year from 1901 to 2099
        days[2]++
    for (i = 1; i < m; i++)
        n += days[i]
    return n + d
}
    { print daynum($1, $2, $3) }

# Example of using substrings
# substr($2,9,7) picks out characters 9 thru 15 of column 2
{print "imarith", substr($2,1,7) " - " $3, "out."substr($2,5,3)}
{print "imarith", substr($2,9,7) " - " $3, "out."substr($2,13,3)}
{print "imarith", substr($2,17,7) " - " $3, "out."substr($2,21,3)}
{print "imarith", substr($2,25,7) " - " $3, "out."substr($2,29,3)}