Extra Unix Shell Material: AWK

Learning Objectives {.objectives}

  • Explain why AWK is useful and when it is better than pipes.
  • Show a basic usage similar to the command “cut”
  • Introduce the filed separator parameter.
  • Use regulax expressions to perform different instructions.
  • Introduce BEGIN and END keywords.
  • Use the if then structure to change behaviour for the same matching regex.
  • Introduce the array data structure.
  • Use the for loop to cycle through an array

Prerequisite: shell and any programming language

If we need to count the number of lines in a file, we can use the previously showed command for word counting wc

$ wc -l example.txt

As you probably remember, -l is an option that asks for the number of lines only.

However, wc counts the number of newlines in the file, if the last line does not contain a carriage return (i.e. there is no emptyline at the end of the file), the result is going be the actual number of lines minus one.

A workaround is to use Awk. Awk is command line program that takes as input a set of instructions and one or more files. The instructions are executed on each line of the input file(s).

The instructions are enclosed in single quotes or they can be read from a file.

Example:

$ awk '{print $0}' example.txt

This command has the same output of “cat”: it prints each line from the example.fasta file.

The structure of the instruction is the following:

As you can see, the file contains a table.

Awk automatically splits the processed line by looking at spaces: in our case it has knowledge of the different columns in the table.

Each column value for the current line is stored into a variable: $1 for the first column, $2 for the second and so on.

So, if we like to print only the second column from the table, we execute

$ awk '{print $2}' example.txt

We can also print more than one value, or add text to the printed line:

$ awk '{print "chr",$2,$4}' example.txt

The comma puts a space between the printed values. Strings of text should be enclosed in double quotes. In this case we are printing the text “chr”, the second and the fourth column for each row in the table.

So, $0 is the whole line, $1 the first field, $2 the second and so on. What if we want to print the last column, but we don’t know its number? Maybe it is a huge table, or maybe different lines have a different number of columns.

Awk helps us thanks to the variable NF. NF stores the number of fields (our columns) in the row. Let’s see for our table:

$ awk '{print NF}' example.txt

We can see that some lines contain 6 fields while others contain 7 of them. Since NF is the number of the last field, $NF contains its value.

$ awk '{print "This line has",NF,"columns. The last one contains",$NF}' example.txt

Field separator {.callout}

Out there we have different file formats: our data may be comma separated (csv), tab separated (tsv), by semicolon or by any other character.

To specify the field separator, we should provide it at command line like:

$ awk -F "," '{print $2}' example2.txt

In this case , we are printing the second field in each line, using comma as separator. Please notice that the character space is now part of the field value, since it is no longer the separator.

Matching lines {.callout}

Maybe we would like to perform different instruction on different lines.

Awk allows you to specify a matching pattern, like the command grep does.

Let’s look at the file content

$ awk '{print $0}' example.pdb

It seems an abriged PDB file. If we would like to print only lines starting with the word “ATOM”, we type:

awk '/^ATOM/ {print $0}' example.pdb

In this case, we specify the pattern before the instructions: only lines starting with the text “ATOM”. As you remember, ^ means “at the beginning of the line”.

We can specify more that one pattern:

awk '/^ATOM/ {print $7,$8,$9} /^HEADER/ {print $NF}' example.pdb

In this case, we are printing the spatial coordinates of each atom.