Chapter 10 AWK

awk is a line-oriented language for text processing such as data extraction and reporting. It was written by Aho, Weinberger and Kernighan in 1977, but much improved since. Its syntax is quite different from the standard bash syntax, but once you get a hang on it you will see how powerful it can be for data manipulation.

Note: In this section, we will use the Banthracis proteome BanthracisProteome.txt as an example file. You may get the file as follows:

$ # download the zipped file using wget
$ wget --compression=auto https://bitbucket.org/wegmannlabteaching/bash_lecture/raw/master/Files/BanthracisProteome.txt.gz
$ # unzip the file
$ gunzip BanthracisProteome.txt.gz