Lecture for the "Programming for Evolutionary Biology" workshop in Leipzig 2012 (http://evop.bioinf.uni-leipzig.de/)

1. Programming for Evolutionary Biology
March 17th - April 1st 2012
Leipzig, Germany
Introduction to Unix systems
Extra: awk and gawk
Giovanni Marco Dall'Olio
Universitat Pompeu Fabra
Barcelona (Spain)

2. awk
 “awk” is a “swiss army” command line tool to
manipulate tabular files
 Things you can do with awk:
 Extract all the lines of a file that match a pattern, and
print only some of the columns (instead of “grep |
cut”)
 Add a prefix/suffix to all the element of a column
(instead of “cut | paste”)
 Sum values of different columsn

3. awk and gawk
 In these slides we will be talking about awk
 In reality, the original awk is not available
anymore. We will use gawk, a free version of
gawk developed by the GNU project

4. Basic awk usage
 “awk '<pattern to select lines> {instructions to be
executed on each line}' ”

5. Example awk usage
 “awk '$0 ~ AAC {print}' sample_vcf.vcf”
 $0 ~ AAC → select all the lines that contain AAC
 {print} → for each line that matches the previous
expression, print it

6. Column names in awk
 awk assumes that you are working on tabular files
 Each column of the file can be accessed by
$<column­name>. For example, $2 is the second
column of the file
 $0 matches all the columns of the file

7. Accessing columns in awk
 “awk '{print $1, $2, $3}' sample_vcf.vcf” → prints
the first three columns
 “awk '{print $0}' sample_vcf.vcf” → print all the
columns

8. Adding a prefix to a column
with awk
 A common awk usage is to add a prefix or suffix to
all the entries of a column
 Example:
 awk '{print $2 “my_prefix”$2}' myfile.txt

9. Summing columns in awk
 If two columns contain numeric values, we can use
awk to sum them
 Usage:
 “awk '{print $1 + $2}' myfile.txt

10. Selecting columns with awk
 Awk can be used to select columns,
 It is like grep, but more powerful, because it let you
specify on which columns the match must be
 This example will print all the lines that have a
AAC in their first colum:
 “awk '$1 ~ AAC {print}' myfile.txt

11. More on awk
 awk is a complete programming language
 It is the equivalent of a spreadsheet for the
command line
 If you want to know more, check the book “Gawk
effective AWK Programming” at
http://www.gnu.org/software/gawk/manual