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A non-comprehensive list of bash commands

I have listed a number of common bash commands that come in handy when working in a shell.
You can try the following basic commands on the example file to understand what they are doing.

Slightly more advanced bash

AWK

This command is also considered a programming language on its own. It is particularly useful when you need to process the elements of a table. The basic syntax is as follows:

awk- F “\t” '{print $2 “\t” $1}'

use after reading the contents of your table, i.e. after cat file.txt
indicate the delimiter of your table to tabs in this case (default is space)
$ indicates the column numberyou want to return
Text added to your tablemust be written inside quotation marks; in this case, the text is just the addition of a new tab.
You can also process columns by mathematical operations. For instance, print $1+ $2

awk -F “\t”'$3==“+“ {print $0}'

You can indicate you want only the rows in which a column meets certain condition.In this case the column 3 has to be exactly a plus sign.
- Equal ==
- Non equal =!
- > Greater than
In this example $0 will print all columns of the table.

Sort

sort -r -g -k2

-r if you want descending order
-g if you want to sort by number
-k sort by a specific column

Sort more

sort -u -t ' ' -k1,1

-u for unique
-t to select a delimiter as space (default is tab)
-k1,1 to apply the unique only for the value of the first column, but still keeping the rest of the row.

Translate

tr '[ATGC]' '[TACG]' | rev

This is a trick if you are working on the complementary strand.
It will convert each “A” into “T” and so on.
rev will make everything read backwards.

sed (slightly more advanced)

sed -n -e '/AAA/,/BBB/ p'

This will find AAA, and keep all the lines inafileuntilitreachesBBB.
Pro tip: use this one to extract a sequence in a multi-line fasta.*

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