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.

Feel free to complement your notes on the compilation of basic commands.

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} file.txt

• -F to indicate the delimiter of your table as tabs (default is space).
• '{print}' to select with “$” the column number you want in the output.
• Text added to the output must 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 > 10 {print $0}'

• You can indicate you want only the rows in which a column meets certain condition. For example, the column 3 requires a value greater than 10.
  • Equal ==
  • Non equal =!
  • > Greater than
• '{print $0}' will print all the columns of the table

sort -g -u file.txt

• -r to sort in descending order
• -g to sort by number
• -k1,1 to sort by a specific column, in this example, first column only.
• -u make values unique
• -t ' ' to select a non-default field separator (default is tab, and in this case I changed to a space)

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 -n -e '/AAA/,/BBB/ p' file.txt

• This will find AAA, and keep all the lines in a file until it reaches BBB. Pro tip: use this one to extract a sequence in a multi-line fasta.
• Note that using variables inside a sed command requires double quotation marks “ instead of single '.

Play with the following sample files.comm_join_example.tar.gz

To compare contents of both files (in this case, the identifiers of the first column of the two files):

comm <() <()

• Within each ”<()“ we place the command of the input to compare.
• These should be sorted out
• I use the second part of the command (the sed) to adjust the output to have the correct number of columns

comm <(cut -f1 1_table.txt | sort) <(cut -f1 2_table.txt | sort) | sed -e 's/$/\t\t/' | cut -f1,2,3

• Output:
• First column: identifiers exclusive of the table in input 1
• Second column: identifiers exclusive of the table in input 2
• Third column: identifiers present in both tables

Join two tables based on a column in common.

join -t $'\t' <() <()

• Input within the ”<()“ must be sorted out.
• I highly recommend using only the first column with the identifiers to join.
• If one of the tables has repeated identifiers, the output will generate all combinations possible.
• The standard output will display only lines with columns in common. We can add option -a1 or -a2 to also include the entries of one of the tables, with no joined values from other. Do not use both.

join -t $'\t' -a1 <(sort -k1,1 1_table.txt) <(sort -k1,1 2_table.txt)