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:

<font 14px/Courier New,Courier,monospace;;inherit;;inherit>awk</font><font 14px/Courier New,Courier,monospace;;#27ae60;;inherit>-</font> <font inherit/Courier New,Courier,monospace;;#27ae60;;inherit>F</font><font inherit/Courier New,Courier,monospace;;#27ae60;;inherit> “\t”</font> '{print <font inherit/inherit;;#2980b9;;inherit>$2</font> <font inherit/inherit;;#8e44ad;;inherit>“\t”</font> $1}'

• use after reading the contents of your table, i.e. after cat file.txt
• indicate the <font inherit/inherit;;#27ae60;;inherit>delimiter</font> <font inherit/inherit;;#27ae60;;inherit>of your table</font> to tabs in this case (default is space)
• <font inherit/inherit;;#2980b9;;inherit>$ indicates the column</font> <font inherit/inherit;;#2980b9;;inherit>number</font>you want to return
• <font inherit/inherit;;#8e44ad;;inherit>Text added to your</font> <font inherit/inherit;;#8e44ad;;inherit>table</font>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

<font 16px/Courier New,Courier,monospace;;inherit;;inherit>awk -F “\t”</font><font 16px/Courier New,Courier,monospace;;#e74c3c;;inherit>'$3==“+“</font> {print <font inherit/inherit;;#f39c12;;inherit>$0</font>}'

• You can indicate you want only the rows in which a <font inherit/inherit;;#e74c3c;;inherit>column meets certain condition.</font>In this case the column 3 has to be exactly a plus sign.
  • Equal ==
  • Non equal =!
  • > Greater than
• In this example $0 will <font inherit/inherit;;#f39c12;;inherit>print</font> <font inherit/inherit;;#f39c12;;inherit>all columns of the table.</font>

<font inherit/Courier New,Courier,monospace;;inherit;;inherit>sort -r -g -k2</font>

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

<font inherit/Courier New,Courier,monospace;;inherit;;inherit>sort -u -t ' ' -k1,1</font>

• -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.

<font inherit/Courier New,Courier,monospace;;inherit;;inherit>tr '[ATGC]' '[TACG]' | rev</font>

• 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.

<font inherit/Courier New,Courier,monospace;;inherit;;inherit>sed -n -e '/AAA/,/BBB/ p'</font>

• <font inherit/Arial,Helvetica,sans-serif;;inherit;;inherit>This will find AAA, and keep all the lines in</font><font inherit/Arial,Helvetica,sans-serif;;inherit;;inherit>a</font><font inherit/Arial,Helvetica,sans-serif;;inherit;;inherit>file</font><font inherit/Arial,Helvetica,sans-serif;;inherit;;inherit>until</font><font inherit/Arial,Helvetica,sans-serif;;inherit;;inherit>it</font><font inherit/Arial,Helvetica,sans-serif;;inherit;;inherit>reaches</font>BBB.
• <font inherit/Arial,Helvetica,sans-serif;;inherit;;inherit>Pro tip: use this one to extract a sequence in a multi-line fasta.</font>*