Script: A series of commands or instructions to automate a task. The commands are written in a text file that is then executed by a program without being first compiled (converted into the binary machine code).
Scripting language: A computer programming language that supports scripts. The scripts are typically interpreted by the program and do not have to be compiled.
In this exercise, we’ll discuss variable assignment and manipulation. The goal is to demonstrate the need to automate repeated tasks, which will be done in the next exercise in which we introduce scripts.
1. Open a shell or terminal window.
2. Assign a DNA sequence to a variable (sequence):
3. Complement the sequence using tr:
$ echo $sequence | tr [ACTGactg] [TGACtgac]
4. Reverse the sequence using rev:
$ echo $sequence | rev
5. Reverse complement the sequence using tr and rev:
$ echo $sequence | rev | tr [ACTGactg] [TGACtgac]
6. Calculate the length of the sequence using wc -c:
$ echo -n $sequence | wc -c
This exercise required multiple steps and if it is something we wanted to repeat, it could be easily automated with a script, as demonstrated below.
A good text editor is essential for writing scripts. Microsoft Word and Mac TextEdit should not be used for writing scripts.
Common Free Text Editors
In this exercise, we will write a bash script to identify the length, the complement, the reverse, and the reverse complement of a DNA sequence.
1. Open a shell or terminal window.
2. Create a new directory named Bash_Scripts using mkdir.
3. Change into the Bash_Scripts directory using cd.
4. Open a text editor, such as TextWrangler or Notepad++, using open and use it to create a new file called iseq.sh within the Bash_Scripts directory. In the next steps, we will write a bash script by adding commands to the file.
5. Confirm that you are in the Bash_Scripts directory using pwd and that the iseq.sh script is in the directory using ls.
6. Insert a shebang that directs the terminal to bash within the iseq.sh file: #!/bin/bash
7. Prompt the user for a sequence and store as a variable (seq) using read -p:
read -p "Enter a sequence: " seq
8. Determine if the sequence entered is DNA or RNA using a conditional statement:
if [[ $seq =~ U ]] then type=RNA elif [[ $seq =~ T ]] then type=DNA else type=unknown fi
9. Complement the sequence using tr and store as new variable (comp):
comp=`echo $seq | tr [ACTGactg] [TGACtgac]`
10. Reverse the sequence using rev and store as a new variable (reverse):
reverse=`echo $seq | rev`
11. Reverse complement a sequence using tr and rev and store as a new variable (revcomp):
revcomp=`echo $seq | tr [ACTGactg] [TGACtgac] | rev`
12. Calculate the length of the sequence using wc -c and store as a new variable (length):
length=`echo -n $seq | wc -c`
13. Print to the shell the output of each of the above steps along with a brief description:
echo "" echo "Original sequence: $seq" echo "Your sequence is $type" echo "Complement: $comp" echo "Reverse: $reverse" echo "Reverse complement: $revcomp" echo ""
14. Return to your terminal window and execute the script using ./iseq.sh. Did you receive an error message? How can you make the script executable?
15. Edit iseq.sh to repeat indefinitely using a while loop as follows.
a. Add while before the read command.
while read -p "Enter a sequence: " seq
b. Insert a new line and the command do directly after the previous line containing while….:
c. At the end of the script add a new line and the command done:
16. Return to your terminal window and execute the script again.