Introduction to Command Line

This lab is designed to practice basic Unix commands and prepare students for shell scripting in the upcoming classes.

1. Create a new screen named "LAB_1".

2. Create a new directory named "Commandline_Lab".

3. Change into the directory you just created.

4. Check the contents of the directory.

5. Make a text file named "Text_1.txt" and write "Welcome to Applied Genome Analytics" into it.

6. Save the file.

7. Rename the file to "Myfile_1.txt".

8. Export the file from Sphinx to your Local computer.

9. Delete the file "Myfile_1.txt".

10. Import the file "Myfile_1.txt" from local to Sphinx.

11. Download the data onto your computer. Data

12. Import the folder to the current working directory.

13. count the number of files in the folder.

14. Peek into the file named "mgGenes.txt".

15. Count the number of genes in the file "mgGenes.txt".

16. List the first 10 and last 10 lines of file "mgGenes.txt".

17. Count the no. of genes on positive strand in "mgGenes.txt".

18. Count the no. of genes on negative strand in "mgGenes.txt".

19. Compare it to the number of gene.

20. Find the flaw.

21. Edit the file "mgGenes.txt". in the text editor and repeat step 17 & 18 and count the number of genes again.

22. Extract the "+" genes excluding the gene names into new file "Plus_genes.txt".

23. Extract the "-" genes excluding the gene names into new file "Minus_genes.txt".

24. Count the number of genes again in both the files.

25. Extract line 250 from the file "mgGenes.txt".

26. Exit the screen.