1. Introduction to Programming and Algorithms
Paolo Marcatili
“Sapienza” University of Rome
Biocomputing group
Bioinformatics master course, ‘11/’12
Paolo Marcatili

2. Course Calendar & structure
Fri 2, Dec: Introduction & Unix
Fri 13, Jan: Perl – Data types
Fri 20, Jan: Perl – IO and loops
Fri 27, Jan: Algorithms: Sort and Search
Thu 2, Feb: Perl – Parsing
Thu 9, Feb: Seminar – Machine Learning
Fri 10, Feb: Perl – Practicals
Fri 17, Feb: Perl – Practicals
Bioinformatics master course, ‘11/’12
Paolo Marcatili

3. Unix for Bioinformaticians
A survival guide
Bioinformatics master course, ‘11/’12
Paolo Marcatili

4. Agenda
• Unix
• Folders
• Files
• Processes
• Redirection
Bioinformatics master course, ‘11/’12
Paolo Marcatili

5. Unix
Bioinformatics master course, ‘11/’12
Paolo Marcatili

6. What is Unix? Unix
Bioinformatics master course, ‘11/’12
Paolo Marcatili

7. What is Unix?
Operating system
stable,
multi-user,
multi-tasking
for servers,
desktops
and laptops.
Bioinformatics master course, ‘11/’12
Paolo Marcatili

8. Types of Unix
• Solaris"
• OS-X"
• Linux!
Bioinformatics master course, ‘11/’12
Paolo Marcatili

9. Unix Operating System
Bioinformatics master course, ‘11/’12
Paolo Marcatili

10. What’s in Unix?
Files (data)
Processes (actions)
Bioinformatics master course, ‘11/’12
Paolo Marcatili

11. Unix Filesystem
Bioinformatics master course, ‘11/’12
Paolo Marcatili

12. Terminal
It makes the difference!
Powerful
Transparent
User-unfriendly
Bioinformatics master course, ‘11/’12
Paolo Marcatili

13. Our Task Today
Bioinformatics master course, ‘11/’12
Paolo Marcatili

14. Human Immunoglobulins
Bioinformatics master course, ‘11/’12
Paolo Marcatili

15. Human Immunoglobulins
Bioinformatics master course, ‘11/’12
Paolo Marcatili

16. The data
We have 3 files
Fasta Sequences of
Heavy (heavy.fasta)
Lambda (lambda.fasta)
Kappa (kappa.fasta)
Bioinformatics master course, ‘11/’12
Paolo Marcatili

17. The Task
• Look data
• Correct errors
• Do some analysis
• Make a single fasta file
Bioinformatics master course, ‘11/’12
Paolo Marcatili

18. Folders: read and write
Bioinformatics master course, ‘11/’12
Paolo Marcatili

19. Change Directory
To know where you are
>pwd
/home/bioinfoSMFN
Let’s move!
>cd /home/bioinfoSMFN/Desktop/task
Or
>cd Desktop/
Bioinformatics master course, ‘11/’12
Paolo Marcatili

20. Folder content
Let’s check what’s in the folder:
>ls
Better
>ls -la
Cheat: parameters are useful!
>ls -lart
Bioinformatics master course, ‘11/’12
Paolo Marcatili

21. Wildcards
Extremely useful!
>ls -la *heavy*
>ls -la heavy.?asta
*= 0,1,2,…. occurences of whatever
?= exactly 1 occurence of whatever
Bioinformatics master course, ‘11/’12
Paolo Marcatili

22. Commands
To know more about a command:
>man ls
>whatis ls
>apropos ls
Or Google!
Bioinformatics master course, ‘11/’12
Paolo Marcatili

23. Unix Permissions
Bioinformatics master course, ‘11/’12
Paolo Marcatili

24. Folders - summary
Command
Meaning
ls
list files and directories
ls -a
list all files and directories
mkdir
make a directory
cd directory
change to named directory
cd
change to home-directory
cd ~
change to home-directory
cd ..
change to parent directory
pwd
path of the current directory
Bioinformatics master course, ‘11/’12
Paolo Marcatili

25. Files: read and write
Bioinformatics master course, ‘11/’12
Paolo Marcatili

26. Backup original data
Create a directory
>mkdir backup
Copy all the files in the directory
>cp heavy.fasta backup/
>cp heavy.fasta heavy_copy.fasta
>mv heavy_copy.fasta backup/
heavy_backup.fasta
Bioinformatics master course, ‘11/’12
Paolo Marcatili

27. Read a file
Let’s see…
>cat heavy.fasta
Bioinformatics master course, ‘11/’12
Paolo Marcatili

28. Read a file
Let’s see…
>cat heavy.fasta
Mmh…
>less heavy.fasta
Hint: q to quit…
but if you are stuck try ctrl+c
Bioinformatics master course, ‘11/’12
Paolo Marcatili

29. Look for text
If we want to look for something
while in less:
/
91979410 (enter)
Bioinformatics master course, ‘11/’12
Paolo Marcatili

30. Edit a file
Let’s remove the first H sequence
>vi heavy.fasta
>nano heavy.fasta
For those who live in 2008
>gedit heavy.fasta
Bioinformatics master course, ‘11/’12
Paolo Marcatili

31. Look for text
How many Igs in each file?
We can count the lines!
>wc heavy.fasta
Bioinformatics master course, ‘11/’12
Paolo Marcatili

32. Look for text
How many Igs in each file?
We can count the lines!
>wc heavy.fasta
Lines > proteins!!!
Bioinformatics master course, ‘11/’12
Paolo Marcatili

33. Grep
# of proteins = # of “>” in a file
>grep “>” heavy.fasta
>grep -c “>” heavy.fasta
Do it for all the files and write the result
(I think they are too many…)
Bioinformatics master course, ‘11/’12
Paolo Marcatili

34. Grep
>grep -c V-region heavy.fasta
>grep -c v-region heavy.fasta
>grep -ci v-region heavy.fasta
Ok, better!
Bioinformatics master course, ‘11/’12
Paolo Marcatili

35. Files: sumary
cp file1 file2
copy file1 and call it file2
mv file1 file2
move or rename file1 to file2
rm file
remove a file
cat file
display a file
less file
display a file a page at a time
head file
display the first few lines
tail file
display the last few lines
grep 'key' file
search a file for keywords
wc file
number of lines
Bioinformatics master course, ‘11/’12
Paolo Marcatili

36. Processes
Bioinformatics master course, ‘11/’12
Paolo Marcatili

37. Run a process
Process = execution of some instructions
Usually the instructions are in a file.
e.g. less -> /usr/bin/less
So
>/usr/bin/less heavy.fasta
Bioinformatics master course, ‘11/’12
Paolo Marcatili

38. Run - It’s simple
Ok, so let’s try
>./loop.pl
Bioinformatics master course, ‘11/’12
Paolo Marcatili

39. Run - It’s simple
Ok, so let’s try
>./loop.pl
Ok, and now?
Bioinformatics master course, ‘11/’12
Paolo Marcatili

40. Controlling processes
Ctrl+z -> go to sleep
Now you’ve got the control again!
But it’s not still dead…
bg
Ctrl+C
Bioinformatics master course, ‘11/’12
Paolo Marcatili

41. Controlling processes
Or:
>./loop.pl
Ctrl+z
>ps
>top (q to exit)
>kill the_number_that_you_have_just_read
Bioinformatics master course, ‘11/’12
Paolo Marcatili

42. Redirection
Control the force
Bioinformatics master course, ‘11/’12
Paolo Marcatili

43. Inputs and outputs
Keyboard
Mouse
Tablet
Kernel
Display
Printer
File
Bioinformatics master course, ‘11/’12
Paolo Marcatili

44. Write into a file
>Cat > lista.txt
Heavy 29061
Ctrl+d
And
>less lista.txt
Bioinformatics master course, ‘11/’12
Paolo Marcatili

45. Append to a file
>Cat >> lista.txt
Kappa 7476
Ctrl+d
And
>less lista.txt
Bioinformatics master course, ‘11/’12
Paolo Marcatili

46. The big one!
>cat heavy.fasta > bigone.fasta
>cat kappa >> bigone.fasta
>cat lambda.fasta >> bigone.fasta
>grep -c “>” bigone.fasta
Bioinformatics master course, ‘11/’12
Paolo Marcatili

47. Extract headers
>grep “>” bigone.fasta > headers.head
>sort headers.head > headers_sort.head
Do we need the first file?
Bioinformatics master course, ‘11/’12
Paolo Marcatili

48. Extract headers
>grep “>” bigone.fasta > headers.head
>sort headers.head > headers_sort.head
Do we need the first file? No!
>grep “>” bigone.fasta | sort >
headers_sorted.head
| is called pipe, and it’s something
Bioinformatics master course, ‘11/’12
Paolo Marcatili

49. Redirect everything!
>grep ">" biggone.fasta 2> err.log
>less err.log
Bioinformatics master course, ‘11/’12
Paolo Marcatili

50. Redirect - summary
command > file
redirect std output to a file
command >> file
append std output to a file
command < file
redirect std input from a file
cmd1 | cmd2
pipe the output of cmd1 to the
input of cmd2
cat f1 f2 > f0
concatenate f1 and f2 to f0
sort
sort data
Bioinformatics master course, ‘11/’12
Paolo Marcatili

51. Quiz
• What does this command perform?"
>grep -v ">" heavy.fasta
• How many proteins in each file?
• How many residues in each file?"
(hint: wc -m counts the # of char in a line)
• Average length of proteins in each file?
• Average content of Prolines of VH, VL and
VK?"
(hint: look at grep parameters)
Bioinformatics master course, ‘11/’12
Paolo Marcatili