1. Trinity College Dublin, The University of Dublin GE3M25: Computer Programming for Biologists Python Karsten Hokamp, PhD Genetics TCD, 03/11/2015

2. Trinity College Dublin, The University of Dublin GE3M25 Data Handling Module Content Python Programming Bioinformatics ChIP-Seq analysis

3. Trinity College Dublin, The University of Dublin GE3M25 Data Handling Module Content Python Programming Bioinformatics ChIP-Seq analysis Evaluation: 1.Weekly tasks 2.Project report

4. Trinity College Dublin, The University of Dublin Overview Programming First Python script/program Why Python? Examples Additional resources

5. Trinity College Dublin, The University of Dublin Overview Programming First Python script/program Why Python? Examples Additional resources http://bioinf.gen.tcd.ie/GE3M25/

6. Trinity College Dublin, The University of Dublin What is programming and why bother?  Data processing  Automation  Combination of programs for analysis pipelines  More control and flexibility  Better understanding of how programs work

7. Trinity College Dublin, The University of Dublin Programming Concepts  Turn into a very meticulous problem solver  Break problems into small details  Keep it variable  Give very precise instructions

8. Trinity College Dublin, The University of Dublin Programming Concepts "human" recipe

9. Trinity College Dublin, The University of Dublin Programming Concepts "computerised" recipe

10. Trinity College Dublin, The University of Dublin Mac for Windows users The main differences:  cmd instead of ctrl (e.g. cmd-C for copying)  right-click mouse: ctrl-click  hashtag (#): alt-3  switch between applications: cmd-tab  Spotlight (top right) for finding files/programs  Apple symbol (top left) for logging out

11. Trinity College Dublin, The University of Dublin IDLE: Integrated DeveLopment Environment open through Spotlight

12. Trinity College Dublin, The University of Dublin IDLE: Integrated DeveLopment Environment

13. Trinity College Dublin, The University of Dublin IDLE: Integrated DeveLopment Environment Alternatively: open through Finder

14. Trinity College Dublin, The University of Dublin IDLE: Integrated DeveLopment Environment interactive Python console

15. Trinity College Dublin, The University of Dublin IDLE: Integrated DeveLopment Environment simple Python statement

16. Trinity College Dublin, The University of Dublin IDLE: Integrated DeveLopment Environment user input output

17. Trinity College Dublin, The University of Dublin Simple Operations try a few simple numeric operations try a few simple numeric operations user input output

18. Trinity College Dublin, The University of Dublin Simple Operations repeat/combine previous commands by clicking into them and hitting return (use left/right arrows and delete to edit them) repeat/combine previous commands by clicking into them and hitting return (use left/right arrows and delete to edit them)

19. Trinity College Dublin, The University of Dublin Special Operators 13 / 5 = 2.6 = 2 * 5 + 3 13 // 5 = 2 13 % 5 = 3 floor division modulus

20. Trinity College Dublin, The University of Dublin EXERCISE: Print greetings to the screen Tip: Use the built-in function 'print'

21. Trinity College Dublin, The University of Dublin IDLE: Integrated DeveLopment Environment Console vs Editor ConsoleEditor interactiverequires extra click for running great for trying out codeadditional IDLE functionality not suited for long scriptssuited for long scripts no saving of codeallows to save code

22. Trinity College Dublin, The University of Dublin IDLE: Writing Python Scripts open a new file

23. Trinity College Dublin, The University of Dublin IDLE: Writing Python Scripts Opening bracket triggers 'call tip'

24. Trinity College Dublin, The University of Dublin IDLE: Writing Python Scripts Quotes needed around words/sentences!

25. Trinity College Dublin, The University of Dublin IDLE: Writing Python Scripts First Python script!

26. Trinity College Dublin, The University of Dublin IDLE: Writing Python Scripts run your code shortcut: F5

27. Trinity College Dublin, The University of Dublin IDLE: Writing Python Scripts save file first

28. Trinity College Dublin, The University of Dublin IDLE: Writing Python Scripts specify a file name

29. Trinity College Dublin, The University of Dublin IDLE: Writing Python Scripts Shortcut for save and run: cmd-S followed by F5 Shortcut for save and run: cmd-S followed by F5

30. Trinity College Dublin, The University of Dublin Learnt so far: IDLE allows executing Python code Python understands mathematical operators Floor division and modulus Scripts can be saved in files and run within IDLE Shortcuts: cmd-S and F5 Comments start with hashtag Character strings enclosed by quotes Built-in function 'print' for writing messages

31. Trinity College Dublin, The University of Dublin Why Python?  easy to learn  great for beginners  enforces clean coding  great for teachers  comes with IDE  avoids command-line usage  object-orientated  code reuse and recycling  very popular  many peers  BioPython  many bioinformatics modules

32. Trinity College Dublin, The University of Dublin Python Help

33. Trinity College Dublin, The University of Dublin IDLE: Writing Python Scripts make it personal

34. Trinity College Dublin, The University of Dublin IDLE: Writing Python Scripts built-in function prints message waits for user input built-in function prints message waits for user input variable stores user input variable stores user input variable content gets printed to screen

35. Trinity College Dublin, The University of Dublin Single vs Double Quotes Can you use single quotes here?

36. Trinity College Dublin, The University of Dublin Escaping special meaning of characters Now you can!

37. Trinity College Dublin, The University of Dublin EXERCISE: Can you print an exclamation mark at the end?

38. Trinity College Dublin, The University of Dublin SOLUTION: Add it as a string to the list of arguments

39. Trinity College Dublin, The University of Dublin EXERCISE: How to get rid of the extra space?

40. Trinity College Dublin, The University of Dublin TIP: Check call tip by deleting and typing opening bracket. separator, space as default

41. Trinity College Dublin, The University of Dublin SOLUTION: sep='' (empty string) Now all the spaces are gone!

42. Trinity College Dublin, The University of Dublin SOLUTION: sep='' (empty string) add an extra space here

43. Trinity College Dublin, The University of Dublin Learnt so far: Variables store and release values Functions take arguments and parameters Built-in function 'input' The computer knows nothing. The devil is in the detail!

44. Trinity College Dublin, The University of Dublin First project: Make a Python Calculator Description: Write a script that asks the user for two numbers and prints out the sum of them.

45. Trinity College Dublin, The University of Dublin First project: Make a Python Calculator Pseudocode: - receive two numbers - calculate sum - print result to screen

46. Trinity College Dublin, The University of Dublin First project: Make a Python Calculator Refine Pseudocode: -Prompt user for first number and store in variable -Prompt user for second number and store in variable -Calculate and store sum of two numbers -Print numbers and sum to screen

47. Trinity College Dublin, The University of Dublin First project: Make a Python Calculator Put pseudocode as comments into new file: Save script, e.g. calculator.py

48. Trinity College Dublin, The University of Dublin First project: Make a Python Calculator Add code after each comment line: Save and run (cmd-s + F5) often!

49. Trinity College Dublin, The University of Dublin First project: Make a Python Calculator First attempt: Not what we want!

50. Trinity College Dublin, The University of Dublin First project: Make a Python Calculator Better: What about non-integers?

51. Trinity College Dublin, The University of Dublin First project: Make a Python Calculator Even better: Works also for integers!

52. Trinity College Dublin, The University of Dublin Repeated calculations:

53. Trinity College Dublin, The University of Dublin Repeated calculations: Error when trying to run script!

54. Trinity College Dublin, The University of Dublin Repeated calculations: Highlight block and indent:

55. Trinity College Dublin, The University of Dublin Repeated calculations: Save and Run (cmd-s + F5)

56. Trinity College Dublin, The University of Dublin EXERCISE: Make it stop!

57. Trinity College Dublin, The University of Dublin Learnt so far: Start project with pseudocode Turn pseudocode into comments Save and run your script often! 'while' and ':' introduces a loop Indentation is important Editor provides formatting help

58. Trinity College Dublin, The University of Dublin Online courses  http://biopython.org/DIST/docs/tutorial/Tutorial.html http://biopython.org/DIST/docs/tutorial/Tutorial.html  http://dowell.colorado.edu/education-python.html  http://www.pasteur.fr/formation/infobio/python http://www.pasteur.fr/formation/infobio/python  https://www.codecademy.com/tracks/python  http://anh.cs.luc.edu/python/hands-on/ http://anh.cs.luc.edu/python/hands-on/  https://www.coursera.org

59. Trinity College Dublin, The University of Dublin Books

60. Trinity College Dublin, The University of Dublin Thank You! http://bioinf.gen.tcd.ie/GE3M25/

61. Trinity College Dublin, The University of Dublin Don't forget to log out!