1. Python programs How can I run a program? Input and output

2. In this module you can learn How to read, process, and output text How to read from the keyboard How to write to the screen How to repeat things How to create your own modules

4. Counting amino acids

6. What is a program? It is a text file that contains Python commands or, in other words, lines of code

7. Exercise 1 1) Open a text file, write: print "This is the output of my first program" save the file with the name my_print.py and exit. Open a terminal, go to the directory where you saved my_print.py and type at the cursor: python my_print.py

10. Input program in the program from the keyboard from a file from a Python module

11. Input from the program itself a = 3 print a

12. Input from the keyboard >>> a = raw_input("Type a number: ") Type a number: 3 >>> print a 3

13. Exercise 2 2) Write a program that reads something from the keyboard and print it to the screen.

14. a = raw_input("Type something: ") print a

15. Input from a text file We need to “access” an existing input file And read its content Infile = open("insulin.txt") content = Infile.read() print content

16. From a Python module A Python module is a text file (with the.py extension) that contains (Python) definitions/assignments Python modules can be accessed from programs using the import statement from insulin import insulin print insulin insulin = "GIVEQCCTSICSLYQLENYCNFVNQHLCGSHL\ VEALYLVCGERGFFYTPKT" Python module insulin.py Python program my_first_import.py

17. Exercise 3 3) Write a program that reads a sequence from a file and print it to the screen. Run it.

18. Output program to the computer screen to a text file

19. To the computer screen ?

20. To a text file We need to “open” a text file in the “writing” mode We have to write to it. from insulin import insulin outfile = open("my_output.txt", "w") outfile.write(insulin) outfile.close()

21. seq.count("A") counts the number of letters

22. Exercise 4 4) Calculate DNA base occurrences. Write a program that counts how many times the four bases occur in a DNA sequence. The program should: -Store the DNA sequence in a variable. -Count how often each base occurs. -Write all four numbers to the screen. Test it with a DNA sequence for which you know the result, for instance “AAAACCCGGT”. This approach makes it much easier to discover small program errors.

23. dna = "AGCTTCGA" print dna.count("A") print dna.count("C") print dna.count("T") print dna.count("G")

24. Loops with for The for command repeats other commands: The commands that are repeated must be indented (shifted right by four spaces). dna = "AGCTTCGA” for base in "ACTG": print dna.count(base)

25. dna = "AGCTTCGA” for base in "ACTG": print dna.count(base) Compare Would you prefer this implementation? dna = "AGCTTCGA" print dna.count("A") print dna.count("C") print dna.count("T") print dna.count("G") Why or why not?

26. Exercise 5 5) Retrieve the 1132-residue sequence of human telomerase reverse transcriptase isoform 1 from the NCBI protein database. Choose the FASTA format. Copy the sequence to a text file (telomerase.txt). Write a program that reads the telomerase.txt file and prints first the whole sequence and then the sequence residue by residue.

27. telomerase = open("telomerase.txt") seq = telomerase.read() print seq for aa in seq: print aa

28. You can use a for loop to read a file line by line Input_file = open(“my_file.txt”) for line in Input_file: print line

29. Exercise 6 6) Write a program that reads the telomerase.txt file and prints its content line by line.

30. telomerase = open("telomerase.txt") for line in telomerase: print line

32. Exercise 7 7) Which amino acid is the most frequent in the sequence of the telomerase reverse transcriptase isoform 1?

33. telomerase = open("telomerase.txt") seq = telomerase.read() for aa in "ACDEFGHKILMNPQRSTVYW": aa_count = seq.count(aa) aa_freq = aa_count/float(len(seq)) print aa, round(aa_freq, 3)

34. Recap

35. Recap I string variables contain text print writes to the screen you can use functions to do things you can enter text with raw_input() write() writes to an open file for loops repeat commands comments starts with # or '''

36. Recap II