1. Builtins, namespaces, functions

2. There are objects that are predefined in Python Python built-ins When you use something without defining it, it means that you are using a built-in object Statements: for,in,import,… Numbers: 3, 16.2,… Strings: ‘AUG’ Functions: dir(), lower(),…

3. Namespaces The collection of object names defined in a module represents the global namespace of that module The same name (e.g. src) in two different modules (e.g. module_1.py and module_2.py), indicates two distinct objects and the dot syntax makes it possible to avoid confusion between the namespaces of the two modules Each module defines its own namespace Module_1.srcModule_2.srcis NOT the same as

4. What actually happens when the command import is executed?

5. The code written in the imported module is entirely interpreted and the module global namespace is imported as well

6. Where the Python interpreter searches a module when you import it? Where do you have to save a module in order the interpreter can find it? The module can be saved in the same directory of the script importing it The module path can be added to the list of directories where the Python interpreter automatically search things (this list is contained in the variable path of the special module sys)

7. >>> import sys >>> sys.path ['','/System/Library/Frameworks/Python.frame work/Versions/2.5/lib/python25.zip','/System /Library/Frameworks/Python.framework/Version s/2.5/Extras/lib/python','/Library/Python/2. 5/site-packages'] >>>

8. The built-in function dir() dir() returns a list of the names defined in the namespace of an object

9. Functions A block of code that performs a specific task They are useful to organise your script, in particular if you need to repeat actions (e.g. a complex calculation) several times A function can be accessed from different parts of a script or even from different scripts

10. In order to use a function, you have first to define it and then to call it def MyFunction(arg1, arg2,…): “ documentation ” MyFunction(3,5,…) definition arguments (optional) optional may or may not include a return statement call

11. def triangle_area(b, h): A = (b*h)/2.0 return A print triangle_area(2.28, 3.55) function body def triangle_area(b, h): return (b*h)/2.0 print triangle_area(2.28, 3.55)

12. The statement to define a function is def A function must be defined and called using brackets The body of a function is a block of code that is initiated by a colon character followed by indented instructions The last indented statement marks the end of a function definition General remarks

13. You can insert in the body of a function a documentation string in quotation marks. This string can be retrieved using the __doc__ attribute of the function object You can pass arguments to a function A function may or may not return a value General remarks

14. Exercise 1 1) Define a function with two arguments: get_values(arg1, arg2) that returns the sum, the difference, and the product of arg1 and arg2.

15. def get_values(arg1, arg2): s = arg1 + arg2 d = arg1 - arg2 p = arg1 * arg2 return s, d, p print get_values(15, 8)

16. The statement return exits a function, optionally passing back a value to the caller. A return statement with no arguments is the same as returning None. The returned value can be assigned to a variable >>> def j(x,y):... return x + y... >>> s = j(1, 100) >>> print s 101 >>>

17. Function arguments >>> def increment(x):... return x + 1... >>> def print_arg(y):... print y... >>> print_arg(increment(5)) 6 >>> Every Python object can be passed as argument to a function. A function call can be the argument of a function too.

18. >>> def print_funct(num, seq):... print num, seq... return... >>> print_funct(10, "ACCTGGCACAA") 10 ACCTGGCACAA >>> Multiple parameters can be passed to a function. In this case, the order of the arguments in the caller must be exactly the same as that in the function definition

19. The sequence of arguments passed to a function is a tuple Functions return multiple values in the form of tuples as well AND

20. tuples A tuple is an immutable sequence of object This means that, once you have defined it, you cannot change/replace its elements

21. tuples Brackets are optional, i.e. you can use either: Tuple = (1,2,3) or Tuple = 1,2,3 variabile = (item1, item2, item3,…) Tuple = (1,) or Tuple = 1, A tuple of a single item must be written either:

22. >>> my_tuple = (1,2,3) >>> my_tuple[0]#indexing 1 >>> my_tuple[:]#slicing (1, 2, 3) >>> my_tuple[2:]#slicing (3, )

23. >>> my_tuple[0] = 0 #re-assigning (Forbidden) Traceback (most recent call last): File " ", line 1, in TypeError: 'tuple' object does not support item assignment >>> BUT

24. def f(a,b): return a + b, a*b, a – b sum, prod, diff = f(20, 2) print sum result = f(20, 2) print result Print result[0]

25. It is possible to assign a name to the arguments of a function. In this case, the order is not important >>> def print_funct(num, seq):... print num, seq... return... >>> print_funct(seq = "ACCTGGCACAA", num = 10) 10 ACCTGGCACAA >>>

26. It is also possible to use default arguments (optional). These optional arguments must be placed in the last position(s) of the function definition def print_funct(num, seq = "A"): print num, seq return print_funct(10, "ACCTGGCACAA") print_funct(10)

27. Summary - def F(x,y): - F(3,’codon’) - function arguments - return

28. 2) Write a function that : Takes as input a file name (of a FASTA file). Opens the file. Returns the header of the sequence record. Print the header. Exercise 2

29. def return_header(filename): fasta = open(filename) for line in fasta: if line[0] == '>': return line print return_header('SingleSeq.fasta')

30. Exercise 3 3) Insert the function call in a for loop running on a list of 3 sequence file names.

31. def return_header(filename): fasta = open(filename) for line in fasta: if line[0] == '>': return line filenames = ['SingleSeq1.fasta', 'SingleSeq2.fasta', 'SingleSeq3.fasta'] for name in filenames: print return_header(name)

32. Exercise 4 4) Consider two output schemes for exercise 3): All the the headers are written to the same output file Each header is written in a separate output file

33. def return_header(filename): fasta = open(filename) for line in fasta: if line[0] == '>': return line filenames = ['SingleSeq1.fasta', 'SingleSeq2.fasta', 'SingleSeq3.fasta'] output = open("headers.txt", "w") for name in filenames: output.write(return_header(name) + '\n') output.close()

34. def return_header(filename): fasta = open(filename) for line in fasta: if line[0] == '>': return line filenames = ['SingleSeq1.fasta', 'SingleSeq2.fasta', 'SingleSeq3.fasta'] n = 0 for name in filenames: n = n + 1 output = open("header" + str(n) + ".txt", "w") output.write(return_header(name)) output.close()

35. Exercise 5 5) Write a function that takes as argument a Genbank record and returns the nucleotide sequence in FASTA format.

36. def genbank2fasta(filename): name = filename.split('.')[0] InputFile = open(filename) OutputFile = open(name + ".fasta","w") flag = 0 for line in InputFile: if line[0:9] == 'ACCESSION': AC = line.split()[1].strip() OutputFile.write('>'+AC+'\n') if line[0:6] == 'ORIGIN': flag = 1 continue if flag == 1: fields = line.split() if fields != []: seq = ''.join(fields[1:]) OutputFile.write(seq +'\n') OutputFile.close() filename = "ap006852.gbk" genbank2fasta(filename)

37. Exercise 6 6) Write a function that takes as arguments two points [x1, y1, z1] and [x2, y2, z2] and returns the distance between the two points.

38. import math def distance(p1, p2): dist = math.sqrt((p1[0]-p2[0])**2 + (p1[1]-p2[1])**2 + (p1[2]-p2[2])**2) return dist p1 = (43.64, 30.72, 88.95) p2 = (45.83, 31.11, 92.04) print "Distance:", distance(p1, p2)

40. Python uses dynamical namespaces: when a function is called, its namespace is automatically created The variables defined in the body of a function live in its local namespace and not in the script (or module) global namespace Local objects can be made global using the global statement When a function is called, names of the objects used in its body are first searched in the function namespace and subsequently, if they are not found in the function body, they are searched in the script (module) global namespace. General remarks

41. >>> def f():... x = 100... return x... >>> print x Traceback (most recent call last): File " ", line 1, in NameError: name 'x' is not defined >>> f() 100 >>> print x Traceback (most recent call last): File " ", line 1, in NameError: name 'x' is not defined >>> x is a local name of the function f() namespace and it is not recognised by the “print” statement in the main script even after the function call

42. >>> def g():... global x... x = 200... return x... >>> print x Traceback (most recent call last): File " ", line 1, in NameError: name 'x' is not defined >>> g() 200 >>> print x 200 >>> The variable x, defined in the body of the g() function, is made global using the “global” statement but is recognised by the “print” statement in the main script only after the function call

43. >>> y = "ACCTGGCACAA" >>> def h():... print y... >>> h() 'ACCTGGCACAA' y is recognised when h() is called as it is a global name.

44. The number of arguments can be variable (i.e. can change from one function call to the other); in this case, you can use * or ** symbols. 1 st case(*args) => tuple of arguments 2 nd case(**args)=> dictionary of arguments >>> def print_args(*args):... print args... return... >>> print_args(1,2,3,4,5) (1, 2, 3, 4, 5) >>> print_args("Hello world!") (‘Hello world!’,) >>> print_args(100, 200, "ACCTGGCACAA") (100, 200, ‘ACCTGGCACAA’) >>> def print_args2(**args):... print args... return... >>> print_args2(num = 100, num2 = 200, seq = "ACCTGGCACAA") {'num': 100, 'seq': 'ACCTGGCACAA', 'num2': 200}