1. Programming: Input and Output in Python Bruce Beckles University of Cambridge Computing Service Day One

2. 2 Introduction ● Who: – Bruce Beckles, e-Science Specialist, UCS ● What: – Programming: Input and Output in Python course, Day One – Part of the Scientific Computing series of courses ● Contact (questions, etc): – escience-support@ucs.cam.ac.uk escience-support@ucs.cam.ac.uk ● Health & Safety, etc: – Fire exits Please switch off mobile phones!

3. 3 Related/Follow-on courses “Programming: Checkpointing in Python”:Programming: Checkpointing in Python – More robust Python programs that can save their current state and restart from that saved state at a later date – “Programming: Input and Output in Python” is a pre-requisite for the “Programming: Checkpointing in Python” course “Pattern Matching Using Regular Expressions”:Pattern Matching Using Regular Expressions – Understanding and constructing regular expressionsregular expressions “Programming: Gnuplot for Simple Graphs”:Programming: Gnuplot for Simple Graphs – Using gnuplot to create graphical output from datagnuplot

4. 4 Pre-requisites ● Ability to use a text editor under Unix/Linux: – Try gedit if you aren’t familiar with any other Unix/Linux text editors ● Basic familiarity with the Python language (as would be obtained from the “Programming: Python for Absolute Beginners” course):Programming: Python for Absolute Beginners – Interactive and batch use of Python – Basic concepts: variables, flow of control, functions – Simple data manipulation – Simple file I/O (reading and writing to files) – Structuring programs (using functions, modules, etc)

5. 5 Start a shell

6. 6 Screenshot of newly started shell

7. 7 Python Interpreter on PWF Linux

8. 8 Python Interpreter: initial screen

9. 9 Input and Output 1. Files 3. The command line 2. Standard input and output

10. 10 input data file Python script output data file > command output

11. 11 input data file Python script output data file input data file input data file output data file output data file

12. 12 Reading a file 3. Closing the file 1. Opening a file 2. Reading from the file

13. 13 Opening a file 'data.txt' line one\n line two\n line three\n line four\n filesystem node position in file type: file file name type: string the data on disc

14. 14 'data.txt' >>> data = open () file nametype: string Python command Python file object type: file refers to the file with name 'data.txt' initial position at start of data

15. 15 >>>data= open('data.txt') >>> data.readline() the Python file object a dot a “method” 'line one\n' first line of the file complete with “\n” >>> 'line two\n' data.readline() same command again second line of file Reading a file

16. 16 >>> data = open('data.txt') line one\n line two\n line three\n line four\n data position: start of file

17. 17 >>> data = open('data.txt') line one\n line two\n line three\n line four\n >>> data.readline() 'line one\n' data position: after end of first line, at start of second line

18. 18 >>> data = open('data.txt') line one\n line two\n line three\n line four\n >>> data.readline() 'line two\n' >>> data.readline() 'line one\n' data position: after end of read data, at start of unread data

19. 19 >>>datareadlines(). [ 'line three\n', 'line four\n' ] >>>datareadline(). 'line one\n' >>>datareadline(). 'line two\n' remaining unread lines in the file

20. 20 >>> data = open('data.txt') line one\n line two\n line three\n line four\n >>> data.readlines() [ 'line three\n', 'line four\n' ] >>> data.readline() 'line one\n' >>> data.readline() 'line two\n' data position: at end of file

21. 21 data >>> data.readlines() [ 'line three\n', 'line four\n' ] >>> data.close() disconnect Closing a file

22. 22 >>> data.readlines() [ 'line three\n', 'line four\n' ] >>>data.close() >>> del data delete the variable if we aren't going to use it again

23. 23 Common trick Python “magic”: treat the file like a list and it will behave like a list for line in data.readlines(): stuff for line in data: stuff

24. 24 Putting it all together in a function 1.Take a file name as the function argument. 2.Read a file of “key/value” lines. 3.Create the equivalent dictionary. 4.Return the dictionary. Hhydrogen Hehelium Lilithium Beberyllium Bboron elements.txt

25. 25 1. Create an empty dictionary. 2. Open the file. 3. For each line in the file: 3a. Split the line into two strings (key & value). 3b. Add the key and value to the dictionary. 4. Close the file. 5. Return the dictionary. The function

26. 26 utils.py def file2dict(filename): dict = {} data = open(filename) for line in data: [ key, value ] = line.split() dict[key] = value data.close () return dict Simple, really.

27. 27 #!/usr/bin/python import utils elements = utils.file2dict('elements.txt') utils.print_dict(elements) mkdict.py

28. 28 >>> data = open('output') Traceback (most recent call last): File " ", line 1, in ? IOError: [Errno 2] No such file or directory: 'output' What if something goes wrong? data.txt output >>> data = open('data.txt') >>> data.readlines() Traceback (most recent call last): File " ", line 1, in ? IOError: [Errno 13] Permission denied

29. 29 >>> data = open('output') Traceback (most recent call last): File " ",line 1, in ? IOError:No such file or directory “Traceback”: the command's history “stdin”: “standard input” = the terminal Only one line of command Type of exception (error) Error message : 'output' [Errno 2] Error number

31. 31 def file2dict(filename): import sys dict={} try: data = open(filename) for line in data: [ key, value ] = line.split() dict[key] = value data.close() except IOError: print "Problem with file %s" % filename print "Aborting!" data.close() sys.exit(1) return dict utils.py

32. 32 >>> import utils >>> mydict = utils.file2dict('output') Problem with file output Aborting! Traceback (most recent call last): File " ", line 1, in ? File "utils.py", line 82, in file2dict data.close() UnboundLocalError: local variable 'data' referenced before assignment

33. 33 def file2dict(filename): import sys dict={} data = None try: data = open(filename) for line in data: [ key, value ] = line.split() dict[key] = value data.close() except IOError: print "Problem with file %s" % filename print "Aborting!" if type(data) == file: data.close() sys.exit(1) return dict utils.py

34. 34 >>> import utils >>> mydict = utils.file2dict('output') Problem with file output Aborting! >

35. 35 def file2dict(filename): import sys dict={} data = None try: data = open(filename) for line in data: [ key, value ] = line.split() dict[key] = value data.close() except IOError, error: (errno, errdetails) = error print "Problem with file %s: %s" % (filename, errdetails) print "Aborting!" if type(data) == file: data.close() sys.exit(1) return dict utils.py

36. 36 >>> import utils >>> mydict = utils.file2dict('output') Problem with file output: No such file or directory Aborting! >

37. 37 >>> line = "Too many values" >>> [ key, value ] = line.split() Traceback (most recent call last): File " ", line 1, in ? ValueError: too many values to unpack >>> line = "notenough!" >>> [ key, value ] = line.split() Traceback (most recent call last): File " ", line 1, in ? ValueError: need more than 1 value to unpack

38. 38 What about output? input=open('input.txt') 'r' input=open('input.txt'), 'w' output=open('output.txt'), equivalent open for reading open for writing

39. 39 Opening a file for writing 'output.txt' filesystem node position in file empty file start of file

40. 40 >>>output=open( 'output.txt', 'w ' ) file nameopen for writing

41. 41 >>>output=open('output.txt','w ' ) >>>output. write ( 'alpha\n' ) alpha\n method to write a lump of data lump of data to be written lump: not necessarily a whole line

42. 42 >>>output=open('output.txt','w ' ) >>>output.write( 'bet' ) alpha\n bet >>>output.write('alpha\n') lump of data to be written

43. 43 >>>output=open('output.txt','w ' ) >>>output.write( 'a\n' ) alpha\n beta\n >>>output.write('alpha\n') >>>output.write('bet') remainder of the line

44. 44 >>>output=open('output.txt','w ' ) >>>output. writelines ( 'a\n' ) alpha\n beta\n gamma\n delta\n >>>output.write('alpha\n') >>>output.write('bet') >>>output.write( ['gamma\n', 'delta\n'] ) method to write a list of lumps the list of lumps (typically lines)

45. 45 >>>output=open('output.txt','w ' ) >>>output. writelines( 'a\n' ) >>>output.write('alpha\n') >>>output.write('bet') >>>output.write( ['gamma\n', 'delta\n'] ) >>>output. close() Python is done with this file. Only at this point is it guaranteed that the data is on the disc!

46. 46 Accessing the system 1. Files 3. The command line 2. Standard input and output The “sys” module

47. 47 The “sys” module >>> import sys Access to general “system” things Standard input and output The command line Information about the Python environment

48. 48 command.py<input.dat>output.dat Python script as a command Standard input from input.dat Standard output to output.dat

49. 49 Inside the python script import sys sys.stdin sys.stdout “standard output” “standard input” import the module treat exactly like an open(…, 'r') file treat exactly like an open(…, 'w') file

50. 50 So, what does this script do? #!/usr/bin/python import sys for line in sys.stdin: sys.stdout.write(lin e) Read lines in from standard input Write them out again to standard output It copies files, line by line

51. 51 ● Access to files ● Opening ● Reading/writing ● Closing ● sys module ● standard input ● standard output

52. 52 > curve.py0.25 Command line arguments Python script as a command Single command line argument

53. 53 curve.py #!/usr/bin/python import sys sys.argv print import the sys module sys.argv — the command line arguments argument values

54. 54 >curve.py0.25 [ '/home/rjd4/bin/curve.py', '0.25' ] The file name of the script itself The command line argument as a string! sys.argv[0] sys.argv[1]

55. 55 curve.py #!/usr/bin/python import sys sys.argv[1] print sys.argv[1] — the 1 st command line argument

56. 56 >curve.py0.25 '0.25' 1 st command line argument as a string

57. 57 0.25 '0.25' string float printfloat('0.25')

58. 58 curve.py #!/usr/bin/python import sys sys.argv[1]print float() float() converts strings to floats float() converts things to floats

59. 59 >curve.py0.25 1 st command line argument as a float

60. 60 2a.Write a function that parses the command line for a float and an integer. #!/usr/bin/python import sys def parse_args(): pow = float(sys.argv[1]) num = int(sys.argv[2]) return (pow, num) def power_curve(pow, num_points): … curve.py

61. 61 2b.Write a script that tests that function. #!/usr/bin/python …functions… # power_curve(0.5, 5) (r, N) = parse_args() print 'Power: ', r, type(r) print 'Points: ', N, type(N) > curve.py 0.5 5 Power: 0.5 Points: 5 ✔ Right values Right types ✔ curve.py

62. 62 3.Combine the two functions. #!/usr/bin/python …functions… …tests (commented out)… (pow, num) = parse_args() power_curve(pow, num) curve.py

63. 63 Any questions?