1. CS190/295 Programming in Python for Life Sciences: Lecture 4
Instructor: Xiaohui Xie
University of California, Irvine

2. Announcements
Homework assignment #2 is out, due on Jan 31 (Tue) before class
Jake will lead a lab session this Thursday (Jan 26). Bring your laptop.

3. Computing with Strings

4. The String Data Type
A string is a sequence of characters

5. The String Data Type A string is a sequence of characters
Remember that the input statement treats whatever the user types as an expression to be evaluated

6. Indexing of the String A string is a sequence of characters
Individual characters can be accessed through the operation of indexing. The general form for indexing is <string>[<expr>].

7. Slicing of the String A string is a sequence of characters
Access a contiguous sequence of characters or substring from a string is called slicing. The general form for slicing is <string>[<start>:<end>].
Both start and end should be int-valued expressions. A slice produces the substring starting at the position given by start and running up to, but not including, position end.

8. The string data type is immutable

9. Operations for putting strings together
+ concatenation
* repetition

10. Summary of basic string operations

11. Example: single string processing

12. String Representation
How does a computer represent strings?
Each character is translated into a number, and the entire string is stored as a sequence of (binary) numbers in computer memory.
It doesn’t really matter what number is used to represent any given character as long as the computer is consistent about the encoding/decoding process.
One important standard , called ASCII, uses the numbers 0 through 127 to represent the characters typically found on a computer keyboard. For example, the capital letters A–Z are represented by the values 65–90, and the lowercase versions have codes 97–122.
UniCode is an extended standard to include characters of other written languages

13. The String Library
split - This function is used to split a string into a sequence of substrings. By default, it will split the string wherever a space occurs

14. The String Library

15. The eval() function
eval - This function takes any string and evaluates it as if it were
a Python expression.

16. Converting Numbers to Strings

17. String Formatting
Notice that the final value is given as a fraction with only one decimal place. How to output something like $1.50 ?
You can do this by using the string formatting operator:

18. String Formatting The string formatting operator is used like this:
<template-string> % (<values>)
% signs inside the template-string mark “slots” into which the values are inserted. There must be exactly one slot for each value. Each of the slots is described by a format specifier that tells Python how the value for that slot should appear.
A formatting specifier has this general form:
%<width>.<precision><type-char>
type-char: decimal, float, or string
width: how many spaces are used to display the value? If a value requires more room than is given in width, Python will just expand the width so that the value fits.
precision: used with floating point values to indicate the desired number of digits after the decimal.

19. String Formatting

20. Multi-Line Strings Special characters:
’\n’ - newline (as if you are typing <Enter> key on your keyboard
’\t’ - <Tab>

21. File Processing
Three Key steps of file-processing in all programming languages:
Associate a file on disk with a variable in a program. This process is called opening a file. Once a file has been opened, it is manipulated through the variable we assign to it.
Define a set of operations that can manipulate the file variable. At the very least, this includes operations that allow us to read the information from a file and write new information to a file.
When we are finished with a file, it is closed. Closing a file makes sure that any bookkeeping that was necessary to maintain the correspondence between the file on disk and the file variable is finished up. (For example, if you write information to a file variable, the changes might not show up on the disk version until the file has been closed.)

22. File Processing: open a file
Associate a file on disk with a variable in a program. This process is called opening a file. <filevar> = open(<name>, <mode>) mode: “r” for read, “w” for write Example: infile = open(“numbers.data”,”r”) Now we can use the variable inflie to read the contents of numbers.data from the disk.

23. File Processing: read
Once a file is open, Python provides three related operations for reading information from a file:
<filevar>.read()
Returns the entire contents of the file as a single string. If the file contains more than one line of text, the resulting string has embedded newline characters between the lines
<filevar>.readline()
read one line from a file (read all the characters up through the next newline character); the string returned by readline will always end with a newline character
<filevar>.readlines()
returns a sequence of strings representing the lines of the file

24. File Processing: read

25. File Processing: write
Open a file for output:
Outfile = open(“mydata.out”, “w”)
A word of warning: if a file with the given name does exist, Python will delete it and create a new, empty file.
Put data into a file using the write operation:
<file-var>.write(<string>)

26. Coming Attraction: Objects
Notice the operations of the file processing are in the format of:
infile.read()
infile.close()
which are different from the normal function applications such as abs(x)
In Python, a file is an example of an object. Objects combine both data and operations together. An object’s operations, called methods, are invoked using the dot notation.
Notice that strings are also objects in Python. You can invoke methods of strings:
myString.split()
Is equivalent to
string.split(myString)

27. Defining Functions

28. Functions, Informally
You can think of a function as a subprogram—a small program inside of a program. The basic idea of a function is that we write a sequence of statements and give that sequence a name. The instructions can then be executed at any point in the program by referring to the function name.
The part of the program that creates a function is called a function definition. When a function is subsequently used in a program, we say that the definition is called or invoked.
A single function definition may be called at many different points of a program.

29. Functions – simple example
Examples: “Happy Birthday” song. The standard lyrics look like this. Happy birthday to you! Happy birthday, dear <insert-name>.

30. Functions – simple example

31. Parameters of a function

32. Functions and Parameters
A function definition looks like this:
A function is called by using its name followed by a list of actual parameters or arguments
A function can have several parameters (arguments):
The actual parameters are matched up with the formal parameters by position
def <name>(<formal-parameter-1>,…,<formal-parameter-n>)
<name>(<actual-parameter-1>,…,<actual-parameter-n>)

33. When a function is called
When Python comes to a function call, it initiates a four-step process.
The calling program suspends at the point of the call.
The formal parameters of the function get assigned the values supplied by the actual parameters in the call.
The body of the function is executed.
Control returns to the point just after where the function was called.

34. Functions with return values
Using return statement:

35. Functions can return more than one value
When calling this function, place it in a simultaneous statement:

36. Part I: Decision structures
Control Structures
Part I: Decision structures

37. Motivation
So far, we have viewed computer programs as sequences of instructions that are followed one after the other. Sequencing is a fundamental concept of programming, but alone, it is not sufficient to solve every problem.
Often it is necessary to alter the sequential flow of a program to suit the needs of a particular situation. This is done with special statements known as control structures.
Decision structures, one type of control structures, are statements that allow a program to execute different sequences of instructions for different cases,

38. An example: temperature warning
Suppose now we want to enhance the program by providing temperature warning like this:

39. Flowchart of the temperature conversion program with warning

40. The temperature conversion program with warning
decision structure

41. Simple if-statement
Control flow of simple if-statement:

42. Forming simple conditions
Simple conditions that compare the values of two expressions:
<expr> <relop> <expr>
<relop> is short for relational operator. There are six relational operators in Python:
Conditions may compare either numbers or strings. When comparing strings, the ordering is lexicographic. Basically, this means that strings are put in alphabetic order according to the underlying ASCII codes. So all upper-case letters come before lower case letters (e.g., “Bbbb” comes before “aaaa”, since “B” precedes “a”).

43. Boolean expression
Conditions are actually a type of expression, called a Boolean expression
When a Boolean expression is evaluated, it produces a value of either True (the condition holds) or False (it does not hold).

44. Boolean operators
Python provides three Boolean operators: and, or and not.
The Boolean operators and and or are used to combine two Boolean expressions and produce a Boolean result.
<expr> and <expr>
<expr> or <expr>
The and of two expressions is true exactly when both of the expressions are true.
The or of two expressions is true when either expression is true
The not operator computes the opposite of a Boolean expression. It is a unary operator, meaning that it operates on a single expression.

45. Precedence of Boolean operators
Build arbitrarily complex Boolean expressions using Boolean operators
Consider this expression:
a or not b and c
Python follows a standard convention that the order of precedence is: not, followed by and, followed by or. So the expression would be equivalent to this parenthesized version.
(a or ((not b) and c))
I suggest that you always parenthesize your complex expressions to prevent confusion.

46. Two-way decisions: if-else statement
When the Python interpreter encounters this structure, it will first evaluate the condition.
If the condition is true, the statements under the if are executed.
If the condition is false, the statements under the else are executed.
In either case, control then passes to the statement following the if-else

47. Two-way decisions: example

48. Two-way decisions: an example

49. Multi-way decisions: if-elif-else
Python will evaluate each condition in turn looking for the first one that is true. If a true condition is found, the statements indented under that condition are executed, and control passes to the next statement after the entire if-elif-else.
If none of the conditions are true, the statements under the else are performed.
The else clause is optional; if omitted, it is possible that no indented statement block will be executed.

50. Control Structures
Part 2: Loop Structures

51. For Loops It allows us to iterate through a sequence of values
The loop index variable var takes on each successive value in the sequence, and the statements in the body of the loop are executed once for each value.

52. For Loop example: computer the average of a series of numbers

53. Indefinite Loops: while-statement
An indefinite loop keeps iterating until certain conditions are met.
Here condition is a Boolean expression, just like in if statements. The body is, as usual, a sequence of one or more statements.
The body of the loop executes repeatedly as long as the condition remains true. When the condition is false, the loop terminates

54. Indefinite loop example: computing the average of a series of numbers

55. Indefinite loop example: computing the average of a series of numbers
Another implementation:

56. File Loops
One disadvantage of all the averaging programs presented so far is that they are interactive. A better approach to the problem is to type all of the numbers into a file. The data in the file can be perused and edited before sending it to a program that generates a report.

57. File Loops
One potential problem with readlines()is that the entire contents of the file are first read into main memory.
With very large data files, it is better to read and process small sections of the file at a time. In the case of text files, a simple approach is to process the file one line at a time
The readline method gets the next line from a file as a string. When we come to the end of the file, readline returns an empty string.

58. Nested Loops
Again in the number averaging example, suppose instead of one-per-line we allow any number of values on a line, separated by comma.

59. Post-Test Loop
Suppose you are writing an input algorithm that is supposed to get a nonnegative number from the user. If the user types an incorrect input, the program asks for another value. It continues to reprompt until the user enters
a valid value. This process is called input validation.
Here is a simple algorithm:
repeat
get a number from the user
until number is >= 0

60. Post-Test Loop
Python does not have a statement that directly implements a post-test loop. However you can implemented with a while statement using the trick of “seeding”:
Or use the break statement:

61. Data Collections

62. Most real-world programs deal with large collections of data
A few examples:
Words in a document.
Students in a course.
Data from an experiment.
Customers of a business.
Graphics objects drawn on the screen.
Cards in a deck.

63. Example problem: simple statistics
Extend this program so that it computes not only the mean, but also the median and standard deviation of the data

64. Lists
Lists are ordered sequences of items, a collection of values denoted by the enclosing square brackets
Lists can be created by listing items inside square brackets

65. Lists vs. Strings
In Python strings and lists are both sequences that can be indexed. In fact, all of the built-in string operations that we discussed previously are sequence operations and can also be applied to lists:

66. Lists vs. Strings: differences
The items in a list can be any data type, including instances of programmer-defined classes. Strings, obviously, are always sequences of characters.
Second, lists are mutable. That means that the contents of a list can be modified. Strings cannot be changed “in place.”

67. List operations
Python lists are dynamic. They can grow and shrink on demand. They are also heterogeneous. You can mix arbitrary data types in a single list. In a nutshell, Python lists are mutable sequences of arbitrary objects. This is very different from arrays in other programming languages.
A list of identical items can be created using the repetition operator.
Typically, lists are built up one piece at a time using the append method.

68. List operations: remove elements

69. List operations

70. Using lists is easy if you keep these basic principles in mind
A list is a sequence of items stored as a single object.
Items in a list can be accessed by indexing, and sublists can be accessed by slicing.
Lists are mutable; individual items or entire slices can be replaced through assignment statements.
Lists will grow and shrink as needed.

71. Statistics with Lists
# get a list of numbers and store in a list

72. Statistics with Lists: Mean

73. Statistics with Lists: Standard Deviation

74. Statistics with Lists: Median

75. Simple Statistics: put together

76. Non-sequential collections
Dictionary is a build-in data type for non-sequential collections in Python.
Python dictionaries are mappings: Keys -> values
A dictionary can be created by listing key-value pairs inside a curly braces.
We can access the value associated with a particular key using:
Dictionaries are mutable:

77. Dictionary Operations
You can also extend a dictionary by adding new entries
In fact, a common method for building dictionaries is to start with an empty collection and add the key-value pairs one at a time

78. Dictionary Operations

79. Dictionary methods: exammples