lec_1.txt

Bio 133, REBMI
Art Lee
10/10/2008

[ Note: This was a short tutorial that I prepared on Python for the
        Bio 133 students at the Claremont Colleges in the Fall of
        2008.  If you find it useful, feel free to read it.
]


                          P Y T H O N


"Python is a dynamic object-oriented programming language that can be
used for many kinds of software development. It offers strong support
for integration with other languages and tools, comes with extensive
standard libraries, and can be learned in a few days. Many Python
programmers report substantial productivity gains and feel the
language encourages the development of higher quality, more
maintainable code."

      - from the Python Official Website, http://www.python.org -


- Installing Python on your machine:

  I am going to assume that you have access to an installation of
  Python, which would be the case if you are a Bio 133 student.

  If you don't have access to an installation, see Appendix at the end
  of this tutorial (yet to be written - I will wirte it after I finish
  writing this tutorial).  If you can't wait until then and if you are
  using a Windows machine, see the first part of last year's lecture
  notes.  You will find a detailed note on how to install both python
  and ipython there for Windows.  I am pretty sure that the 
  information is still valid.  What I will have in the Appendix will
  basically be a cleaned up version of what I had last year.

  If you are using a Mac OS X machine, you would have a version of
  Python pre-installed on your machine.  Go to a Terminal window and
  try 'python'.  My Mac is OS X 10.5.5 (Leopard) and that is what I am
  using.  

  If you are using another version or a different operating system,
  e.g., Windows, don't worry.  What I am doing in this tutorial should
  be operating system independent.


- Note:

  * This tutorial is operating system independent.  Whether you are
    using python or ipython or some other version of Python on a Unix,
    Linux, Windows, Mac machine, it should not matter.
  
  * You will many program examples in the tutorial.  I expect you to
    try them out using a python system - no exception!  The code
    included in the tutorial has been tested using a python system, a
    Mac OS X 10.5.5.  It should work on your python system as well.


- Learning the language Python

  There is an excellent book that you can read to learn the basics of
  Python and some important concepts in computer science at the same
  time.  It is: 

     How to Think Like a Computer Scientist: Learning with Python
     Allen B. Downey, Jeffery Elkner and Chris Myers [DEM]

  and it is available free online here:

     http://www.ibiblio.org/obp/thinkCSpy/ 


  I found a tutorial online on Python.  It may be a good supplement:
  http://docs.python.org/tutorial/. 



- Several different ways to run the Python interpreter

  1. shell mode

     You start a python session using a terminal window like this:

     see shellmode.txt

     After you see shellmode.txt, come back to this file and continue
     with the rest of the tutorial.  That is how it will work and I
     won't remind you again when I say see xxx again and again below.

  2. script mode

     You would prepare a file containing a Python program and
     execute/run the contents of the script file.

     see scriptmode.txt

  3. Combining shell and script mode

     See the "Modules" section later for detail.



- Basic type of data (values) that programs manipulate

  Note: I am not adding very much explanation on these simple concepts
  since I am assuming that you would already be familiar with them.
  If not, the book by Downey, Elkner, and Myers [DEM] is a good source
  to find more information.  In fact, I would recommend that you keep
  a copy of [DEM] as you read my tutorial.

  . integers: 34, 2, -300, ...

  . floats:   3.4, 2.0, -300.0, 3.14, 4.98090909333, ...

  . strings:  "This is a string of letters", "Hello world!", ...

    Note: Strings are defined by enclosing a string of text in a pair
    of double quotes.  Python as in other languages recognizes them as
    a single entity (value) that can be manipulated much like a number
    (integer or a floating point number).

  . booleans: True, False.
  

- Comments

  # Any line starting with a pound sign (#) is a considered a comment
  # and will be ignored by the Python interpreter.  I will often add
  # my explanation as a comment in a program file as you will see in
  # types.py next.


- Basic types of values we use in Python (or programming in general)

  . see types.py

  . Types such as int, float, boolean are called primitive data
    types.  Later we will see some compound data types.  Actually we
    already saw one: string.  We will see others such as lists and
    tuples and strings in more detail later.


- Variables

  . Storing a value with a name so we can refer to the value
    repeatedly by the name.

  . Updating the value with an assignment operator (=) : Once a value
    is given a name, we can even update the value of the variable by
    assigning a new value as we will see in the example next.

  . see variables.py



- Operating on values: operators and operands

  . combining simple data to form more complex ones

  . see operators.py



- Order of precedence among operations

  . rules on operator precedence

  . same as what you would expect for common operators

    4 + 3 * 2 evaluates to 24, not 14.



- Operations on strings

  . We have alredy seen some of them in operators.py



- Input from keyboard

  . There are two built-in functions for getting keyboard input, and
    they are:

    - rqw_input
    - input

  . see input.py



- Functions

  . see functions.py



- Conditionals: doing it conditionally

  . see conditionals.py



- Loops: doing it multiple times

  . see loops.py




- Compound data types: strings, lists, tuples

  . next lecture