PYTHON LECTURE OUTLINE
BME 205, Fall 2010
Contact: auzilov@ucsc.edu


(0) Disclaimers and Background

We will probably run out of time; can continue in a workshop outside of class.

Why Python?
    - Easy for beginners, but many advanced features.
    - Consistent syntax (more or less).
    - Good for prototyping (fast to write).
    - Good for debugging (e.g. stack traces).
    - Powerful standard library:
        - unit tests (module "unitest")
        - profiler (module "profile")
        - regular expressions (module "re")
        - iterators (module "itertools")
        - tests of docstring-embedded examples (module "doctest")
        - and many more!
    - Widely adopted, including by bioinformatics community.
    - Thriving development community for language itself and associated tools

But remember: there is no "one true/best language"; you will have to
learn others.

Several Python implementations: CPython, Jython, IronPython, etc.


(1) Resources

- docs.python.org
  - "index" is most useful
  - "Library Reference" is next in usefulness
- These are the most relevant pages for BME205 Assignment #1:
    Tutorial docs:
      http://docs.python.org/tutorial/interpreter.html
      http://docs.python.org/tutorial/introduction.html
      http://docs.python.org/tutorial/controlflow.html
      http://docs.python.org/tutorial/inputoutput.html
    Understanding strings (and more generally, sequences):
      http://docs.python.org/library/stdtypes.html#string-methods
      http://docs.python.org/library/stdtypes.html#string-formatting-operations
      http://docs.python.org/library/stdtypes.html#sequence-types-str-unicode-list-tuple-buffer-xrange
    Useful standard library modules:
      http://docs.python.org/library/string.html
      http://docs.python.org/library/re.html
      http://docs.python.org/library/sys.html
- Python in a Nutshell (useful for advanced users only)

emacs/aquamacs packages John St. John likes:
    http://www.emacswiki.org/emacs/AutoComplete
    - easy to install
    - will look in current buffer to append to current dictionary on-the-fly
    - comes with Python dictionary, but can extend with other dictionaries, e.g.
        YaSnippet (http://code.google.com/p/yasnippet/)
    - but nontrivial to integrate YaSnipped with AutoComplete, although possible


(2) Starting it up

- Python versions: do NOT use 3.x yet!
- Python installation on SOE machines (refer to Kevin for this one)
- Command-line interpreter
  - using it as a calculator; basic caveats about type conversion
  - getting help:
  - whitespace only matters for indentation
  - history (readline support)
  - Ctrl+D to exit


(3) Python types and interpreter features

- type overview
  - int, float, list, string, tuple, dict, None

- basics: int and float

- an aside about the Python data model
  - everything is a reference; the object to which we refer has the type
  - what is an object?  what is a method?  why not just use functions?
  - the concept of "binding": associating a name to a reference
  - re-binding: powerful but dangerous!
    - caveat about re-binding built-in functions like "type" and "chr" and "next":
        see http://docs.python.org/library/functions.html
        and http://docs.python.org/library/stdtypes.html
      - or use interpreter to tell if a built-in function or type
- caveats about "modifying" a reference
  - you don't modify references other than re-binding;
    you modify the object TO WHICH the reference(s) point

- help() function, takes strings or references:
    help ('help')
    help (help)  # same, as long as name is bound to a reference
    help ('modules')
    x = 205
    help (x)
    s = 'some arbitrary string'
    help (s.rstrip)  # help on object methods

- some standard types
  (with special attention paid to the binding/reference model)
  - see http://docs.python.org/reference/datamodel.html#the-standard-type-hierarchy
  - always keep in mind: is object of this type mutable or immutable?
     iterable or not iterable?

  - None type

  - sequences: mutable and immutable

    - lists (mutable):
      - creating
      - .append()
      - .sort() versus sorted()
        - in place (no return value) versus new copy returned
        - sorting 'listOrig' and 'listNew' (test understanding of references)
      - min() and max()
      - an aside: method versus function
      - looking at contents; modifying contents
      - lists store REFERENCES (which can get rebound)
      - slices
        - I will not cover this --- see additional notes instead (BME_205_Python_lecture_code.txt)
      - list comprehensions
        - only in Python 2.5 or newer!

    - strings (immutable): single versus double quotes
      - all slice operations on lists can also be done on strings
      - some string methods: {l,r}strip, join, replace

    - tuples (immutable)
      - useful for:
        - string formatting (will cover later)
        - as keys to dictionaries

    - dictionaries
        - I will not cover this --- see additional notes instead (BME_205_Python_lecture_code.txt)

  - brief note about other types: dictionaries, sets, modules, callables, classes, files, etc.


(4) Printing and string formatting

- print keywords
- string formatting with % operator and tuples


(5) Writing your first Python program (BME_205_Python_lecture_firstProg)

- shebang
- chmod

Two ways to run a Python program:
    - use shebang to locate interpreter:
            ./progName
    - ignore shebang, specify explicitly which Python interpreter to
      use (also ignores chmod +x setting):
            python progName
            /usr/bin/python progName

- comments and docstrings
- imports
- sys module
  - sys.argv
  - sys.exit()
- printing to STDOUT, STDERR
- loops over input
- conditionals and whitespace/indentation
- assert


(6) Writing a more advanced Python program (BME_205_Python_lecture_secondProg)


(7) Questions and feedback

- another workshop outside of class time?