Ed's Big Plans

Python Crash Course is a Practical Python Programming Programme for Pragmatic People

Last Offering

• 2010: January, February.

Lecture 1 [download slides (pdf)]: A Mad Mad Intro – Using Python in Interactive Mode

• Downloading, Installing, Running Python (Windows, Mac, Linux)
• Windows Users: See this tutorial to set DOS path environment variable (external link) — makes Python by typing “python” in console
• Python as a console calculator
• The print statement
• Variables
• A little on Exceptions and a Preview of Functions and Conditionals

Lecture 2 [download slides (pdf) | download all scripts.py (tgz)]: Finishing a Mad Mad Intro

• Introduces features beginners and pros alike should know (conditionals, loops, functions, lists, tuples)
• Scripts that are discussed and modules that they need (put them all in the same folder)
  • main.py, pointless.py, pccInput.py, pccMathModule.py
• Scripts for the sneak preview (GUI example, put them in the same folder as pccMathModule.py above)
  • mainx.py, pccGuiModule.py
  • Instructions:
    1. Run mainx.py
    2. Fill in any Four fields out of Five fields with numbers
    3. Hit the button!
• Full GUI / Object Orientation explanation in Lecture 4.

Lecture 3 [download slides (pdf) | download related files (tgz | zip) | solution script (py)]: Intro to Handling Files and Humans

• Dictionaries and Exceptions
• Beginning file handling (open())
• About the files in the archive (note: the csvmain.py puzzle was solved in class because of its difficulty):
  • Instructions for argvmain.py:
    1. Run argvmain.py using “python argvmain.py“
    2. Now try running it with a few arguments, e.g. “python argvmain.py The cow eats grass!“
    3. Look at the script and notice that the sys.argv variable is a list that contains the arguments!
  • Instructions for csvmain.py:
    1. Run it using “python csvmain.py igem_strain_list.csv” to see what happens–
       • it should create make a file “output.txt” filled with question marks!
       • Note: more instructions are in the comment at the start of the file
    2. There are several blanks in the file labelled “FILL_IN_THE_BLANK“, your job is to fix the script!
    3. Replace the the variable “FILL_IN_THE_BLANK” with other previously defined variables in the script.
    4. Solutions will be posted soon– next week’s puzzles will be a lot easier!
       • Original script with blanks: csvmain.py
       • Working solution script: csvmain_solved.py

Lecture 4 [download related files (tgz | zip) -- does not include PDBs or SDFs]: In Stark Review

• A review of everything we’ve done so far
• Continuing file handling (close())
• Five smaller, more manageable exercises
  • puzzle0.py
  • puzzle1.py
  • puzzle2.py
  • puzzle3.py
    • 2OVC.pdb (external link) care of RCSB Protein Data Bank
    • do a text search (CTRL + F or APPLE + F) for “download files”.
      
  • puzzle4.py
    • CID_6305.sdf (external link) care of The PubChem Project
    • scroll to the bottom of the page and click on the button labeled “SDF”, then “3D SDF: Save”.
      
• Cheating with POSIX pipes (sys.stdin, sys.stdout)
• Command line arguments (sys.argv)

Lecture 5 [download slides (pdf)]: Regular Expressions and List Comprehension

• Regular expressions offer powerful degenerate string searching, extracting and replacing facilities
• List comprehension is syntactic sugar for list generation
• We also cover higher order functions and how filter, map, fold appears in Python

Future Items: OOP and Python software I’d like to cover in future incarnations of this course

• Object orientation is the backbone of coding Python GUIs
• Classes
• Most of the code is provided, students will stitch the code together (beginners won’t be fazed)
• Touches on new features for advanced students (object orientation, GUIs, modules)
• SciPy, NumPy modules for advanced mathematical functions
• PyMol software for chemistry (end user AND API)
• Chimera software (I’m currently learning it for CS683)
• Address concerns about style, efficiency: exceptions vs. conditionals (e.g. {}.has_key() vs. except KeyError)