week7.md

Week 7 Outline

Reading

• It will be increasingly important to keep up with reading from Practical Computing and other supplementary sources.
• For this week, take a look at Chapters 7 and 8.

Final Project

• We'll talk about these in more detail after Fall Break, but now is an important time to start thinking about what you want to work on.
• As we develop our skills in Python, you should start thinking about how to use your new skills to meet the goals of your project
• Here are some broad questions to start answering:
  • What area of biology would you like to explore?
  • What types of data might be collected and analyzed for studies in this area?
  • Do you want to write code that would analyze data? Or provide new visualizations? Or simulate data?
  • Try looking through the primary literature for ideas. Google Scholar or the Web of Science are good tools for exploring.

Introduction to Python

• What is Python?

  • Interpreted, high-level language
  • Very popular among computational biologists
  • Perhaps the most "human readable" programming language
  • One of the few languages where line indentation is actually interpreted as part of the code
  • Python is much less picky than bash about spacing within lines, though
  • Dynamically typed (we'll get to this later)

• Getting Python Up and Running

  • Your VM comes with Python natively as part of its Ubuntu Linux distribution
  • However, by default the name python is associated with version 2. In this class, we'll be using version 3.
  • To update where the name python points, run this command: sudo ln -sf /usr/bin/python3.6 /usr/bin/python
  • Now when you type python on the command line, you should see a line at the top indicating that you're running Python 3.6.5.
  • You are now running Python interactively!

• Basic Python Data Types

  • Numbers
    • Note that, unlike bash, Python can handle both integers and floating point (decimal) numbers.
    • Integers - myInt = 10
    • Floating point numbers (decimals) - myFloat = 3.21312
    • Define myInt and myFloat as above. Now calculate myInt / myFloat. What type of number is the result?
    • Now try float(myInt) and int(myFloat). What are the results? Look back at the values of myInt and myFloat. Have they changed?
    • Changing numbers from one type to another is one form of "type casting".
  • Strings - myStr = "This is a string."
    • Strings can be of any length, but are always defined with quotes.
    • Individual characters, or subsets of characters, can be accessed using square brackets - []
      • String indices (and all indices in Python) start at 0
      • myStr = "biology"
      • myStr[0]
      • A range of indices can be defined with a colon
      • myStr[2:5]
    • Strings can be concatenated together with the + operator.
      • myStr = "biology"
      • newString = myStr + "_is_super_interesting"
      • newString
  • Booleans - True or False
    • These variables can take the values True or False only.
      • myBool = True
    • These are the data types used in things like if...else statements and while loops.
    • Logical statements, like myNum > 3 or myStr == "test", return a boolean variable indicating the result of the comparison
    • In Python, the value of a Boolean can be reversed by preceding it with not.

• String Formatting

  • Python has a special way to format strings so that the values of variables can be included
  • The operator % is used to indicate that the values of certain variables should be used to fill in a string
  • The parts of the string where the values should go is indicated with placeholders (kinda like wildcards)
  • The three most basic placeholders are:
    • %d - An integer
    • %f - A floating point number (i.e., a decimal)
    • %s - A string
  • Try this:
    • faveInt = 7
    • faveFloat = 3.14
    • faveString = phyleaux
    • print("Favorite integer is %d, favorite float is %f, and favorite string is %s." % (faveInt,faveFloat,faveString))
  • Note how the variables holding the values are provided in the same order inside parentheses after the %.

• Functions

  • Functions are the verbs of a programming language
  • Functions take some variables or objects as input (arguments) and either do something with them or return a new variable/object.
  • Functions are always written like this - myFunction(object1,object2,...)
  • They always have parentheses, even if they don't need any arguments to be passed to them
    • For example, myFunction()
  • The number and type of arguments needed is specific to each function
  • Perhaps the simples function to use is print(). print() can take an arbitrary number of variables as arguments and will print them to the screen.
  • Here are a few other really useful functions and what they do:
    • len(string) - Takes one argument (a string) and returns its length
    • abs(number) - Takes one argument (either an integer or a float) and returns its absolute value
    • round(float) - Takes one floating point number as an argument and rounds it to the nearest integer
    • type(variable) - Takes one variable as an argument and returns its type

• Methods

  • Methods are functions (sort of like actions or verbs) that belong to a variable
  • Methods are accessed and used by appending them to the name of a variable, separated by a .
  • For instance, let's say we define a string - myStr = "biOLogy ". Here are some really useful methods that can be used with that string:
    • myStr.upper() - Converts all characters in the string to uppercase
    • myStr.lower() - Converts all characters in the string to lowercase
    • myStr.strip() - Removes whitespace from the beginning or ending of the string
    • Methods can also be chained! - myStr.strip().lower()
    • myStr.replace("y","ical") - This method functions like find and replace, where the first argument is the text to find and the second argument is the text to use when replacing.
    • myStr.split("O") - Breaks up the string, using the character provided as an argument as the delimiter. This method then returns a list of new strings. We'll talk more about lists later.

• Creating a Python Script

  • Python scripts can be created in a similar way to bash scripts
  • Open a blank text file and add a "shebang" line at the top
    • #!/usr/bin/env python
  • Add some Python code to the file
  • Print something to the screen using the print() command.
  • Add execute permissions to the file with chmod
  • Execute the script in Terminal

• Comments in Python

  • Especially now that we will be writing more complicated code, comments are essential
  • Comments are included in Python by putting a # at the beginning of a line.
  • Many text editors have a shortcut keystroke to toggle lines between being commented and uncommented. For instance, check the Edit menu in Atom.
  • # This is an example of a comment

• User Input

  • Python has a special function, input("Message:" ), to accept input from a user.
  • This function reads the user input and returns it. But be sure to store it in a variable!
    • userStr = input("Input some string: ")
  • You can use the string methods outlined above to standardize user input - like stripping out excess whitespace, changing character case, etc.

Additional Resources

• Python
• Software Carpentry - Intro. to Python

Week 7 Assignment (due Tuesday, Oct. 9th)

• Fork this repository, then clone it to your computer
• In the Assignments folder, add the following script.
• Remember the bash script we wrote to count the frequencies of different bases in a DNA sequence? Write a version of this program in Python that prompts the user to provide a DNA sequence and then calculates and prints the relevant values.
• Commit this script to your branch, push it to your fork, and submit a pull request.