Python - Week 3

Updating to Python 3

To ensure that we're all using the same, recent version of Python, please execute these commands after opening up a Terminal on SuperMike

echo "module load python/3.6.4-anaconda" >> ~/.modules

Then close the browser window with your Terminal, and open a new one. Now open up the Python interpreter using the python command. At the top, it should start with "Python 3.6.4 |Anaconda, Inc.|".

Practice Exercises

A Jupyter notebook with practice exercises for the topics covered this week is available here.

While loops

• Sometimes we want to do something repetitively, but we don't know ahead of time how many times we need to repeat it (as in a for loop.
• In these cases, we can use a while loop. A while loop will continue to do something until a certain condition is no longer satisfied.

num = 0
while num < 10:
    print(num)
    num += 1

• WARNING - You need to make sure to update variables such that the condition will eventually be satisified. If you don't, you could create an infinite loop!

Dictionaries

• Dictionaries are incredibly useful for storing pairs of things - known as "keys" and "values"
• They don't store these pairs in a particular order, like lists do, but they make looking up values from keys much faster.
• The keys and values can each be different types of variables
• To create a new dictionary, you can use this syntax:
  • myDict = {"keyOne":"valueOne", "keyTwo":"valueTwo"}
• To look at the methods available for dictionaries, try this:
  • dir(myDict)
• You can access a value, as long as you know its key, either of these ways:
  • myDict.get("keyOne")
  • myDict["keyOne"]
• You can change a value using its key, this way:
  • myDict["keyOne"] = <NEW_VALUE>
• You can add a new key/value pair using the update method:
  • myDict.update({<NEW_KEY:NEW_VALUE})

Importing libraries and drawing random numbers

• Sometimes it will be helpful to use functionality that's not part of the core python functionality.
• Thankfully, python has a built-in way to import new functions that other people have written to extend the core functions
• Once you know the name of a library, you can use the import command to load it (if it's already been installed).
• One library that we're going to use today is called random.
• Once it's loaded, you'll need to precede any of its functions with random. in order to use them.
• Try this:
  • import random
  • random.random() - Do this a few times
  • random.uniform(0,1) - Do this a few times
  • random.uniform(0,5) - Do this a few times
  • random.choice([5,6,7,8]) - Do this a few times
  • firstList
  • random.shuffle(firstList)
  • firstList
  • random.shuffle(firstList)
  • firstList
  • random.shuffle(firstList)
  • firstList

Reading from files

• To read or write from a file, you'll first need to define the file name
  • e.g., inFileName = "FileToRead.txt"
• However, this is just a string variable with the file name. We need to create an object that can actually read the contents of a file.
• Python has a built-in function to create a file object - open(<FILENAME>,<MODE>)
• The <FILENAME> argument is just a string with the file's name (or path to the file)
• The <MODE> argument tells Python whether we are reading from a file (r), writing to a file (w), or appending to a file (a).
• To open up a new File object to read file contents, use syntax like this:
  • inFile = open(inFileName,'r')
• There are several useful methods associated with file objects, but one of the most commonly used is readline(). This method will read lines one-by-one from the file. Note that the end of line character (\n) is retained when the line is read in.
  • firstLine = inFile.readline()
• Files opened for reading can be used in a for loop, as follows, to go through all the lines in the file:

        for line in file:
            print("Length of line is: %d" % (len(line)))

• Note that line is just a variable name we've chosen to hold each line as we iterate through the file. You can use any variable name you choose, as with any other for loop.

Writing to Files

• Writing to a file is very similar to reading from a file. First, you define an output file name
  • outFileName = "FileToWrite.txt"
• To create a file object to use for writing, we'll again use the open() function, but we'll specify 'w' for the <MODE>.
  • outFile = open(outFileName,'w')
• To write to the file line-by-line, we can use the .write() method.
  • outFile.write("This is a new sentence.\n")
  • Note that the write() method does NOT, by default, add a new line character to strings. If we want to end a line, we have to explicitly include \n.

Command-line Arguments

• As with bash scripts, Python scripts can also take advantage of command-line arguments.
• To easily deal with command-line arguments, we're going to take advantage of some functions in the sys library. So we'll need to start by importing that library:
  • import sys
• Any command-line arguments we pass to a script can then be accessed using the sys.argv variable.
  • print(sys.argv[2])
  • Which argument is printed when you run the line above? Does that make sense with the 0-based indexing in Python?
• We can also loop through all command-line arguments: for arg in sys.argv: print(arg)
• These abilities are very useful in a variety of contexts, but particularly when a set of filenames are provided as command-line arguments and you want to iteratively process each file.

Assignment - Week 9

Open the Jupyter notebook SimulateDNAEvolution.ipynb in this week's repository. In this assignment, you will complete code to simulate random changes in a DNA sequence over time, and then translate the DNA sequence to an amino acid sequence. Fill in the missing code in the notebook and use it to answer the questions. Submit your completed Jupyter notebook in the assignments folder.

This assignment is due next Tuesday, March 17th.