Week 15: December 7 - 11

Computing With Text

We use Python's text processing functions to explore the distribution of words in some classic texts.

Bioinformatics

Biopython is a set of Python modules containing tools for computational molecular biology. We install Biopython and learn to use one such tool to identify a set of unknown genetic sequences.

Python

• String processing - lower, replace, split, strip and join.
• Dictionaries
• Sorting sequences using sorted.
• random.choice

Matplotlib

• pie

Quiz

There will be no quiz this week.

Class Activity: Bioinformatics

• Use the tools available in Biopython to identify the origin of six real nucleotide sequences presented in class.
• Determine which nucleotide sequence is the fake one.

Assignment 11: Computing with Text

Activity: Word Frequency Analysis

• Download the text of Shakespeare's "Hamlet" from Project Gutenberg.
• Make a list of all the words in this text, ordered by frequency of use.
• Identify the most commonly used words.
• Make a pie chart of the words, showing their frequency.
• Plot the frequency of the words against their rank in frequency order, and comment on any patterns seen.
• Perform the word frequency analysis with another text of your choice.
• Generate a random text, and compare to the word frequency patterns seen for real texts.

Assignment: Report Compilation

• Include all reports from the entire semester.
• Create one master document with each report inserted as a section.
• Title the document 337f15_yourname.odt.
• Start each report on a separate page.
• Add a title page.
• Add a table of contents.
• Export the document as a pdf.