Programming For Biology 2018

Instructors

James Baldwin-Brown

Jacob Cooper

Robert Greenhalgh

Based on course created by

Simon Prochnik

Sofia Robb

• Big Picture
  • Why?
  • Helpful Tips
• Unix
  • Unix 0
    • Installing Linux on a PC
  • Unix 1
    • Unix Overview
      • What is the Command-Line?
    • The Basics
      • Logging into Your Workstation
      • Bringing up the Command-Line
      • OK. I've Logged in. What Now?
      • Command-Line Prompt
      • Issuing Commands
      • Command-Line Editing
      • Wildcards
      • Home Sweet Home
      • Getting Around
      • Essential Unix Commands
      • Getting Information About Commands
      • Finding Out What Commands are on Your Computer
      • Arguments and Command Line Switches
      • Spaces and Funny Characters
      • Useful Commands
      • Manipulating Directories
      • Networking
      • Standard I/O and Redirection
      • A Simple Example
      • Redirection Meta-Characters
      • Filters, Filenames, and Standard Input
      • Standard I/O and Pipes
      • More Pipe Idioms
    • Advanced Unix
    • Link to Unix 1 Problem Set
  • Unix 2
    • Text Editors
• Python Lectures
  • Python 1
    • Python Overview
    • Running Python
      • Interactive Interpreter
      • Python Scripts are Text Files
      • Running Python Scripts
      • A quicker/better way to run python scripts
    • Syntax
      • Python Variable Names
      • Naming conventions for Python Variable Names
      • Reserved Words
      • Lines and Indentation
      • Comments
      • Blank Lines
    • Data Types and Variables
      • Numbers and Strings
      • Lists
      • Tuples
      • Dictionary
      • Command line parameters: A Special Built-in List
      • What kind of object am I working with?
    • Link to Python 1 Problem Set
  • Python 2
    • Operators
      • Arithmetic Operators
      • Assignment Operators
      • Comparison Operators
      • Logical Operators
      • Membership Operators
      • Operator Precedence
    • Truth
      • Use bool() to test for truth
    • Logic: Control Statements
      • If Statement
      • if/elif
    • Numbers
      • integer
      • floating point number
      • complex number
      • Conversion functions
      • Numeric Functions
    • Comparing two numbers
    • Link to Python 2 Problem Set
  • Python 3
    • Sequences
    • What functions go with my object?
    • Strings
      • Quotation Marks
      • Strings and the print() function
      • print() and Common Errors
      • Special/Escape Characters
      • Concatenation
      • The difference between string and integer
      • Determine the length of a string
      • Changing String Case
      • Find and Count
      • Replace one string with another
      • Extracting a Substring, or Slicing
      • Reverse a string or a list
      • Other String Methods
    • String Formatting
      • The format() mini-language
      • Summary of special formatting symbols so far
      • What's the point?
    • Link to Python 3 Problem Set
  • Python 4
    • Lists and Tuples
      • Lists
      • Tuples
      • Back to Lists
      • Accessing Values in Lists
      • Changing Values in a List
      • Extracting a Subset of a List, or Slicing
      • List Operators
      • List Functions
      • List Methods
      • Building a List one Value at a Time
    • Loops
      • While loop
      • While Loop Syntax
      • Infinite Loops
      • While/Else
      • For Loops
      • For Loop Syntax
      • For/Else
      • Loop Control
      • Loop Control: Break
      • Loop Control: Continue
      • Iterators
      • List Comprehension
    • Link to Python 4 Problem Set
  • Python 5
    • I/O and Files
      • Writing to the Screen
      • Reading input from the keyboard
      • Reading from a File
      • Open a File
      • Reading the contents of a file
      • Opening a file with with open() as fh:
      • Writing to a File
      • Building a Dictionary from a File
    • Link to Python 5 Problem Set
  • Python 6
    • Dictionaries
      • Creating a Dictionary
      • Accessing Values in Dictionaries
      • Changing Values in a Dictionary
      • Accessing Each Dictionary Key/Value
      • Building a Dictionary one Key/Value at a Time
      • Checking That Dictionary Keys Exist
      • Dictionary Operators
      • Sorting Dictionary Keys
      • Dictionary Functions
      • Dictionary Methods
    • Sets
      • Set Operators
      • Set Functions
      • Set Methods
    • Link to Python 6 Problem Set
  • Python 7
    • Functions
      • Defining a Function that calculates GC Content
      • Using your function to calculate GC content
      • The details
      • Naming Arguments
      • Keyword Arguments
      • Default Values for Arguments
      • Lambda expressions
    • Scope
      • Local Variables
      • Global
    • Modules
      • Getting information about modules with pydoc
      • os.path
      • os.system
      • subprocess
        • Capturing output from a shell pipeline
        • Capturing output the long way (for a single command)
        • Check the exit status of a command
        • Redirect stdout to a file inside python subprocess
      • sys
      • re
      • collections
      • copy
      • math
      • random
      • statistics
      • glob
      • argparse
    • Many more modules that do many things
    • Link to Python 7 Problem Set
  • Python 8
    • Regular Expressions
      • Individual Characters
      • Character Classes
      • Anchors
      • Quantifiers
      • Variables and Patterns
      • Either Or
      • Subpatterns
      • Using Subpatterns Inside the Regular Expression Match
      • Using Subpatterns Outside the Regular Expression
      • Get position of the subpattern with finditer()
      • Subpatterns and Greediness
      • Practical Example: Codons
      • Truth and Regular Expression Matches
      • Using Regular expressions in substitutions
      • Using subpatterns in the replacement
      • Regular Expression Option Modifiers
    • Link to Python 8 Problem Set
  • Python 9
    • Data Structures
      • List of lists
      • Lists of dictionaries
      • Dictionaries of lists
      • Dictionaries of dictionaries
      • Building Complex Datastructures
    • Exceptions
      • try/except/else/finally
      • Getting more information about an exception
      • Raising an Exception
      • Creating Custom Exceptions
    • Link to Python 9 Problem Set
  • Python 10
    • Classes
      • You have been using classes to create objects
      • attributes and methods
      • Creating a Class
      • Retrieving attribute values
      • Using class methods
      • Getting data into a new instance of our class
        • init
    • Link to Python 10 Problem Set
• Workshops
  • BioPython -- Sofia Robb
  • NGS -- Mike Campbell
  • Structural Variation -- Tomas Marques
  • Sequence Homology -- Brandi Cantarel
  • Genome Assembly -- Deb Triant
  • Bioinformatics and Useful Tools -- Simon Prochnik
  • STAR RNA Aligner -- Alex Dobin
  • RNAseq -- Brian Haas
  • Ethics and Responsibility in Bioinformatics -- Simon Prochnik
  • GMOD -- Scott Cain
  • Ontologies -- Nicole Vasilevsky
  • Protein Function -- Paul Thomas
• Git lectures (extra content)
  • Git for Beginners
    • The Big Picture.
      • Collaboration
      • Storing Versions
      • Restoring Previous Versions
      • Backup
      • The Details
    • The Basics
      • Creating a new repository
      • Cloning a Repository
      • Bringing Changes in from the Remote Repository to your Local Repository
      • Keeping track of differences between local and remote repositories
      • Links to slightly less basic topics
    • Link To Unix 2 Problem Set
• Projects