Python for EVOP2019

Sofia Robb

Lecture Material [pdf] [markdown]
Lecture Files
Lecture Scripts

To download all files and scripts, run this command:
git clone https://github.com/prog4biol/evop2019.git

Table of Contents

• Python for EVOP 2019
  • Why Python?
  • Why Script?
  • Teaching Format
  • Installing Python
  • Python References * Books * Websites * Practice
  • Python Overview
    • Running Python
      • Interactive Interpretor
      • Python Scripts
      • Running Python Scripts
      • A quicker/better way to run python scripts
    • Syntax
      • Python Identifiers
      • Naming conventions for Python Identifiers
      • 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?
    • Operators
      • Arithmetic Operators
      • Assignment Operators
      • Comparison Operators
      • Logical Operators
      • Membership Operators
      • Operator Precedence
    • Truth
      • Test for truth
    • Logic: Control Statements
      • If Statement
      • if/elif
    • Numbers
      • integer
      • floating point number
      • complex number
      • Conversion functions
      • Numeric Functions
    • Comparing two numbers
    • Sequences
      • Strings
        • Quotation Marks
        • Strings and the print() function
        • Special/Escape Characters
        • Concatenation
        • The difference between string and integer
        • Determine the length of a string
        • Changing String Case
        • Find and Count
        • Find and Replace
        • Extracting a Substring, or Slicing
        • Locate and Report
        • Other String Methods
      • String Formatting
      • 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
      • For Loops
        • For Loop Syntax
      • Loop Control
        • Loop Control: Break
        • Loop Control: Continue
      • Iterators
      • List Comprehension
    • 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
        • Difference
        • Union
        • Intersection
        • Symmetric Difference
      • Set Functions
      • Set Methods
    • 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
    • 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
    • Basic FASTA Parser
    • 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
      • Global Variables
      • Local Variables
      • Global
    • Data Structures
      • List of lists
      • Lists of dictionaries
      • Dictionaries of lists
      • Dictionaries of dictionaries
      • Building Complex Datastructures
    • Pipelines
      • subprocess Module
      • shell=True
      • Use Error Code to Control Pipeline
  • Biopython
    • What is biopython?
    • Installing Biopython
    • Biopython documentation
    • Working with DNA and protein sequences
    • From ... import ...
    • Bio.Alphabets
    • Extracting a subsequence
    • Read a FASTA file
    • Convert fasta file to python dictionary in one line
    • Seq methods
    • SeqRecord objects
    • Retrieving annotations from GenBank file
    • File Format Conversions
    • Parsing BLAST output
    • There are many other uses for Biopython
    • Why use biopython

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