Introduction to Programming with python!

This course, aims to introduce the basics of programming to the biologists using the Python language.

About the Course

The audience for this course is biologists without any skills in programming but strong motivation to learn how to do his own programs or for advanced beginners who need to develop his skills with concepts.

At the end of the week, the student will be able to automate some repetitive tasks, and open a file, parse it, do basics computation and writes results in file.

Although all exercises are based on biological data, this course will not be focused on how to analysed data. And will not cover the using of external bioinformatics tools.

Recommended Background

There are no prerequisite skills in programming but notions in unix (structure of file systems, file, directories, absolute/relative path, and permissions, or equivalent to Unix-I course would be an advantage, although this is not essential.

This course is very intensive and needs highly motivated candidates.

Contents

Contents:

• Introduction
  • Getting and installing Python
  • Creating and running Python Programs
  • High and low level language
  • What is a program
  • Formal and natural language
  • Style of programming
  • Python 2.x vs 3.x
  • Exercices
  • Python Documentation
  • Summary
  • References
• Variables, Expression and statements
  • Variables and Object References
  • Immutable objects
  • Mutable objects
  • Variable name and keywords
  • Summary
• Creating and Calling Functions
  • Creating and Calling Functions
• Data Types
  • NoneType
  • Boolean
  • Integers
  • Floating Point types
  • Strings
  • Exercices
• Collection Data Types
  • Sequence Types
  • Set Types
  • Mapping Types
  • Iterating and copying collections
  • Exercises
• Logical Operations
  • The Identity Operator
  • Comparison Operators
  • The Membership Operator
  • Logical Operators
• Control Flow Statements
  • Control Structures
  • Exception Handling
  • Exercises
• Dive into Functions
  • Dive into Functions
  • References
  • Exercises
• Modules and Packages
  • Modules
  • Packages
  • Standard Library
  • Exercises
• Input/Output
  • File Object
  • Why It’s important to close files
  • helpful functions to manipulate files
  • Exercises
• Scripting
  • Shell True vs False
  • Environment Variables
  • Get the standard and error output
• Object Oriented Programming
  • Modularity
  • Reusability
  • Abstract Data Types
  • Concepts and Terminology
  • Namespace and attributes lookup
  • deleting object
  • Exercises
  • References
• Object-oriented Architecture and Design
  • Inheritance
  • Polymorphism
  • Multiple inheritance
  • Abstract classes
  • Composition
  • Exercises
• From script to a project in Python
  • Which Python version to use?
  • Follow the conventions
  • Managing code
  • Documenting Your Project
  • Don’t reinvent the wheel
  • Tests
  • Debuging
  • Optimization
  • Virtualenv
• Further Reading
• Appendix
  • Python 3 what’s new

Indices and tables

• Search Page