Introduction to Programming with Python.

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

About the Course

This course is intended for biologists without any skills in programming but strong motivation to learn how to write their own programs, or for advanced beginners who need to complement their 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 basic computations and write the results in a file.

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

Recommended Background

There are no prerequisite skills in programming but notions in unix (structure of file systems, files, directories, absolute/relative paths, 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.

Syllabus:

• Introduction

• Variables, Expressions and Statements

• Introduction to Functions

• Data Types

• Collection Data Types

• Logical Operations

• Control Flow Statements

• Dive into Functions

• Input/Output

• Modules and Packages

• Object Oriented Programming

Conventions

In this course, you will encounter blocks containing code. It is important to realize that this code can belong to two completely distinct interfaces.

Lines prefixed with $ are meant to represent a command-line prompt in a Unix-like shell:

$ python3

Those prefixed with >>> are meant to represent the prompt of an interactive Python interpreter:

>>> print("Hello world!")

When you try those commands:

• Type them in the appropriate interface.

• Don’t include the prompt symbols ($ or >>>`).

Please note that commands are case-sensitive: The effect will be different if you use capitals instead of small case characters, or the contrary.

Miscellanea

Although the support is in English, this course can be given in French, if all students agree.

To know the schedule of the next sessions or register to this course contact the “service formation”.

Contents

• 1. Introduction
  • 1.1. Getting and installing Python
  • 1.2. Some preliminary programming notions
  • 1.3. Exercices
  • 1.4. Python Documentation
  • 1.5. Summary
  • 1.6. References
• 2. Variables, Expressions and Statements
  • 2.1. Variables and Object References
  • 2.2. Immutable objects
  • 2.3. Mutable objects
  • 2.4. Variable names and keywords
  • 2.5. Summary
• 3. Introduction to Functions
  • 3.1. Creating and Calling Functions
  • 3.2. Names and Docstrings
  • 3.3. Functions are objects
• 4. Data Types
  • 4.1. NoneType
  • 4.2. Boolean
  • 4.3. Numeric types
  • 4.4. Strings
  • 4.5. Exercices
• 5. Collection Data Types
  • 5.1. Sequence Types
  • 5.2. Set Types
  • 5.3. Mapping Types
  • 5.4. Iterating and copying collections
  • 5.5. Exercises
• 6. Logical Operations
  • 6.1. The Identity Operator
  • 6.2. Comparison Operators
  • 6.3. The Membership Operator
  • 6.4. Boolean Operators
• 7. Control Flow Statements
  • 7.1. Control Structures
  • 7.2. Exception Handling
  • 7.3. Exercises
• 8. Dive into Functions
  • 8.1. Dive into Functions
  • 8.2. References
  • 8.3. Exercises
• 9. Input/Output
  • 9.1. File Object
  • 9.2. Why it is important to close files
  • 9.3. Helpful functions to manipulate files
  • 9.4. Exercises
  • 9.5. Command-line arguments
• 10. Modules and Packages
  • 10.1. Modules
  • 10.2. Packages
  • 10.3. Standard Library
  • 10.4. Exercises
• 11. Object Oriented Programming
  • 11.1. Concepts and Terminology
  • 11.2. Namespace and attributes lookup
  • 11.3. Deleting object
  • 11.4. Inheritance
  • 11.5. Polymorphism
  • 11.6. Exercises
• 12. From script to a project in Python
  • 12.1. Which Python version to use?
  • 12.2. Follow the conventions
  • 12.3. Managing code
  • 12.4. Documenting Your Project
  • 12.5. Don’t reinvent the wheel
  • 12.6. Tests
  • 12.7. Debuging
  • 12.8. Optimization
  • 12.9. Virtualenv
• 13. Scripting
  • 13.1. Shell True vs False
  • 13.2. Environment Variables
  • 13.3. Get the standard and error output
• 14. Further Reading
• 15. Appendix
  • 15.1. Python 3 what’s new

Indices and tables

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