.. Python course documentation master file, created by
   sphinx-quickstart on Fri Aug 18 17:46:39 2017.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.


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 <http://hub-courses.pages.pasteur.fr/unix-training/>`_)
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 <https://hub-courses.pages.pasteur.fr/refresher_utilities_hts/Program_interfaces.html>`_.

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
--------

.. toctree::
   :maxdepth: 2
   :numbered:

   Introduction
   Variables
   Introduction_to_Functions
   Data_Types
   Collection_Data_Types
   Logical_Operations
   Control_Flow_Statements
   Dive_into_Functions
   Input_Output
   Modules_and_Packages
   Object_Oriented_Programming
   From_script_to_project
   Scripting
   Further_Reading
   Appendix


Indices and tables
==================

* :ref:`search`