diff --git a/README.md b/README.md
index d813869c8a340295603a772dcc166ecac3bebe8d..7345fecf93ace469895810a4f2627e2e1e90e635 100644
--- a/README.md
+++ b/README.md
@@ -65,7 +65,7 @@ The top-level directory contains materials for the following lessons:
8. Object-oriented programming ([slides][lesson_08])
9. A sip of Biopython ([notebook 1][lesson_09_01], [notebook 2][lesson_09_02])
-[lesson_01]: http://nbviewer.ipython.org/urls/git.lumc.nl/courses/programming-course/raw/master/01%20-%20Welcome.ipynb
+[lesson_01]: http://nbviewer.ipython.org/urls/git.lumc.nl/courses/programming-course/raw/master/introduction/01_welcome.ipynb
[lesson_02_01]: http://nbviewer.ipython.org/urls/git.lumc.nl/courses/programming-course/raw/master/02%20-%20Introduction%20to%20Python%20(1).ipynb
[lesson_02_02]: http://nbviewer.ipython.org/urls/git.lumc.nl/courses/programming-course/raw/master/02%20-%20Introduction%20to%20Python%20(2).ipynb
[lesson_02_03]: http://nbviewer.ipython.org/urls/git.lumc.nl/courses/programming-course/raw/master/02%20-%20Introduction%20to%20Python%20(3).ipynb
diff --git a/introduction/01_welcome.ipynb b/introduction/01_welcome.ipynb
new file mode 100644
index 0000000000000000000000000000000000000000..dd1d9299576d53ebcf61b793e928a0822ca8b724
--- /dev/null
+++ b/introduction/01_welcome.ipynb
@@ -0,0 +1,240 @@
+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "<span style=\"font-size: 200%\">Programming in Python</span>\n",
+ "===\n",
+ "\n",
+ "<br>\n",
+ "\n"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "About the course\n",
+ "===\n",
+ "\n",
+ "* Aimed at PhD students, Postdocs, researchers, analysts, ...\n",
+ "* Programming as a tool to do your research.\n",
+ "* Slightly focussed on bioinformatics.\n",
+ "\n",
+ "**Note:** This is its third session."
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "Teachers\n",
+ "===\n",
+ "\n",
+ "* Jeroen Laros<br>\n",
+ " [j.f.j.laros@lumc.nl](mailto:j.f.j.laros@lumc.nl)\n",
+ "\n",
+ "\n",
+ "* Mihai Lefter<br>\n",
+ " [m.lefter@lumc.nl](mailto:m.lefter@lumc.nl)\n",
+ "\n",
+ "\n",
+ "* Jonathan Vis<br>\n",
+ " [j.k.vis@lumc.nl](mailto:j.k.vis@lumc.nl)\n",
+ "\n",
+ "\n",
+ "* Mark Santcroos<br>\n",
+ " [m.a.santcroos@lumc.nl](mailto:m.a.santcroos@lumc.nl)\n",
+ "\n",
+ "\n",
+ "* Guy Allard<br>\n",
+ " [w.g.Allard@lumc.nl](mailto:w.g.allard@lumc.nl)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "Program\n",
+ "===\n",
+ "\n",
+ "| Day | Time | Lesson | Teacher | \n",
+ "|-----------------|-------|------------------------------------ |----------|\n",
+ "| Monday, 18/9 | 9-10 | Welcome, Introduction to Python (1) | Mihai | \n",
+ "| | 10-11 | Introduction to Python (2) | Jeroen | \n",
+ "| | 11-12 | Introduction to Python (3) | Mihai | \n",
+ "| | 12-13 | Practical help | | \n",
+ "| Tuesday, 19/9 | 9-10 | Assignments review | |\n",
+ "| | 10-11 | More Python Goodness (1) | Mihai | \n",
+ "| | 11-12 | More Python Goodness (2) | Mihai | \n",
+ "| | 12-13 | IPython Notebook | Mark | \n",
+ "| Wednesday, 20/9 | 9-10 | Assignments review | | \n",
+ "| | 10-11 | Data manipulation (NumPy, Pandas) | Mark | \n",
+ "| | 11-12 | Data visualisation (1) | Guy | \n",
+ "| | 12-13 | Data visualisation (2) | Guy | \n",
+ "| Thursday, 21/9 | 9-10 | Assignments review | | \n",
+ "| | 10-11 | Object-oriented programming | Jonathan | \n",
+ "| | 11-12 | Biopython | Guy | \n",
+ "| | 12-13 | Putting everything together | Jeroen |\n",
+ "\n",
+ "All slides are linked as one-page documents from the course website: [https://git.lumc.nl/courses/programming-course](https://git.lumc.nl/courses/programming-course)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "Software requirements\n",
+ "===\n",
+ "\n",
+ "* Anaconda\n",
+ " * Python 2.7\n",
+ " * NumPy, matplotlib, Biopython\n",
+ "* Git\n",
+ "\n",
+ "Anaconda installation instructions [here](https://docs.anaconda.com/anaconda/install/)."
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "Exercises\n",
+ "===\n",
+ "\n",
+ "You only learn programming by doing it.\n",
+ "\n",
+ "* Have your laptop open during the lessons.\n",
+ "* Repeat the code from the slides, play around with it.\n",
+ "* Do the exercises.\n",
+ "* There will be a few assignments to submit."
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "Getting help\n",
+ "===\n",
+ "\n",
+ "* Ask a teacher.\n",
+ "* If it's private, mail one of the teachers.\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {
+ "slideshow": {
+ "slide_type": "skip"
+ }
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<style>/* Remove the vertical scrollbar added by nbconvert. */\n",
+ ".reveal {\n",
+ " overflow: hidden;\n",
+ "}\n",
+ "\n",
+ "/* Workaround some highlight.js bugs in language autodetection. */\n",
+ "code.objectivec *,\n",
+ "code.perl *,\n",
+ "code.cs *,\n",
+ "code.javascript *,\n",
+ "code.http * {\n",
+ " color: black ! important;\n",
+ " font-weight: normal ! important;\n",
+ "}\n",
+ "span.title {\n",
+ " color: black ! important;\n",
+ "}\n",
+ "span.tag {\n",
+ " color: black ! important;\n",
+ "}\n",
+ "span.attribute {\n",
+ " color: black ! important;\n",
+ "}\n",
+ "</style>"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "execution_count": 3,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "from IPython.display import HTML\n",
+ "def css_styling():\n",
+ " styles = open('../styles/custom.css', 'r').read()\n",
+ " return HTML('<style>' + styles + '</style>')\n",
+ "css_styling()"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "License: [Creative Commons Attribution 3.0 License (CC-by)](http://creativecommons.org/licenses/by/3.0)\n"
+ ]
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 3",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.5.2"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 1
+}
diff --git a/introduction/02_introduction_to_python_1.ipynb b/introduction/02_introduction_to_python_1.ipynb
new file mode 100644
index 0000000000000000000000000000000000000000..4a01e69444ff586a2851aa1f8ae5eb9dc2ef0851
--- /dev/null
+++ b/introduction/02_introduction_to_python_1.ipynb
@@ -0,0 +1,940 @@
+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "<span style=\"font-size: 200%\">Introduction to Python (1)</span>\n",
+ "===\n",
+ "\n",
+ "<br>\n",
+ "\n",
+ "[Martijn Vermaat](mailto:m.vermaat.hg@lumc.nl), [Department of Human Genetics, Leiden University Medical Center](http://humgen.nl)\n",
+ "\n",
+ "[Jeroen Laros](mailto:j.f.j.laros@lumc.nl), [Department of Human Genetics, Leiden University Medical Center](http://humgen.nl)\n",
+ "\n",
+ "Based on: [Python Scientific Lecture Notes](http://scipy-lectures.github.io/)\n",
+ "\n",
+ "License: [Creative Commons Attribution 3.0 License (CC-by)](http://creativecommons.org/licenses/by/3.0)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "About Python\n",
+ "===\n",
+ "\n",
+ "History\n",
+ "---\n",
+ "\n",
+ "* Created early 90's by Guido van Rossem at CWI.\n",
+ "* General purpose, high-level programming language.\n",
+ "* Design is driven by code readability."
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "subslide"
+ }
+ },
+ "source": [
+ "About Python\n",
+ "===\n",
+ "\n",
+ "Features\n",
+ "---\n",
+ "\n",
+ "* Interpreted, no separate compilation step needed.\n",
+ "* Imperative and object-oriented programming (and some functional programming).\n",
+ "* Dynamic type system.\n",
+ "* Automatic memory management.\n",
+ "\n",
+ "We'll come back to most of this."
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "subslide"
+ }
+ },
+ "source": [
+ "About Python\n",
+ "===\n",
+ "\n",
+ "Why Python?\n",
+ "---\n",
+ "\n",
+ "* Readable and low barrier to entry.\n",
+ "* Rich scientific libraries.\n",
+ "* Many other libraries available.\n",
+ "* Widely used with a large community."
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "subslide"
+ }
+ },
+ "source": [
+ "About Python\n",
+ "===\n",
+ "\n",
+ "Python 2 versus Python 3\n",
+ "---\n",
+ "\n",
+ "* Python 3 is backwards incompatible.\n",
+ "* Some libraries don't support it yet.\n",
+ "* Python 2.7 is the last Python 2.\n",
+ "* Some Python 3 features are backported in Python 2.7.\n",
+ "* Default Python on most distributions is Python 2.7.\n",
+ "\n",
+ "We use Python 2.7 for the time being."
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "Running Python code\n",
+ "===\n",
+ "\n",
+ "Two main ways of writing and executing Python code.\n",
+ "\n",
+ "Interactively\n",
+ "---\n",
+ "\n",
+ "* Statement by statement directly in the interpreter.\n",
+ "\n",
+ "Non-interactively\n",
+ "---\n",
+ "\n",
+ "* By editing in a file and running the code afterwards."
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "fragment"
+ }
+ },
+ "source": [
+ "We'll start with the first option."
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "subslide"
+ }
+ },
+ "source": [
+ "Running Python code\n",
+ "===\n",
+ "\n",
+ "The standard Python interpreter\n",
+ "---\n",
+ "\n",
+ "Start it by typing `python` on the command line:\n",
+ "\n",
+ " $ python\n",
+ " Python 2.7.3 (default, Jan 2 2013, 13:56:14) \n",
+ " [GCC 4.7.2] on linux2\n",
+ " Type \"help\", \"copyright\", \"credits\" or \"license\" for more information.\n",
+ " >>>\n",
+ "\n",
+ "* It shows an interpreter prompt.\n",
+ "* You can give it Python code to interpret."
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "subslide"
+ }
+ },
+ "source": [
+ "Running Python code\n",
+ "===\n",
+ "\n",
+ "The IPython interpreter\n",
+ "---\n",
+ "\n",
+ "* Similar to the standard Python interpreter, but with\n",
+ "* syntax highlighting,\n",
+ "* tab completion,\n",
+ "* cross-session history, etcetera...\n",
+ "\n",
+ "Start it by typing `ipython` on the command line:\n",
+ "\n",
+ " $ ipython\n",
+ " Python 2.7.3 (default, Jan 2 2013, 13:56:14) \n",
+ " Type \"copyright\", \"credits\" or \"license\" for more information.\n",
+ "\n",
+ " IPython 0.13.1 -- An enhanced Interactive Python.\n",
+ " ? -> Introduction and overview of IPython's features.\n",
+ " %quickref -> Quick reference.\n",
+ " help -> Python's own help system.\n",
+ " object? -> Details about 'object', use 'object??' for extra details.\n",
+ "\n",
+ " In [1]:"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "fragment"
+ }
+ },
+ "source": [
+ "From now on, play along in your own IPython interpreter."
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "Python as a calculator\n",
+ "===\n",
+ "\n",
+ "Integers\n",
+ "---"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "17"
+ ]
+ },
+ "execution_count": 1,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "17"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "42"
+ ]
+ },
+ "execution_count": 2,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "(17 + 4) * 2"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "subslide"
+ }
+ },
+ "source": [
+ "Python as a calculator\n",
+ "===\n",
+ "\n",
+ "Floating point numbers\n",
+ "---"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "55.5"
+ ]
+ },
+ "execution_count": 3,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "3.2 * 18 - 2.1"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "7.2"
+ ]
+ },
+ "execution_count": 4,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "36. / 5"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Scientific notation:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "1.3e+20"
+ ]
+ },
+ "execution_count": 5,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "1.3e20 + 2"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "1.3e+20"
+ ]
+ },
+ "execution_count": 6,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "1.3 * 10**20"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "subslide"
+ }
+ },
+ "source": [
+ "Python as a calculator\n",
+ "===\n",
+ "\n",
+ "The division operator\n",
+ "---"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 7,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "7"
+ ]
+ },
+ "execution_count": 7,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "35 / 5"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 8,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "7"
+ ]
+ },
+ "execution_count": 8,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "36 / 5"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Division is a bit weird: if you give it integer arguments, the result will also be an integer."
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "subslide"
+ }
+ },
+ "source": [
+ "Python as a calculator\n",
+ "===\n",
+ "\n",
+ "The division operator\n",
+ "---"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 9,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "7"
+ ]
+ },
+ "execution_count": 9,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "35 / 5"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 10,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "7"
+ ]
+ },
+ "execution_count": 10,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "36 / 5"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Solution 1\n",
+ "---\n",
+ "\n",
+ "Give floating point arguments instead of integer arguments."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 11,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "7.2"
+ ]
+ },
+ "execution_count": 11,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "36. / 5."
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "subslide"
+ }
+ },
+ "source": [
+ "Python as a calculator\n",
+ "===\n",
+ "\n",
+ "The division operator\n",
+ "---"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 12,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "7"
+ ]
+ },
+ "execution_count": 12,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "35 / 5"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 13,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "7"
+ ]
+ },
+ "execution_count": 13,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "36 / 5"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Solution 2\n",
+ "---\n",
+ "\n",
+ "From Python 3 onwards, division behaves differently. You can actually get that behaviour in Python 2.7:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 14,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "7.2"
+ ]
+ },
+ "execution_count": 14,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "from __future__ import division\n",
+ "36 / 5"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "subslide"
+ }
+ },
+ "source": [
+ "Python as a calculator\n",
+ "===\n",
+ "\n",
+ "Variables\n",
+ "---\n",
+ "\n",
+ "* We can use names to reference values (variables).\n",
+ "* No need to declare them first or define the type."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 15,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "a = 1.3e20"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 16,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "1.3e+20"
+ ]
+ },
+ "execution_count": 16,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "a"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 17,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "2.84e+20"
+ ]
+ },
+ "execution_count": 17,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "b = a + 1.2e19\n",
+ "b * 2"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "Python's type system (1/2)\n",
+ "===\n",
+ "\n",
+ "Every value has a type, view it using `type`:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 18,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "int"
+ ]
+ },
+ "execution_count": 18,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "type(27)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 19,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "float"
+ ]
+ },
+ "execution_count": 19,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "type(3.0 * 2.7)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 20,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "float"
+ ]
+ },
+ "execution_count": 20,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "type(a)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Another example of a builtin datatype is `str`, we'll see more later:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 21,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "str"
+ ]
+ },
+ "execution_count": 21,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "type('I am a homo sapiens')"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "subslide"
+ }
+ },
+ "source": [
+ "Python's type system (2/2)\n",
+ "===\n",
+ "\n",
+ "Some operations are defined on more than one type, possibly with different meanings."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 22,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "'beerbeerbeerbeerbeerwhiskey'"
+ ]
+ },
+ "execution_count": 22,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "'beer' * 5 + 'whiskey'"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Dynamic typing means that variables can be assigned values of different types during runtime."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 23,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "str"
+ ]
+ },
+ "execution_count": 23,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "a = 'spezi'\n",
+ "type(a)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Python is strongly typed, meaning that operations on values with incompatible types are forbidden."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 24,
+ "metadata": {},
+ "outputs": [
+ {
+ "ename": "TypeError",
+ "evalue": "cannot concatenate 'str' and 'int' objects",
+ "output_type": "error",
+ "traceback": [
+ "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m\n\u001b[1;31mTypeError\u001b[0m Traceback (most recent call last)",
+ "\u001b[1;32m<ipython-input-24-ec918fbfdf41>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[1;34m'beer'\u001b[0m \u001b[1;33m+\u001b[0m \u001b[1;36m34\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
+ "\u001b[1;31mTypeError\u001b[0m: cannot concatenate 'str' and 'int' objects"
+ ]
+ }
+ ],
+ "source": [
+ "'beer' + 34"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "metadata": {
+ "slideshow": {
+ "slide_type": "skip"
+ }
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<style>/* Remove the vertical scrollbar added by nbconvert. */\n",
+ ".reveal {\n",
+ " overflow: hidden;\n",
+ "}\n",
+ "\n",
+ "/* Workaround some highlight.js bugs in language autodetection. */\n",
+ "code.objectivec *,\n",
+ "code.perl *,\n",
+ "code.cs *,\n",
+ "code.javascript *,\n",
+ "code.http * {\n",
+ " color: black ! important;\n",
+ " font-weight: normal ! important;\n",
+ "}\n",
+ "span.title {\n",
+ " color: black ! important;\n",
+ "}\n",
+ "span.tag {\n",
+ " color: black ! important;\n",
+ "}\n",
+ "span.attribute {\n",
+ " color: black ! important;\n",
+ "}\n",
+ "</style>"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML at 0x3463a50>"
+ ]
+ },
+ "execution_count": 1,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "from IPython.display import HTML\n",
+ "def css_styling():\n",
+ " styles = open('styles/custom.css', 'r').read()\n",
+ " return HTML('<style>' + styles + '</style>')\n",
+ "css_styling()"
+ ]
+ }
+ ],
+ "metadata": {
+ "celltoolbar": "Slideshow",
+ "kernelspec": {
+ "display_name": "Python 3",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.5.2"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 1
+}
diff --git a/02 - Introduction to Python (2).ipynb b/introduction/02_introduction_to_python_2.ipynb
similarity index 100%
rename from 02 - Introduction to Python (2).ipynb
rename to introduction/02_introduction_to_python_2.ipynb
diff --git a/02 - Introduction to Python (3).ipynb b/introduction/02_introduction_to_python_3.ipynb
similarity index 100%
rename from 02 - Introduction to Python (3).ipynb
rename to introduction/02_introduction_to_python_3.ipynb
diff --git a/01 - Welcome.ipynb b/past_sessions/2014_july/01 - Welcome.ipynb
similarity index 100%
rename from 01 - Welcome.ipynb
rename to past_sessions/2014_july/01 - Welcome.ipynb
diff --git a/02 - Introduction to Python (1).ipynb b/past_sessions/2014_july/02 - Introduction to Python (1).ipynb
similarity index 100%
rename from 02 - Introduction to Python (1).ipynb
rename to past_sessions/2014_july/02 - Introduction to Python (1).ipynb
diff --git a/past_sessions/2014_july/02 - Introduction to Python (2).ipynb b/past_sessions/2014_july/02 - Introduction to Python (2).ipynb
new file mode 100644
index 0000000000000000000000000000000000000000..d7010ad5a4bc1c27708e86ce779188c6d3977840
--- /dev/null
+++ b/past_sessions/2014_july/02 - Introduction to Python (2).ipynb
@@ -0,0 +1,1883 @@
+{
+ "metadata": {
+ "celltoolbar": "Slideshow",
+ "name": "",
+ "signature": "sha256:7b4c4307ccc127e749bcc6fae78706177f4e98973022d13424e5a50a8325f24e"
+ },
+ "nbformat": 3,
+ "nbformat_minor": 0,
+ "worksheets": [
+ {
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "<span style=\"font-size: 200%\">Introduction to Python (2)</span>\n",
+ "===\n",
+ "\n",
+ "<br>\n",
+ "\n",
+ "[Martijn Vermaat](mailto:m.vermaat.hg@lumc.nl), [Department of Human Genetics, Leiden University Medical Center](http://humgen.nl)\n",
+ "\n",
+ "[Jeroen Laros](mailto:j.f.j.laros@lumc.nl), [Department of Human Genetics, Leiden University Medical Center](http://humgen.nl)\n",
+ "\n",
+ "Based on: [Python Scientific Lecture Notes](http://scipy-lectures.github.io/)\n",
+ "\n",
+ "License: [Creative Commons Attribution 3.0 License (CC-by)](http://creativecommons.org/licenses/by/3.0)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "Sequence types\n",
+ "===\n",
+ "\n",
+ "Lists\n",
+ "---\n",
+ "\n",
+ "Mutable sequences of values."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "l = [2, 5, 2, 3, 7]\n",
+ "type(l)"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 1,
+ "text": [
+ "list"
+ ]
+ }
+ ],
+ "prompt_number": 1
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Lists can be heterogeneous, but we typically don't use that."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "a = 'spezi'\n",
+ "[3, 'abc', 1.3e20, [a, a, 2]]"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 2,
+ "text": [
+ "[3, 'abc', 1.3e+20, ['spezi', 'spezi', 2]]"
+ ]
+ }
+ ],
+ "prompt_number": 2
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "subslide"
+ }
+ },
+ "source": [
+ "Sequence types\n",
+ "===\n",
+ "\n",
+ "Tuples\n",
+ "---\n",
+ "\n",
+ "Immutable sequences of values."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "t = 'white', 77, 1.5\n",
+ "type(t)"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 3,
+ "text": [
+ "tuple"
+ ]
+ }
+ ],
+ "prompt_number": 3
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "color, width, scale = t\n",
+ "width"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 4,
+ "text": [
+ "77"
+ ]
+ }
+ ],
+ "prompt_number": 4
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "subslide"
+ }
+ },
+ "source": [
+ "Sequence types\n",
+ "===\n",
+ "\n",
+ "Strings (1/2)\n",
+ "---\n",
+ "\n",
+ "Immutable sequences of characters."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "'a string can be written in single quotes'"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 5,
+ "text": [
+ "'a string can be written in single quotes'"
+ ]
+ }
+ ],
+ "prompt_number": 5
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Strings can also be written with double quotes, or over multiple lines with triple-quotes."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "\"this makes it easier to use the ' character\""
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 6,
+ "text": [
+ "\"this makes it easier to use the ' character\""
+ ]
+ }
+ ],
+ "prompt_number": 6
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "\"\"\"This is a multiline string.\n",
+ "\n",
+ "You see? I continued after a blank line.\"\"\""
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 7,
+ "text": [
+ "'This is a multiline string.\\n\\nYou see? I continued after a blank line.'"
+ ]
+ }
+ ],
+ "prompt_number": 7
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "subslide"
+ }
+ },
+ "source": [
+ "Sequence types\n",
+ "===\n",
+ "\n",
+ "Strings (2/2)\n",
+ "---\n",
+ "\n",
+ "A common operation is formatting strings using argument substitutions."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "'{} times {} equals {:.2f}'.format('pi', 2, 6.283185307179586)"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 8,
+ "text": [
+ "'pi times 2 equals 6.28'"
+ ]
+ }
+ ],
+ "prompt_number": 8
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Accessing arguments by position or name is more readable."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "'{1} times {0} equals {2:.2f}'.format('pi', 2, 6.283185307179586)"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 9,
+ "text": [
+ "'2 times pi equals 6.28'"
+ ]
+ }
+ ],
+ "prompt_number": 9
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "'{number} times {amount} equals {result:.2f}'.format(number='pi', amount=2,\n",
+ " result=6.283185307179586)"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 10,
+ "text": [
+ "'pi times 2 equals 6.28'"
+ ]
+ }
+ ],
+ "prompt_number": 10
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "subslide"
+ }
+ },
+ "source": [
+ "Sequence types\n",
+ "===\n",
+ "\n",
+ "Common operations (1/2)\n",
+ "---\n",
+ "\n",
+ "All sequence types support concatenation, membership/substring tests, indexing, and slicing."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "[1, 2, 3] + [4, 5, 6]"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 11,
+ "text": [
+ "[1, 2, 3, 4, 5, 6]"
+ ]
+ }
+ ],
+ "prompt_number": 11
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "'bier' in 'we drinken bier vanaf half 5'"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 12,
+ "text": [
+ "True"
+ ]
+ }
+ ],
+ "prompt_number": 12
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "'abcdefghijkl'[5]"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 13,
+ "text": [
+ "'f'"
+ ]
+ }
+ ],
+ "prompt_number": 13
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "subslide"
+ }
+ },
+ "source": [
+ "Sequence types\n",
+ "===\n",
+ "\n",
+ "Slicing\n",
+ "---\n",
+ "\n",
+ "Slice `s` from `i` to `j` with `s[i:j]`."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "'abcdefghijkl'[4:8]"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 14,
+ "text": [
+ "'efgh'"
+ ]
+ }
+ ],
+ "prompt_number": 14
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "'abcdefghijkl'[:3]"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 15,
+ "text": [
+ "'abc'"
+ ]
+ }
+ ],
+ "prompt_number": 15
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "We can also define the step `k` with `s[i:j:k]`."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "'abcdefghijkl'[7:3:-1]"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 16,
+ "text": [
+ "'hgfe'"
+ ]
+ }
+ ],
+ "prompt_number": 16
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "subslide"
+ }
+ },
+ "source": [
+ "Sequence types\n",
+ "===\n",
+ "\n",
+ "Common operations (2/2)\n",
+ "---\n",
+ "\n",
+ "Contrary to strings and tuples, lists are mutable. We can also get their length, smallest/largest item, and number/position of certain items."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "len('attacgataggcatccgt')"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 17,
+ "text": [
+ "18"
+ ]
+ }
+ ],
+ "prompt_number": 17
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "max([17, 86, 34, 51])"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 18,
+ "text": [
+ "86"
+ ]
+ }
+ ],
+ "prompt_number": 18
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "('atg', 22, True, 'atg').count('atg')"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 19,
+ "text": [
+ "2"
+ ]
+ }
+ ],
+ "prompt_number": 19
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "subslide"
+ }
+ },
+ "source": [
+ "Sequence types\n",
+ "===\n",
+ "\n",
+ "Additional operations with lists\n",
+ "---\n",
+ "\n",
+ "We can replace, add, remove, reverse and sort items in-place."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "l = [1, 2, 3, 4]\n",
+ "l[3] = 7\n",
+ "l.append(1)\n",
+ "l[1:3] = [3, 2]\n",
+ "l.sort()\n",
+ "l.reverse()"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [],
+ "prompt_number": 20
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "l"
+ ],
+ "language": "python",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "fragment"
+ }
+ },
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 21,
+ "text": [
+ "[7, 3, 2, 1, 1]"
+ ]
+ }
+ ],
+ "prompt_number": 21
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "Dictionaries\n",
+ "===\n",
+ "\n",
+ "Dictionaries map *hashable* values to arbitrary objects\n",
+ "---\n",
+ "\n",
+ "* All built-in immutable objects are hashable.\n",
+ "* No built-in mutable objects are hashable."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "d = {'a': 27, 'b': 18, 'c': 12}\n",
+ "type(d)"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 22,
+ "text": [
+ "dict"
+ ]
+ }
+ ],
+ "prompt_number": 22
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "d['e'] = 17\n",
+ "'e' in d"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 23,
+ "text": [
+ "True"
+ ]
+ }
+ ],
+ "prompt_number": 23
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "d.update({'a': 18, 'f': 2})\n",
+ "d"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 24,
+ "text": [
+ "{'a': 18, 'b': 18, 'c': 12, 'e': 17, 'f': 2}"
+ ]
+ }
+ ],
+ "prompt_number": 24
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "subslide"
+ }
+ },
+ "source": [
+ "Dictionaries\n",
+ "===\n",
+ "\n",
+ "Accessing dictionary content\n",
+ "---"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "d['b']"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 25,
+ "text": [
+ "18"
+ ]
+ }
+ ],
+ "prompt_number": 25
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "d.keys()"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 26,
+ "text": [
+ "['a', 'c', 'b', 'e', 'f']"
+ ]
+ }
+ ],
+ "prompt_number": 26
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "d.values()"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 27,
+ "text": [
+ "[18, 12, 18, 17, 2]"
+ ]
+ }
+ ],
+ "prompt_number": 27
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "d.items()"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 28,
+ "text": [
+ "[('a', 18), ('c', 12), ('b', 18), ('e', 17), ('f', 2)]"
+ ]
+ }
+ ],
+ "prompt_number": 28
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "Sets\n",
+ "===\n",
+ "\n",
+ "Mutable unordered collections of hashable values without duplication\n",
+ "---"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "x = {12, 28, 21, 17}\n",
+ "type(x)"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 29,
+ "text": [
+ "set"
+ ]
+ }
+ ],
+ "prompt_number": 29
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "x.add(12)\n",
+ "x"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 30,
+ "text": [
+ "{12, 17, 21, 28}"
+ ]
+ }
+ ],
+ "prompt_number": 30
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "x.discard(21)\n",
+ "x"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 31,
+ "text": [
+ "{12, 17, 28}"
+ ]
+ }
+ ],
+ "prompt_number": 31
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "subslide"
+ }
+ },
+ "source": [
+ "Sets\n",
+ "===\n",
+ "\n",
+ "Operations with sets\n",
+ "---\n",
+ "\n",
+ "We can test for membership and apply many common set operations such as union and intersect."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "17 in {12, 28, 21, 17}"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 32,
+ "text": [
+ "True"
+ ]
+ }
+ ],
+ "prompt_number": 32
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "{12, 28, 21, 17} | {12, 18, 11}"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 33,
+ "text": [
+ "{11, 12, 17, 18, 21, 28}"
+ ]
+ }
+ ],
+ "prompt_number": 33
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "{12, 28, 21, 17} & {12, 18, 11}"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 34,
+ "text": [
+ "{12}"
+ ]
+ }
+ ],
+ "prompt_number": 34
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "Booleans\n",
+ "===\n",
+ "\n",
+ "Boolean values and operations\n",
+ "---\n",
+ "\n",
+ "The two boolean values are written `False` and `True`."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "True or False"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 35,
+ "text": [
+ "True"
+ ]
+ }
+ ],
+ "prompt_number": 35
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "True and False"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 36,
+ "text": [
+ "False"
+ ]
+ }
+ ],
+ "prompt_number": 36
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "not False"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 37,
+ "text": [
+ "True"
+ ]
+ }
+ ],
+ "prompt_number": 37
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "subslide"
+ }
+ },
+ "source": [
+ "Booleans\n",
+ "===\n",
+ "\n",
+ "Comparisons\n",
+ "---\n",
+ "\n",
+ "Comparisons can be done on all objects and return a boolean value."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "22 * 3 > 66"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 38,
+ "text": [
+ "False"
+ ]
+ }
+ ],
+ "prompt_number": 38
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "We have two equivalence relations: value equality (`==`) and object identity (`is`)."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "a, b = [1, 2, 3], [1, 2, 3]\n",
+ "a == b"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 39,
+ "text": [
+ "True"
+ ]
+ }
+ ],
+ "prompt_number": 39
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "a is b"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 40,
+ "text": [
+ "False"
+ ]
+ }
+ ],
+ "prompt_number": 40
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "subslide"
+ }
+ },
+ "source": [
+ "Booleans\n",
+ "===\n",
+ "\n",
+ "`if` statements\n",
+ "---\n",
+ "\n",
+ "(The `print` statement writes a string representation of the given value.)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "if 26 <= 17:\n",
+ " print 'Fact: 26 is less than or equal to 17'\n",
+ "elif (26 + 8 > 14) == True:\n",
+ " print 'Did we need the ` == True` part here?'\n",
+ "else:\n",
+ " print 'Nothing seems true'"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "output_type": "stream",
+ "stream": "stdout",
+ "text": [
+ "Did we need the ` == True` part here?\n"
+ ]
+ }
+ ],
+ "prompt_number": 41
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "subslide"
+ }
+ },
+ "source": [
+ "Booleans\n",
+ "===\n",
+ "\n",
+ "`while` statements\n",
+ "---\n",
+ "\n",
+ "Our first looping control structure just repeats until the given expression evaluates to `False`."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "i = 0\n",
+ "while i < 5:\n",
+ " print i\n",
+ " i += 1"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "output_type": "stream",
+ "stream": "stdout",
+ "text": [
+ "0\n",
+ "1\n",
+ "2\n",
+ "3\n",
+ "4\n"
+ ]
+ }
+ ],
+ "prompt_number": 42
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "Notes about syntax\n",
+ "===\n",
+ "\n",
+ "Indentation\n",
+ "---\n",
+ "\n",
+ "Python uses indentation to delimit blocks\n",
+ "\n",
+ "* Instead of `begin ... end` or `{ ... }` in other languages.\n",
+ "* Always increase indentation by *4 spaces*, never use tabs.\n",
+ "* In any case, be consistent."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "if False:\n",
+ " if False:\n",
+ " print 'Why am I here?'\n",
+ " else:\n",
+ " while True:\n",
+ " print 'When will it stop?'\n",
+ " print \"And we're back to the first indentation level\""
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [],
+ "prompt_number": 43
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Some editors can be configured to behave just like that."
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "subslide"
+ }
+ },
+ "source": [
+ "Notes about syntax\n",
+ "===\n",
+ "\n",
+ "Comments\n",
+ "---\n",
+ "\n",
+ "Comments are prepended by `#` and completely ignored."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "# Add 42 to this list.\n",
+ "l.append(42)"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [],
+ "prompt_number": 44
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "`pass` statements\n",
+ "---\n",
+ "\n",
+ "If you ever need a statement syntactically but don't want to do anything, use `pass`."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "while False:\n",
+ " # This is never executed anyway.\n",
+ " pass"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [],
+ "prompt_number": 45
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "Useful built-ins\n",
+ "===\n",
+ "\n",
+ "Getting help\n",
+ "---\n",
+ "\n",
+ "You can get help on almost any object with `help`."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "help(range)"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "output_type": "stream",
+ "stream": "stdout",
+ "text": [
+ "Help on built-in function range in module __builtin__:\n",
+ "\n",
+ "range(...)\n",
+ " range([start,] stop[, step]) -> list of integers\n",
+ " \n",
+ " Return a list containing an arithmetic progression of integers.\n",
+ " range(i, j) returns [i, i+1, i+2, ..., j-1]; start (!) defaults to 0.\n",
+ " When step is given, it specifies the increment (or decrement).\n",
+ " For example, range(4) returns [0, 1, 2, 3]. The end point is omitted!\n",
+ " These are exactly the valid indices for a list of 4 elements.\n",
+ "\n"
+ ]
+ }
+ ],
+ "prompt_number": 46
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "In IPython you can do it faster by typing:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "range?"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [],
+ "prompt_number": 47
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "subslide"
+ }
+ },
+ "source": [
+ "Useful built-ins\n",
+ "===\n",
+ "\n",
+ "We'll shortly use the following built-in functions."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "range(5, 16)"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 48,
+ "text": [
+ "[5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15]"
+ ]
+ }
+ ],
+ "prompt_number": 48
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "zip(['red', 'white', 'blue'], range(3))"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 49,
+ "text": [
+ "[('red', 0), ('white', 1), ('blue', 2)]"
+ ]
+ }
+ ],
+ "prompt_number": 49
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "list('abcdefghijk')"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 50,
+ "text": [
+ "['a', 'b', 'c', 'd', 'e', 'f', 'g', 'h', 'i', 'j', 'k']"
+ ]
+ }
+ ],
+ "prompt_number": 50
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "Iteration\n",
+ "===\n",
+ "\n",
+ "Iterating over a sequence\n",
+ "---"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "colors = ['red', 'white', 'blue', 'orange']\n",
+ "cities = ['leiden', 'utrecht', 'warmond', 'san francisco']"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [],
+ "prompt_number": 51
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "The `for` statement can iterate over sequence items."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "for color in colors:\n",
+ " print color"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "output_type": "stream",
+ "stream": "stdout",
+ "text": [
+ "red\n",
+ "white\n",
+ "blue\n",
+ "orange\n"
+ ]
+ }
+ ],
+ "prompt_number": 52
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "for character in 'blue':\n",
+ " print character"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "output_type": "stream",
+ "stream": "stdout",
+ "text": [
+ "b\n",
+ "l\n",
+ "u\n",
+ "e\n"
+ ]
+ }
+ ],
+ "prompt_number": 53
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "subslide"
+ }
+ },
+ "source": [
+ "Iteration\n",
+ "===\n",
+ "\n",
+ "Python anti-patterns\n",
+ "---\n",
+ "\n",
+ "These are common for programmers coming from other languages."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "i = 0\n",
+ "while i < len(colors):\n",
+ " print colors[i]\n",
+ " i += 1"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "output_type": "stream",
+ "stream": "stdout",
+ "text": [
+ "red\n",
+ "white\n",
+ "blue\n",
+ "orange\n"
+ ]
+ }
+ ],
+ "prompt_number": 54
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "for i in range(len(colors)):\n",
+ " print colors[i]"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "output_type": "stream",
+ "stream": "stdout",
+ "text": [
+ "red\n",
+ "white\n",
+ "blue\n",
+ "orange\n"
+ ]
+ }
+ ],
+ "prompt_number": 55
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "We call them *unpythonic*."
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "subslide"
+ }
+ },
+ "source": [
+ "Iteration\n",
+ "===\n",
+ "\n",
+ "Using values *and* indices\n",
+ "---"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "for i, color in enumerate(colors):\n",
+ " print i, '->', color"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "output_type": "stream",
+ "stream": "stdout",
+ "text": [
+ "0 -> red\n",
+ "1 -> white\n",
+ "2 -> blue\n",
+ "3 -> orange\n"
+ ]
+ }
+ ],
+ "prompt_number": 56
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Taking two sequences together\n",
+ "---"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "for city, color in zip(cities, colors):\n",
+ " print city, '->', color"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "output_type": "stream",
+ "stream": "stdout",
+ "text": [
+ "leiden -> red\n",
+ "utrecht -> white\n",
+ "warmond -> blue\n",
+ "san francisco -> orange\n"
+ ]
+ }
+ ],
+ "prompt_number": 57
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "subslide"
+ }
+ },
+ "source": [
+ "Iteration\n",
+ "===\n",
+ "\n",
+ "Other iterables\n",
+ "---\n",
+ "\n",
+ "Iterating over a dictionary yields keys."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "for key in {'a': 33, 'b': 17, 'c': 18}:\n",
+ " print key"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "output_type": "stream",
+ "stream": "stdout",
+ "text": [
+ "a\n",
+ "c\n",
+ "b\n"
+ ]
+ }
+ ],
+ "prompt_number": 58
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Iterating over a file yields lines."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "for line in open('data/short_file.txt'):\n",
+ " print line"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "output_type": "stream",
+ "stream": "stdout",
+ "text": [
+ "this short file has two lines\n",
+ "\n",
+ "it is used in the example code\n",
+ "\n"
+ ]
+ }
+ ],
+ "prompt_number": 59
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "There are many more useful iterables in Python."
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "$\\S$ Exercise: Iterate over a list\n",
+ "===\n",
+ "\n",
+ "First we are going to make a list and fill it with a simple sequence. Then we are going to use this list to print something.\n",
+ "\n",
+ "* Make a list containing the numbers 0, 1, ... 9.\n",
+ "* Print the last 10 lines of the song ''99 bottles of beer'' using this list."
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "$\\S$ Exercise: Analyse a repeat structure\n",
+ "===\n",
+ "\n",
+ "We are going to make a repeating DNA sequence and extract some subsequences from it.\n",
+ "\n",
+ "* Make a short tandem repeat that consists of three \"ACGT\" units and five \"TTATT\" units.\n",
+ "* Print all suffixes of the repeat structure.\n",
+ "\n",
+ "**Note:** A suffix is an ending. For example, the word \"spam\" has five suffixes: \"spam\", \"pam\", \"am\", \"m\" and \"\".\n",
+ "\n",
+ "* Print all substrings of length 3.\n",
+ "* Print all unique substrings of length 3.\n",
+ "\n",
+ "**Hint:** All elements in a set are unique."
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "$\\S$ Exercise: Boolean comparison\n",
+ "===\n",
+ "\n",
+ "Try to guess the outcome of the following statements:\n",
+ "\n",
+ " 2 * 3 > 4\n",
+ " 2 * (3 > 4)\n",
+ " 2 * (4 > 3)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "$\\S$ Exercise: Combining lists\n",
+ "===\n",
+ "\n",
+ "Calculate all coordinates of the line x=y with x < 100.\n",
+ "\n",
+ "**Note:** This is the sequence (0, 0), (1, 1), ... (99, 99)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "$\\S$ Exercise: Dictionaries\n",
+ "===\n",
+ "We are going to store the output of a function ($f(x) = x^2$) together with its input in a dictionary.\n",
+ "\n",
+ "* Make a dictionary containing all squares smaller than 100.\n",
+ "* Print the content of this dictionary in english, e.g., \"4 is the square of 2\"."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "from IPython.display import HTML\n",
+ "def css_styling():\n",
+ " styles = open('styles/custom.css', 'r').read()\n",
+ " return HTML('<style>' + styles + '</style>')\n",
+ "css_styling()"
+ ],
+ "language": "python",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "skip"
+ }
+ },
+ "outputs": [
+ {
+ "html": [
+ "<style>/* Remove the vertical scrollbar added by nbconvert. */\n",
+ ".reveal {\n",
+ " overflow: hidden;\n",
+ "}\n",
+ "\n",
+ "/* Workaround some highlight.js bugs in language autodetection. */\n",
+ "code.objectivec *,\n",
+ "code.perl *,\n",
+ "code.cs *,\n",
+ "code.javascript *,\n",
+ "code.http * {\n",
+ " color: black ! important;\n",
+ " font-weight: normal ! important;\n",
+ "}\n",
+ "span.title {\n",
+ " color: black ! important;\n",
+ "}\n",
+ "span.tag {\n",
+ " color: black ! important;\n",
+ "}\n",
+ "span.attribute {\n",
+ " color: black ! important;\n",
+ "}\n",
+ "</style>"
+ ],
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 1,
+ "text": [
+ "<IPython.core.display.HTML at 0x1873a50>"
+ ]
+ }
+ ],
+ "prompt_number": 1
+ }
+ ],
+ "metadata": {}
+ }
+ ]
+}
\ No newline at end of file
diff --git a/past_sessions/2014_july/02 - Introduction to Python (3).ipynb b/past_sessions/2014_july/02 - Introduction to Python (3).ipynb
new file mode 100644
index 0000000000000000000000000000000000000000..792c0926b7c98083cfb53aa045d31ddf4fff937a
--- /dev/null
+++ b/past_sessions/2014_july/02 - Introduction to Python (3).ipynb
@@ -0,0 +1,892 @@
+{
+ "metadata": {
+ "celltoolbar": "Slideshow",
+ "name": "",
+ "signature": "sha256:255f999074050e52200e04b7179ca89a373daf14311e382c4ab05b4444cf392e"
+ },
+ "nbformat": 3,
+ "nbformat_minor": 0,
+ "worksheets": [
+ {
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "<span style=\"font-size: 200%\">Introduction to Python (3)</span>\n",
+ "===\n",
+ "\n",
+ "<br>\n",
+ "\n",
+ "[Martijn Vermaat](mailto:m.vermaat.hg@lumc.nl), [Department of Human Genetics, Leiden University Medical Center](http://humgen.nl)\n",
+ "\n",
+ "[Jeroen Laros](mailto:j.f.j.laros@lumc.nl), [Department of Human Genetics, Leiden University Medical Center](http://humgen.nl)\n",
+ "\n",
+ "Based on: [Python Scientific Lecture Notes](http://scipy-lectures.github.io/)\n",
+ "\n",
+ "License: [Creative Commons Attribution 3.0 License (CC-by)](http://creativecommons.org/licenses/by/3.0)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "Functions\n",
+ "===\n",
+ "\n",
+ "Defining a function\n",
+ "---\n",
+ "\n",
+ "A function definition includes its name, arguments and body."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "def add_two(number):\n",
+ " return number + 2"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [],
+ "prompt_number": 1
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "for i in range(5):\n",
+ " print add_two(i)"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "output_type": "stream",
+ "stream": "stdout",
+ "text": [
+ "2\n",
+ "3\n",
+ "4\n",
+ "5\n",
+ "6\n"
+ ]
+ }
+ ],
+ "prompt_number": 2
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "subslide"
+ }
+ },
+ "source": [
+ "Functions\n",
+ "===\n",
+ "\n",
+ "Keyword arguments\n",
+ "---\n",
+ "\n",
+ "Besides regular arguments, functions can have keyword arguments."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "def add_some_other_number(number, other_number=12):\n",
+ " return number + other_number"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [],
+ "prompt_number": 3
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "add_some_other_number(2, 6)"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 4,
+ "text": [
+ "8"
+ ]
+ }
+ ],
+ "prompt_number": 4
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "add_some_other_number(3, other_number=4)"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 5,
+ "text": [
+ "7"
+ ]
+ }
+ ],
+ "prompt_number": 5
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "add_some_other_number(5)"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 6,
+ "text": [
+ "17"
+ ]
+ }
+ ],
+ "prompt_number": 6
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "subslide"
+ }
+ },
+ "source": [
+ "Functions\n",
+ "===\n",
+ "\n",
+ "Docstrings\n",
+ "---\n",
+ "\n",
+ "Like many other definitions, functions can have docstrings.\n",
+ "\n",
+ "* Docstrings are regular string values which you start the definition body with.\n",
+ "* You can access an object's docstring using `help`."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "def factorial(n):\n",
+ " \"\"\"Compute factorial of n in the obious way.\"\"\"\n",
+ " if n == 0:\n",
+ " return 1\n",
+ " else:\n",
+ " return factorial(n - 1) * n"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [],
+ "prompt_number": 7
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "help(factorial)"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "output_type": "stream",
+ "stream": "stdout",
+ "text": [
+ "Help on function factorial in module __main__:\n",
+ "\n",
+ "factorial(n)\n",
+ " Compute factorial of n in the obious way.\n",
+ "\n"
+ ]
+ }
+ ],
+ "prompt_number": 8
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "subslide"
+ }
+ },
+ "source": [
+ "Functions\n",
+ "===\n",
+ "\n",
+ "Functions are values\n",
+ "---\n",
+ "\n",
+ "We can pass functions around just like other values, and call them."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "functions = [add_two, add_some_other_number]\n",
+ "for function in functions:\n",
+ " print function(7)"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "output_type": "stream",
+ "stream": "stdout",
+ "text": [
+ "9\n",
+ "19\n"
+ ]
+ }
+ ],
+ "prompt_number": 9
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Simple anonymous functions can be created with `lambda`."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "functions.append(lambda x: x * 7)\n",
+ "for function in functions:\n",
+ " print function(4)"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "output_type": "stream",
+ "stream": "stdout",
+ "text": [
+ "6\n",
+ "16\n",
+ "28\n"
+ ]
+ }
+ ],
+ "prompt_number": 10
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "subslide"
+ }
+ },
+ "source": [
+ "Functions\n",
+ "===\n",
+ "\n",
+ "Higher-order functions\n",
+ "---\n",
+ "\n",
+ "A function that takes a function as argument is a higher-order function."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "help(map)"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "output_type": "stream",
+ "stream": "stdout",
+ "text": [
+ "Help on built-in function map in module __builtin__:\n",
+ "\n",
+ "map(...)\n",
+ " map(function, sequence[, sequence, ...]) -> list\n",
+ " \n",
+ " Return a list of the results of applying the function to the items of\n",
+ " the argument sequence(s). If more than one sequence is given, the\n",
+ " function is called with an argument list consisting of the corresponding\n",
+ " item of each sequence, substituting None for missing values when not all\n",
+ " sequences have the same length. If the function is None, return a list of\n",
+ " the items of the sequence (or a list of tuples if more than one sequence).\n",
+ "\n"
+ ]
+ }
+ ],
+ "prompt_number": 11
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "map(add_two, [1, 2, 3, 4])"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 12,
+ "text": [
+ "[3, 4, 5, 6]"
+ ]
+ }
+ ],
+ "prompt_number": 12
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "$\\S$ Exercise: k-mer counting (1/2)\n",
+ "===\n",
+ "\n",
+ "Remember the previous exercise of finding (unique) substrings of length 3.\n",
+ "\n",
+ "* Make a function from your implementation.\n",
+ "* Have `k` as an argument to the function.\n",
+ "* Test the function on several input strings.\n",
+ "\n",
+ "**Note:** Editing multi-line statements in the console can be frustrating. You can try the QT console (`ipython qtconsole`) or edit your function in an editor with `%edit`:\n",
+ "\n",
+ " def my_function(arg):\n",
+ " print arg * 4\n",
+ " %edit my_function"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "subslide"
+ }
+ },
+ "source": [
+ "$\\S$ Exercise: k-mer counting (2/2)\n",
+ "===\n",
+ "\n",
+ "Modify your function to use a dictionary with substring counts.\n",
+ "\n",
+ "* Use the substrings as dictionary keys.\n",
+ "* Use the counts as dictionary values.\n",
+ "* Have the function return the dictionary.\n",
+ "* Add a docstring to the function.\n",
+ "* Use the function to print k-mer counts for some strings."
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "Comprehensions\n",
+ "===\n",
+ "\n",
+ "List comprehensions\n",
+ "---\n",
+ "\n",
+ "Similar to mathematical set notation (e.g., $\\{ x ~|~ x \\in \\mathbf R \\land x > 0\\}$), we can create lists."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "[(x, x * x) for x in range(10) if x % 2]"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 13,
+ "text": [
+ "[(1, 1), (3, 9), (5, 25), (7, 49), (9, 81)]"
+ ]
+ }
+ ],
+ "prompt_number": 13
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "We can do the same thing using `map` and `filter`, but list comprehensions are often more readable."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "map(lambda x: (x, x * x), filter(lambda x: x %2, range(10)))"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 14,
+ "text": [
+ "[(1, 1), (3, 9), (5, 25), (7, 49), (9, 81)]"
+ ]
+ }
+ ],
+ "prompt_number": 14
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "subslide"
+ }
+ },
+ "source": [
+ "Comprehensions\n",
+ "===\n",
+ "\n",
+ "Set and dictionary comprehensions\n",
+ "---\n",
+ "\n",
+ "Similar notation can be used for (non-empty) sets."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "{c for c in 'LUMC-standard' if 'a' <= c <= 'z'}"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 15,
+ "text": [
+ "{'a', 'd', 'n', 'r', 's', 't'}"
+ ]
+ }
+ ],
+ "prompt_number": 15
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "And dictionaries."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "colors = ['red', 'white', 'blue', 'orange']\n",
+ "{c: len(c) for c in colors}"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 16,
+ "text": [
+ "{'blue': 4, 'orange': 6, 'red': 3, 'white': 5}"
+ ]
+ }
+ ],
+ "prompt_number": 16
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "Everything is an object\n",
+ "===\n",
+ "\n",
+ "* Objects have properties and methods. \n",
+ "* Explore them using `dir(o)`, or by typing `o.<tab>` in the IPython interpreter."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "dir('abc')[-5:]"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 17,
+ "text": [
+ "['swapcase', 'title', 'translate', 'upper', 'zfill']"
+ ]
+ }
+ ],
+ "prompt_number": 17
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "help('abc'.upper)"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "output_type": "stream",
+ "stream": "stdout",
+ "text": [
+ "Help on built-in function upper:\n",
+ "\n",
+ "upper(...)\n",
+ " S.upper() -> string\n",
+ " \n",
+ " Return a copy of the string S converted to uppercase.\n",
+ "\n"
+ ]
+ }
+ ],
+ "prompt_number": 18
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "'abc'.upper()"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 19,
+ "text": [
+ "'ABC'"
+ ]
+ }
+ ],
+ "prompt_number": 19
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "Code in files\n",
+ "===\n",
+ "\n",
+ "Running code from a file\n",
+ "---"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "cat examples/fsquare.py"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "output_type": "stream",
+ "stream": "stdout",
+ "text": [
+ "d = {}\r\n",
+ "for i in range(10):\r\n",
+ " d[i] = i ** 2\r\n",
+ "\r\n",
+ "for i in d:\r\n",
+ " print \"{0} is the square of {1}.\".format(d[i], i)\r\n"
+ ]
+ }
+ ],
+ "prompt_number": 20
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "%%sh\n",
+ "python examples/fsquare.py"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "output_type": "stream",
+ "stream": "stdout",
+ "text": [
+ "0 is the square of 0.\n",
+ "1 is the square of 1.\n",
+ "4 is the square of 2.\n",
+ "9 is the square of 3.\n",
+ "16 is the square of 4.\n",
+ "25 is the square of 5.\n",
+ "36 is the square of 6.\n",
+ "49 is the square of 7.\n",
+ "64 is the square of 8.\n",
+ "81 is the square of 9.\n"
+ ]
+ }
+ ],
+ "prompt_number": 21
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "subslide"
+ }
+ },
+ "source": [
+ "Code in files\n",
+ "===\n",
+ "\n",
+ "Working with files in IPython\n",
+ "---\n",
+ "\n",
+ "The `%run` magic runs the code from a file directly in IPython:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "%run examples/fsquare.py"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "output_type": "stream",
+ "stream": "stdout",
+ "text": [
+ "0 is the square of 0.\n",
+ "1 is the square of 1.\n",
+ "4 is the square of 2.\n",
+ "9 is the square of 3.\n",
+ "16 is the square of 4.\n",
+ "25 is the square of 5.\n",
+ "36 is the square of 6.\n",
+ "49 is the square of 7.\n",
+ "64 is the square of 8.\n",
+ "81 is the square of 9.\n"
+ ]
+ }
+ ],
+ "prompt_number": 22
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "-"
+ }
+ },
+ "source": [
+ "You can edit and run a file with `%edit`."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "%edit examples/fsquare.py"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [],
+ "prompt_number": 23
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "subslide"
+ }
+ },
+ "source": [
+ "Code in files\n",
+ "===\n",
+ "\n",
+ "Saving your IPython session history to a file\n",
+ "---\n",
+ "\n",
+ "Give the `%save` magic a name and a range of input lines and it will save them to a `.py` file with that name:\n",
+ "\n",
+ " In [4]: %save my_session 1-3\n",
+ " The following commands were written to file `my_session.py`:\n",
+ " a = 4\n",
+ " a += 3\n",
+ " b = a"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "$\\S$ Exercise: Running code from a file\n",
+ "===\n",
+ "\n",
+ "* Save your k-mer counting code to a file `kmer_counting.py`.\n",
+ "* Include some code using it on an example string and printing the results.\n",
+ "* Run the code from the command line."
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "Further reading\n",
+ "===\n",
+ "\n",
+ "* [The Python Tutorial](http://docs.python.org/2/tutorial/index.html)\n",
+ " <br>\n",
+ " From the official Python documentation.\n",
+ "\n",
+ "\n",
+ "* [Learn Python The Hard Way](http://learnpythonthehardway.org/book/)\n",
+ " <br>\n",
+ " Book on learning Python by exercises, online available for free.\n",
+ "\n",
+ "\n",
+ "* [The Hitchhiker's Guide to Python](http://docs.python-guide.org/en/latest/)\n",
+ " <br>\n",
+ " This opinionated guide exists to provide both novice and expert Python developers a best-practice handbook to the installation, configuration, and usage of Python on a daily basis.\n",
+ "\n",
+ "\n",
+ "* [A Primer on Scientific Programming with Python](http://codingcat.com/knjige/python/A%20Primer%20on%20Scientific%20Programming%20with%20Python.pdf)\n",
+ " <br>\n",
+ " Complete PDF version of the book. The aim of this book is to teach computer programming using examples from mathematics and the natural sciences.\n",
+ "\n",
+ "\n",
+ "* [Python Module of the Week](http://pymotw.com/)\n",
+ " <br>\n",
+ " Series of articles providing a tour of the Python standard library through short examples."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "from IPython.display import HTML\n",
+ "def css_styling():\n",
+ " styles = open('styles/custom.css', 'r').read()\n",
+ " return HTML('<style>' + styles + '</style>')\n",
+ "css_styling()"
+ ],
+ "language": "python",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "skip"
+ }
+ },
+ "outputs": [
+ {
+ "html": [
+ "<style>/* Remove the vertical scrollbar added by nbconvert. */\n",
+ ".reveal {\n",
+ " overflow: hidden;\n",
+ "}\n",
+ "\n",
+ "/* Workaround some highlight.js bugs in language autodetection. */\n",
+ "code.objectivec *,\n",
+ "code.perl *,\n",
+ "code.cs *,\n",
+ "code.javascript *,\n",
+ "code.http * {\n",
+ " color: black ! important;\n",
+ " font-weight: normal ! important;\n",
+ "}\n",
+ "span.title {\n",
+ " color: black ! important;\n",
+ "}\n",
+ "span.tag {\n",
+ " color: black ! important;\n",
+ "}\n",
+ "span.attribute {\n",
+ " color: black ! important;\n",
+ "}\n",
+ "</style>"
+ ],
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 1,
+ "text": [
+ "<IPython.core.display.HTML at 0x2e0ea50>"
+ ]
+ }
+ ],
+ "prompt_number": 1
+ }
+ ],
+ "metadata": {}
+ }
+ ]
+}
\ No newline at end of file
diff --git a/03 - More Python goodness (1).ipynb b/past_sessions/2014_july/03 - More Python goodness (1).ipynb
similarity index 100%
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diff --git a/03 - More Python goodness (2).ipynb b/past_sessions/2014_july/03 - More Python goodness (2).ipynb
similarity index 100%
rename from 03 - More Python goodness (2).ipynb
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diff --git a/04 - Working with NumPy arrays.ipynb b/past_sessions/2014_july/04 - Working with NumPy arrays.ipynb
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diff --git a/05 - IPython Notebook.ipynb b/past_sessions/2014_july/05 - IPython Notebook.ipynb
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diff --git a/06 - Plotting with matplotlib.ipynb b/past_sessions/2014_july/06 - Plotting with matplotlib.ipynb
similarity index 100%
rename from 06 - Plotting with matplotlib.ipynb
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diff --git a/07 - Painting Pandas.ipynb b/past_sessions/2014_july/07 - Painting Pandas.ipynb
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diff --git a/08 - Object-oriented programming.ipynb b/past_sessions/2014_july/08 - Object-oriented programming.ipynb
similarity index 100%
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diff --git a/09 - A sip of Biopython (1).ipynb b/past_sessions/2014_july/09 - A sip of Biopython (1).ipynb
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diff --git a/09 - A sip of Biopython (2).ipynb b/past_sessions/2014_july/09 - A sip of Biopython (2).ipynb
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diff --git a/INSTALL.md b/past_sessions/2014_july/INSTALL.md
similarity index 100%
rename from INSTALL.md
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diff --git a/past_sessions/2014_july/README.md b/past_sessions/2014_july/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..75c9c3e9b536c0de6b721e4f898381d7d62bfc19
--- /dev/null
+++ b/past_sessions/2014_july/README.md
@@ -0,0 +1,132 @@
+Programming course
+==================
+
+This repository contains material for the second installment (July 2014) of a
+programming course for scientists organised by the department of Human
+Genetics of the Leiden University Medical Center.
+
+The course is targeted at PhD students, Postdocs, or anyone willing to learn
+how to program in Python. Students are assumed to have some experience with
+programming, but not necessarily in Python, and the UNIX shell.
+
+The program consists of four mornings with lessons and some assignments to
+be done in your own time (i.e., during the afternoons).
+
+See the
+[Trac Wiki](https://humgenprojects.lumc.nl/trac/humgenprojects/wiki/ProgrammingCourse)
+for more information.
+
+Software installation
+---------------------
+
+See the instructions in `INSTALL.md`.
+
+
+Materials
+---------
+
+The top-level directory contains materials for the following lessons:
+
+1. Welcome ([slides][lesson_01])
+2. Introduction to Python ([slides 1][lesson_02_01], [slides 2][lesson_02_02],
+ [slides 3][lesson_02_03])
+3. More Python Goodness ([notebook 1][lesson_03_01], [notebook 2][lesson_03_02])
+4. Working with NumPy arrays ([slides][lesson_04])
+5. IPython Notebook ([notebook][lesson_05])
+6. Plotting with matplotlib ([notebook][lesson_06])
+7. Painting Pandas ([slides][lesson_07])
+8. Object-oriented programming ([slides][lesson_08])
+9. A sip of Biopython ([notebook 1][lesson_09_01], [notebook 2][lesson_09_02])
+
+[lesson_01]: http://nbviewer.ipython.org/urls/git.lumc.nl/courses/programming-course/raw/master/past_sessions/2014_july/01%20-%20Welcome.ipynb
+[lesson_02_01]: http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/02%20-%20Introduction%20to%20Python%20(1).ipynb
+[lesson_02_02]: http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/02%20-%20Introduction%20to%20Python%20(2).ipynb
+[lesson_02_03]: http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/02%20-%20Introduction%20to%20Python%20(3).ipynb
+[lesson_03_01]: http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/03%20-%20More%20Python%20goodness%20(1).ipynb
+[lesson_03_02]: http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/03%20-%20More%20Python%20goodness%20(2).ipynb
+[lesson_04]: http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/04%20-%20Working%20with%20NumPy%20arrays.ipynb
+[lesson_05]: http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/05%20-%20IPython%20Notebook.ipynb
+[lesson_06]: http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/06%20-%20Plotting%20with%20matplotlib.ipynb
+[lesson_07]: http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/07%20-%20Painting%20Pandas.ipynb
+[lesson_08]: http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/08%20-%20Object-oriented%20programming.ipynb
+[lesson_09_01]: http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/09%20-%20A%20sip%20of%20Biopython%20(1).ipynb
+[lesson_09_02]: http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/09%20-%20A%20sip%20of%20Biopython%20(2).ipynb
+
+As indicated, some of the lessons are slideshows, whereas others are just
+notebooks we scroll through during class. The links above are all one-page
+static renderings on [IPython Notebook Viewer](http://nbviewer.ipython.org/).
+
+We also have a
+[repository with material for the assignments](https://git.lumc.nl/humgen/programming-course-assignments).
+
+
+Notebooks
+---------
+
+We apply some custom styling to the notebooks (e.g., body width, font), which
+is loaded in the last cell. This loads `styles/notebook.css` and
+`styles/notebook.js`.
+
+A variant `styles/notebook.css.small` is provided that is more suitable for
+use on low-resolution displays. To use it, manually change the reference to
+this file in the bottom cell, and rerun it.
+
+
+Slideshows
+----------
+
+The sources for the slideshows are also IPython notebooks and you can edit
+them by starting a notebook server:
+
+ ipython notebook
+
+Choose *Slideshow* in the *Cell Toolbar* menu.
+
+Some aditional information on editing slides in the Notebook can be found
+here in
+[this presentation](http://www.slideviper.oquanta.info/tutorial/slideshow_tutorial_slides.html).
+
+We also apply some custom styling to the slideshows, which is loaded in the
+last cell.
+
+
+Live rendering of the slides
+----------------------------
+
+You can use nbconvert to convert the slides to HTML and serve them. For
+example:
+
+ ipython nbconvert --to slides --post serve numpy.ipynb
+
+This will open the slides in a new browser window. If you don't want that, add
+this argument:
+
+ --ServePostProcessor.open_in_browser=False
+
+To serve on another IP address than the default 127.0.0.1, use the `ip`
+configuration of the serve postprocessing. For example, to listen on all IP
+addresses:
+
+ --ServePostProcessor.ip=0.0.0.0
+
+Changing the port can be done similarly with `port`.
+
+By default, the reveal.js library is loaded over the internet from a CDN. I
+think it's usually not a good idea to rely on internet connectivity for your
+slides, so you can also place a copy of reveal.js on your local computer and
+specify the location like this:
+
+ --reveal-prefix reveal.js
+
+This would look for the reveal.js library in the `reveal.js` directory. A Git
+submodule is already setup for this, so you can just do:
+
+ git submodule init
+ git submodule update
+
+(Unfortunately, there are other online dependencies such Font Awesome, so
+without an internet connection, not everything will look ok, but it will
+work.)
+
+Also, if you just want to compile the slides to HTML without serving them to
+your browser, leave out the `--post serve` argument.
diff --git a/person.py b/past_sessions/2014_july/person.py
similarity index 100%
rename from person.py
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diff --git a/solutions/More_goodness_progression.ipynb b/past_sessions/2014_july/solutions/More_goodness_progression.ipynb
similarity index 100%
rename from solutions/More_goodness_progression.ipynb
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diff --git a/solutions/matplotlib.ipynb b/past_sessions/2014_july/solutions/matplotlib.ipynb
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diff --git a/solutions/more_python_seq_toolbox.py b/past_sessions/2014_july/solutions/more_python_seq_toolbox.py
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rename from solutions/more_python_seq_toolbox.py
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diff --git a/solutions/notebook.ipynb b/past_sessions/2014_july/solutions/notebook.ipynb
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diff --git a/solutions/numpy.ipynb b/past_sessions/2014_july/solutions/numpy.ipynb
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diff --git a/solutions/python_01_bottles_of_beer.py b/past_sessions/2014_july/solutions/python_01_bottles_of_beer.py
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diff --git a/solutions/python_02_repeat_structure.py b/past_sessions/2014_july/solutions/python_02_repeat_structure.py
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rename from solutions/python_02_repeat_structure.py
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diff --git a/solutions/python_03_combining_lists.py b/past_sessions/2014_july/solutions/python_03_combining_lists.py
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rename from solutions/python_03_combining_lists.py
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diff --git a/solutions/python_04_dictionaries.py b/past_sessions/2014_july/solutions/python_04_dictionaries.py
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diff --git a/solutions/python_05_kmer_counting.py b/past_sessions/2014_july/solutions/python_05_kmer_counting.py
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rename from solutions/python_05_kmer_counting.py
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diff --git a/solutions/python_08_scientific_calculator.py b/past_sessions/2014_july/solutions/python_08_scientific_calculator.py
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diff --git a/reveal.js b/reveal.js
index 131c00689a4c7a18e5c991fc8102347e4594b5d4..43eada79901830702bd40dce857831aef8e76759 160000
--- a/reveal.js
+++ b/reveal.js
@@ -1 +1 @@
-Subproject commit 131c00689a4c7a18e5c991fc8102347e4594b5d4
+Subproject commit 43eada79901830702bd40dce857831aef8e76759