From 14546372d26f512414ccf1ccc3ee2570a4434f92 Mon Sep 17 00:00:00 2001
From: "J.F.J. Laros" <jlaros@obscured.morspoort.fixedpoint.nl>
Date: Wed, 7 Aug 2013 17:36:51 +0200
Subject: [PATCH] Updated the slides on object oriented programming.
---
classes.ipynb | 104 +++++++++++++++++++++++++++++++++++++++++++++-----
1 file changed, 95 insertions(+), 9 deletions(-)
diff --git a/classes.ipynb b/classes.ipynb
index 51c008a..5ea4e0d 100644
--- a/classes.ipynb
+++ b/classes.ipynb
@@ -42,7 +42,7 @@
"\n",
"You can use nbconvert to convert the slides to HTML and serve them:\n",
"\n",
- " ipython nbconvert --to slides --post serve matplotlib.ipynb\n",
+ " ipython nbconvert --to slides --post serve classes.ipynb\n",
"\n",
"This will open the slides in a new browser window."
]
@@ -73,7 +73,11 @@
},
{
"cell_type": "markdown",
- "metadata": {},
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
"source": [
"Imagine we are collecting a number of attributes of some persons:\n",
"\n",
@@ -378,7 +382,11 @@
},
{
"cell_type": "markdown",
- "metadata": {},
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
"source": [
" class Person(object):\n",
" ...\n",
@@ -436,7 +444,11 @@
},
{
"cell_type": "markdown",
- "metadata": {},
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
"source": [
" class Person(object):\n",
" ...\n",
@@ -556,7 +568,11 @@
},
{
"cell_type": "markdown",
- "metadata": {},
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
"source": [
" class Person(object):\n",
" ...\n",
@@ -607,7 +623,11 @@
" self.eye_colour, self.hair_colour, self.weight, self.length)"
],
"language": "python",
- "metadata": {},
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
"outputs": [],
"prompt_number": 127
},
@@ -633,9 +653,75 @@
"prompt_number": 86
},
{
- "cell_type": "markdown",
- "metadata": {},
- "source": []
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "class Read(object):\n",
+ " def __init__(self):\n",
+ " self.read = \"\"\n",
+ " self.qual = []\n",
+ " \n",
+ " def __str__(self):\n",
+ " return self.read\n",
+ " \n",
+ " def add(self, base):\n",
+ " self.read += base[0]\n",
+ " self.qual.append(base[1])\n",
+ " \n",
+ " def quality(self):\n",
+ " return sum(self.qual) / len(self.read)\n",
+ " \n",
+ " def trim(self, score):\n",
+ " for position in range(len(self.read) - 1, -1, -1):\n",
+ " if self.qual[position] >= score:\n",
+ " return self.read[:position]"
+ ],
+ "language": "python",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "outputs": [],
+ "prompt_number": 7
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "from sequencer import Sequencer\n",
+ "\n",
+ "spots = 2\n",
+ "run = Sequencer(spots, readlength=60)\n",
+ "\n",
+ "reads = [Read() for _ in range(spots)]\n",
+ "for tile in run:\n",
+ " for read_id, base in enumerate(tile):\n",
+ " reads[read_id].add(base)\n",
+ "\n",
+ "for i in reads:\n",
+ " print i, i.quality()\n",
+ " print i.trim(39)"
+ ],
+ "language": "python",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "outputs": [
+ {
+ "output_type": "stream",
+ "stream": "stdout",
+ "text": [
+ "GGTGTGATTCCCGTTCGGTGGGCCGCCTTGGGTCATTGCTCGGTTGAGGAGGGAAGACCT 30\n",
+ "GGTGTGATTCCCGTTCGGTGGGCCGCCTTGGGTCAT\n",
+ "GGCTTTAGAATGTCTCCTGCATCTGATGCTATTAAAAGCTATGTTTTTCACATAGTACGG 29\n",
+ "GGCTTTAGAATGTCTCCTGCATCTGATGCTATTAAAAGCTATGTTTTTCACATAGT\n"
+ ]
+ }
+ ],
+ "prompt_number": 8
}
],
"metadata": {}
--
GitLab