Skip to content
Snippets Groups Projects
Commit 26accada authored by Vermaat's avatar Vermaat
Browse files

Merge remote-tracking branch 'gitlab/jfjlaros_2014'

parents 139915b2 9885ba3d
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
.gitmodules
+ 3
− 0
View file @ 26accada
[submodule "reveal.js"]
path = reveal.js
url = https://github.com/hakimel/reveal.js.git
[submodule "programming-course-assignments"]
path = programming-course-assignments
url = git@git.lumc.nl:humgen/programming-course-assignments.git
matplotlib.ipynb → 06 - Plotting with matplotlib.ipynb
+ 437
− 271
View file @ 26accada
Source diff could not be displayed: it is too large. Options to address this: view the blob.
classes.ipynb → 08 - Object-oriented programming.ipynb
+ 144
− 94
View file @ 26accada
......@@ -50,7 +50,7 @@
]
}
],
"prompt_number": 1
"prompt_number": 2
},
{
"cell_type": "markdown",
......@@ -67,7 +67,7 @@
"\n",
"You can use nbconvert to convert the slides to HTML and serve them:\n",
"\n",
" ipython nbconvert --to slides --post serve classes.ipynb\n",
" ipython nbconvert --to slides --post serve \"08 - Object-oriented programming.ipynb\" \n",
"\n",
"This will open the slides in a new browser window."
]
......@@ -120,13 +120,13 @@
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 2,
"prompt_number": 3,
"text": [
"('blue', 90, 161)"
]
}
],
"prompt_number": 2
"prompt_number": 3
},
{
"cell_type": "markdown",
......@@ -147,13 +147,13 @@
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 3,
"prompt_number": 4,
"text": [
"90"
]
}
],
"prompt_number": 3
"prompt_number": 4
},
{
"cell_type": "markdown",
......@@ -194,13 +194,13 @@
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 4,
"prompt_number": 5,
"text": [
"['blue', 90, 161]"
]
}
],
"prompt_number": 4
"prompt_number": 5
},
{
"cell_type": "markdown",
......@@ -221,13 +221,13 @@
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 5,
"prompt_number": 6,
"text": [
"161"
]
}
],
"prompt_number": 5
"prompt_number": 6
},
{
"cell_type": "markdown",
......@@ -268,13 +268,13 @@
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 6,
"prompt_number": 7,
"text": [
"{'hair_colour': 'blue', 'length': 161, 'weight': 90}"
]
}
],
"prompt_number": 6
"prompt_number": 7
},
{
"cell_type": "code",
......@@ -288,13 +288,13 @@
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 7,
"prompt_number": 8,
"text": [
"90"
]
}
],
"prompt_number": 7
"prompt_number": 8
},
{
"cell_type": "markdown",
......@@ -339,13 +339,13 @@
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 8,
"prompt_number": 9,
"text": [
"90"
]
}
],
"prompt_number": 8
"prompt_number": 9
},
{
"cell_type": "markdown",
......@@ -383,13 +383,13 @@
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 9,
"prompt_number": 10,
"text": [
"90"
]
}
],
"prompt_number": 9
"prompt_number": 10
},
{
"cell_type": "markdown",
......@@ -435,13 +435,13 @@
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 10,
"prompt_number": 11,
"text": [
"(90, 'blue')"
]
}
],
"prompt_number": 10
"prompt_number": 11
},
{
"cell_type": "code",
......@@ -457,13 +457,13 @@
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 11,
"prompt_number": 12,
"text": [
"(93, 'white')"
]
}
],
"prompt_number": 11
"prompt_number": 12
},
{
"cell_type": "markdown",
......@@ -519,13 +519,13 @@
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 12,
"prompt_number": 13,
"text": [
"(205.02965999999998, 93000)"
]
}
],
"prompt_number": 12
"prompt_number": 13
},
{
"cell_type": "markdown",
......@@ -593,13 +593,13 @@
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 13,
"prompt_number": 14,
"text": [
"80"
]
}
],
"prompt_number": 13
"prompt_number": 14
},
{
"cell_type": "code",
......@@ -614,13 +614,13 @@
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 14,
"prompt_number": 15,
"text": [
"79"
]
}
],
"prompt_number": 14
"prompt_number": 15
},
{
"cell_type": "code",
......@@ -637,13 +637,13 @@
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 15,
"prompt_number": 16,
"text": [
"90"
]
}
],
"prompt_number": 15
"prompt_number": 16
},
{
"cell_type": "markdown",
......@@ -714,7 +714,7 @@
]
}
],
"prompt_number": 16
"prompt_number": 17
},
{
"cell_type": "markdown",
......@@ -744,7 +744,7 @@
}
},
"outputs": [],
"prompt_number": 17
"prompt_number": 18
},
{
"cell_type": "markdown",
......@@ -772,54 +772,32 @@
]
}
],
"prompt_number": 18
"prompt_number": 19
},
{
"cell_type": "markdown",
"metadata": {
"slideshow": {
"slide_type": "slide"
"slide_type": "subslide"
}
},
"source": [
"The Sequencer assignment\n",
"$\\S$ A stack calculator\n",
"==="
]
},
{
"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 \"\".join(self.read)\n",
" \n",
" def append(self, base):\n",
" self.read.append(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",
" self.read = self.read[:position + 1]\n",
" self.qual = self.qual[:position + 1]\n",
" break"
],
"language": "python",
"cell_type": "markdown",
"metadata": {
"slideshow": {
"slide_type": "-"
}
},
"outputs": [],
"prompt_number": 19
"source": [
"A stack is a datastructure that only allows access to the ''top'' element.\n",
"\n",
"<img src=\"files/images/stack.png\" />"
]
},
{
"cell_type": "markdown",
......@@ -829,7 +807,41 @@
}
},
"source": [
"The Sequencer assignment\n",
"$\\S$ A stack calculator\n",
"==="
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Stack operations\n",
"---\n",
"\n",
"* Push - Add one element to the top of the stack.\n",
"* Pop - Retrieve the top element from the stack.\n",
"\n",
"Arithmetic with a stack\n",
"---\n",
"\n",
"* Pop the operands from the stack.\n",
"* Perform an arithmetic operation.\n",
"* Push the result back to the stack.\n",
"\n",
"Example (add two numbers):\n",
"\n",
" stack.push(stack.pop() + stack.pop())"
]
},
{
"cell_type": "markdown",
"metadata": {
"slideshow": {
"slide_type": "subslide"
}
},
"source": [
"$\\S$ A stack calculator\n",
"==="
]
},
......@@ -837,40 +849,78 @@
"cell_type": "code",
"collapsed": false,
"input": [
"from sequencer import Sequencer\n",
"%load programming-course-assignments/calculator/calculator.py"
],
"language": "python",
"metadata": {
"slideshow": {
"slide_type": "skip"
}
},
"outputs": [],
"prompt_number": 40
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"#!/usr/bin/env python\n",
"\n",
"spots = 2\n",
"run = Sequencer(spots, readlength=60)\n",
"class Stack(list):\n",
" def push(self, element):\n",
" self.append(element)\n",
"\n",
" def __str__(self):\n",
" return str(self[-1])\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].append(base)\n",
"\n",
"for i in reads:\n",
" print i, i.quality()\n",
" i.trim(39)\n",
" print i, i.quality()"
"class Calculator(Stack):\n",
" def add(self):\n",
" self.push(self.pop() + self.pop())\n",
"\n",
" def sub(self):\n",
" temp = self.pop()\n",
" self.push(self.pop() - temp)\n",
"\n",
" def mul(self):\n",
" self.push(self.pop() * self.pop())\n",
"\n",
" def div(self):\n",
" temp = self.pop()\n",
" self.push(self.pop() / temp)\n"
],
"language": "python",
"metadata": {},
"outputs": []
},
{
"cell_type": "markdown",
"metadata": {
"slideshow": {
"slide_type": "-"
"slide_type": "subslide"
}
},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"AACAGTGAGCAATGCGCACTTCCAGTGCCATGCCTATACGCCGGGCCGTTAAGAATTTAT 31\n",
"AACAGTGAGCAATGCGCACTTCCAGTGCCATGCCTATACGCCG 34\n",
"CACCTTGAGGTATACGGGCACTACACGAACGTATAATTACCGTATTATGGGTCTCCCAGA 30\n",
"CACCTTGAGGTATACGGGCACTACACGAACGTATAATTACCGTATTATG 33\n"
]
}
],
"prompt_number": 20
"source": [
"$\\S$ A stack calculator\n",
"==="
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Assignment\n",
"---\n",
"\n",
"* Make a scientific calculator.\n",
"* Add exponentiation and square root functions.\n",
"\n",
"Hints:\n",
"\n",
"* Do not edit the `calculator.py` file, use `import` instead.\n",
"* Use inheritance.\n",
"* To use mathematical functions, use the `math` library."
]
},
{
"cell_type": "code",
......@@ -884,7 +934,7 @@
"language": "python",
"metadata": {
"slideshow": {
"slide_type": "slide"
"slide_type": "skip"
}
},
"outputs": [
......@@ -892,7 +942,7 @@
"html": [
"<style>/* Remove the vertical scrollbar added by nbconvert. */\n",
".reveal {\n",
" overflow-y: hidden;\n",
" overflow: hidden;\n",
"}\n",
"\n",
"/* Workaround some highlight.js bugs in language autodetection. */\n",
......@@ -917,13 +967,13 @@
],
"metadata": {},
"output_type": "pyout",
"prompt_number": 21,
"prompt_number": 22,
"text": [
"<IPython.core.display.HTML at 0x3cc71d0>"
"<IPython.core.display.HTML at 0xb182306c>"
]
}
],
"prompt_number": 21
"prompt_number": 22
}
],
"metadata": {}
......
images/stack.png 0 → 100644
+ 0
− 0
View file @ 26accada
images/stack.png

8.23 KiB

programming-course-assignments @ 44222ed4
Subproject commit 44222ed4f2d9b932d6bde32b1587d2668b9dd7da
solutions/python_08_scientific_calculator.py 0 → 100644
+ 22
− 0
View file @ 26accada
#!/usr/bin/env python
import math
from calculator import Calculator
class ScientificCalculator(Calculator):
def pow(self):
temp = self.pop()
self.push(self.pop() ** temp)
def sqrt(self):
self.push(math.sqrt(self.pop()))
s = ScientificCalculator()
s.push(2)
s.push(3)
s.pow()
print s
s.sqrt()
print s
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment