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Uploading assignment solutions for review
=========================================
Some assignments need additional data or come with some example startup code
for you to use. These are stored in a Git repository. Git can also be used to
share your solutions for review.
Start by configuring Git (only need to do this once per computer). In a
terminal, type:
git config --global user.name "John Doe"
git config --global user.email johndoe@example.com
Clone the assignments repository
--------------------------------
Use your webbrowser to go to:
https://git.lumc.nl/humgen/programming-course-assignments
Sign in using your LUMC account or the account you were emailed (notify a
teacher if you cannot login). Click the *Fork repository* button on the
right.
The resulting page is your fork of the repository. Bookmark this page in your
browser.
On your fork, click the *HTTPS* button on the top and copy the resulting URL,
e.g.,
`https://git.lumc.nl/johndoe/programming-course-assignments.git`.
Use this URL to clone the repository on your local computer. In a terminal,
type:
git clone https://git.lumc.nl/johndoe/programming-course-assignments.git
You now have a copy of the material on your computer. Change directory to it:
cd programming-course-assignments
Do an assignment
----------------
You'll have to figure this out yourself. Just make sure you do your work
within the directory we just created.
Commit and publish your solution
--------------------------------
For any files you created as part of your solution, run `git add`. For
example:
git add solution_1.py
Commit your changes to Git:
git commit -am 'Solution for assignment 1'
Push your changes to the server:
git push
You can repeat this section later when you did another assignment.
Share your solution
-------------------
Go to your project page (the one you bookmarked) where you should now see what
you pushed earlier.
You can of course share your solution simply by sharing a link to your project
page. However, there is a nice feature in GitLab called *merge requests* which
you can use to directly submit you solution to the teachers.
On your project page, click the green square button on the right (with three
horizontal white stripes) an choose *New merge request*. Make sure the *Source
branch* is set to *master* on your fork and the *Target branch* is set to
*master* on the original (*humgen*).
Click *Compare branches*. Enter an appropriate title and perhaps a description
before clicking *Submit merge request*. The resulting page can be used by you
and the teachers to discuss your solution.
This diff is collapsed.
Programming course assignments
==============================
This repository contains some assignment material for the first installment
(August 2013) of a programming course for scientists organised by the
department of Human Genetics of the Leiden University Medical Center.
See the [Trac Wiki](https://humgenprojects.lumc.nl/trac/programming-course)
for more information.
Programming course assignments
==============================
This repository contains some assignment 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.
See the
[course website](https://humgenprojects.lumc.nl/trac/humgenprojects/wiki/ProgrammingCourse)
for more information.
Also see the [instructions on using this repository](INSTRUCTIONS.md).
#!/usr/bin/env python
class Stack(list):
def push(self, element):
self.append(element)
def __str__(self):
return str(self[-1])
class Calculator(Stack):
def add(self):
self.push(self.pop() + self.pop())
def sub(self):
temp = self.pop()
self.push(self.pop() - temp)
def mul(self):
self.push(self.pop() * self.pop())
def div(self):
temp = self.pop()
self.push(self.pop() / temp)
@HWI-ST1019:196:D121WACXX:5:1101:1538:2300/1
CCGCGACCTCTGTTCTGCAGCCCCTTCCCTTCCCCGCCTCCTGCTCTGCCGGGACTACGCACCGGCCTGATTGGTTACCCCCGGGGTGTCCTCGGTCACCA
+
1+++4)<@<A<+2A9A2++:3C8:)1?BDBDBBDC@::6@(.8..7)777:<?@@##############################################
5.1,3.5,1.4,0.2,Iris-setosa
4.9,3.0,1.4,0.2,Iris-setosa
4.7,3.2,1.3,0.2,Iris-setosa
4.6,3.1,1.5,0.2,Iris-setosa
5.0,3.6,1.4,0.2,Iris-setosa
5.4,3.9,1.7,0.4,Iris-setosa
4.6,3.4,1.4,0.3,Iris-setosa
5.0,3.4,1.5,0.2,Iris-setosa
4.4,2.9,1.4,0.2,Iris-setosa
4.9,3.1,1.5,0.1,Iris-setosa
5.4,3.7,1.5,0.2,Iris-setosa
4.8,3.4,1.6,0.2,Iris-setosa
4.8,3.0,1.4,0.1,Iris-setosa
4.3,3.0,1.1,0.1,Iris-setosa
5.8,4.0,1.2,0.2,Iris-setosa
5.7,4.4,1.5,0.4,Iris-setosa
5.4,3.9,1.3,0.4,Iris-setosa
5.1,3.5,1.4,0.3,Iris-setosa
5.7,3.8,1.7,0.3,Iris-setosa
5.1,3.8,1.5,0.3,Iris-setosa
5.4,3.4,1.7,0.2,Iris-setosa
5.1,3.7,1.5,0.4,Iris-setosa
4.6,3.6,1.0,0.2,Iris-setosa
5.1,3.3,1.7,0.5,Iris-setosa
4.8,3.4,1.9,0.2,Iris-setosa
5.0,3.0,1.6,0.2,Iris-setosa
5.0,3.4,1.6,0.4,Iris-setosa
5.2,3.5,1.5,0.2,Iris-setosa
5.2,3.4,1.4,0.2,Iris-setosa
4.7,3.2,1.6,0.2,Iris-setosa
4.8,3.1,1.6,0.2,Iris-setosa
5.4,3.4,1.5,0.4,Iris-setosa
5.2,4.1,1.5,0.1,Iris-setosa
5.5,4.2,1.4,0.2,Iris-setosa
4.9,3.1,1.5,0.1,Iris-setosa
5.0,3.2,1.2,0.2,Iris-setosa
5.5,3.5,1.3,0.2,Iris-setosa
4.9,3.1,1.5,0.1,Iris-setosa
4.4,3.0,1.3,0.2,Iris-setosa
5.1,3.4,1.5,0.2,Iris-setosa
5.0,3.5,1.3,0.3,Iris-setosa
4.5,2.3,1.3,0.3,Iris-setosa
4.4,3.2,1.3,0.2,Iris-setosa
5.0,3.5,1.6,0.6,Iris-setosa
5.1,3.8,1.9,0.4,Iris-setosa
4.8,3.0,1.4,0.3,Iris-setosa
5.1,3.8,1.6,0.2,Iris-setosa
4.6,3.2,1.4,0.2,Iris-setosa
5.3,3.7,1.5,0.2,Iris-setosa
5.0,3.3,1.4,0.2,Iris-setosa
7.0,3.2,4.7,1.4,Iris-versicolor
6.4,3.2,4.5,1.5,Iris-versicolor
6.9,3.1,4.9,1.5,Iris-versicolor
5.5,2.3,4.0,1.3,Iris-versicolor
6.5,2.8,4.6,1.5,Iris-versicolor
5.7,2.8,4.5,1.3,Iris-versicolor
6.3,3.3,4.7,1.6,Iris-versicolor
4.9,2.4,3.3,1.0,Iris-versicolor
6.6,2.9,4.6,1.3,Iris-versicolor
5.2,2.7,3.9,1.4,Iris-versicolor
5.0,2.0,3.5,1.0,Iris-versicolor
5.9,3.0,4.2,1.5,Iris-versicolor
6.0,2.2,4.0,1.0,Iris-versicolor
6.1,2.9,4.7,1.4,Iris-versicolor
5.6,2.9,3.6,1.3,Iris-versicolor
6.7,3.1,4.4,1.4,Iris-versicolor
5.6,3.0,4.5,1.5,Iris-versicolor
5.8,2.7,4.1,1.0,Iris-versicolor
6.2,2.2,4.5,1.5,Iris-versicolor
5.6,2.5,3.9,1.1,Iris-versicolor
5.9,3.2,4.8,1.8,Iris-versicolor
6.1,2.8,4.0,1.3,Iris-versicolor
6.3,2.5,4.9,1.5,Iris-versicolor
6.1,2.8,4.7,1.2,Iris-versicolor
6.4,2.9,4.3,1.3,Iris-versicolor
6.6,3.0,4.4,1.4,Iris-versicolor
6.8,2.8,4.8,1.4,Iris-versicolor
6.7,3.0,5.0,1.7,Iris-versicolor
6.0,2.9,4.5,1.5,Iris-versicolor
5.7,2.6,3.5,1.0,Iris-versicolor
5.5,2.4,3.8,1.1,Iris-versicolor
5.5,2.4,3.7,1.0,Iris-versicolor
5.8,2.7,3.9,1.2,Iris-versicolor
6.0,2.7,5.1,1.6,Iris-versicolor
5.4,3.0,4.5,1.5,Iris-versicolor
6.0,3.4,4.5,1.6,Iris-versicolor
6.7,3.1,4.7,1.5,Iris-versicolor
6.3,2.3,4.4,1.3,Iris-versicolor
5.6,3.0,4.1,1.3,Iris-versicolor
5.5,2.5,4.0,1.3,Iris-versicolor
5.5,2.6,4.4,1.2,Iris-versicolor
6.1,3.0,4.6,1.4,Iris-versicolor
5.8,2.6,4.0,1.2,Iris-versicolor
5.0,2.3,3.3,1.0,Iris-versicolor
5.6,2.7,4.2,1.3,Iris-versicolor
5.7,3.0,4.2,1.2,Iris-versicolor
5.7,2.9,4.2,1.3,Iris-versicolor
6.2,2.9,4.3,1.3,Iris-versicolor
5.1,2.5,3.0,1.1,Iris-versicolor
5.7,2.8,4.1,1.3,Iris-versicolor
6.3,3.3,6.0,2.5,Iris-virginica
5.8,2.7,5.1,1.9,Iris-virginica
7.1,3.0,5.9,2.1,Iris-virginica
6.3,2.9,5.6,1.8,Iris-virginica
6.5,3.0,5.8,2.2,Iris-virginica
7.6,3.0,6.6,2.1,Iris-virginica
4.9,2.5,4.5,1.7,Iris-virginica
7.3,2.9,6.3,1.8,Iris-virginica
6.7,2.5,5.8,1.8,Iris-virginica
7.2,3.6,6.1,2.5,Iris-virginica
6.5,3.2,5.1,2.0,Iris-virginica
6.4,2.7,5.3,1.9,Iris-virginica
6.8,3.0,5.5,2.1,Iris-virginica
5.7,2.5,5.0,2.0,Iris-virginica
5.8,2.8,5.1,2.4,Iris-virginica
6.4,3.2,5.3,2.3,Iris-virginica
6.5,3.0,5.5,1.8,Iris-virginica
7.7,3.8,6.7,2.2,Iris-virginica
7.7,2.6,6.9,2.3,Iris-virginica
6.0,2.2,5.0,1.5,Iris-virginica
6.9,3.2,5.7,2.3,Iris-virginica
5.6,2.8,4.9,2.0,Iris-virginica
7.7,2.8,6.7,2.0,Iris-virginica
6.3,2.7,4.9,1.8,Iris-virginica
6.7,3.3,5.7,2.1,Iris-virginica
7.2,3.2,6.0,1.8,Iris-virginica
6.2,2.8,4.8,1.8,Iris-virginica
6.1,3.0,4.9,1.8,Iris-virginica
6.4,2.8,5.6,2.1,Iris-virginica
7.2,3.0,5.8,1.6,Iris-virginica
7.4,2.8,6.1,1.9,Iris-virginica
7.9,3.8,6.4,2.0,Iris-virginica
6.4,2.8,5.6,2.2,Iris-virginica
6.3,2.8,5.1,1.5,Iris-virginica
6.1,2.6,5.6,1.4,Iris-virginica
7.7,3.0,6.1,2.3,Iris-virginica
6.3,3.4,5.6,2.4,Iris-virginica
6.4,3.1,5.5,1.8,Iris-virginica
6.0,3.0,4.8,1.8,Iris-virginica
6.9,3.1,5.4,2.1,Iris-virginica
6.7,3.1,5.6,2.4,Iris-virginica
6.9,3.1,5.1,2.3,Iris-virginica
5.8,2.7,5.1,1.9,Iris-virginica
6.8,3.2,5.9,2.3,Iris-virginica
6.7,3.3,5.7,2.5,Iris-virginica
6.7,3.0,5.2,2.3,Iris-virginica
6.3,2.5,5.0,1.9,Iris-virginica
6.5,3.0,5.2,2.0,Iris-virginica
6.2,3.4,5.4,2.3,Iris-virginica
5.9,3.0,5.1,1.8,Iris-virginica
1. Title: Iris Plants Database
Updated Sept 21 by C.Blake - Added discrepency information
2. Sources:
(a) Creator: R.A. Fisher
(b) Donor: Michael Marshall (MARSHALL%PLU@io.arc.nasa.gov)
(c) Date: July, 1988
3. Past Usage:
- Publications: too many to mention!!! Here are a few.
1. Fisher,R.A. "The use of multiple measurements in taxonomic problems"
Annual Eugenics, 7, Part II, 179-188 (1936); also in "Contributions
to Mathematical Statistics" (John Wiley, NY, 1950).
2. Duda,R.O., & Hart,P.E. (1973) Pattern Classification and Scene Analysis.
(Q327.D83) John Wiley & Sons. ISBN 0-471-22361-1. See page 218.
3. Dasarathy, B.V. (1980) "Nosing Around the Neighborhood: A New System
Structure and Classification Rule for Recognition in Partially Exposed
Environments". IEEE Transactions on Pattern Analysis and Machine
Intelligence, Vol. PAMI-2, No. 1, 67-71.
-- Results:
-- very low misclassification rates (0% for the setosa class)
4. Gates, G.W. (1972) "The Reduced Nearest Neighbor Rule". IEEE
Transactions on Information Theory, May 1972, 431-433.
-- Results:
-- very low misclassification rates again
5. See also: 1988 MLC Proceedings, 54-64. Cheeseman et al's AUTOCLASS II
conceptual clustering system finds 3 classes in the data.
4. Relevant Information:
--- This is perhaps the best known database to be found in the pattern
recognition literature. Fisher's paper is a classic in the field
and is referenced frequently to this day. (See Duda & Hart, for
example.) The data set contains 3 classes of 50 instances each,
where each class refers to a type of iris plant. One class is
linearly separable from the other 2; the latter are NOT linearly
separable from each other.
--- Predicted attribute: class of iris plant.
--- This is an exceedingly simple domain.
--- This data differs from the data presented in Fishers article
(identified by Steve Chadwick, spchadwick@espeedaz.net )
The 35th sample should be: 4.9,3.1,1.5,0.2,"Iris-setosa"
where the error is in the fourth feature.
The 38th sample: 4.9,3.6,1.4,0.1,"Iris-setosa"
where the errors are in the second and third features.
5. Number of Instances: 150 (50 in each of three classes)
6. Number of Attributes: 4 numeric, predictive attributes and the class
7. Attribute Information:
1. sepal length in cm
2. sepal width in cm
3. petal length in cm
4. petal width in cm
5. class:
-- Iris Setosa
-- Iris Versicolour
-- Iris Virginica
8. Missing Attribute Values: None
Summary Statistics:
Min Max Mean SD Class Correlation
sepal length: 4.3 7.9 5.84 0.83 0.7826
sepal width: 2.0 4.4 3.05 0.43 -0.4194
petal length: 1.0 6.9 3.76 1.76 0.9490 (high!)
petal width: 0.1 2.5 1.20 0.76 0.9565 (high!)
9. Class Distribution: 33.3% for each of 3 classes.
@IRIS:7:1:17:394#0/1
GTCAGGACAAGAAAGACAANTCCAATTNACATTATG
+IRIS:7:1:17:394#0/1
aaabaa`]baaaaa_aab]D^^`b`aYDW]abaa`^
@IRIS:7:1:17:800#0/2
GGAAACACTACTTAGGCTTATAAGATCNGGTTGCGG
+IRIS:7:1:17:800#0/2
ababbaaabaaaaa`]`ba`]`aaaaYD\\_a``XT
@IRIS:7:1:17:1757#0/1
TTTTCTCGACGATTTCCACTCCTGGTCNACGAATCC
+IRIS:7:1:17:1757#0/1
aaaaaa``aaa`aaaa_^a```]][Z[DY^XYV^_Y
@IRIS:7:1:17:1479#0/2
CATATTGTAGGGTGGATCTCGAAAGATATGAAAGAT
+IRIS:7:1:17:1479#0/2
abaaaaa`a```^aaaaa`_]aaa`aaa__a_X]``
@IRIS:7:1:17:150#0/1
TGATGTACTATGCATATGAACTTGTATGCAAAGTGG
+IRIS:7:1:17:150#0/1
abaabaa`aaaaaaa^ba_]]aaa^aaaaa_^][aa
@IRIS:7:1:18:443#0/2
CGATTCCACGTGATCAAAGAAACTAGAGTGGGTCTG
+IRIS:7:1:18:443#0/2
abbbbbababababababbaaaababababa``aaa
@IRIS:7:1:18:622#0/1
TGGGCTCCGGGAGGGGGGGATGTAAGAAAAATTACA
+IRIS:7:1:18:622#0/1
ababaaaabaa_``aa``]^aa_`aa_Z_aaaaa^b
@IRIS:7:1:18:628#0/2
AAAACAATTAGATGATGATAAAATTAACAAAGATTG
+IRIS:7:1:18:628#0/2
aaaaaaaaaaaaaaaaaa`^```a`aaa`^`a`a^a
@IRIS:7:1:18:1642#0/1
AATAAGTTTTAAACAGCTAACCTTGTTTACTTCTTT
+IRIS:7:1:18:1642#0/1
aaaaaa_aaababba_baa\aaaaa`a`baaaaa`a
@IRIS:7:1:18:1260#0/2
AGATGTACAAATTTGTATTTCAAGACAGATTTATAA
+IRIS:7:1:18:1260#0/2
abaab`bab`abaab`bbaaab_babb]aaaabba^
@IRIS:7:1:18:16#0/1
AGGTTCGTGTTGAGTGTTGCCTCTTTTTCTGTTAAT
+IRIS:7:1:18:16#0/1
abb`bbbabbbaWa`baba_Z``babaa[_aa`\X_
@IRIS:7:1:18:1150#0/2
AGCTAGGTAAAGTTATACATACAGATGGCCGAACTT
+IRIS:7:1:18:1150#0/2
abaaabb^bbabaabbbaaaaaaaaa`W^`a`_^``
@IRIS:7:1:18:1819#0/1
CTTACCGCGGTTTTAATAATTTTACCATCACTTCGT
+IRIS:7:1:18:1819#0/1
abbbbbbbba[aba``ba`bbba^]]``___]`_^W
@IRIS:7:1:18:1232#0/2
AAGAAATATATCGAAGAGTTAGTGCTGGACTGGCTG
+IRIS:7:1:18:1232#0/2
a^aY\Y^]^Y[WYUBBBBBBBBBBBBBBBBBBBBBB
@IRIS:7:1:19:1343#0/1
GGCATCTCCAGAGGAGGCTGTACCTGTGGAATAGCA
+IRIS:7:1:19:1343#0/1
abbbbbbbbababaaba_a\FXQXNVKO^F[RWYSQ
@IRIS:7:1:19:1885#0/2
TGAATTTCAATACGTGCAATTCCCTCCATACCAGAG
+IRIS:7:1:19:1885#0/2
abbbbbbbbbbbabaa[a_aba_^aa^_a``UZaab
@IRIS:7:1:19:691#0/1
GACATGAATTGTGTTTTAGGATAATTGATTAAAAAT
+IRIS:7:1:19:691#0/1
aaabbb`aaab`baaaaaba`aaababaaaaaaaab
@IRIS:7:1:19:1159#0/2
CAAGAATCATACTCAACATGCAAGCGATGATGAACA
+IRIS:7:1:19:1159#0/2
`a^`bbabba\_a^[_a\\]][GY]YBBBBBBBBBB
@IRIS:7:1:19:1310#0/1
GGAGATGATTTGACGATTCGCAGTCGGATCATCTGC
+IRIS:7:1:19:1310#0/1
aaabbabbabbbbbbbbbbbbbbabbbaabaa^a^Z
@IRIS:7:1:19:1108#0/2
GGATAATAAGCTCATGGGTTTGGTCTTACTTCACCG
+IRIS:7:1:19:1108#0/2
abaaaaaaaaaaaaaaa`^aaaa]]a``_a`aa^_Z
Source diff could not be displayed: it is too large. Options to address this: view the blob.
@HWI-ST1019:196:D121WACXX:5:1101:1538:2300/1
CCGCGACCTCTGTTCTGCAGCCCCTTCCCTTCCCCGCCTCCTGCTCTGCCGGGACTACGCACCGGCCTGATTGGTTACCCCCGGGGTGTCCTCGGTCACCA
+
1+++4)<@<A<+2A9A2++:3C8:)1?BDBDBBDC@::6@(.8..7)777:<?@@##############################################
@HWI-ST1019:196:D121WACXX:5:1101:1538:2300/2
CCGCGACCTCTGTTCTGCAGCCCCTTCCCTTCCCCGCCTCCTGCTCTGCCGGGACTACGCACCGGCCTGATTGGTTACCCCCGGGGTGTCCTCGGTCACCA
+
1+++4)<@<A<+2A9A2++:3C8:)1?BDBDBBDC@::6@(.8..7)777:<?@@##############################################
File added
File added
>sp|P12464|RPOE_BACSU DNA-directed RNA polymerase subunit delta OS=Bacillus subtilis (strain 168) GN=rpoE PE=1 SV=1
MGIKQYSQEELKEMALVEIAHELFEEHKKPVPFQELLNEIASLLGVKKEELGDRIAQFYT
DLNIDGRFLALSDQTWGLRSWYPYDQLDEETQPTVKAKKKKAKKAVEEDLDLDEFEEIDE
DDLDLDEVEEELDLEADDFDEEDLDEDDDDLEIEEDIIDEDDEDYDDEEEEIK