INSTRUCTIONS.md

+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.

README

-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.

README.md

+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).

calculator/calculator.py

+#!/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)

data/easy.fastq

+@HWI-ST1019:196:D121WACXX:5:1101:1538:2300/1
+CCGCGACCTCTGTTCTGCAGCCCCTTCCCTTCCCCGCCTCCTGCTCTGCCGGGACTACGCACCGGCCTGATTGGTTACCCCCGGGGTGTCCTCGGTCACCA
++
+1+++4)<@<A<+2A9A2++:3C8:)1?BDBDBBDC@::6@(.8..7)777:<?@@##############################################

data/iris.data

+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
+

data/iris.names

+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.

data/mangled.fq

+@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

data/parse.fastq

+@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:<?@@##############################################

data/simple.fa

+>sp|P12464|RPOE_BACSU DNA-directed RNA polymerase subunit delta OS=Bacillus subtilis (strain 168) GN=rpoE PE=1 SV=1
+MGIKQYSQEELKEMALVEIAHELFEEHKKPVPFQELLNEIASLLGVKKEELGDRIAQFYT
+DLNIDGRFLALSDQTWGLRSWYPYDQLDEETQPTVKAKKKKAKKAVEEDLDLDEFEEIDE
+DDLDLDEVEEELDLEADDFDEEDLDEDDDDLEIEEDIIDEDDEDYDDEEEEIK