Merge branch 'master' of https://git.lumc.nl/humgen/programming-course

INSTALL.md

@@ -46,10 +46,9 @@ any name here):
 
     mkvirtualenv programming-course
 
-Install IPython (version 1.0):
+Install IPython:
 
-    pip install -e git+https://github.com/ipython/ipython#egg=ipython
-    # or after its 1.0 release: pip install ipython
+    pip install ipython
 
 Install some of the other package we'll use:
 

README.md

@@ -33,6 +33,8 @@ The top-level directory contains slides for the following lessons.
 4. [More Python Goodness](http://nbviewer.ipython.org/urls/raw.github.com/LUMC/programming-course/master/more-python.ipynb)
 5. [Working with NumPy arrays](http://nbviewer.ipython.org/urls/raw.github.com/LUMC/programming-course/master/numpy.ipynb)
 6. [Plotting with matplotlib](http://nbviewer.ipython.org/urls/raw.github.com/LUMC/programming-course/master/matplotlib.ipynb)
+7. [Object-oriented programming](http://nbviewer.ipython.org/urls/raw.github.com/LUMC/programming-course/master/classes.ipynb)
+8. [A sip of Biopython](http://nbviewer.ipython.org/urls/raw.github.com/LUMC/programming-course/master/biopython.ipynb)
 
 Note: These links are to one-page renderings on [IPython Notebook Viewer](http://nbviewer.ipython.org/), see below how to get the real slideshows.
 

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/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

styles/notebook.css

@@ -31,14 +31,19 @@ div.text_cell_render{
 .prompt{
     display: None;
 }
-.text_cell_render h5 {
+.text_cell_render .exercise {
     font-weight: 300;
-    font-size: 22pt;
+    /*font-size: 22pt;*/
     color: #4057A1;
     font-style: italic;
-    margin-bottom: .5em;
+    /*margin-bottom: .5em;
     margin-top: 0.5em;
-    display: block;
+    display: block;*/
+}
+.text_cell_render .example {
+    font-weight: 300;
+    color: #40A157;
+    font-style: italic;
 }
 
 .warning{

styles/notebook.css.small

@@ -31,14 +31,19 @@ div.text_cell_render{
 .prompt{
     display: None;
 }
-.text_cell_render h5 {
+.text_cell_render .exercise {
     font-weight: 300;
-    font-size: 22pt;
+    /*font-size: 22pt;*/
     color: #4057A1;
     font-style: italic;
-    margin-bottom: .5em;
+    /*margin-bottom: .5em;
     margin-top: 0.5em;
-    display: block;
+    display: block;*/
+}
+.text_cell_render .example {
+    font-weight: 300;
+    color: #40A157;
+    font-style: italic;
 }
 
 .warning{