| Date | Lecture | Exercises | Remarks |
| Mon 30/10 |
Practical matters. Introduction to Unix and Python and the
dynamic interpreter. Read: Emacs tricks, Course notes chapters 1 and 2. |
File organization,
Pattern counting using Unix commands,
Python mode,
Math functions,
Math functions in a file
|
|
| Thu 2/11 |
String formatting, string methods, if/else, while loops, for loops, functions, .. Read: Course notes, chapters 3 and 4. |
Floats,
Vowels,
Reverse complementing DNA,
Name scrambling,
Boxes,
Counting nucleotides,
Number guessing,
Treasure hunt |
|
| Mon 6/11 |
Modules, scope, namespaces, default arguments, keyword arguments, .. Read: Course notes, chapter 5, Note on importing modules. |
Hypothenuses, Grade averages, Reverse complement function, Codon translation 1, GCD, Scope, Non-recursive factorial, Codon translation 2, Mutually recursive functions, Cheating dice | Note on program names |
| Thu 9/11 |
Sequences, dictionaries, .. Read: Course notes, chapter 6. |
Top-N, List membership, Incomplete DNA patterns, Random DNA sequences, List min/max, Character counting, Sieve of Eratosthenes, Character table, GCD2, Premier League stats, The function reduce | |
| Mon 13/11 |
Objects and classes. Read: Course notes, chapter 7 |
New Hamming distance method,
Node siblings,
Rational number operations,
Exact lookup,
Alignment,
Tree node printing,
String analyzer,
Search tree class,
Recursive printing |
|
| Thu 16/11 |
Exceptions,
reading/writing files, .. Read: Sections 12.1 - 12.4, 12.6, and chapter 14 from the book "Python - How To Program" by Deitel et al. Postscript PDF |
File scrambler, Phylogeny class, Phylogeny class 2, Illegal rational numbers, Codon translation 3, Codon translation 4, Unsuccesful load/save, CD extensions | |
| Mon 20/11
|
String functions, regular expressions. Read: Course notes, chapter 8 (part 1). |
Censorship,
Trypsin,
Fasta file,
Microsatellites,
Pruning Fasta headers,
A game of patience
|
|
| Thu 23/11
|
Regular expressions. Read: Course notes, rest of chapter 8, pages 149-162. (No changes made to pages 138-148). |
Censorship 2,
DNA chip synthesis,
Regular expressions,
Regular expressions 2,
Regular expressions 3,
Microsatellites 2,
Codon translation 5,
|
|
| Mon 27/11
|
Parsing and recursive data structures (Nothing to read) |
TTT markers, Chicken repeats, DNA fingerprinting, Blast parser | |
| Thu 30/11
|
Filters. Nothing to read. |
Isequence load/save
methods,
Table parsing,
Depth-first search,
Node depth,
Phylogeny search,
Phylogeny
construction |
|
| Mon 4/12
|
Python and XML. Read: Sections 15.1 - 12.5 and the essentials of 16.1 - 16.4 from the Deitel book: Postscript PDF (First page blurred, here is a rescan: Postscript PDF) |
Efficient Fasta reader, XML, New XML sequence format, Phylogeny/XML, Breadth-first search | |
| Thu 7/12
|
Inheritance and project relevant stuff. Read: Deitel Sections 9.1 - 9.4: Postscript PDF (First page blurred, here is a rescan: Postscript PDF) |
Vikings, Newick trees, Mass spectrometry, Newick conversion | Mandatory project |
| Mon 11/12
|
Drawing trees, os and os.path modules | Leaf counting, Node depth 2, Node tree drawing, Node tree drawing 2, General tree drawing | Please give your opinion about this couse |
| Thu 16/12
|
Cake/beer/sodas, questions regarding the project or
Python in general. No lecture. |
Just for fun: The Centinel game ANONYMOUS COURSE EVALUATION if you haven't already given your opinion |
Project questions session: Tuesday January 9th 14:15 in the meeting room, BiRC building, 1st floor. |