Introductory Programming in Python
Assignments

Assignment 1

1. Write an accountants calculator. The user may enter a number, an operator (+, -, *, /), a blank line, or the word 'quit'. The first entry must be a number. Every time a number is entered, it is added to the current total (which starts at 0), unless the previous line was an operator, in which case, instead of adding, use the operator given to combine the number entered and the total to form a new total. Every time a blank line is entered, print a line of dashes followed by a line containing the current total. If the entry is the word 'quit' the program ends. Here is an example of output for the input; 4, 9, blank line, *, 2, -, 6, /, 10, blank line, quit

   4
   9
   
   -----
   13
   *
   2
   -
   6
   /
   10
   
   -----
   2
   quit
   

Assignment 2

2. Write a simple noughts and crosses game, with a simple artificial intelligence, i.e. the computer will always place their nought or cross to win the game if possible, otherwise it will prevent the player forming a line, or where there are multiple choices, the computer chooses randomly. The player should be able to decide who is noughts and who is crosses, with crosses always starting first. To get the players move, allow them to enter their move in the format "A2", where the alphabetic character represents the column, and the number the row. Check that the input is valid, but allow the alphabetic character to be in any case. If the input isn't valid (too many characters, out of bounds, etc...), let the player enter their move again. Entering the word 'quit' allows the player to forfeit the game early. Output should present a grid showing the state of the game at each of the players turns.

   Noughts (0) or Crosses (X): X
     A B C
    |-|-|-|
   1| | | |
    |-|-|-|
   2| | | |
    |-|-|-|
   3| | | |
    |-|-|-|
   Your move? B2
     A B C
    |-|-|-|
   1| | | |
    |-|-|-|
   2| |X|O|
    |-|-|-|
   3| | | |
    |-|-|-|
   Your move? D3x
   Input not valid, too many characters. Try again: D3
   Input not valid, out of bounds. Try again: C3
     A B C
    |-|-|-|
   1|O| | |
    |-|-|-|
   2| |X|O|
    |-|-|-|
   3| | |X|
    |-|-|-|
   Your move? B3
     A B C
    |-|-|-|
   1|O|O| |
    |-|-|-|
   2| |X|O|
    |-|-|-|
   3| |X|X|
    |-|-|-|
   Your move? A3
     A B C
    |-|-|-|
   1|O|O| |
    |-|-|-|
   2| |X|O|
    |-|-|-|
   3|X|X|X|
    |-|-|-|
   You win!
   

Assignment 3

3. A wet lab has given you the task of writing a program to do some basic statistics on their data. Every now and then they sequence oligos from different organisms. Their wet lab machinery provides them with a file for each organism they sequence containing the date of the sequencing, the name of the organism sequenced, a short name for it with no spaces or punctuation, and the list of oligos obtained, and their starting positions in the genome. There may or may not be 100% coverage of the entire genome. No oligo is greater than 12 base pairs in length. They want the following functionality, using command line parameters.
   • Given a new file, of the format following, they wish to be able to merge it's data into the database if organism hasn't been merged already, i.e. the short name doesn't already exist in the database. (--merge <filename>)
   • They want to know for a given oligo which organisms it occurred in, and their positions (--belongs <oligo sequence>)
   • They want to know for a given organism, all of the oligos belonging to it, in order (--genome <organism short name>)
   • They want to know any shared oligos between two specified organisms, and their positions in each oligo, displayed in a neat table (--shared <organism short name 1> <organism short name 2>)
   • They want to know the frequency of a given oligo in the entire database (--freq <oligo sequence>)
   Notes:
   • You will need to use a file to store the database, and you will need to modify its contents. You can either overwrite the entire thing (easiest), or modify it in place (+3 bonus marks above 100%, can offset poor marks from previous assignments). Your decision heavily influences the format of database file.
   • Remember to use command line parameters for input exclusively, this means no raw_input()...
   • There is no reason your database can't consist of more than one file
   • Oligos must match exactly. Do not combine adjacent oligos, nor search for for sub-oligos within the ones in the database
   • You may not use any form of database module, inter alia; any relational database, the shelve or pickle modules, berkdb, ODBC etc... flat standard python files only.
   Following are 2 example files and the example outputs for the program using various command line parameters.

   31 Mar 2008: Bugblatter of Traal Neuron
   BugBlatNeuron
   AACGATCTTACG 0
   TGTTGAGACA   16
   GCAGATGTCGA  43
   CCGAGGCG     86
   TGCAGACCATC  111
   CACAAACCC    145

   02 Apr 2008: Babel Fish Brain Matrix Neuron
   BabelMatrix
   AGCTAGCATGC  3
   CATGATGACGAT 45
   TACGAGGA     78
   CCGAGGCG     109
   GTCCCAG      205

   $ oligodb --merge bugblatter.dat
   $ oligodb --merge babel.dat
   $ oligodb --genome BabelMatrix
   AGCTAGCATGC (3)
   CATGATGACGAT (45)
   TACGAGGA (78)
   CCGAGGCG (109)
   GTCCCAG (205)
   $ oligodb --freq GTCCCAG
   1
   $ oligodb --belongs CCGAGGCG
   BugBlatNeuron: 86
   BabelMatrix: 109
   $ oligodb --shared BugBlatNeuron BabelMatrix
                   BugBlatNeuron  BabelMatrix
   CCGAGGCG        86             109

Assignment 4

4. A local laboratory is doing experiments in accelerated mutation. Taking starting unicellular organisms, they bombard them with radiation causing increased mutation rates, then place the offspring on a medium containing cellulose. For those organisms that digest the cellulose, the process is repeated this time with the offspring as the initial organisms, and the final medium containing a slightly higher cellulose content. The lab has already identified a site on the various organisms genomes of interest, 10 base pairs long. For each surviving organism they have recorded in a file (assignment.dat):
   • The lab code for the individual organism (unique)
   • The date the organism was sequenced
   • The sequence of interest from the organism
   • The percentage of cellulose digested by the organism in a given time
   • The ancestry of the organism by its relative indentation
   While the organisms do exhibit increased cellulose degradation capabilities, they also exhibit a variety of undesirable phenotypes. The lab now needs to identify individual SNPs that cause the greatest average positive changes in cellulose consumption percentages (CCP), so they can focus on those mutations to achieve only the cellulose degradation phenotype. Your crack team of programmers has just been awarded the contract, the deposit cheque is in your sweaty little palms, the data file is available for download, get coding.
   • Your program should process files specified on the command line, and merge them into one large dataset for processing
   • A change in CCP is the difference in a child's CCP and its parent's CCP (child - parent), for a given sequence position
   • Only if a nucleotide is changed from parent to child in a given position, does that change in CCP contribute to the average change in CCP for that position
   • Your program should output in descending order of average CCP change, the value of the average CCP change, and the nucleotide position relative to the start of the gene of interest
   • Create a slide show presentation of maximum 5 minutes, explaining your approach to the problem. Be prepared for question from myself, and the class.
   • The mark for the assignment is out of 10, 5 from the presentation and questions, 5 from the code. You will be expected to demonstrate your code, on screen during your presentation, using the example file.
   Example output from the given example input file follows...