Assignment 4

Question #1

A DNA sequence can be represented as a string over the alphabet {A, C, G, T}. Let a DNA structure consist of either a single DNA string or an ordered pair of DNA strings (x, y) with an integer-pair (l,u) specifying lower (x) and upper (y) bounds on the number of DNA symbols that are allowed between the end of an occurrence of x and the beginning of an occurrence of y in a DNA sequence. Denote the string-pieces of a structure as motifs. For example, given DNA sequence ACAGGTA, structure ['CAGG'] occurs at position 2, structure ['CA', (1,5), 'TA'] occurs at position 2 (with individual motif start-positions 2 and 6, respectively), and structure ['AAAA'] does not occur.

Write and document a Python script dnastruct.py which takes as command-line arguments a DNA sequence file and a DNA structure file and determines for each structure whether or not it occurs in the sequence. If it occurs, a list is printed describing via tuple-pairs each motif and its start-position. A DNA sequence file may represent the sequence over multiple lines. Each line in a DNA structure file describes an individual structure that consists of either a single motif or a pair of motifs separated by a lower/upper bound-pair written as l/u. Your script must work on DNA sequence file seq1.dat and DNA structure file struct1.dat to produce the output given in typescript-file dnastruct.script. You may assume that all given files are formatted correctly.

Question #2

Write and document a Python script stats2.py which takes as command-line arguments the names of a real-valued data matrix file and a command file describing various row, column, and diagonal vectors in the data matrix, and for each described data vector, computes the length, sum, minimum, mean, maximum, standard deviation, and variance of that vector (see Q2 in Assignment #2) and outputs these statistics to a data-vector-specific file. An n x m data matrix is encoded as an n-line file in which each line consists of m real numbers. For example the data matrix in data1.dat is encoded as

 1  2  3  4
 5  6  7  8
 9 10 11 12

and has the following associated row, column, and diagonal data-vectors:

• row 1: [1, 2, 3, 4]
• row 2: [5, 6, 7, 8]
• row 3: [9, 10, 11, 12]
• column 1: [1, 5, 9]
• column 2: [2, 6, 10]
• column 3: [3, 7, 11]
• column 4: [4, 8, 12]
• diagonal 3: [4]
• diagonal 2: [3, 8]
• diagonal 1: [2, 7, 12]
• diagonal 0: [1, 6, 11]
• diagonal -1: [5, 10]
• diagonal -2: [9]

Each line of the command file consists of X in {row, column, diagonal} and a number Yspecifying a data vector relative to the data matrix in file Z.dat; the statistics for this data vector are written to data-vector-specific file Z.XY.stt. Your script must work on data matrix file data1.dat and command-file cmd1.dat to produce statistics-file data1.row3.stt, data1.col2.stt, data1.dia3.stt, data1.dia2.stt, data1.dia1.stt, data1.dia0.stt, data1.dia-1.stt, and data1.dia-2.stt as specified in typescript-file stats2.script. You may assume that all given files are formatted correctly.

Hints

You may find the various example scripts in the course notes of use.

In Q2, you may find it useful to store the data matrix internally as a nested list and extract data vectors to process as required.

Submission

Please hand in printed copies of all of your Python script files. You must also submit these files electronically using the submit-assignment command. Note that each script file must have the following comment block at the top, where the X's are replaced with the appropriate information, followed by a docstring briefly describing the program in that script. For instance, my script for Question #1 of this assignment would begin with the following comment block:

#########################################################
##  CS 2500 (Fall 2009), Assignment #4, Question #1    ##
##   Script File Name: numdesc.py                      ##
##       Student Name: Todd Wareham                    ##
##         Login Name: harold                          ##
##              MUN #: 8008765                         ##
#########################################################

You do not have to develop your code on our CS departmental systems. However, as your code will be interpreted and tested on our CS departmental systems as part of the assignment marking process, you should ensure that your code interprets and runs correctly on at least one of these systems.

Additional Notes:

• August 21, 10:20am
  Assignment #4 posted.

Created: August 21, 2009
Last Modified: August 21, 2009