MilanG-git-A5 1.0.10

MilanG's Python package for APBC A0-A4

#Collection of assignments for APBC2021 as a single package

Usage: $ MilanG-Git_A5 [options] [filename]

Options: -h, --help show this help message and exit -A0 Use the Hello World module. -A1 Use the Word Count module. -I WordCount option: count words in case ignore mode. -l WordCount option: print a list of counted words, instead of pure counts. -A2 Use the Administration module to optimise costs. -o Administration option: Optimises the cost and prints the best solution. -A3 Use the Manhattan module to find the best path through a weighted matrix. -d Manhattan option: Include diagonal_matrix paths. -t Manhattan option: Print the path from start to finish -A4 {dice,mono,klet} Use the Random sequence module to shuffle sequences. Three methods are available: 1. rolling dice, 2. mono shuffle, 3. k-let shuffle. -N N Random sequence option: Number of random sequences printed. Default=1 --verbose Random sequence option: Print verbose output -k K Random sequence, k-let shuffle option: Length of k-lets. Default=2

Modules: -A0 HelloWorld: Will take a text file and print "Hello World!" and the contents of the file in the next line to screen.

-A1 WordCount: Counts the words in a text file and prints " / " to screen. The count can be case insensitive with -I. And the sorted list of words can be printed with -l.

-A2 Administration: Needs a file containing the number of capitals and the maximum cost in the first line, aswell as a matrix containing the cost of pairs. With -o flag only the best combination will be printe with the corresponding score. Example input:

  8 10                     # number of capitals; cost limit
   B  E  G  I  K  L  P  S  # names of capitals
   - 10 10  2 10 10 10 10  # symmetric cost matrix
  10  -  2 10 10 10  1 10
  10  2  - 10  2  3  3  3
   2 10 10  -  4 10 10  2
  10 10  2  4  - 10 10  3
  10 10  3 10 10  -  2  2
  10  1  3 10 10  2  - 10
  10 10  3  2  3  2 10  -

-A3 Manhattan: Calculates the best (highest pointed) path through a matrix. -d will include diagonal weights in the calculation -t will calculate the path through the grid. Example input:

#G_down: 4 5
  0.60   0.65   0.91   0.94   0.14
  0.85   0.27   0.70   0.31   0.63
  0.63   0.23   0.35   0.77   0.20
  0.37   0.76   0.41   0.30   0.67
#---
#G_right: 5 4
  0.76   0.41   0.72   0.13
  0.57   0.64   0.62   0.62
  0.37   0.98   0.36   0.24
  0.99   0.77   0.39   0.35
  0.37   0.34   0.62   0.82
#---
#G_diag: 4 4
  6.74   7.03   2.47   6.25
  4.48   3.75   2.98   3.62
  7.90   3.63   3.67   3.18
  9.30   8.40   9.02   2.58
#---

-A4 Random Sequences: Will take sequences and return -N N random sequencs. Three methods are available: -Rolling dice: Calculates the frequencies of letters (nucleotides) in a sequence and randomly generates new sequences with the same frequencies as the input sequenc. -Mono shuffle: Iterates through the sequence and swaps each letter with a randomly chosen one later in the sequence. -K-let shuffle: Shuffles k-lets of a given length (-k K) to generate random sequences, preserving the k-let composition.