Phase 1 - Borderlands Science Documentation

Processing script data files

File-dictionary containing general information about puzzles. It can be used as a lookup table for further analysis.

All the pickle files described in this section use dnapuzzle.py .
Make sure you have “dnapuzzle.py” in the working directory.
Pandas library is used in the Code section, however it is not required to open the file.

To open the pickle file (replace filepath with appropriate string):

#python
import pandas as pd
from dnapuzzle import Puzzle
filepath = "05312021pikdiks.pickle "
obj = pd.read_pickle(filepath)

Pickle file encodes a dictionary where:

ATTRIBUTE	DESCRIPTION
Add New keys	originalCode [str] of puzzle - used as ID in BLS system
values	"pikdik" dictionary (see below)

ATTRIBUTE	TYPE	DESCRIPTION
pikdik.puzzle	[list]	Collapsed symbol-wise split puzzle sequences (e.g. [['T', 'T', 'G', 'A', '-', '-', '-'], ['G', 'T', 'A', 'A', '-', '-', '-'], ['G', 'C', 'G', 'A', '-', '-', '-'], ['T', 'G', 'C', 'A', '-', '-', '-'], ['C', 'T', '-', '-', '-', '-', '-'], ['C', 'T', 'G', 'A', '-', '-', '-']] )
pikdik.par_puzzle	[list]	Symbol-wise split pareto solution of the puzzle (e.g. [['T', 'T', '-', 'G', 'A', '-', '-'], ['G', 'T', '-', 'A', 'A', '-', '-'], ['G', 'C', '-', 'G', 'A', '-', '-'], ['T', 'G', '-', 'C', 'A', '-', '-'], ['C', 'T', '-', '-', '-', '-', '-'], ['C', 'T', '-', 'G', 'A', '-', '-']] )
pikdik.columns	[str(list)]	Column indexes in original alignment (e.g. '[99, 100, 101, 102, 103, 104, 105]' )
pikdik.flanks	[list]	Column indexes used as a flanks for a puzzle (e.g [105, 106])
pikdik.consensus	[list]	Predefined guides for a puzzle (used in scoring) (e.g. [('C', 'T'), ('C', 'T'), ('-', 'C'), ('C', 'T'), ('-', 'A'), ('G', 'A'), ('-', 'C'), ('-', 'G')] )
pikdik.cons_scores	[list]	Counter for each nucleotide from consenus to appear in the alignment (e.g. [(6287, 2552), (3416, 2688), (9666, 1), (2938, 2669), (9545, 55)] )
pikdik.n	[int]	Number of sequences. (e.g. 6)
pikdik.bonus	[float]	Multiplier for aligned "line" perfectly matching given consensus / guide (e.g. 1.15)
pikdik.level	[int]	Difficulty level of the puzzle in range [1, 9] (e.g. 2)