tt.py

CRED = '\033[91m'
CEND = '\033[0m'

# Reference: https://www.cs.cmu.edu/~02710/Lectures/ScoringMatrices2015.pdf

import utils
import numpy as np
import save

def generate(X, seqType, args):
    '''
    # Reference: It is a very common feature.
    :param X:
    :param seqType:
    :param args:
    :return:
    '''

    if seqType == 'DNA':
        d = {
            'A': [0, 5, 5, 1],
            'C': [5, 1, 0, 5],
            'G': [1, 5, 5, 0],
            'T': [5, 0, 1, 5],
            'p': [0, 0, 0, 0],  # padding
        }
    else:
        if seqType == 'RNA':
            d = {
                'A': [0, 5, 5, 1],
                'C': [5, 1, 0, 5],
                'G': [1, 5, 5, 0],
                'U': [5, 0, 1, 5],
                'p': [0, 0, 0, 0],  # padding
            }
        else:
            if seqType == 'PROT':
                print(CRED + 'Error: The \'Transition-Transversion\' feature is NOT applicable for PROT.' + CEND)
                return None
            else: None
    #end-if
    # print(X)

    X = utils.processMono(X, d, args)
    # print(X.shape)

    totalFeature = 0
    if seqType == 'DNA' or seqType == 'RNA':
        totalFeature = 4
    else:
        if seqType == 'PROT': None
        else:
            None
    # end-if

    save.datasetSave(X, totalFeature, 'tt')
#end-def