bpf.py

import utils
import numpy as np
import save

def generate(X, seqType, args):
    '''
    # Reference: https://doi.org/10.1016/j.omtn.2019.04.025 (It is also called "identity matrix".)
    :param X:
    :param seqType:
    :param args:
    :return:
    '''

    if seqType == 'DNA':
        d = {
            'A': [1, 0, 0, 0],
            'C': [0, 1, 0, 0],
            'G': [0, 0, 1, 0],
            'T': [0, 0, 0, 1],
            'p': [0, 0, 0, 0],  # padding
        }
    else:
        if seqType == 'RNA':
            d = {
                'A': [1, 0, 0, 0],
                'C': [0, 1, 0, 0],
                'G': [0, 0, 1, 0],
                'U': [0, 0, 0, 1],
                'p': [0, 0, 0, 0],  # padding
            }
        else:
            if seqType == 'PROT':
                # Protein/Peptide One-Zero Encoding
                d = {
                    'A': [1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
                    'C': [0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
                    'D': [0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
                    'E': [0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
                    'F': [0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
                    'G': [0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
                    'H': [0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
                    'I': [0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
                    'K': [0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
                    'L': [0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
                    'M': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0],
                    'N': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0],
                    'P': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0],
                    'Q': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0],
                    'R': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0],
                    'S': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0],
                    'T': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0],
                    'V': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0],
                    'W': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0],
                    'Y': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1],
                    'p': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],  # padding
                }
            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':
            totalFeature = 20
        else:
            None
    # end-if

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