utils_dataset.py

import numpy as np
import csv

def load_GO_annot(filename):
    # Load GO annotations
    onts = ['mf', 'bp', 'cc']
    prot2annot = {}
    goterms = {ont: [] for ont in onts}
    gonames = {ont: [] for ont in onts}
    with open(filename, mode='r') as tsvfile:
        reader = csv.reader(tsvfile, delimiter='\t')

        # molecular function
        next(reader, None)  # skip the headers
        goterms[onts[0]] = next(reader)
        next(reader, None)  # skip the headers
        gonames[onts[0]] = next(reader)

        # biological process
        next(reader, None)  # skip the headers
        goterms[onts[1]] = next(reader)
        next(reader, None)  # skip the headers
        gonames[onts[1]] = next(reader)

        # cellular component
        next(reader, None)  # skip the headers
        goterms[onts[2]] = next(reader)
        next(reader, None)  # skip the headers
        gonames[onts[2]] = next(reader)

        next(reader, None)  # skip the headers
        counts = {ont: np.zeros(len(goterms[ont]), dtype=float) for ont in onts}
        for row in reader:
            prot, prot_goterms = row[0], row[1:]
            prot2annot[prot] = {ont: [] for ont in onts}
            for i in range(3):
                goterm_indices = [goterms[onts[i]].index(goterm) for goterm in prot_goterms[i].split(',') if goterm != '']
                prot2annot[prot][onts[i]] = np.zeros(len(goterms[onts[i]]))
                prot2annot[prot][onts[i]][goterm_indices] = 1.0
                counts[onts[i]][goterm_indices] += 1.0
    return prot2annot, goterms, gonames, counts


def load_EC_annot(filename):
    # Load EC annotations """
    prot2annot = {}
    with open(filename, mode='r') as tsvfile:
        reader = csv.reader(tsvfile, delimiter='\t')

        # molecular function
        next(reader, None)  # skip the headers
        ec_numbers = {'ec': next(reader)}
        next(reader, None)  # skip the headers
        counts = {'ec': np.zeros(len(ec_numbers['ec']), dtype=float)}
        for row in reader:
            prot, prot_ec_numbers = row[0], row[1]
            ec_indices = [ec_numbers['ec'].index(ec_num) for ec_num in prot_ec_numbers.split(',')]
            prot2annot[prot] = {'ec': np.zeros(len(ec_numbers['ec']), dtype=np.int64)}
            prot2annot[prot]['ec'][ec_indices] = 1.0
            counts['ec'][ec_indices] += 1