compara-deep-learning/finalize_dataset.py

import numpy as np
import pickle
import os
import sys
from tree_data import create_tree_data
from process_negative import read_database_txt
from select_data import read_db_homology


def read_data_homology(dirname, nfname):
    lf = os.listdir(dirname)
    if len(lf) == 0:
        print("No Files in the Directory!!!!!!!")
        sys.exit(1)
    a_h = []
    d_h = []
    for x in lf:
        df, n = read_db_homology(dirname, x)
        n = n.split()[0]
        try:
            indexes = np.load(
                "processed/synteny_matrices/" +
                n +
                "_indexes.npy")
        except BaseException:
            print("Incomplete data for:", n)
        df = df.loc[indexes]
        a_h.append(df)
        d_h.append(n)
    # read the negative dataset
    df = read_database_txt(nfname)
    indexes = np.load(
        "processed/synteny_matrices/" +
        nfname.split(".")[0] +
        "_indexes.npy")
    df = df.loc[indexes]
    a_h.append(df)
    d_h.append(nfname.split(".")[0])
    return a_h, d_h


def prepare_features(a_h, d_h, sptree, label):
    rows = []
    smg_name = "_synteny_matrices_global.npy"
    sml_name = "_synteny_matrices_local.npy"
    smi_name = "_indexes.npy"
    dir_name = "processed/synteny_matrices/"
    for i in range(len(a_h)):
        df = a_h[i]
        n = d_h[i]
        try:
            smg = np.load(dir_name + n + smg_name)
            sml = np.load(dir_name + n + sml_name)
            indexes = np.load(dir_name + n + smi_name)
        except BaseException:
            print("Incomplete data for:", n)
            continue
        df = df.loc[indexes]

        branch_length_species, \
            branch_length_homology_species, \
            distance, dist_p_s, dist_p_hs = create_tree_data(
                                            sptree, df)
        assert(len(branch_length_species) == len(df))
        assert(len(sml) == len(distance))

        for i in range(len(df)):
            index = indexes[i]
            row = df.loc[index]
            r = {}
            r["species"] = row["species"]
            r["homology_species"] = row["homology_species"]
            r["gene_stable_id"] = row["gene_stable_id"]
            r["homology_gene_stable_id"] = row["homology_gene_stable_id"]
            r["label"] = label[row["homology_type"]]
            r["global_alignment_matrix"] = smg[i]
            r["local_alignment_matrix"] = sml[i]
            r["index_homology_dataset"] = index
            r["bls"] = branch_length_species[i]
            r["blhs"] = branch_length_homology_species[i]
            r["dis"] = distance[i]
            r["dps"] = dist_p_s[i]
            r["dphs"] = dist_p_hs[i]
            rows.append(r)
    return rows


def main():
    arg = sys.argv
    nfname = arg[-1]
    a_h, d_h = read_data_homology("data_homology", nfname)
    labels = dict(ortholog_one2one=1,
                  other_paralog=0,
                  non_homolog=2,
                  ortholog_one2many=1,
                  ortholog_many2many=1,
                  within_species_paralog=0,
                  gene_split=4)
    rows = prepare_features(a_h, d_h, "species_tree.tree", labels)
    with open("dataset", "wb") as file:
        pickle.dump(rows, file)
    print("Dataset_Finalized")


if __name__ == "__main__":
    main()