compara-deep-learning/neighbor_genes.py

import sys
import numpy as np
import pandas as pd
import json
import os
import gc
import pickle
from select_data import read_db_homology
from process_data import create_data_homology_ls

def read_genome_maps():
    data={}
    with open("genome_maps","rb") as file:
        data=pickle.load(file)
    cmap=data["cmap"]
    cimap=data["cimap"]
    ld=data["ld"]
    ldg=data["ldg"]
    a=data["a"]
    d=data["d"]
    return a,d,ld,ldg,cmap,cimap

def read_data_homology(dirname):
    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/"+n+"_selected_indexes.npy")
        except:
            print("Incomplete data for:",n)
        df=df.loc[indexes]
        print(len(df))
        a_h.append(df)
        d_h.append(n)
    return a_h,d_h

def main():
    a,d,ld,ldg,cmap,cimap=read_genome_maps()
    print("Genome Maps Loaded.")
    a_h,d_h=read_data_homology("data_homology")
    print("Data Read.")
    n=3
    _=create_data_homology_ls(a_h,d_h,n,a,d,ld,ldg,cmap,cimap,1)
    print("Neighbor Genes Found and Saved Successfully:)")

if __name__=="__main__":
    main()