diff --git a/prepare_data.py b/prepare_data.py
deleted file mode 100644
index 3f41ecc..0000000
--- a/prepare_data.py
+++ /dev/null
@@ -1,94 +0,0 @@
-import sys
-import numpy as np
-import pandas as pd
-import json
-import os
-import gc
-from get_data import get_data_homology,get_data_genome
-from process_data import create_data_homology_ls
-from read_get_gene_seq import read_gene_sequences
-from create_synteny_matrix import synteny_matrix
-from tree_data import create_tree_data
-from prepare_train_data import train_data
-
-if not os.path.exists("processed"):
-    os.mkdir("processed")
-
-arg=sys.argv
-arg=arg[1:]
-
-enable_break=0
-
-if arg[-1]=="-test":
-    enable_break=1
-
-arg=arg[:-1]
-
-if len(arg)!=5:
-    print("No. of arguments more or less. Please check")
-    sys.exit(1)
-
-dir_g="data"
-ld,ldg,a,d=get_data_genome(arg,dir_g)
-
-dir_hom="data_homology"
-a_h,d_h=get_data_homology(arg,dir_hom)
-
-if arg[-1]=="-d":
-    sys.exit(1)
-
-print("Data Read")
-
-n=3 #no. of numbers neighbors
-save_after=0 #to save data after n steps
-
-if enable_break==1:
-    save_after=3
-else:
-    save_after=1000000
-
-lsy=create_data_homology_ls(a_h,d_h,n,a,d,ld,ldg,save_after,enable_break,0)
-print(len(lsy))
-
-a=[]
-d=[]
-ld=[]
-ldg=[]
-gc.collect()
-
-print("Neighbor Genes Found")
-
-if enable_break==1:
-    gene_sequences=read_gene_sequences(a_h[0][0:10],lsy,"geneseq","gene_sequences")
-else:    
-    gene_sequences=read_gene_sequences(a_h[0],lsy,"geneseq","gene_sequences")
-
-if enable_break==1:
-    synteny_matrices_global,synteny_matrices_local,indexes=synteny_matrix(gene_sequences,a_h[0][0:10],lsy,n,enable_break)
-else:    
-    synteny_matrices_global,synteny_matrices_local,indexes=synteny_matrix(gene_sequences,a_h[0],lsy,n,enable_break)
-
-print("Synteny Matrices are created successfully\n",len(indexes),"\n",len(synteny_matrices_global))
-np.save("processed/synteny_matrices_global",synteny_matrices_global)
-np.save("processed/synteny_matrices_local",synteny_matrices_local)
-np.save("processed/indexes",indexes)
-
-with open("processed/gene_seq_updated.json","w") as file:
-    json.dump(gene_sequences,file)
-
-df=a_h[0].loc[indexes]
-branch_length_species,branch_length_homology_species,distance,dist_p_s,dist_p_hs=create_tree_data("species_tree.tree",df)
-
-train_synteny_matrices_global,train_synteny_matrices_local,train_branch_length_species,train_branch_length_homology_species,train_mean_gene_length,train_dist_p_s,train_dist_p_hs,train_distance,train_labels=train_data(indexes,synteny_matrices_global,synteny_matrices_local,df,branch_length_species,branch_length_homology_species,distance,dist_p_s,dist_p_hs,gene_sequences)
-
-np.save("processed/train_synteny_matrices_global",train_synteny_matrices_global)
-np.save("processed/train_synteny_matrices_local",train_synteny_matrices_local)
-np.save("processed/train_branch_length_species",train_branch_length_species)
-np.save("processed/train_branch_length_homology_species",train_branch_length_homology_species)
-np.save("processed/train_mean_gene_length",train_mean_gene_length)
-np.save("processed/train_dist_p_s",train_dist_p_s)
-np.save("processed/train_dist_p_hs",train_dist_p_hs)
-np.save("processed/train_distance",train_distance)
-np.save("processed/train_labels",train_labels)
-
-print("Data Saved Successfully to processed :)")