Delete prepare_other_factors.py

prepare_other_factors.py

@@ -1,55 +0,0 @@
-import pandas as pd
-import numpy as np 
-import json
-import gc
-import pickle
-from read_data import read_data_homology
-from tree_data import create_tree_data
-
-a_h,d_h=read_data_homology("data_homology")
-d_h=list(d_h.keys())
-
-smg_name="_synteny_matrices_global.npy"
-sml_name="_synteny_matrices_local.npy"
-smi_name="_indexes.npy"
-dir_name="processed/synteny_matrices/"
-label=dict(ortholog_one2one=0,other_paralog=1,ortholog_one2many=1,ortholog_many2many=1,within_species_paralog=0)
-
-rows=[]
-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:
-        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("species_tree.tree",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)
-
-with open("dataset","wb") as file:
-    pickle.dump(rows,file)
-
-print("Data Saved Successfully:)")