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prepare_other_features.py

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+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())
+print("Data Read")
+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=1,other_paralog=0,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:)")