mirror of
https://github.com/Priyatham-sai-chand/compara-deep-learning.git
synced 2026-10-05 08:11:34 -07:00
55 lines
No EOL
1.6 KiB
Python
55 lines
No EOL
1.6 KiB
Python
import pandas as pd
|
|
import numpy as np
|
|
import json
|
|
import gc
|
|
import pickle
|
|
import progressbar
|
|
import sys
|
|
from tree_data import create_tree_data
|
|
|
|
|
|
|
|
smg_name="negative_dataset_synteny_matrices_global"
|
|
sml_name="negative_dataset_synteny_matrices_local"
|
|
smi_name="negative_dataset_indexes"
|
|
dir_name="processed/synteny_matrices/"
|
|
label=2
|
|
|
|
rows=[]
|
|
df=pd.read_hdf("negative_dataset.h5",key="ndf")
|
|
try:
|
|
smg=np.load(dir_name+smg_name+".npy")
|
|
sml=np.load(dir_name+sml_name+".npy")
|
|
indexes=np.load(dir_name+smi_name+".npy")
|
|
except:
|
|
print("Incomplete data")
|
|
sys.exit(1)
|
|
df=df.loc[indexes]
|
|
for _,row in progressbar.progressbar(df.iterrows()):
|
|
row["homology_species"]=row["homology_species"].lower()
|
|
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
|
|
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("negative_dataset","wb") as file:
|
|
pickle.dump(rows,file)
|
|
|
|
print("Data Saved Successfully:)") |