mirror of
https://github.com/Priyatham-sai-chand/compara-deep-learning.git
synced 2026-10-05 08:11:34 -07:00
55 lines
1.6 KiB
Python
55 lines
1.6 KiB
Python
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import pandas as pd
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import numpy as np
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import json
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import gc
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import pickle
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import progressbar
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import sys
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from tree_data import create_tree_data
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smg_name="negative_dataset_synteny_matrices_global"
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sml_name="negative_dataset_synteny_matrices_local"
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smi_name="negative_dataset_indexes"
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dir_name="processed/synteny_matrices/"
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label=2
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rows=[]
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df=pd.read_hdf("negative_dataset.h5",key="ndf")
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try:
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smg=np.load(dir_name+smg_name+".npy")
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sml=np.load(dir_name+sml_name+".npy")
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indexes=np.load(dir_name+smi_name+".npy")
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except:
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print("Incomplete data")
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sys.exit(1)
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df=df.loc[indexes]
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for _,row in progressbar.progressbar(df.iterrows()):
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row["homology_species"]=row["homology_species"].lower()
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branch_length_species,branch_length_homology_species,distance,dist_p_s,dist_p_hs=create_tree_data("species_tree.tree",df)
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assert(len(branch_length_species)==len(df))
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assert(len(sml)==len(distance))
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for i in range(len(df)):
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index=indexes[i]
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row=df.loc[index]
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r={}
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r["species"]=row["species"]
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r["homology_species"]=row["homology_species"]
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r["gene_stable_id"]=row["gene_stable_id"]
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r["homology_gene_stable_id"]=row["homology_gene_stable_id"]
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r["label"]=label
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r["global_alignment_matrix"]=smg[i]
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r["local_alignment_matrix"]=sml[i]
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r["index_homology_dataset"]=index
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r["bls"]=branch_length_species[i]
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r["blhs"]=branch_length_homology_species[i]
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r["dis"]=distance[i]
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r["dps"]=dist_p_s[i]
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r["dphs"]=dist_p_hs[i]
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rows.append(r)
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with open("negative_dataset","wb") as file:
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pickle.dump(rows,file)
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print("Data Saved Successfully:)")
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