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https://github.com/Priyatham-sai-chand/compara-deep-learning.git
synced 2026-10-05 08:11:34 -07:00
54 lines
1.4 KiB
Python
54 lines
1.4 KiB
Python
import pandas as pd
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import numpy as np
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import os
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import sys
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import progressbar
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import json
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from read_data import read_data_homology
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from read_get_gene_seq import read_gene_sequences
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from create_synteny_matrix import synteny_matrix
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if not os.path.isdir("processed/synteny_matrices"):
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os.mkdir("processed/synteny_matrices")
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arg=sys.argv
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arg=arg[1:]
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nos=int(arg[0])
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lsy={}
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a_h,d_h=read_data_homology("data_homology")
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print(d_h)
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d_h=list(d_h.keys())
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print("Homology Data Read")
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for i in range(len(a_h)):
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df=a_h[i]
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random_indexes=np.random.permutation(len(df))
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random_indexes=random_indexes[:nos]
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df=df.loc[random_indexes]
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assert(len(df)==nos)
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a_h[i]=df
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with open("processed/neighbor_genes.json","r") as file:
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lsy=dict(json.load(file))
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print(len(lsy))
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print("Neighbor Genes Loaded")
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gene_sequences=read_gene_sequences(a_h,lsy,"geneseq","gene_sequences")
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print("Gene Sequences Loaded")
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n=3
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ndir="processed/synteny_matrices/"
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nf1="synteny_matrices_global"
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nf2="synteny_matrices_local"
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nf3="indexes"
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for i in range(len(a_h)):
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df=a_h[i]
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synteny_matrices_global,synteny_matrices_local,indexes=synteny_matrix(gene_sequences,df,lsy,n,0)
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np.save(ndir+str(d_h[i])+"_"+nf1,synteny_matrices_global)
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np.save(ndir+str(d_h[i])+"_"+nf2,synteny_matrices_local)
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np.save(ndir+str(d_h[i])+"_"+nf3,indexes)
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print("Synteny Matrices Created Successfully :)")
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