mirror of
https://github.com/Priyatham-sai-chand/compara-deep-learning.git
synced 2026-10-05 08:11:34 -07:00
43 lines
1.4 KiB
Python
43 lines
1.4 KiB
Python
|
import pandas as pd
|
||
|
|
import numpy as np
|
||
|
|
import os
|
||
|
|
import sys
|
||
|
|
import progressbar
|
||
|
|
import json
|
||
|
|
from read_get_gene_seq import read_gene_sequences
|
||
|
|
from create_synteny_matrix import synteny_matrix
|
||
|
|
|
||
|
|
if not os.path.isdir("processed/synteny_matrices"):
|
||
|
|
os.mkdir("processed/synteny_matrices")
|
||
|
|
|
||
|
|
df=pd.read_hdf("negative_dataset.h5",key="ndf")
|
||
|
|
for _,row in progressbar.progressbar(df.iterrows()):
|
||
|
|
row["homology_species"]=row["homology_species"].lower()
|
||
|
|
print(df[0:10])
|
||
|
|
|
||
|
|
with open("processed/neighbor_genes.json","r") as file:
|
||
|
|
lsy=dict(json.load(file))
|
||
|
|
print(len(lsy))
|
||
|
|
print("Neighbor Genes Loaded")
|
||
|
|
|
||
|
|
a_h=[]
|
||
|
|
a_h.append(df)
|
||
|
|
#gene_sequences=read_gene_sequences(a_h,lsy,"geneseq","gene_sequences")
|
||
|
|
with open("processed/gene_sequences.json","r") as file:
|
||
|
|
gene_sequences=dict(json.load(file))
|
||
|
|
print("Gene Sequences Loaded")
|
||
|
|
|
||
|
|
|
||
|
|
|
||
|
|
n=3
|
||
|
|
ndir="processed/synteny_matrices/"
|
||
|
|
nf1="synteny_matrices_global"
|
||
|
|
nf2="synteny_matrices_local"
|
||
|
|
nf3="indexes"
|
||
|
|
for i in range(10):
|
||
|
|
synteny_matrices_global,synteny_matrices_local,indexes=synteny_matrix(gene_sequences,df[i*100000:(i+1)*100000],lsy,n,0)
|
||
|
|
np.save(ndir+"negative_dataset"+"_"+nf1+str(i),synteny_matrices_global)
|
||
|
|
np.save(ndir+"negative_dataset"+"_"+nf2+str(i),synteny_matrices_local)
|
||
|
|
np.save(ndir+"negative_dataset"+"_"+nf3+str(i),indexes)
|
||
|
|
print("Synteny Matrices Created Successfully :)")
|