mirror of
https://github.com/Priyatham-sai-chand/compara-deep-learning.git
synced 2026-10-05 08:11:34 -07:00
53 lines
1.9 KiB
Python
53 lines
1.9 KiB
Python
import sys
|
|
import numpy as np
|
|
import pandas as pd
|
|
import json
|
|
from get_data import get_data_homology,get_data_genome
|
|
from process_data import create_data_homology_ls
|
|
from read_get_gene_seq import read_gene_sequences
|
|
from create_synteny_matrix import synteny_matrix
|
|
from tree_data import create_tree_data
|
|
from create_train_data import train_data
|
|
from train import train
|
|
|
|
arg=sys.argv
|
|
arg=arg[1:]
|
|
|
|
if len(arg)!=5:
|
|
print("No. of arguments more or less. Please check")
|
|
sys.exit(1)
|
|
|
|
dir_g="data"
|
|
ld,ldg,a,d=get_data_genome(arg,dir_g)
|
|
|
|
dir_hom="data_homology"
|
|
a_h,d_h=get_data_homology(arg,dir_hom)
|
|
|
|
if arg[-1]=="-d":
|
|
sys.exit(1)
|
|
|
|
print("Data Read")
|
|
|
|
n=2 #no. of numbers neighbors
|
|
save_after=50000 #to save data after n steps
|
|
lsy=create_data_homology_ls(a_h,d_h,n,a,d,ld,ldg,save_after)
|
|
print(len(lsy))
|
|
|
|
print("Neighbor Genes Found")
|
|
|
|
gene_sequences=read_gene_sequences(a_h[0],lsy,"geneseq","gene_sequences")
|
|
|
|
synteny_matrices,indexes=synteny_matrix(gene_sequences,a_h[0],lsy,n)
|
|
print("Synteny Matrices are created successfully\n",len(indexes),"\n",len(synteny_matrices))
|
|
np.save("synteny_matrices",synteny_matrices)
|
|
np.save("indexes",indexes)
|
|
|
|
with open("gene_seq_updated.json","w") as file:
|
|
json.dump(gene_sequences,file)
|
|
|
|
df=a_h[0].loc[indexes]
|
|
branch_length_species,branch_length_homology_species,distance,dist_p_s,dist_p_hs=create_tree_data("species_tree.tree",df)
|
|
|
|
train_synteny_matrices,train_branch_length_species,train_branch_length_homology_species,train_mean_gene_length,train_dist_p_s,train_dist_p_hs,train_distance,train_labels=train_data(indexes,synteny_matrices,df,branch_length_species,branch_length_homology_species,distance,dist_p_s,dist_p_hs,gene_sequences)
|
|
|
|
train(train_synteny_matrices,train_branch_length_species,train_branch_length_homology_species,train_mean_gene_length,train_dist_p_s,train_dist_p_hs,train_distance,train_labels)
|