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https://github.com/Priyatham-sai-chand/compara-deep-learning.git
synced 2026-10-05 08:11:34 -07:00
69 lines
2 KiB
Python
69 lines
2 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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import gc
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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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from access_data_rest import update_rest
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from select import select,create_map_reverse
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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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with open("dist_matrix","r") as file:
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matrix=file.readlines()
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matrix=[x.split("\t") for x in matrix]
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matrix=[[float(y) for y in x] for x in matrix]
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matrix=np.array(matrix)
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with open("sp_names","r") as file:
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dname=file.readlines()
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dname=[x.split("\n")[0] for x in dname]
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spnmap,nspmap=create_map_reverse(dname)
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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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d_h=[x.split()[0] for x in d_h]
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print("Homology Data Read")
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for i in range(len(a_h)):
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a_h[i]=select(a_h[i],nos,matrix,spnmap,nspmap,d_h[i])
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assert(len(a_h[i])==nos)
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gc.collect()
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print("Data Selected")
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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={}
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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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print("Going to update not found sequences:")
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gene_sequences=update_rest(gene_sequences)
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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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print(len(df))
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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(len(indexes))
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print("Synteny Matrices Created Successfully :)")
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