priyatham/compara-deep-learning
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HarshitGupta11 2019-06-27 14:01:50 +05:30 committed by GitHub
parent ea37c29761
commit 0b4610bffc
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2 changed files with 8 additions and 3 deletions
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4
create_synteny_matrix.py
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@ -65,9 +65,13 @@ def create_synteny_matrix_mul(gene_seq,g1,g2,n):
for i in range(n):
if g1[i]=="NULL_GENE":
continue
if gene_seq[g1[i]]=="":
return np.zeros((n,n,2)),np.zeros((n,n,2))
for j in range(n):
if g2[j]=="NULL_GENE":
continue
if gene_seq[g2[j]]=="":
return np.zeros((n,n,2)),np.zeros((n,n,2))
norm_len=max(len(gene_seq[g1[i]]),len(gene_seq[g2[j]]))
try:
result = ed.align(gene_seq[g1[i]],gene_seq[g2[j]], mode="NW", task="distance")

7
test_prepare_functions.py
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@ -2,7 +2,8 @@ import pandas as pd
import progressbar
import json
import numpy as np
import multiprocessing
import time
from multiprocessing import Process
from threading import Thread
from ete3 import Tree
from read_get_gene_seq import read_gene_seq,create_dict
@ -114,7 +115,6 @@ def intermediate_process(gene_seq,x,y,n,index,sl,sg,ind):
sl.append(smltemp)
ind.append(index)
def synteny_matrix(gene_seq,hdf,lsy,n,enable_break,sg,sl,ind):
#sg=[]
#sl=[]
@ -160,8 +160,9 @@ def synteny_matrix(gene_seq,hdf,lsy,n,enable_break,sg,sl,ind):
th.start()
th.join(30)
if th.is_alive():
th.join()
raise SystemError("Long Time")
print(row)
th.join()
except Exception as e:
print(e)
if t==5 and enable_break==1: