From 0b4610bffcdadfb4a29bccc51508dae043f86baf Mon Sep 17 00:00:00 2001
From: HarshitGupta11 <50410275+HarshitGupta11@users.noreply.github.com>
Date: Thu, 27 Jun 2019 14:01:50 +0530
Subject: [PATCH] Add files via upload

---
 create_synteny_matrix.py  | 4 ++++
 test_prepare_functions.py | 7 ++++---
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/create_synteny_matrix.py b/create_synteny_matrix.py
index dd795eb..a995bb7 100644
--- a/create_synteny_matrix.py
+++ b/create_synteny_matrix.py
@@ -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")
diff --git a/test_prepare_functions.py b/test_prepare_functions.py
index d072ea0..4a9a178 100644
--- a/test_prepare_functions.py
+++ b/test_prepare_functions.py
@@ -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: