Merge pull request #73 from CBIIT/LDlink_3.8.1

L dlink 3.8.1
CBIIT · Nov 7, 2019 · e202e48 · e202e48
2 parents a4eebf7 + 75ca92b
commit e202e48
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Showing 12 changed files with 31 additions and 31 deletions.
diff --git a/LDlink/LDassoc.py b/LDlink/LDassoc.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 import yaml
 import csv
 import json
@@ -552,13 +552,13 @@ def get_coords_gene(gene_raw):
 	print("Create LDassoc_sub subprocesses")
 	for i in range(threads):
 		if i==min(range(threads)) and i==max(range(threads)):
-			command="python LDassoc_sub.py "+snp+" "+chromosome+" "+"_".join(assoc_coords)+" "+request+" "+str(i)
+			command="python3 LDassoc_sub.py "+snp+" "+chromosome+" "+"_".join(assoc_coords)+" "+request+" "+str(i)
 		elif i==min(range(threads)):
-			command="python LDassoc_sub.py "+snp+" "+chromosome+" "+"_".join(assoc_coords[:block])+" "+request+" "+str(i)
+			command="python3 LDassoc_sub.py "+snp+" "+chromosome+" "+"_".join(assoc_coords[:block])+" "+request+" "+str(i)
 		elif i==max(range(threads)):
-			command="python LDassoc_sub.py "+snp+" "+chromosome+" "+"_".join(assoc_coords[(block*i)+1:])+" "+request+" "+str(i)
+			command="python3 LDassoc_sub.py "+snp+" "+chromosome+" "+"_".join(assoc_coords[(block*i)+1:])+" "+request+" "+str(i)
 		else:
-			command="python LDassoc_sub.py "+snp+" "+chromosome+" "+"_".join(assoc_coords[(block*i)+1:block*(i+1)])+" "+request+" "+str(i)
+			command="python3 LDassoc_sub.py "+snp+" "+chromosome+" "+"_".join(assoc_coords[(block*i)+1:block*(i+1)])+" "+request+" "+str(i)
 		commands.append(command)
 
 
@@ -1122,7 +1122,7 @@ def get_output(process):
 		if web:
 			# Open thread for high quality image exports
 			print("Open thread for high quality image exports.")
-			command = "python LDassoc_plot_sub.py " + tmp_dir + 'assoc_args' + request + ".json" + " " + file + " " + region + " " + pop + " " + request + " " + myargsName + " " + myargsOrigin
+			command = "python3 LDassoc_plot_sub.py " + tmp_dir + 'assoc_args' + request + ".json" + " " + file + " " + region + " " + pop + " " + request + " " + myargsName + " " + myargsOrigin
 			subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
 
 
@@ -1264,7 +1264,7 @@ def get_output(process):
 		if web:
 			# Open thread for high quality image exports
 			print("Open thread for high quality image exports.")
-			command = "python LDassoc_plot_sub.py " + tmp_dir + 'assoc_args' + request + ".json" + " " + file + " " + region + " " + pop + " " + request + " " + myargsName + " " + myargsOrigin
+			command = "python3 LDassoc_plot_sub.py " + tmp_dir + 'assoc_args' + request + ".json" + " " + file + " " + region + " " + pop + " " + request + " " + myargsName + " " + myargsOrigin
 			subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
 
 	###########################

diff --git a/LDlink/LDassoc_plot_sub.py b/LDlink/LDassoc_plot_sub.py
@@ -386,17 +386,17 @@ def get_coords_gene(gene_raw):
     else:
         threads=4
 
-    block=len(assoc_coords)/threads
+    block=len(assoc_coords)//threads
     commands=[]
     for i in range(threads):
         if i==min(range(threads)) and i==max(range(threads)):
-            command="python LDassoc_sub.py "+snp+" "+chromosome+" "+"_".join(assoc_coords)+" "+request+" "+str(i)
+            command="python3 LDassoc_sub.py "+snp+" "+chromosome+" "+"_".join(assoc_coords)+" "+request+" "+str(i)
         elif i==min(range(threads)):
-            command="python LDassoc_sub.py "+snp+" "+chromosome+" "+"_".join(assoc_coords[:block])+" "+request+" "+str(i)
+            command="python3 LDassoc_sub.py "+snp+" "+chromosome+" "+"_".join(assoc_coords[:block])+" "+request+" "+str(i)
         elif i==max(range(threads)):
-            command="python LDassoc_sub.py "+snp+" "+chromosome+" "+"_".join(assoc_coords[(block*i)+1:])+" "+request+" "+str(i)
+            command="python3 LDassoc_sub.py "+snp+" "+chromosome+" "+"_".join(assoc_coords[(block*i)+1:])+" "+request+" "+str(i)
         else:
-            command="python LDassoc_sub.py "+snp+" "+chromosome+" "+"_".join(assoc_coords[(block*i)+1:block*(i+1)])+" "+request+" "+str(i)
+            command="python3 LDassoc_sub.py "+snp+" "+chromosome+" "+"_".join(assoc_coords[(block*i)+1:block*(i+1)])+" "+request+" "+str(i)
         commands.append(command)
 
 

diff --git a/LDlink/LDhap.py b/LDlink/LDhap.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 import yaml
 import json
 import math

diff --git a/LDlink/LDmatrix.py b/LDlink/LDmatrix.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 import yaml
 import json
 import math
@@ -907,7 +907,7 @@ def set_alleles(a1, a2):
     # Generate high quality images only if accessed via web instance
     if web:
         # Open thread for high quality image exports
-        command = "python LDmatrix_plot_sub.py " + \
+        command = "python3 LDmatrix_plot_sub.py " + \
             snplst + " " + pop + " " + request + " " + r2_d
         subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
 

diff --git a/LDlink/LDpair.py b/LDlink/LDpair.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 import yaml
 import json
 import math

diff --git a/LDlink/LDpop.py b/LDlink/LDpop.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 import yaml
 import json
 import math

diff --git a/LDlink/LDproxy.py b/LDlink/LDproxy.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 import yaml
 import csv
 import json
@@ -249,18 +249,18 @@ def replace_coord_rsid(snp):
     commands = []
     for i in range(threads):
         if i == min(range(threads)) and i == max(range(threads)):
-            command = "python LDproxy_sub.py " + str(web) + " " + snp + " " + \
+            command = "python3 LDproxy_sub.py " + str(web) + " " + snp + " " + \
                 snp_coord['chromosome'] + " " + str(coord1) + " " + \
                 str(coord2) + " " + request + " " + str(i)
         elif i == min(range(threads)):
-            command = "python LDproxy_sub.py " + str(web) + " " + snp + " " + \
+            command = "python3 LDproxy_sub.py " + str(web) + " " + snp + " " + \
                 snp_coord['chromosome'] + " " + str(coord1) + " " + \
                 str(coord1 + block) + " " + request + " " + str(i)
         elif i == max(range(threads)):
-            command = "python LDproxy_sub.py " + str(web) + " " + snp + " " + snp_coord['chromosome'] + " " + str(
+            command = "python3 LDproxy_sub.py " + str(web) + " " + snp + " " + snp_coord['chromosome'] + " " + str(
                 coord1 + (block * i) + 1) + " " + str(coord2) + " " + request + " " + str(i)
         else:
-            command = "python LDproxy_sub.py " + str(web) + " " + snp + " " + snp_coord['chromosome'] + " " + str(coord1 + (
+            command = "python3 LDproxy_sub.py " + str(web) + " " + snp + " " + snp_coord['chromosome'] + " " + str(coord1 + (
                 block * i) + 1) + " " + str(coord1 + (block * (i + 1))) + " " + request + " " + str(i)
         commands.append(command)
 
@@ -818,7 +818,7 @@ def get_output(process):
     # Generate high quality images only if accessed via web instance
     if web:
         # Open thread for high quality image exports
-        command = "python LDproxy_plot_sub.py " + snp + " " + pop + " " + request + " " + r2_d
+        command = "python3 LDproxy_plot_sub.py " + snp + " " + pop + " " + request + " " + r2_d
         subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
 
     ###########################

diff --git a/LDlink/LDproxy_plot_sub.py b/LDlink/LDproxy_plot_sub.py
@@ -179,18 +179,18 @@ def replace_coord_rsid(db, snp):
     commands = []
     for i in range(threads):
         if i == min(range(threads)) and i == max(range(threads)):
-            command = "python LDproxy_sub.py " + "True " + snp + " " + \
+            command = "python3 LDproxy_sub.py " + "True " + snp + " " + \
                 snp_coord['chromosome'] + " " + str(coord1) + " " + \
                 str(coord2) + " " + request + " " + str(i)
         elif i == min(range(threads)):
-            command = "python LDproxy_sub.py " + "True " + snp + " " + \
+            command = "python3 LDproxy_sub.py " + "True " + snp + " " + \
                 snp_coord['chromosome'] + " " + str(coord1) + " " + \
                 str(coord1 + block) + " " + request + " " + str(i)
         elif i == max(range(threads)):
-            command = "python LDproxy_sub.py " + "True " + snp + " " + snp_coord['chromosome'] + " " + str(
+            command = "python3 LDproxy_sub.py " + "True " + snp + " " + snp_coord['chromosome'] + " " + str(
                 coord1 + (block * i) + 1) + " " + str(coord2) + " " + request + " " + str(i)
         else:
-            command = "python LDproxy_sub.py " + "True " + snp + " " + snp_coord['chromosome'] + " " + str(coord1 + (
+            command = "python3 LDproxy_sub.py " + "True " + snp + " " + snp_coord['chromosome'] + " " + str(coord1 + (
                 block * i) + 1) + " " + str(coord1 + (block * (i + 1))) + " " + request + " " + str(i)
         commands.append(command)
 

diff --git a/LDlink/RegisterAPI.py b/LDlink/RegisterAPI.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 import json
 import os.path
 import binascii

diff --git a/LDlink/SNPchip.py b/LDlink/SNPchip.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 ###########
 # SNPchip #

diff --git a/LDlink/SNPclip.py b/LDlink/SNPclip.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 import yaml
 import json
 import math

diff --git a/LDlink/UnlockStaleTokens.py b/LDlink/UnlockStaleTokens.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 import datetime
 import dateutil.parser
 import yaml