updating time.clock() to time.time() for Python 3.8

python_scripts/DIAMOND_COG_analysis_counter.py

@@ -50,7 +50,7 @@ def string_find(usage_term):
 		if elem == usage_term:
 			 return next_elem
 
-t0 = time.clock()
+t0 = time.time()
 
 # loading starting file
 if "-I" in sys.argv:
@@ -71,7 +71,7 @@ def string_find(usage_term):
 	line_counter += 1
 	splitline = line.split("\t")
 	if line_counter % 1000000 == 0:
-		t99 = time.clock()
+		t99 = time.time()
 		print (str(line_counter)[:-6] + "M lines processed so far in " + str(t99-t0) + " seconds.")
 
 	unique_seq_db[splitline[0]] = 1
@@ -85,7 +85,7 @@ def string_find(usage_term):
 		hit_count_db[splitline[1]] = 1
 		continue
 
-t1 = time.clock()
+t1 = time.time()
 
 # results reporting
 print ("\nAnalysis of " + infile_name + " complete.")
@@ -109,7 +109,7 @@ def string_find(usage_term):
 
 print ("\nStarting database analysis now.")
 
-t2 = time.clock()
+t2 = time.time()
 
 # building a dictionary of the reference database
 db_hier_dictionary = {}
@@ -136,10 +136,10 @@ def string_find(usage_term):
 
 		# line counter to show progress
 		if db_line_counter % 1000000 == 0:							# each million
-			t95 = time.clock()
+			t95 = time.time()
 			print (str(db_line_counter) + " lines processed so far in " + str(t95-t2) + " seconds.")
 
-t3 = time.clock()
+t3 = time.time()
 
 print ("\nSuccess!")
 print ("Time elapsed: " + str(t3-t2) + " seconds.")

python_scripts/DIAMOND_analysis_counter.py

@@ -51,7 +51,7 @@ def string_find(usage_term):
 		if elem == usage_term:
 			 return next_elem
 
-t0 = time.clock()
+t0 = time.time()
 
 # checking for an option (organism or function) to be specified
 if "-O" not in sys.argv:
@@ -86,7 +86,7 @@ def string_find(usage_term):
 	line_counter += 1
 	splitline = line.split("\t")
 	if line_counter % 1000000 == 0:
-		t99 = time.clock()
+		t99 = time.time()
 		print (str(line_counter)[:-6] + "M lines processed so far in " + str(t99-t0) + " seconds.")
 
 	unique_seq_db[splitline[0]] = 1
@@ -97,7 +97,7 @@ def string_find(usage_term):
 		RefSeq_hit_count_db[splitline[1]] = 1
 		continue
 
-t1 = time.clock()
+t1 = time.time()
 
 print ("\nAnalysis of " + infile_name + " complete.")
 print ("Number of total lines: " + str(line_counter))
@@ -111,7 +111,7 @@ def string_find(usage_term):
 
 print ("\nStarting database analysis now.")
 
-t2 = time.clock()
+t2 = time.time()
 
 # optional outfile of specific organism results
 if "-SO" in sys.argv:
@@ -185,10 +185,10 @@ def string_find(usage_term):
 
 		# line counter to show progress
 		if db_line_counter % 1000000 == 0:							# each million
-			t95 = time.clock()
+			t95 = time.time()
 			print (str(db_line_counter)[:-6] + "M lines processed so far in " + str(t95-t2) + " seconds.")
 
-t3 = time.clock()
+t3 = time.time()
 
 print ("\nSuccess!")
 print ("Time elapsed: " + str(t3-t2) + " seconds.")

python_scripts/DIAMOND_general_RefSeq_analysis_counter.py

@@ -51,7 +51,7 @@ def string_find(usage_term):
 		if elem == usage_term:
 			 return next_elem
 
-t0 = time.clock()
+t0 = time.time()
 
 # checking for an option (organism or function) to be specified
 if "-O" not in sys.argv:
@@ -85,7 +85,7 @@ def string_find(usage_term):
 	line_counter += 1
 	splitline = line.split("\t")
 	if line_counter % 1000000 == 0:
-		t99 = time.clock()
+		t99 = time.time()
 		print str(line_counter)[:-6] + "M lines processed so far in " + str(t99-t0) + " seconds."
 
 	unique_seq_db[splitline[0]] = 1
@@ -96,7 +96,7 @@ def string_find(usage_term):
 		RefSeq_hit_count_db[splitline[1]] = 1
 		continue
 
-t1 = time.clock()
+t1 = time.time()
 
 print ("\nAnalysis of " + infile_name + " complete.")
 print ("Number of total lines: " + str(line_counter))
@@ -110,7 +110,7 @@ def string_find(usage_term):
 
 print ("\nReading in reference database...")
 
-t2 = time.clock()
+t2 = time.time()
 
 # optional outfile of specific organism results
 if "-SO" in sys.argv:
@@ -187,11 +187,11 @@ def string_find(usage_term):
 
 		# line counter to show progress
 		if db_line_counter % 1000000 == 0:							# each million
-			t95 = time.clock()
+			t95 = time.time()
 			print (str(db_line_counter)[:-6] + "M lines processed so far in " + str(t95-t2) + " seconds.")
 
 db.close()
-t3 = time.clock()
+t3 = time.time()
 
 print ("Database read successfully.\n")
 print ("Time elapsed: " + str(t3-t2) + " seconds.")

python_scripts/DIAMOND_results_filter.py

@@ -86,15 +86,15 @@ def string_find(usage_term):
 db_line_counter = 0
 db_error_counter = 0
 
-t0 = time.clock()
+t0 = time.time()
 
 for line in db:
 	if line.startswith(">") == True:
 		db_line_counter += 1
 
 		# line counter to show progress
 		if db_line_counter % 1000000 == 0:							# each million
-			t95 = time.clock()
+			t95 = time.time()
 			print (str(db_line_counter) + " lines processed so far in " + str(t95-t0) + " seconds.")
 
 		if target_org in line:
@@ -153,7 +153,7 @@ def string_find(usage_term):
 line_counter = 0
 hit_counter = 0
 
-t1 = time.clock()
+t1 = time.time()
 
 # reading through the infile
 for line in infile:
@@ -167,11 +167,11 @@ def string_find(usage_term):
 		continue
 
 	if line_counter % 1000000 == 0:
-		t99 = time.clock()
+		t99 = time.time()
 		print (str(line_counter)[:-6] + "M lines processed so far in " + str(t99-t1) + " seconds.")
 
 # results stats
-t100 = time.clock()
+t100 = time.time()
 print ("Run complete!")
 print ("Number of sequences found matching target query, " + target_org + ":\t" + str(hit_counter))
 print ("Time elapsed: " + str(t100-t0) + " seconds.")

python_scripts/DIAMOND_specific_organism_retriever.py

@@ -85,15 +85,15 @@ def string_find(usage_term):
 db_line_counter = 0
 db_error_counter = 0
 
-t0 = time.clock()
+t0 = time.time()
 
 for line in db:
 	if line.startswith(">") == True:
 		db_line_counter += 1
 
 		# line counter to show progress
 		if db_line_counter % 1000000 == 0:							# each million
-			t95 = time.clock()
+			t95 = time.time()
 			print (str(db_line_counter) + " lines processed so far in " + str(t95-t0) + " seconds.")
 
 		if target_org not in line:
@@ -153,7 +153,7 @@ def string_find(usage_term):
 line_counter = 0
 hit_counter = 0
 
-t1 = time.clock()
+t1 = time.time()
 
 # reading through the infile
 for line in infile:
@@ -167,11 +167,11 @@ def string_find(usage_term):
 		continue
 
 	if line_counter % 1000000 == 0:
-		t99 = time.clock()
+		t99 = time.time()
 		print (str(line_counter)[:-6] + "M lines processed so far in " + str(t99-t1) + " seconds.")
 
 # results stats
-t100 = time.clock()
+t100 = time.time()
 print ("Run complete!")
 print ("Number of sequences found matching target organism, " + target_org + ": " + str(hit_counter))
 print ("Time elapsed: " + str(t100-t0) + " seconds.")

python_scripts/DIAMOND_subsystems_analysis_counter.py

@@ -50,7 +50,7 @@ def string_find(usage_term):
 		if elem == usage_term:
 			 return next_elem
 
-t0 = time.clock()
+t0 = time.time()
 
 # loading starting file
 if "-I" in sys.argv:
@@ -71,7 +71,7 @@ def string_find(usage_term):
 	line_counter += 1
 	splitline = line.split("\t")
 	if line_counter % 1000000 == 0:
-		t99 = time.clock()
+		t99 = time.time()
 		print (str(line_counter)[:-6] + "M lines processed so far in " + str(t99-t0) + " seconds.")
 
 	unique_seq_db[splitline[0]] = 1
@@ -85,7 +85,7 @@ def string_find(usage_term):
 		hit_count_db[splitline[1]] = 1
 		continue
 
-t1 = time.clock()
+t1 = time.time()
 
 # results reporting
 print ("\nAnalysis of " + infile_name + " complete.")
@@ -114,7 +114,7 @@ def string_find(usage_term):
 
 print ("\nStarting database analysis now.")
 
-t2 = time.clock()
+t2 = time.time()
 
 # building a dictionary of the reference database
 db_hier_dictionary = {}
@@ -144,10 +144,10 @@ def string_find(usage_term):
 
 		# line counter to show progress
 		if db_line_counter % 1000000 == 0:							# each million
-			t95 = time.clock()
+			t95 = time.time()
 			print (str(db_line_counter) + " lines processed so far in " + str(t95-t2) + " seconds.")
 
-t3 = time.clock()
+t3 = time.time()
 
 print ("\nSuccess!")
 print ("Time elapsed: " + str(t3-t2) + " seconds.")

python_scripts/db_results_swapper.py

@@ -23,16 +23,16 @@
 # Sam Westreich, [email protected], github.com/transcript
 #
 # This program takes a list of IDs from one database, such as the RefSeq
-# database, and gets all IDs for those entries retrieved against another 
+# database, and gets all IDs for those entries retrieved against another
 # database, such as Subsystems.
 #
-# Usage: 
+# Usage:
 #
-# -I		infile			specifies the infile (a DIAMOND results file 
+# -I		infile			specifies the infile (a DIAMOND results file
 #								in m8 format)
-# -A		annotation		specifies annotated results to search against 
+# -A		annotation		specifies annotated results to search against
 #
-# -O		outfile			specifies a name for the outfile (otherwise defaults 
+# -O		outfile			specifies a name for the outfile (otherwise defaults
 #								to $name_hierarchy.tsv)
 # -P 		partial			partial outfile; a list of all reads with their
 #								hierarchy results (OPTIONAL)
@@ -50,7 +50,7 @@ def string_find(usage_term):
 		if elem == usage_term:
 			 return next_elem
 
-t0 = time.clock()
+t0 = time.time()
 
 # loading starting file
 if "-I" in sys.argv:
@@ -69,20 +69,20 @@ def string_find(usage_term):
 	line_counter += 1
 	splitline = line.split("\t")
 	if line_counter % 1000000 == 0:
-		t99 = time.clock()
+		t99 = time.time()
 		print str(line_counter)[:-6] + "MM lines processed so far in " + str(t99-t0) + " seconds."
-	
+
 	id_list.append(splitline[0])
 
-t1 = time.clock()
+t1 = time.time()
 
 # results reporting
 print "\nAnalysis of " + infile_name + " complete."
 print "Number of IDs found: " + str(len(id_list))
 print "Time elapsed: " + str(t1-t0) + " seconds."
 
 infile.close()
-	
+
 # time to search for these in the annotated file
 if "-A" in sys.argv:
 	af_name = string_find("-A")
@@ -100,7 +100,7 @@ def string_find(usage_term):
 
 print "\nStarting annotation filtering now."
 
-t2 = time.clock()
+t2 = time.time()
 
 # data storage
 af_line_counter = 0
@@ -112,7 +112,7 @@ def string_find(usage_term):
 	splitline = line.split("\t", 1)
 	af_dic[splitline[0]] = splitline[1]
 	if af_line_counter % 1000000 == 0:
-		t3 = time.clock()
+		t3 = time.time()
 		print str(af_line_counter)[:-6] + "MM lines processed so far in " + str(t3-t2) + " seconds."
 
 print "Annotation file read in."