main exception handling

main.py

@@ -4,6 +4,8 @@ import sys
 import os
 import shutil
 import click
+from datetime import datetime
+from subprocess import CalledProcessError
 
 from Bio import SeqIO
 
@@ -24,34 +26,39 @@ def cleanup():
 @click.option('--input_fasta', '-i', required=True, type=str, help='Input fasta file.')
 @click.option('--sketch_only', '-s', is_flag=True)
 def main(input_fasta, sketch_only):
+	numberOfErrors = 0
+	startTime = datetime.now()
 	setup()
 
-	#RUN
 	sequences = list(SeqIO.parse(open(input_fasta), 'fasta'))
 	for sequence in sequences:
+		seqStartTime = datetime.now()
+		print('Processing {}...'.format(sequence.id), end='\r')
 		try:
 			if not os.path.exists('data/{}'.format(sequence.id)):
 				os.makedirs('data/{}'.format(sequence.id))
 			if not os.path.exists('data/{}/TE'.format(sequence.id)):
 				os.makedirs('data/{}/TE'.format(sequence.id))
-			print('Running Nester for {}...'.format(sequence.id))
 			
 			if not sketch_only:
 				nester = Nester(sequence)
-				#for a in nester.nestedList:
-				#	print(a)
-				#	for b in a.features['domains']:
-				#		print('--------------------')
-				#		print(b)
-				#	print('##########################')
 				sketch.createGFF(sequence.id, sequence.seq, nester.nestedList)
 			sketch.sketch(sequence.id)
+			seqEndTime = datetime.now()
+			print('Processing {}: done [{}]'.format(sequence.id, seqEndTime - seqStartTime))	
 		except KeyboardInterrupt:
 			raise
-		#except:
-		#	print('Unexpected error:', sys.exc_info()[0])			
+		except CalledProcessError:
+			numberOfErrors += 1
+			print('Processing {}: SUBPROCESS ERROR'.format(sequence.id))		
+		except:
+			numberOfErrors += 1
+			print('Processing {}: UNEXPECTED ERROR:'.format(sequence.id), sys.exc_info()[0])		
 
 	cleanup()
+	endTime = datetime.now()
+	print('Total time: {}'.format(endTime - startTime))
+	print('Number of errors: {}'.format(numberOfErrors))
 
 if __name__ == '__main__':
     main()
\ No newline at end of file

python/sketch.py

+import os
 import subprocess
 
 from Bio import SeqIO
@@ -83,5 +84,8 @@ def createGFF(id, sequence, nestedList):
         GFF.write([rec], out_handle)
 
 def sketch(id):
-    process = subprocess.Popen([config.gt_sketch_path] + config.gt_sketch_args + ['data/{}/{}.png'.format(id, id)] + ['data/{}/{}.gff'.format(id, id)])
+    null = open(os.devnull, 'w')
+    process = subprocess.check_output([config.gt_sketch_path] + config.gt_sketch_args + ['data/{}/{}.png'.format(id, id)] + ['data/{}/{}.gff'.format(id, id)], stderr=null)
+    
+