fix bug?

Author: zhangrengang

soi/mcscan.py

@@ -212,14 +212,20 @@ def _parse_list(self, _collinearities):
 		collinearities = []
 		if isinstance(_collinearities, str):  # file
 			return [_collinearities]
+		_unknown = []
 		for collinearity in _collinearities:
+			if not test_s(collinearity):
+				_unknown += [collinearity]
+				continue
 			# *.collinearity file
 			if lazy_decode(open(collinearity).read(1)) == '#':
 				collinearities += [collinearity]
 			else:  # list file
-				files, _unknown = [], []
+				files = []
 				i = 0
 				for line in open(collinearity):
+					if not line.strip():
+						continue
 					_file = line.strip().split()[0]
 					if _file:
 						i += 1
@@ -232,9 +238,13 @@ def _parse_list(self, _collinearities):
 				elif len(files) == 0:
 					collinearities += [collinearity]
 				else:
-					logger.warn(
-						'Files empty or not exists: {}'.format(_unknown))
 					collinearities += files
+		if _unknown:
+			logger.warn(
+                        'Files empty or not exists: {}'.format(_unknown))
+		if len(collinearities) == 0:
+			logger.error('No collinearity file(s) are recognized. Please check the input.')
+			sys.exit()
 		return collinearities
 
 	def _parse(self):

soi/options.py

@@ -214,7 +214,7 @@ def makeArgs():
 	# subcommands
 	subparsers = parser.add_subparsers(help='sub-command help')
 	parser_dot = subparsers.add_parser('dotplot',
-									   help='Generate colored dot plots')
+									   help='Generate Ks/OI-colored dot plots')
 	args_dotplot(parser_dot)
 	parser_flt = subparsers.add_parser('filter',
 									   help='Filter synteny with Orthology Index (standard output)')