diff --git a/flake8/pep8.py b/flake8/pep8.py
index 01d512e..da9a112 100644
--- a/flake8/pep8.py
+++ b/flake8/pep8.py
@@ -482,6 +482,9 @@ def continuation_line_indentation(logical_line, tokens, indent_level, verbose):
         print(">>> " + tokens[0][4].rstrip())
 
     for token_type, text, start, end, line in tokens:
+        if line.strip().lower().endswith('# nopep8'):
+            continue
+
         newline = row < start[0] - first_row
         if newline:
             row = start[0] - first_row
@@ -1205,8 +1208,7 @@ class Checker(object):
         self.line_number += 1
         if self.line_number > len(self.lines):
             return ''
-        line = self.lines[self.line_number - 1]
-        return '' if line.lower().strip().endswith('# nopep8') else line
+        return self.lines[self.line_number - 1]
 
     def readline_check_physical(self):
         """
diff --git a/flake8/run.py b/flake8/run.py
index f5cb831..f7b5b52 100644
--- a/flake8/run.py
+++ b/flake8/run.py
@@ -52,7 +52,7 @@ def _get_python_files(paths):
                         yield fullpath
 
         else:
-            if not skip_file(path) or pep8style.excluded(fullpath):
+            if not skip_file(path) or pep8style.excluded(path):
                 yield path