New eggs which contain the NiceReaderWrapper, and removed it from Gops. bx.intervals.io.NiceReaderWrapper. Enjoy.

tools/new_operations/galaxyops/__init__.py

@@ -24,35 +24,6 @@ def parse_cols_arg( cols ):
     else:
         return BED_DEFAULT_COLS
 
-class NiceReaderWrapper( GenomicIntervalReader ):
-    def __init__( self, reader, **kwargs ):
-        GenomicIntervalReader.__init__( self, reader, **kwargs )
-        self.outstream = kwargs.get("outstream", None)
-        self.print_delegate = kwargs.get("print_delegate", None)
-        self.skipped = 0
-        self.skipped_lines = []
-        self.input_wrapper = iter( self.input )
-        self.input_iter = self.iterwrapper()
-    def __iter__( self ):
-        return self
-    def next( self ):
-        while 1:
-            try:
-                nextitem = GenomicIntervalReader.next( self )
-                return nextitem
-            except ParseError, e:
-                if self.outstream:
-                    if self.print_delegate and hasattr(self.print_delegate,"__call__"):
-                        self.print_delegate( self.outstream, e, self )
-                self.skipped += 1
-                # no reason to stuff an entire bad file into memmory
-                if self.skipped < 10:
-                    self.skipped_lines.append( (self.linenum, self.current_line) )
-    def iterwrapper( self ):
-        while 1:
-            self.current_line = self.input_wrapper.next()
-            yield self.current_line
-
 def default_printer( stream, exc, obj ):
     print >> stream, "%d: %s" % ( obj.linenum, obj.current_line )
     print >> stream, "\tError: %s" % ( str(exc) )