diff --git a/tools/new_operations/galaxyops/__init__.py b/tools/new_operations/galaxyops/__init__.py index 224d10e7fb7..73123ae110b 100644 --- a/tools/new_operations/galaxyops/__init__.py +++ b/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) )