1.1 --- a/allpy/processors.py	Tue Jul 12 15:00:37 2011 +0400
     1.2 +++ b/allpy/processors.py	Tue Jul 12 16:16:08 2011 +0400
     1.3 @@ -36,14 +36,17 @@
     1.4  #
     1.5  
     1.6  class _Muscle(ExternalCommand):
     1.7 -    """Realign block with muscle."""
     1.8 +    """Realign block with muscle.
     1.9 +
    1.10 +    Arguments:
    1.11 +
    1.12 +    - remove_gaps -- drop all gaps from alignment before realigning
    1.13 +    """
    1.14  
    1.15      def __init__(self, remove_gaps=False):
    1.16 -        """
    1.17 -        remove_gaps -- drop all gaps from alignment before treating it with muscle
    1.18 -        """
    1.19          self.remove_gaps = remove_gaps
    1.20 -        ExternalCommand.__init__(self, 'muscle -stable -in %(infile)s -out %(outfile)s')
    1.21 +        cmd = 'muscle -stable -in %(infile)s -out %(outfile)s >/dev/null 2>&1'
    1.22 +        ExternalCommand.__init__(self, cmd)
    1.23  
    1.24      def __call__(self, block):
    1.25          if self.remove_gaps: