old_contents: #!/usr/bin/env python2.3
  
  """
  Read a maf file from stdin and write out a new maf with only blocks having all
  of the required in species, after dropping any other species and removing
  columns containing only gaps.
  
  usage: %prog species,species2,... < maf
  """
  
  import psyco_full
  
  import bx.align.maf
  import copy
  import sys
  
  from itertools import *
  
  def main():
  
      species = sys.argv[1].split( ',' )
  
      maf_reader = bx.align.maf.Reader( sys.stdin )
      maf_writer = bx.align.maf.Writer( sys.stdout )
  
      for m in maf_reader:        
          new_components = []    
          for comp in m.components:
              if comp.src.split( '.' )[0] in species:
                  new_components.append( comp )
          m.components = new_components
          if len( m.components ) > 1:
              maf_writer.write( m )
          
      maf_reader.close()
      maf_writer.close()
  
  if __name__ == "__main__": 
      main()
  
new_contents: #!/usr/bin/env python2.3
  
  """
  Read a maf file from stdin and write out a new maf with only blocks having all
  of the required in species, after dropping any other species and removing
  columns containing only gaps.
  
  usage: %prog species,species2,... < maf
  """
  
  import psyco_full
  
  import bx.align.maf
  import copy
  import sys
  
  from itertools import *
  
  def main():
  
      species = sys.argv[1].split( ',' )
  
      maf_reader = bx.align.maf.Reader( sys.stdin )
      maf_writer = bx.align.maf.Writer( sys.stdout )
  
      for m in maf_reader:        
          new_components = []    
          for comp in m.components:
              if comp.src.split( '.' )[0] in species:
                  new_components.append( comp )
          m.components = new_components
          m.remove_all_gap_columns()
          if len( m.components ) > 1:
              maf_writer.write( m )
          
      maf_reader.close()
      maf_writer.close()
  
  if __name__ == "__main__": 
      main()
  
subject: Remove all-gap columns after removing rows of the alignment