old_contents: from helps import *
  
  def formatdb(**args):
      ''' run NCBI formatdb '''
      
      database = args['database']
      
      cmd = ' '.join([
          '~/cram/bin/formatdb',
          '-i %s' % database,
      ])
      
      ohai('running formatdb')
      
      run(cmd, generates='%s.psq' % database)
  
  def blastp(**args):
      ''' run BLASTALL (default is blastp, can be overriden with program=) '''
      
      cmd = ' '.join([
          '~/cram/bin/blastall',
          '-p %s' % args.get('program', 'blastp'),
          '-d %s' % args['database'],
          '-i %s' % args['query'],
          '-e %s' % args.get('evalue', 10),
          '-o %s' % args['out'],
          '-v %s' % args.get('alignments', 1),
          '-b %s' % args.get('descriptions', 1),
          '-a %s' % args.get('threads', 1),
          '-m %s' % args.get('format', 1)
      ])
      
      ohai('running blastp')
      
      run(cmd, generates=args['out'])
new_contents: from helps import *
  
  def formatdb(**args):
      ''' run NCBI formatdb '''
      
      database = args['database']
      
      cmd = ' '.join([
          '~/cram/bin/formatdb',
          '-i %s' % database,
      ])
      
      ohai('running formatdb')
      
      run(cmd, generates='%s.psq' % database)
  
  def blastp(**args):
      ''' run BLASTALL (default is blastp, can be overriden with program=) '''
      
      cmd = ' '.join([
          '~/cram/bin/blastall',
          '-p %s' % args.get('program', 'blastp'),
          '-d %s' % args['database'],
          '-i %s' % args['query'],
          '-e %s' % args.get('evalue', 10),
          '-o %s' % args['out'],
          '-v %s' % args.get('alignments', 1),
          '-b %s' % args.get('descriptions', 1),
          '-a %s' % args.get('threads', 1),
          '-m %s' % args.get('format', 8)
      ])
      
      ohai('running blastp')
      
      run(cmd, generates=args['out'])
  
subject: format = 8 not 1