code: def run_hmmbuild(self):
  
          '''
          Generate hmm with hhbuild,
          output to file. Also stores query names.
          '''
  
          for alignment in self.alignment_list:
  
              print 'building Hmm for', alignment
  
              alignment_full_path = self.alignment_dir + alignment
              query_name = alignment.split("_")[0]
              self.query_names.append(query_name)
  
              new_hmm= self.hmm_dir + query_name + ".hmm"
  
              hmmbuild_output = subprocess.call(["hmmbuild", new_hmm,
               alignment_full_path])
  
          print 'hhbuild complete for', self.query_namef run_hmmbuild(self):
  
          '''
          Generate hmm with hhbuild,
          output to file. Also stores query names.
          '''
  
          for alignment in self.alignment_list:
  
              print 'building Hmm for', alignment
  
              alignment_full_path = self.alignment_dir + alignment
              query_name = alignment.split("_")[0]
              self.query_names.append(query_name)
  
              new_hmm= self.hmm_dir + query_name + ".hmm"
  
              hmmbuild_output = subprocess.call(["hmmbuild", new_hmm,
               alignment_full_path])
  
          print 'hhbuild complete for', self.query_names
docs: Generate hmm with hhbuild,
          output to file. Also stores query names.