docs: def cmalign_from_file(cm_file_path, seqs, moltype=DNA, alignment_file_path=None,\
      include_aln=False,return_stdout=False,params=None):
      """Uses cmalign to align seqs to alignment in cm_file_path.
  
          - cm_file_path: path to the file created by cmbuild, containing aligned
              sequences. This will be used to align sequences in seqs.
          - seqs: unaligned sequendes that are to be aligned to the sequences in
              cm_file.
          - moltype: cogent.core.moltype object.  Must be DNA or RNA
          - alignment_file_path: path to stockholm alignment file used to create
              cm_file.
              __IMPORTANT__: This MUST be the same file used by cmbuild
              originally.  Only need to pass in this file if include_aln=True.
              This helper function will NOT check if the alignment file is correct
              so you must use it correctly.
          - include_aln: Boolean to include sequences in aln_file in final
              alignment. (Default=False)
          - return_stdout: Boolean to return standard output from infernal.  This
              includes alignment and structure bit scores and average
              probabilities for each sequence. (Default=False)
      """
      #NOTE: Must degap seqs or Infernal well seg fault!
      seqs = SequenceCollection(seqs,MolType=moltype).degap()
  
      #Create mapping between abbreviated IDs and full IDs
      int_map, int_keys = seqs.getIntMap()
      #Create SequenceCollection from int_map.
      int_map = SequenceCollection(int_map,MolType=moltype)
  
      if params is None:
          params = {}
      params.update({MOLTYPE_MAP[moltype]:True})
  
      app = Cmalign(InputHandler='_input_as_paths',WorkingDir='/tmp',\
          params=params)
      app.Parameters['--informat'].on('FASTA')
  
      #turn on --withali flag if True.
      if include_aln:
          if alignment_file_path is None:
              raise DataError, """Must have path to alignment file used to build CM if include_aln=True."""
          else:
              app.Parameters['--withali'].on(alignment_file_path)
  
      seqs_path = app._input_as_multiline_string(int_map.toFasta())
      paths = [cm_file_path,seqs_path]
  
      _, tmp_file = mkstemp(dir=app.WorkingDir)
      app.Parameters['-o'].on(tmp_file)
      res = app(paths)
  
      info, aligned, struct_string = \
          list(MinimalRfamParser(res['Alignment'].readlines(),\
              seq_constructor=SEQ_CONSTRUCTOR_MAP[moltype]))[0]
  
  
      #Make new dict mapping original IDs
      new_alignment={}
      for k,v in aligned.items():
          new_alignment[int_keys.get(k,k)]=v
      #Create an Alignment object from alignment dict
      new_alignment = Alignment(new_alignment,MolType=moltype)
      std_out = res['StdOut'].read()
      res.cleanUp()
      if return_stdout:
          return new_alignment, struct_string, std_out
      else:
          return new_alignment, struct_string