original_docstring: 
      Considering matrix files specified by a list, performs cross-matrix
      correlative analysis.
  
      \b
      Arguments:
      - matrix_list_fn:   List of matrix files to be considered in analysis. Each
                          row in the list corresponds to a matrix to be
                          considered in the analysis. The list contains three
                          columns:
                              1) unique integer ID for matrix
                              2) unique name for each matrix
                              3) absolute path to matrix file
      - window_start:     The first position of the analysis window relative to
                          the features in the associated feature list.
      - bin_number:       Number of bins used
      - bin_size:         Size of each bin
      - output_json:      Filename of output JSON
      
docstring: Considering matrix files specified by a list, performs cross-matrix
  correlative analysis.
  
  \b
  Arguments:
  matrix_list_fn:   List of matrix files to be considered in analysis. Each
  row in the list corresponds to a matrix to be
  considered in the analysis. The list contains three
  columns:
  1) unique integer ID for matrix
  2) unique name for each matrix
  3) absolute path to matrix file
  window_start:     The first position of the analysis window relative to
  the features in the associated feature list.
  bin_number:       Number of bins used
  bin_size:         Size of each bin
  output_json:      Filename of output JSON
docstring_tokens: Considering matrix files specified by a list performs cross - matrix correlative analysis . \ b Arguments : matrix_list_fn : List of matrix files to be considered in analysis . Each row in the list corresponds to a matrix to be considered in the analysis . The list contains three columns : 1 ) unique integer ID for matrix 2 ) unique name for each matrix 3 ) absolute path to matrix file window_start : The first position of the analysis window relative to the features in the associated feature list . bin_number : Number of bins used bin_size : Size of each bin output_json : Filename of output JSON
code: def cli(feature_bed, matrix_list_fn, annotation, window_start, bin_number,
          bin_size, output_json, sort_vector):
      """
      Considering matrix files specified by a list, performs cross-matrix
      correlative analysis.
  
      \b
      Arguments:
      - matrix_list_fn:   List of matrix files to be considered in analysis. Each
                          row in the list corresponds to a matrix to be
                          considered in the analysis. The list contains three
                          columns:
                              1) unique integer ID for matrix
                              2) unique name for each matrix
                              3) absolute path to matrix file
      - window_start:     The first position of the analysis window relative to
                          the features in the associated feature list.
      - bin_number:       Number of bins used
      - bin_size:         Size of each bin
      - output_json:      Filename of output JSON
      """
  
      assert os.path.exists(matrix_list_fn)
      with open(matrix_list_fn) as f:
          matrix_list = [
              line.strip().split()
              for line in f.readlines()
          ]
  
      mm = MatrixByMatrix(
          feature_bed, matrix_list, annotation, window_start, bin_number,
          bin_size, sort_vector
      )
      mm.writeJson(output_json)
code_tokens: def cli ( feature_bed , matrix_list_fn , annotation , window_start , bin_number , bin_size , output_json , sort_vector ) : assert os . path . exists ( matrix_list_fn ) with open ( matrix_list_fn ) as f : matrix_list = [ line . strip ( ) . split ( ) for line in f . readlines ( ) ] mm = MatrixByMatrix ( feature_bed , matrix_list , annotation , window_start , bin_number , bin_size , sort_vector ) mm . writeJson ( output_json )
short_docstring: Considering matrix files specified by a list, performs cross-matrix
  correlative analysis.
short_docstring_tokens: Considering matrix files specified by a list performs cross - matrix correlative analysis .
comment: """
      Considering matrix files specified by a list, performs cross-matrix
      correlative analysis.
  
      \b
      Arguments:
      - matrix_list_fn:   List of matrix files to be considered in analysis. Each
                          row in the list corresponds to a matrix to be
                          considered in the analysis. The list contains three
                          columns:
                              1) unique integer ID for matrix
                              2) unique name for each matrix
                              3) absolute path to matrix file
      - window_start:     The first position of the analysis window relative to
                          the features in the associated feature list.
      - bin_number:       Number of bins used
      - bin_size:         Size of each bin
      - output_json:      Filename of output JSON
      """