I have tried to create a new wrapper for MStatx in biopython. But it gives me the following error. For my university project I need to include MStatx .

    Running doctests...
Traceback (most recent call last):
  File "_mstax_wrapper.py", line 31, in <module>
    run_doctest()
  File "/home/osh/miniconda3/envs/vir_env/lib/python3.5/site-packages/Bio/_utils.py", line 115, in run_doctest
    os.chdir(find_test_dir(target_dir))
  File "/home/osh/miniconda3/envs/vir_env/lib/python3.5/site-packages/Bio/_utils.py", line 98, in find_test_dir
    os.path.abspath(start_dir))
ValueError: Not within Biopython source tree: '/home/osh/Desktop/FYP/MSA'

Following is my code.

 """Command line wrapper for the Mstatx"""

 from __future__ import print_function

 from Bio.Application import _Option, _Switch, AbstractCommandline

class MstatxCommandline(AbstractCommandline):


    def __init__(self, cmd="mstatx", **kwargs):
        self.parameters = [
            _Option(["-o", "--output"],
                    "Output file name",
                    filename=False,
                    equate=False),
            _Option(["-g", "--global"],
                    "Output the global score"),
           # Input file name
            _Argument(["-i","--i"],
                      "--input is needed",
                      filename=True,
                      is_required=True)
            ]
        AbstractCommandline.__init__(self, cmd, **kwargs)


if __name__ == "__main__":
    from Bio._utils import run_doctest
    run_doctest()