User interface improvements

[ArtPoon]

I'm not crazy about the current command-line invocation:

python3 -m openrdp ./openrdp/tests/test_neisseria.fasta ./test.csv -cfg ./openrdp/tests/test_cfg.ini -all

• I would much prefer to enable users to simply call openrdp as an executable script in /usr/local/bin or /home/USER/.local/bin
• There should be a default configuration, so the user does not have to use the -cfg flag.
• Calling the script without setting -cfg proceeds to run the analysis until it throws an exception:

Setting Up Siscan Analysis
Scanning triplet 1 / 4
Traceback (most recent call last):
  File "/usr/lib/python3.8/runpy.py", line 194, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/usr/lib/python3.8/runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "/home/art/git/OpenRDP/openrdp/__main__.py", line 4, in <module>
    main()
  File "/home/art/git/OpenRDP/openrdp/main.py", line 173, in main
    openrdp(infile, outfile, cfg, run_geneconv, run_three_seq, run_rdp,
  File "/home/art/git/OpenRDP/openrdp/main.py", line 146, in openrdp
    scanner.run_scans(aln)
  File "/home/art/git/OpenRDP/openrdp/scripts/run_scans.py", line 139, in run_scans
    maxchi.execute(triplet)
  File "/home/art/git/OpenRDP/openrdp/scripts/maxchi.py", line 147, in execute
    win_size = triplet.get_win_size(0, self.win_size, self.fixed_win_size, self.num_var_sites,
AttributeError: 'MaxChi' object has no attribute 'win_size'

-cfg is listed as an optional argument in the help text, so it should behave as such!

[ArtPoon]

The current Python interface is also not ideal:

>>> from openrdp.main import openrdp
>>> res = openrdp("openrdp/tests/test_neisseria.fasta", "test.csv", "openrdp/tests/test_cfg.ini")
Starting 3Seq Analysis
...
Siscan               2                    45                   X64866               X64869               X64873               0.7654518134939761  
>>> res
>>> 

openrdp should return some object that makes the outputs available to the user for downstream processing.

[ArtPoon]

Python interface should not depend on an external file, e.g., test_cfg.ini

[ArtPoon]

Started ripping things out in new branch interface

[ArtPoon]

Moved command-line interface code to executable script under new /bin folder.

[ArtPoon]

Moved core code from main.py and run_scans.py into openrdp/__init__.py

[ArtPoon]

• Made default_config.ini into default settings, i.e., user does not have to explicitly specify these.
• Need to come up with some way of displaying a summary of configuration for Scanner object.
• Need to allow users to modify configuration via accessory functions of Scanner.

[ArtPoon]

Of course refactoring broke stuff:

art@Wernstrom OpenRDP % openrdp tests/test_neisseria.fasta test
Starting 3Seq Analysis
[Errno 2] No such file or directory: '/Users/art/git/OpenRDP/test_neisseria.fasta.3s.rec'
Finished 3Seq Analysis
Starting GENECONV Analysis
Finished GENECONV Analysis
Setting up geneconv analysis...
Setting up bootscan analysis...
Starting Scanning Phase of Bootscan/Recscan
Traceback (most recent call last):
  File "/usr/local/bin/openrdp", line 4, in <module>
    __import__('pkg_resources').run_script('OpenRDP==0.0.1', 'openrdp')
  File "/usr/local/lib/python3.10/site-packages/pkg_resources/__init__.py", line 672, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/usr/local/lib/python3.10/site-packages/pkg_resources/__init__.py", line 1472, in run_script
    exec(code, namespace, namespace)
  File "/usr/local/lib/python3.10/site-packages/OpenRDP-0.0.1-py3.10.egg/EGG-INFO/scripts/openrdp", line 30, in <module>
    results = openrdp.openrdp(args.infile, args.outfile, cfg=args.cfg,
  File "/usr/local/lib/python3.10/site-packages/OpenRDP-0.0.1-py3.10.egg/openrdp/__init__.py", line 293, in openrdp
    results = scanner.run_scans(aln)
  File "/usr/local/lib/python3.10/site-packages/OpenRDP-0.0.1-py3.10.egg/openrdp/__init__.py", line 174, in run_scans
    tmethods.append(a['method'](alignment, settings=settings, quiet=self.quiet))
  File "/usr/local/lib/python3.10/site-packages/OpenRDP-0.0.1-py3.10.egg/openrdp/bootscan.py", line 33, in __init__
    self.dists = self.do_scanning_phase(alignment)
  File "/usr/local/lib/python3.10/site-packages/OpenRDP-0.0.1-py3.10.egg/openrdp/bootscan.py", line 128, in do_scanning_phase
    with multiprocessing.Pool() as p:
  File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/context.py", line 119, in Pool
    return Pool(processes, initializer, initargs, maxtasksperchild,
  File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/pool.py", line 215, in __init__
    self._repopulate_pool()
  File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/pool.py", line 306, in _repopulate_pool
    return self._repopulate_pool_static(self._ctx, self.Process,
  File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/pool.py", line 329, in _repopulate_pool_static
    w.start()
  File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/process.py", line 121, in start
    self._popen = self._Popen(self)
  File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/context.py", line 288, in _Popen
    return Popen(process_obj)
  File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/popen_spawn_posix.py", line 32, in __init__
    super().__init__(process_obj)
  File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/popen_fork.py", line 19, in __init__
    self._launch(process_obj)
  File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/popen_spawn_posix.py", line 42, in _launch
    prep_data = spawn.get_preparation_data(process_obj._name)
  File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/spawn.py", line 183, in get_preparation_data
    main_mod_name = getattr(main_module.__spec__, "name", None)
AttributeError: module '__main__' has no attribute '__spec__'

[ArtPoon]

The first error:

Starting 3Seq Analysis
[Errno 2] No such file or directory: '/Users/art/git/OpenRDP/test_neisseria.fasta.3s.rec'

is probably associated with these lines:

OpenRDP/openrdp/threeseq.py

Lines 60 to 63 in 1863aca

	# Parse the output of 3Seq
	tseq_out = self.in_name + '.3s.rec'
	out_path = os.path.join(os.getcwd(), tseq_out)
	ts_results = self.parse_output(out_path)

[ArtPoon]

I confirmed that master branch runs fine in this setup. Very strange.
Ah, but the "file not found" error is still there:

Starting 3Seq Analysis
[Errno 2] No such file or directory: '/Users/art/git/OpenRDP/test_neisseria.fasta.3s.rec'
Finished 3Seq Analysis

[ArtPoon]

I'm going to spin these two errors off into separate issues.

[ArtPoon]

• First problem fixed in 3Seq: no such file or directory #39
• Pushed fixes to dev branch and merged into interface
• I think the second problem may have something to do with my converting the main script into an executable file. Open as separate issue.