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: https://github.com/PoonLab/OpenRDP/blob/1863aca41432151c6121ddf336ebd02408ed0c74/openrdp/threeseq.py#L60-L63

[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 #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.

[ArtPoon]

Successful run from interface branch on Linux (Ubuntu 20):

(venv) art@orolo:~/git/OpenRDP$ openrdp tests/test_neisseria.fasta test.out -c tests/test_cfg.ini 
Starting 3Seq Analysis
Finished 3Seq Analysis
Starting GENECONV Analysis
Finished GENECONV Analysis
Setting up bootscan analysis...
Starting Scanning Phase of Bootscan/Recscan
Finished Scanning Phase of Bootscan/Recscan
Setting up maxchi analysis...
Setting up siscan analysis...
Setting up chimaera analysis...
Setting up rdp analysis...
Scanning triplet 1 / 4
Scanning triplet 2 / 4
Scanning triplet 3 / 4
Scanning triplet 4 / 4

Method               StartLocation        EndLocation          Recombinant          Parent1              Parent2              Pvalue              
Geneconv             1                    204                  X64866               X64869               -                    0.00002             
Geneconv             151                  195                  X64860               X64869               -                    0.00210             
Geneconv             203                  507                  X64860               X64866               -                    0.00829             
Geneconv             539                  759                  X64860               X64866               -                    0.15378             
Geneconv             151                  193                  X64873               -                    -                    0.02202             
Geneconv             56                   170                  X64860               -                    -                    0.02728             
Bootscan             760                  765                  X64869               X64860               X64866               0.06513627245570731 
MaxChi               475                  518                  X64860               X64866               X64869               0.04042768199451279 
MaxChi               439                  482                  X64860               X64866               X64873               0.04042768199451279 
MaxChi               475                  518                  X64866               X64869               X64873               0.04042768199451279 
Siscan               2                    45                   X64860               X64866               X64869               0.7663004734577327  
Siscan               2                    45                   X64860               X64866               X64873               0.7593011319150192  
Siscan               2                    45                   X64860               X64869               X64873               0.7629651782860931  
Siscan               2                    45                   X64866               X64869               X64873               0.7624489264586414  
Chimaera             179                  265                  X64860               X64869               X64873               0.004701217146256585
Chimaera             170                  213                  X64869               X64866               X64873               0.0018132288986577026
Chimaera             177                  220                  X64873               X64860               X64866               0.02047438504938101 
3Seq                 202                  787                  X64869               X64860               X64866               5.982096e-10        
3Seq                 181                  787                  X64866               X64869               X64873               5.294757e-06        
RDP                  6                    496                  X64860               X64866               X64869               6.450462737744835e-06
RDP                  6                    504                  X64860               X64866               X64873               0.002454937279797601
RDP                  36                   481                  X64860               X64869               X64873               0.00044032555125241474