madscatt / zazzie

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collection of questions for DWW #105

Closed madscatt closed 6 years ago

madscatt commented 6 years ago

1) in preprocessor.py what is the thought for

self.logger = logging.getLogger(__name__)

2) in preprocessor.py what is the need for this?

        if 'mol' in kwargs:
            self.mol = kwargs['mol']
        else:
            # TODO: Make a better decision on what to do here
            self.mol = None

3) in preprocessor.py ...

As I am prototyping a GUI variable type (i.e. a string) passed in from gui_mimic. Do you expect to have problems if we pass ui_type as a required variable instead of **kwargs

        if 'ui' in kwargs:
            self.ui_type = kwargs['ui']
        else:
            # TODO: Not strictly needed as it is now passed from gui_mimic
            self.ui_type = 'terminal'

4) in cmdline_segname_editor.py:

There are methods that process the data structures and do not involve terminal UI that if re-written in new code to deal with sassie-web UI would be redundant. For example "get_segment_starts" and perhaps others. Would it be okay to move these methods to a new python file or is it running the risk of breaking other calls to these methods?

This doesn't seem to be an issue for preprocessor.py as I can write a method

def sassie-web_edit_options(self)

that mimics the input requirements of "terminal_edit_options" and re-use some of the PreProcessor self methods.

madscatt commented 6 years ago

Please see ticket: dealing with input fasta files #106