[Biopython-dev] Question about "class _Argument(_AbstractParameter):"

[Lenna Peterson]

Subclasses of Bio.Applications.AbstractCommandline set the values. The
docstring for that class gives some examples.

Cheers,

Lenna


On Sat, May 17, 2014 at 9:39 AM, Vincent Davis <vincent at vincentdavis.net>wrote:

> I don't understand how self.value = None can ever be anything but None?
> Which then leads me to wonder how the assert in _ArgumentList can ever pass
> "assert isinstance(self.value, list)"
> Probably something I don't understand about how arguments work with
> subclasses.
>
> Here is an example
> >>> exp1 = _ArgumentList(["input_bam", "in_bam", "input", "bam"], "Input
> BAM", >>> filename=True, is_required=True)
> >>> print(exp1.value)
> >>> print(exp1.names)
> None
>
> ['input_bam', 'in_bam', 'input', 'bam']
>
>
> But this will never work?
>
> print(exp1)
>
>
>
>
> class _Argument(_AbstractParameter):
>     """Represent an argument on a commandline.
>
>     The names argument should be a list containing one string.
>     This must be a valid Python identifer as it is used as the
>     property name and as a keyword argument, and should therefore
>     follow PEP8 naming.
>     """
>     def __init__(self, names, description, filename=False,
>                  checker_function=None, is_required=False):
>         #if len(names) != 1:
>         #    raise ValueError("The names argument to _Argument should be a
> "
>         #                     "single entry list with a PEP8 property
> name.")
>         self.names = names
>         assert isinstance(description, basestring), \
>                "%r for %s" % (description, names[-1])
>         self.is_filename = filename
>         self.checker_function = checker_function
>         self.description = description
>         self.is_required = is_required
>         self.is_set = False
>         *self.value = None*
>
> class _ArgumentList(_Argument):
>     """Represent a variable list of arguments on a command line, e.g.
> multiple filenames."""
>     *def __str__(self):*
> *        assert isinstance(self.value, list), \*
> *                "Arguments should be a list"*
>     ........
>
> Vincent Davis
> 720-301-3003
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