[Biopython-dev] Bio.Motif._Motif has_instances, has_counts

Peter Cock p.j.a.cock at googlemail.com
Fri Aug 10 08:33:43 UTC 2012

On Thu, Aug 9, 2012 at 5:00 PM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> OK, done. Thanks!
> -Michiel.

You'll also need to update the example in the Tutorial, quote:

    The arnt and srf motifs can both do the same things for us,
    but they use different internal representations of the motif.
    We can tell that by inspecting the \verb|has_counts| and
    has_instances properties:

    >>> arnt.has_instances
    >>> srf.has_instances
    >>> srf.has_counts

This means test_Tutorial.py is failing (across all platforms).
Presumably we would suggest switching these to somethinglike:

    >>> arnt.instances is None

etc? In fact given the old methods were documents like
this, I would be happier if we could phase them out with
a deprecation warning via a read only property method,

    def has_instances(self):
        """"Does this motif have instances (DEPRECATED)."""
        import warnings
        from Bio import BiopythonDeprecationWarning
        warnings.warn("Check if motif.instance is None or not instead",
        return self.instances is not None

(untested, but something like that)


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