[Biopython-dev] [Bug 2622] Parsing between position locations like 5933^5934 in GenBank/EMBL files

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2622


chapmanb at 50mail.com changed:

           What    |Removed                     |Added
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             Status|NEW                         |ASSIGNED




------- Comment #3 from chapmanb at 50mail.com  2008-10-28 18:12 EST -------
Peter -- this is a great summary of the problem. The fix you propose in the
_FeatureParser should definitely go in.

In terms of the higher level how should we treat this question, it wasn't
really thought about two heavily in the initial implementation since it's a
fringe case. Your proposal for handling it sounds fine. In this case
BetweenPosition would change to something like:

    def __init__(self, position, extension = 0):
        AbstractPosition.__init__(self, position + 1, 0)
        self._between_position = position
        self._between_extension = extension

    def __str__(self):
        return "(%s^%s)" % (self._between_position, self._between_position +
self._between_extension)

We would just hide the "between" junk from the standard Position stuff and
represent it as your proposal. How does that sound generally?


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