[Biopython-dev] [Bug 1716] Fasta.Dictionary should throw KeyError for invalid keys

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

http://bugzilla.open-bio.org/show_bug.cgi?id=1716

biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
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         OS/Version|Windows 2000                |All



------- Additional Comments From biopython-bugzilla at maubp.freeserve.co.uk  2004-12-11 08:47 -------
Further investigation reveals that the __getitem__ function checks for an
invalid key by exception, and in this case attempts to "try and fetch by alias".
 I'm not sure what that is meant to do, but if this also fails, I think a
KeyError should be raised rather than whatever went wrong with the alias fetch.

An except from old code in Bio/Fasta/__init.py__ from the class Dictionary:
----------------------------------------------------------------------------
def __getitem__(self, key):
    # first try to retrieve by the base id
    try:
        seqs = self._index.lookup(id = key)
    # if we can't do that, we have to try and fetch by alias
    except KeyError:
        seqs = self._index.lookup(aliases = key)
    ...
----------------------------------------------------------------------------

My suggested code:
----------------------------------------------------------------------------
def __getitem__(self, key):
    # first try to retrieve by the base id
    try:
        seqs = self._index.lookup(id = key)
    # if we can't do that, we have to try and fetch by alias
    except KeyError:
        try :
            seqs = self._index.lookup(aliases = key)
        except :
            #That failed too.  Rather than returning some
            #cryptic ZeroDivisionError from Mindy, do this:
            raise KeyError("Key (%s) not found, not even as an alias" % key)
    ...
----------------------------------------------------------------------------

This would appear to fix my original problem of a miss-leading error message. 
The actual wording I have suggested could probably be improved...



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