[Bioperl-l] FW: [Bug 1754] Bio::Location::Fuzzy.pm -> SwissProt FeatureTable locationvalue error (undef values!)

Brian Osborne brian_osborne at cognia.com
Thu Oct 27 08:25:05 EDT 2005

Hi Brian,

finally took some time to check your testcases! They are fine and test
OK on our installation as well. You wrote you were not sure if you are
covering all cases. There are two more possible cases those would need

        "?..?" => [$fuzzy_impl,
           undef, undef, "UNCERTAIN", undef, undef, "UNCERTAIN",
"UNCERTAIN", 1, 1],
        "12..?1" => [$fuzzy_impl,
           1, 1, "UNCERTAIN", 12, 12, "EXACT", "EXACT", 1, 1]

The first (?..?) is a really occuring SP entry - they have annotations
which do not map to an exact location... :S. the second case i'm not
100% sure anymore that i did find it in SP, but your parser definetly
should be/is capable of coping with such a locationstring.

Also these two cases tested fine on my machine as well. So for by part
this bug is CLOSED...

Another problem on the horizon:  are you aware of the new annotations
coming up from the SP-team in the database? Have you had a look at them?
Do you know if your paser is ready for it? If you need help, I'm
available - we will need to verify the parser is working for these when
the new annotations are integrated. I had a talk with some guys from the
SP-team at the ECCB'05, so I guess I could receive some "testrecords" if
I ask very nicely ;).


Florian Leitner
Institute for Molecular Pathology, Vienna (www.imp.univie.ac.at)
Eisenhaber Bioinformatics Group (mendel.imp.univie.ac.at)
e-mail: <florian.leitner at imp.univie.ac.at>
mobile: +43-(0)650-4567 321

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