Allen, your recent change to require only 1 digit instead of 3 after
the colon broke the parser. The change makes the regular expressions
pick up EC numbers as secondary GO accessions. Did the test quoted
below not fail on your machine?
I'm going to reverse that change. The MPATH ontology needs to be
accommodated in a way that doesn't break the parser, possibly by having
its own.
Also, I should urge you to add test cases for all the ontologies for
which you found yourself having to adapt the parser. Otherwise the
ability to parse those too may be abolished silently at any time by
anyone changing the code.
-hilmar
On Tuesday, October 21, 2003, at 06:57 PM, Jason Stajich wrote:
I also get this on perl 5.8.0
not ok 11
# Test 11 got: <UNDEF> (t/simpleGOparser.t at line 82)
# Expected: 'EC:5.3.99.5'
and perl 5.6.0
not ok 11
# Test 11 got: <UNDEF> (t/simpleGOparser.t at line 82)
# Expected: 'EC:5.3.99.5'
On Tue, 21 Oct 2003, Hilmar Lapp wrote:
On 10/18/03 6:34 PM, "Rob Edwards" <redwards@xxxxxxxxx> wrote:
t/simpleGOparser.t 88 1 1.14% 11
Do these just fail under Mac OSX perl 5.8.x? I can only check for perl
5.6.0.
-hilmar
--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
--
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Hilmar Lapp email: lapp at gnf.org
GNF, San Diego, Ca. 92121 phone: +1-858-812-1757
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