[Bioperl-l] Error retrieving sequence from BioSQL

Seth Johnson johnson.biotech at gmail.com
Mon Oct 23 12:36:36 EDT 2006


Chris,

There's definite improvement:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Failed Test     Stat Wstat Total Fail  Failed  List of Failed
-------------------------------------------------------------------------------
t/02species.t                 65    2   3.08%  63 65
t/03simpleseq.t    1   256    59  106 179.66%  7-59
t/04swiss.t                   52   14  26.92%  25 27-34 38-42
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

There's some weirdness going on during the 'swiss.t' test.  It almost seems
to me that expectations of some tests are swapped (27 & 39, 28 & 40, 29 &
41, 31 & 27, 32 & 28, 33 & 29, 39 & 31):
================================
not ok 25
# Test 25 got: '10097078' (t/04swiss.t at line 79)
#    Expected: '91309150'
ok 26
not ok 27
# Test 27 got: 'Jiang,J., Zhang,Y., Krainer,A.R. and Xu,R.M.' (t/04swiss.t
at line 85)
#    Expected: 'Krainer,A.R., Mayeda,A., Kozak,D. and Binns,G.'
not ok 28
# Test 28 got: 'Crystal structure of human p32, a doughnut-shaped acidic
mitochondrial matrix protein' (t/04swiss.t at line 86)
#    Expected: 'Functional expression of cloned human splicing factor SF2:
homology to RNA-binding proteins, U1 70K, and Drosophila splicing
regulators'
not ok 29
# Test 29 got: 'Proc. Natl. Acad. Sci. U.S.A. 96 (7), 3572-3577 (1999)'
(t/04swiss.t at line 87)
#    Expected: 'Cell 66 (2), 383-394 (1991)'
not ok 30
# Test 30 got: <UNDEF> (t/04swiss.t at line 88)
#    Expected: '91309150'
not ok 31
# Test 31 got: 'Krainer,A.R., Mayeda,A., Kozak,D. and Binns,G.' (t/04swiss.t
at line 85 fail #2)
#    Expected: 'Honore,B., Madsen,P., Rasmussen,H.H., Vandekerckhove,J.,
Celis,J.E. and Leffers,H.'
not ok 32
# Test 32 got: 'Functional expression of cloned human splicing factor SF2:
homology to RNA-binding proteins, U1 70K, and Drosophila splicing
regulators' (t/04swiss.t at line 86 fail #2)
#    Expected: 'Cloning and expression of a cDNA covering the complete
coding region of the P32 subunit of human pre-mRNA splicing factor SF2'
not ok 33
# Test 33 got: 'Cell 66 (2), 383-394 (1991)' (t/04swiss.t at line 87 fail
#2)
#    Expected: 'Gene 134 (2), 283-287 (1993)'
not ok 34
# Test 34 got: <UNDEF> (t/04swiss.t at line 88 fail #2)
#    Expected: '94085792'
ok 35
ok 36
ok 37
not ok 38
# Test 38 got: <UNDEF> (t/04swiss.t at line 88 fail #3)
#    Expected: '94253723'
not ok 39
# Test 39 got: 'Honore,B., Madsen,P., Rasmussen,H.H., Vandekerckhove,J.,
Celis,J.E. and Leffers,H.' (t/04swiss.t at line 85 fail #4)
#    Expected: 'Jiang,J., Zhang,Y., Krainer,A.R. and Xu,R.M.'
not ok 40
# Test 40 got: 'Cloning and expression of a cDNA covering the complete
coding region of the P32 subunit of human pre-mRNA splicing factor SF2'
(t/04swiss.t at line 86 fail #4)
#    Expected: 'Crystal structure of human p32, a doughnut-shaped acidic
mitochondrial matrix protein'
not ok 41
# Test 41 got: 'Gene 134 (2), 283-287 (1993)' (t/04swiss.t at line 87 fail
#4)
#    Expected: 'Proc. Natl. Acad. Sci. U.S.A. 96 (7), 3572-3577 (1999)'
not ok 42
# Test 42 got: <UNDEF> (t/04swiss.t at line 88 fail #4)
#    Expected: '99199225'
==============================


On 10/20/06, Chris Fields <cjfields at uiuc.edu> wrote:
>
>
>
> Seth,
>
> Did you work out the problem here?  There was a recent CVS update to OBDA
> tests (16obda.t) that fixed similar problems on Mac OS X.  Old OBDA tests
> apparently left data from tests in the database, which caused problems
> with
> repeated test runs.
>
> Chris
>
> > > -----Original Message-----
> > > From: bioperl-l-bounces <at> lists.open-bio.org [mailto: bioperl-l-
> > > bounces <at> lists.open-bio.org] On Behalf Of Seth Johnson
> > > Sent: Saturday, September 30, 2006 6:35 PM
> > > To: Hilmar Lapp
> > > Cc: Chris Fields; Bioperl List
> > > Subject: Re: [Bioperl-l] Error retrieving sequence from BioSQL
> > >
> > > Here're complete test details:
> > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> >
> > ...
> >
> > > FAILED tests 10-12
> > >     Failed 3/12 tests, 75.00% okay
> > > Failed Test     Stat Wstat Total Fail  Failed  List of Failed
> > >
> >
> --------------------------------------------------------------------------
> > > -----
> > > t\02species.t                 65    2   3.08%  63 65
> > > t\03simpleseq.t    1   256    59  106 179.66%  7-59
> > > t\04swiss.t                   52   14  26.92%  25 27-34 38-42
> > > t\12ontology.t     2   512   738 1471 199.32%  3-738
> > > t\16obda.t                    12    3  25.00%  10-12
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l <at> lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
>
>


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