[Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Sat Nov 29 21:47:56 EST 2008


http://bugzilla.open-bio.org/show_bug.cgi?id=2476





------- Comment #16 from cjfields at bioperl.org  2008-11-29 21:47 EST -------
I'm seeing lots of errors using both HSPI and the latest LocatableSeq patches
(ignore the abi.t and ztr.t, as I have io_lib installed for bioperl-ext and
those fail all the time, and the seq-quality.t seeems unrelated).

I'm sure much of this is due to core code using subseq() expecting behavior
similar to that seen for PrimarySeq, which is more substr()-like and by
position in the string, not by the actual seq residue and start/end/strand.  We
can't change that easily, unfortunately, without dire consequences (as seen in
the test failures).  That's a significant API change, hence the breakage you
see.

Couple of things that would rectify this and meet halfway:

1) make sure the subseq() POD reflects what subseq() is actually doing in both
PrimarySeq and LocatableSeq (subseq positions by default are by column/string
position, not residue position).

2) Make LocatableSeq::subseq() by default act like PrimarySeq::subseq() (i.e.
return SUPER::subseq(@args)), but have it DTRT if passed a specific flag or
param:

my $sseq = $sq->subseq(-start => 10, -end => 30, -flag => 'by_residue') # or
similar

Not sure how to fix HSPI.  That may be trickier, but is worth looking at as the
bug in question here could be due to improper subsequences being used.

Test Summary Report
-------------------
t/AlignIO/AlignIO.t               (Wstat: 65280 Tests: 17 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 28 tests but ran 17.
t/AlignIO/bl2seq.t                (Wstat: 65280 Tests: 1 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 3 tests but ran 1.
t/AlignIO/mega.t                  (Wstat: 256 Tests: 6 Failed: 1)
  Failed test:  5
  Non-zero exit status: 1
t/AlignIO/po.t                    (Wstat: 65280 Tests: 6 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 11 tests but ran 6.
t/AlignStats.t                    (Wstat: 65280 Tests: 9 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 43 tests but ran 9.
t/AlignUtil.t                     (Wstat: 65280 Tests: 19 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 33 tests but ran 19.
t/BlastIndex.t                    (Wstat: 65280 Tests: 7 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 26 tests but ran 7.
t/ContigSpectrum.t                (Wstat: 65280 Tests: 46 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 134 tests but ran 46.
t/CoordinateMapper.t              (Wstat: 65280 Tests: 173 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 175 tests but ran 173.
t/EncodedSeq.t                    (Wstat: 65280 Tests: 27 Failed: 5)
  Failed tests:  12, 15-18
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 37 tests but ran 27.
t/GbrowseGFF.t                    (Wstat: 65280 Tests: 1 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 3 tests but ran 1.
t/Genewise.t                      (Wstat: 65280 Tests: 34 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 53 tests but ran 34.
t/InstanceSite.t                  (Wstat: 65280 Tests: 3 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 6 tests but ran 3.
t/LocatableSeq.t                  (Wstat: 65280 Tests: 19 Failed: 5)
  Failed tests:  13, 16-19
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 112 tests but ran 19.
t/MetaSeq.t                       (Wstat: 65280 Tests: 75 Failed: 15)
  Failed tests:  33, 35-36, 39-40, 42-43, 46-47, 49-51, 54-55
                73
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 128 tests but ran 75.
t/RemoteBlast.t                   (Wstat: 65280 Tests: 4 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 16 tests but ran 4.
t/SearchIO/HTMLWriter.t           (Wstat: 65280 Tests: 2 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 8 tests but ran 2.
t/SearchIO/HitTableWriter.t       (Wstat: 65280 Tests: 2 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 8 tests but ran 2.
t/SearchIO/Writer/HTMLWriter.t    (Wstat: 65280 Tests: 2 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 8 tests but ran 2.
t/SearchIO/Writer/HitTableWriter.t (Wstat: 65280 Tests: 2 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 8 tests but ran 2.
t/SearchIO/blast.t                (Wstat: 65280 Tests: 1 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 1089 tests but ran 1.
t/SearchIO/blast_pull.t           (Wstat: 65280 Tests: 1 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 287 tests but ran 1.
t/SearchIO/blasttable.t           (Wstat: 65280 Tests: 2 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 154 tests but ran 2.
t/SearchIO/blastxml.t             (Wstat: 65280 Tests: 130 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 298 tests but ran 130.
t/SearchIO/cross_match.t          (Wstat: 65280 Tests: 1 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 15 tests but ran 1.
t/SearchIO/erpin.t                (Wstat: 65280 Tests: 1 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 91 tests but ran 1.
t/SearchIO/exonerate.t            (Wstat: 65280 Tests: 1 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 45 tests but ran 1.
t/SearchIO/fasta.t                (Wstat: 65280 Tests: 1 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 287 tests but ran 1.
t/SearchIO/hmmer.t                (Wstat: 65280 Tests: 1 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 116 tests but ran 1.
t/SearchIO/hmmer_pull.t           (Wstat: 65280 Tests: 1 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 290 tests but ran 1.
t/SearchIO/infernal.t             (Wstat: 65280 Tests: 1 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 316 tests but ran 1.
t/SearchIO/megablast.t            (Wstat: 65280 Tests: 1 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 31 tests but ran 1.
t/SearchIO/psl.t                  (Wstat: 65280 Tests: 1 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 49 tests but ran 1.
t/SearchIO/rnamotif.t             (Wstat: 65280 Tests: 1 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 60 tests but ran 1.
t/SearchIO/sim4.t                 (Wstat: 65280 Tests: 1 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 102 tests but ran 1.
t/SearchIO/waba.t                 (Wstat: 65280 Tests: 1 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 64 tests but ran 1.
t/SearchIO/wise.t                 (Wstat: 65280 Tests: 1 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 20 tests but ran 1.
t/SeqIO/abi.t                     (Wstat: 1280 Tests: 7 Failed: 5)
  Failed tests:  3-7
  Non-zero exit status: 5
t/SeqIO/scf.t                     (Wstat: 65280 Tests: 34 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 35 tests but ran 34.
t/SeqIO/ztr.t                     (Wstat: 256 Tests: 3 Failed: 1)
  Failed test:  3
  Non-zero exit status: 1
t/SimilarityPair.t                (Wstat: 65280 Tests: 4 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 12 tests but ran 4.
t/SimpleAlign.t                   (Wstat: 65280 Tests: 62 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 152 tests but ran 62.
t/cigarstring.t                   (Wstat: 65280 Tests: 1 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 4 tests but ran 1.
t/seq_quality.t                   (Wstat: 65280 Tests: 1 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 53 tests but ran 1.
t/sequencetrace.t                 (Wstat: 65280 Tests: 5 Failed: 0)
  Non-zero exit status: 255
Files=304, Tests=13060, 513 wallclock secs ( 3.21 usr  1.84 sys + 133.34 cusr
17.67 csys = 156.06 CPU)
Result: FAIL
Failed 45/304 test programs. 32/13060 subtests failed.


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