[Bioperl-l] Psiblast parser and empty blast reports

Jason Stajich jason@cgt.mc.duke.edu
Thu, 25 Jul 2002 16:18:56 -0400 (EDT)


For the record the SearchIO::blast.pm parser does handle wublast reports -
I though we were going to migrate towards one parser?


On Thu, 25 Jul 2002, Steve Chervitz wrote:

> Ben,
>
> Go ahead and add a descr->footer transition in the @state_transitions array
> of psiblast.pm, as you suggested to me previously. It shouldn't be a problem
> for other flavors of reports.
>
> psiblast.pm hasn't had a lot of testing on WU-BLAST reports, so I'd expect
> there to be some issues.
>
> Be sure to commit on branch-1-0-0 and the trunk. Thanks!
>
> Steve
>
> --- Benjamin Berman <benb@fruitfly.org> wrote:
> >
> > Hi Steve and others,
> >
> > I'm using the SearchIO psiblast parser, which seems to work great.  I am
> > having a problem though when it encounters blast reports without any hits.
> > I get the following error:
> >
> > ------------- EXCEPTION: Bio::Tools::StateMachine::StateException
> > MSG: The desired state change is not valid for this machine: Descriptions ->
> > Footer
> > STACK: Error::throw
> > STACK: Bio::Root::Root::throw
> > /usr/local/lib/perl5/site_perl/5.6.1/Bio/Root/Root.pm:315
> > STACK: Bio::Tools::StateMachine::AbstractStateMachine::validate_transition
> > /users/benb/cvs/bioperl-live/Bio/Tools/StateMachine/AbstractStateMachine.pm:
> > 529
> > STACK: Bio::SearchIO::psiblast::change_state
> > /users/benb/cvs/bioperl-live/Bio/SearchIO/psiblast.pm:362
> > STACK: Bio::Tools::StateMachine::AbstractStateMachine::run
> > /users/benb/cvs/bioperl-live/Bio/Tools/StateMachine/AbstractStateMachine.pm:
> > 319
> > STACK: Bio::SearchIO::psiblast::next_result
> > /users/benb/cvs/bioperl-live/Bio/SearchIO/psiblast.pm:1139
> > STACK: main::blast_sp_seqs blast_sps.pl:200
> > ----------------------------------------------------------------------------
> >
> >
> >
> >
> >
> > Here is the blast report that's being parsed:
> >
> > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > BLASTP 2.0MP-WashU [09-Nov-2000] [linux-i686 19:13:41 11-Nov-2000]
> >
> > Copyright (C) 1996-2000 Washington University, Saint Louis, Missouri USA.
> > All Rights Reserved.
> >
> > Reference:  Gish, W. (1996-2000) http://blast.wustl.edu
> >
> > Query=  SWP:P81160[real] DUCTUS EJACULATORIUS PEPTIDE 99B.
> >         (31 letters)
> >
> > Database:
> > /users/benb/gadb_tools/validation/r2_r3_comparisons/r1_pep_dumps/pep
> >            s.release1.all.071802.fst
> >            14,053 sequences; 6,832,949 total letters.
> > Searching....10....20....30....40....50....60....70....80....90....100% done
> >
> >
> > Smallest
> >                                                                        Sum
> >                                                               High
> > Probability
> > Sequences producing High-scoring Segment Pairs:              Score  P(N)
> > N
> >
> >
> >       *** NONE ***
> >
> >
> >
> > Parameters:
> >   E=1e-08
> >   matrix=MATCH_MORE_PENALTY
> >   W=8
> >   Q=5
> >   R=1
> >   T=1000
> >   warnings
> >   postsw
> >
> >   ctxfactor=1.00
> >
> >   Query                              -----  As Used  -----    -----
> > Computed  ----
> >   Frame  MatID Matrix name           Lambda    K       H      Lambda    K
> > H
> >    +0      0   MATCH_MORE_PENALTY    2.94    0.947   2.94     same    same
> > same
> >                Q=5,R=1         2.94    0.947   2.94      n/a     n/a     n/a
> >
> >   Query
> >   Frame  MatID  Length  Eff.Length     E    S W    T X   E2    S2
> >    +0      0       31        31   1.0e-08  13 8 1000 3  0.060   4
> >                                                      4  0.060   4
> >
> >
> > Statistics:
> >
> >   Database:
> > /users/benb/gadb_tools/validation/r2_r3_comparisons/r1_pep_dumps/peps.releas
> > e1.all.071802.fst
> >    Title:
> > /users/benb/gadb_tools/validation/r2_r3_comparisons/r1_pep_dumps/peps.releas
> > e1.all.071802.fst
> >    Posted:  4:43:21 PM PDT Jul 18, 2002
> >    Format:  BLAST-1.4
> >    # of letters in database:  6,832,949
> >    # of sequences in database:  14,053
> >    # of database sequences satisfying E:  0
> >   No. of states in DFA:  157 (16 KB)
> >   Total size of DFA:  16 KB (64 KB)
> >   Time to generate neighborhood:  0.00u 0.00s 0.00t  Elapsed: 00:00:01
> >   No. of threads or processors used:  2
> >   Search cpu time:  0.07u 0.00s 0.07t  Elapsed: 00:00:00
> >   Total cpu time:  0.08u 0.00s 0.08t  Elapsed: 00:00:01
> >   Start:  Mon Jul 22 13:51:02 2002   End:  Mon Jul 22 13:51:03 2002
> >
> > WARNINGS SUPPRESSED:  1
> > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> >
> >
> >
> >
> > Thanks,
> > Ben.
> >
> > _______________________________________________
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> > http://bioperl.org/mailman/listinfo/bioperl-l
>
>
>
> =====
> Steve Chervitz
> sac@bioperl.org
>
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-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu