[Bioperl-l] Psiblast parser and empty blast reports
Steve Chervitz
sac@bioperl.org
Thu, 25 Jul 2002 14:05:54 -0700 (PDT)
I'm totally behind migrating to one parser, thanks for catching me on this
Jason.
So Ben, if you don't need any PSI-BLAST-specific functionality, why aren't you
using SearchIO::blast?
Steve
--- Jason Stajich <jason@cgt.mc.duke.edu> wrote:
> 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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> > > Bioperl-l@bioperl.org
> > > 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
>
=====
Steve Chervitz
sac@bioperl.org
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