[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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> > 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