[Bioperl-l] Psiblast parser and empty blast reports
Steve Chervitz
sac@bioperl.org
Thu, 25 Jul 2002 13:01:43 -0700 (PDT)
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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=====
Steve Chervitz
sac@bioperl.org
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