[Bioperl-l] Psiblast parser and empty blast reports

[Benjamin Berman]

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.