[Bioperl-guts-l] [Bug 3064] New: unusual blastp output causes SearchIO to crash

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Mon Apr 26 18:06:06 EDT 2010


http://bugzilla.open-bio.org/show_bug.cgi?id=3064

           Summary: unusual blastp output causes SearchIO to crash
           Product: BioPerl
           Version: unspecified
          Platform: Other
        OS/Version: Mac OS
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Bio::Search/Bio::SearchIO
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: jayoung at fhcrc.org
                CC: jayoung at fhcrc.org


Hi,

I'm using NCBI's BLASTP 2.2.23+ and have found an unusual output file that
makes SearchIO's next_result() crash with the following error:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: no data for midline Query      
------------------------------------------------------------  
STACK: Error::throw
STACK: Bio::Root::Root::throw
/home/jayoung/traskdata/perl/bioperl-live/Bio/Root/Root.pm:368
STACK: Bio::SearchIO::blast::next_result
/home/jayoung/traskdata/perl/bioperl-live/Bio/SearchIO/blast.pm:1842
STACK: /home/jayoung/bin/blastparsenew_really_simple.bioperl:14
-----------------------------------------------------------

It's the weird-looking line in the middle with no aligned query residues that's
causing the issue:
Query       ------------------------------------------------------------  

If I edit that line to include positions, parsing proceeds fine:
Query  63   ------------------------------------------------------------  63

I can't tell if NCBI have recently changed their output specs, or if this issue
could have arisen in the past. On an older versions of blast, I tried this
particular query and subject pair produced a slightly different alignment,
where the long gap wasn't quite as long and didn't stretch over a full output
line.

I updated my bioperl via svn today (revision 16954).  I'll attach the blast
result file (as well as the edited version that parses OK) and the query and
subject seqs each in fasta format. Hopefully it'll be easy to fix.

thanks very much,

Janet Young

------------------------------------------------------------------- 

Dr. Janet Young (Trask lab)

Fred Hutchinson Cancer Research Center
1100 Fairview Avenue N., C3-168, 
P.O. Box 19024, Seattle, WA 98109-1024, USA.

tel: (206) 667 1471 fax: (206) 667 6524
email: jayoung  ...at...  fhcrc.org

http://www.fhcrc.org/labs/trask/

-------------------------------------------------------------------


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