[Bioperl-guts-l] [Bug 2181] New: Bio::SearchIO SearchIO can't parse fasta output file MSG: Did not specify a Query End or Query Begin

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Thu Jan 11 05:05:02 EST 2007


http://bugzilla.open-bio.org/show_bug.cgi?id=2181

           Summary: Bio::SearchIO SearchIO can't parse fasta output file
                    MSG: Did not specify a Query End or Query Begin
           Product: Bioperl
           Version: 1.4 branch
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Bio::Search/Bio::SearchIO
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: massocec at yahoo.fr


I tried using Bio::SearchIO to parse blast and fasta output file, but the
script throws exception for fasta output file

Here is the output from my sample script :

------------- EXCEPTION  -------------
MSG: Did not specify a Query End or Query Begin -verbose 0 -algorithm FASTX
-hit_seq DVVVRCVKFLIDKGHYPCYMHCTNG -hit_length 25 -query_length 25 -query_frame
+1 -rank 1 -hit_name Q12454|OCA6_YEAST -query_name BLDpMixOFF002.F03_06103010WF
-evalue 1.5 -score 139.4 -hit_frame 0 -hsp_length 25 -swscore 86 -query_seq
DILINTVKWI*RQKSWECYIHCQNG -homology_seq :...  ::..  .  . ::.:: :: -bits 32.9
(qs='
STACK Bio::Search::HSP::GenericHSP::new
/usr/lib/perl5/site_perl/5.8.7/Bio/Search/HSP/GenericHSP.pm:231
STACK Bio::Search::HSP::FastaHSP::new
/usr/lib/perl5/site_perl/5.8.7/Bio/Search/HSP/FastaHSP.pm:97
STACK Bio::Factory::ObjectFactory::create_object
/usr/lib/perl5/site_perl/5.8.7/Bio/Factory/ObjectFactory.pm:150
STACK Bio::SearchIO::SearchResultEventBuilder::end_hsp
/usr/lib/perl5/site_perl/5.8.7/Bio/SearchIO/SearchResultEventBuilder.pm:275
STACK Bio::SearchIO::fasta::end_element
/usr/lib/perl5/site_perl/5.8.7/Bio/SearchIO/fasta.pm:872
STACK Bio::SearchIO::fasta::next_result
/usr/lib/perl5/site_perl/5.8.7/Bio/SearchIO/fasta.pm:403
STACK toplevel parseblast.pl:49

I have tried it with different files, but I got
always the same error.


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