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Trouble parsing PSI-BLAST
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Trouble parsing PSI-BLAST
by Sharma, Rachita
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I am having trouble parsing PSI-BLAST results. Please help. The code is: my $in = new Bio::SearchIO( -format => 'blast', -file => "BS_XFpsiRblastoutputs/e${ev}/bloutput${i}.txt"); while( my $result = $in->next_result ) { while( my $hit = $result->next_hit ) { $sth->execute($result->query_name, $hit->name, $hit->significance); print "Query executed!\n"; } } The error is: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: no data for midline ***** No hits found ****** STACK: Error::throw STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359 STACK: Bio::SearchIO::blast::next_result /usr/lib/perl5/site_perl/5.8.8/Bio/SearchIO/blast.pm:1813 STACK: BSubVCpsiRblast.pl:92 ----------------------------------------------------------- ******************************* Rachita Sharma Research Assistant (PhD Student) University of New Brunswick, NB, CANADA email: Rachita.Sharma@... Phone no: 503-895-3619 ******************************* _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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Re: Trouble parsing PSI-BLAST
by Chris Fields-5
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Rachita,
Asked and answered yesterday. Please submit as a bug. chris On Nov 3, 2009, at 11:30 AM, Sharma, Rachita wrote: > > I am having trouble parsing PSI-BLAST results. Please help. > > The code is: > my $in = new Bio::SearchIO( -format => 'blast', > -file => "BS_XFpsiRblastoutputs/e${ev}/bloutput${i}.txt"); > > > while( my $result = $in->next_result ) { > while( my $hit = $result->next_hit ) { > > $sth->execute($result->query_name, $hit->name, $hit->significance); > print "Query executed!\n"; > > } > } > > The error is: > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: no data for midline ***** No hits found ****** > STACK: Error::throw > STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/ > Root/Root.pm:359 > STACK: Bio::SearchIO::blast::next_result > /usr/lib/perl5/site_perl/5.8.8/Bio/SearchIO/blast.pm:1813 > STACK: BSubVCpsiRblast.pl:92 > ----------------------------------------------------------- > > > > > ******************************* > Rachita Sharma > Research Assistant (PhD Student) > University of New Brunswick, NB, CANADA > email: Rachita.Sharma@... > Phone no: 503-895-3619 > ******************************* > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@... > http://lists.open-bio.org/mailman/listinfo/bioperl-l _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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