[Bioperl-l] Trouble parsing PSI-BLAST

Sharma, Rachita b3sn7 at UNB.ca
Tue Nov 3 12:30:24 EST 2009


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 at unb.ca
Phone no: 503-895-3619
*******************************



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