[Bioperl-l] Trouble parsing PSI-BLAST

Rachita Sharma rachitasharma at gmail.com
Tue Nov 3 17:12:11 EST 2009

I am having trouble parsing PSI-BLAST results. Please help.

The code is:
my $in = new Bio::SearchIO(        -format => 'blast',
                                -file =>

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
STACK: Bio::SearchIO::blast::next_result
STACK: BSubVCpsiRblast.pl:92

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