[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 $in = new Bio::SearchIO(        -format => 'blast',
                                -file =>
"BS_XFpsiRblastoutputs/e${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
-----------------------------------------------------------


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