[Bioperl-l] Trouble parsing PSI-BLAST

Chris Fields cjfields at illinois.edu
Wed Nov 4 08:55:34 EST 2009


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