Trouble parsing PSI-BLAST

[Rachita Sharma]

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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[Chris Fields-5]

Rachita,

You'll have to give us more to go on than this.  The best thing to do  
is file a bug report and attach an example PSI-BLAST report and code  
that causes the problem.  The $sth->execute(...) is a bit odd, but  
that shouldn't cause the error in question.

Also, make sure to stipulate the OS, version of BioPerl, and perl  
version.

chris

On Nov 3, 2009, at 4:12 PM, Rachita Sharma 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
> -----------------------------------------------------------
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

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