[Bioperl-l] Finding significant hits with BPlite

[gert thijs]

Just, before I went on holidays myself, I found what was causing the problem.

In "Bio::Tools::BPlite::Sbjct::nextHSP" there is some code to parse a
scoreline and to assign the value to $p. 
The code looks like:
($p) = $scoreline =~ /Expect = (\S+)/ ;

But in a Blast report there can be another form than the "Expect = Score": eg.
"Expect(2) = Score". So I only have to add an extra check for this kind of
scoreline.


Gert



Lorenz Pollak wrote:
> 
> hi gert!
> 
> sorry that i didnt reply earlier but i had been on holidays
> in sicily :)
> 
> i'll try to have a look on this, ok?
> 
> cu, Lorenz
> 
> On Tue, 22 Aug 2000, gert thijs wrote:
> 
> > Hello,
> >
> > I am using BPlite to parse a blast report, which works fine, but sometimes I
> > get the following exception using
> > while ( my $hsp = $subject->nextHSP ){
> >   ...
> > }
> >
> > -------------------- EXCEPTION --------------------
> > MSG: asking for tag value that does not exist signif
> > CONTEXT: Error in uNKNOWN CONTEXT
> > SCRIPT: PrintSelectedSequences.pl
> > STACK:
> > Bio::SeqFeature::Generic::each_tag_value(470)
> > Bio::SeqFeature::Similarity::_tag_value(116)
> > Bio::SeqFeature::Similarity::significance(134)
> > Bio::SeqFeature::SimilarityPair::significance(339)
> > Bio::Tools::BPlite::HSP::_initialize(81)
> > Bio::Root::Object::new(462)
> > Bio::Tools::BPlite::Sbjct::nextHSP(125)
> > BlastSequence::BlastSequence(80)
> > main::PrintSelectedSequences.pl(114)
> > ---------------------------------------------------
> >
> > If I look at the report the HSP looks alright to me. I have no idea how I can
> > work around this error and grab the HSP from the report.
> >
> > Can anyone give me some advice here?
> >
> > Thanks,
> > Gert Thijs
> >


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