[Bioperl-l] Re: BPbl2seq.pm

[Heikki Lehvaslaiho]

Juerg,

Unfortunately blast parsing is one of the areas in bioperl I do know well
enough. The parsers are in constant flux. 

Please send your question to bioperl mailing list and state the version of
bioperl you are using.  Note that if you are using on older version of
bioperl things might have changed considerably.

Do not feel shy to ask a question at the mailing list: 
	Bioperl <bioperl-l@bioperl.org>

I do not dare to forward you mail directly for the list. Your disclaimer is
a bit scary. 8-)

Yours,
	-Heikki


Arek Kasprzyk wrote:
> 
> On Thu, 28 Mar 2002 Juerg.Straubhaar@serono.com wrote:
> 
> Hi Juerg,
> I don't use bioperl very much any more and decided to forward your email
> to our bioperl guru Heikki in hope that he would be able to help more
> 
> cheers,
> arek
> 
> > Hi Arek,
> >
> > I wonder whether I can ask you a question about BioPerl. Please, don't
> > spend time if you don't want to be bothered.
> >
> > I am doing something like this as part of a loop:
> >
> > my $factory = Bio::Tools::Run::StandAloneBlast->new( @paramArray );
> > my $report = $factory->bl2seq($querySeq, $subjectSeq );
> >
> > If bl2seq can't generate an alignment the report is empty and bl2seq throws
> > an error and stops the program.
> >
> > I don't want to stop the program, but just print a message and continue
> > with the next query alignment.
> >
> > How do I do that?
> >
> > Kind regards and thank you,
> > Juerg
> >
> >
> >
> >
> >
> >
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> 
> -------------------------------------------------------------------------------
> Dr Arek Kasprzyk
> EMBL-European Bioinformatics Institute.
> Wellcome Trust Genome Campus, Hinxton,
> Cambridge CB10 1SD, UK.
> Tel: +44-(0)1223-494606
> Fax: +44-(0)1223-494468
> -------------------------------------------------------------------------------

-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
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