[Bioperl-l] Re: BPbl2seq.pm

[Heikki Lehvaslaiho]

Heikki Lehvaslaiho wrote:
> 
> 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-)

I unintentionally did it anyway. Sorry, Juerg! No harm done, I hope.

	-Heikki

> 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
> > >
> > >
> > >
> > >
> > >
> > >
> > > *****************************************************************************************
> > >  S- The information in this e.mail and any attachments is confidential and
> > > is intended for the addressee only. Reading, copying, disclosure or
> > > use by anybody else is not authorised. The contents do not represent
> > > the opinion of Serono International S.A. or any of its affiliates except to the
> > > extent that it relates to their official business. If you are not the
> > > intended recipient, please delete this message and any attachments and
> > > advise the sender by return e.mail.
> > > ******************************************************************************************
> > >
> > >
> >
> > -------------------------------------------------------------------------------
> > 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
> ___ _/_/_/_/_/________________________________________________________
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l