[Bioperl-l] Re: zebrafish est database
James Priest
jpriest@uclink.berkeley.edu
Fri, 07 Jun 2002 11:14:49 -0700
Hello-
Actually it turns out that you have to set the database variable manually in addition to the other two variables. Leaving out the $db
variable in the rest of the code the three lines should read...
$Bio::Tools::Run::RemoteBlast::Header{'DATABASE'} = 'Danio_Rerio_EST';
$Bio::Tools::Run::RemoteBlast::Header{'DB_DIR_PREFIX'} = 'Trace';
$Bio::Tools::Run::RemoteBlast::Header{'WWW_BLAST_TYPE'} = 'drtrace';
jrp
bioperl-l-request@bioperl.org wrote:
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> Today's Topics:
>
> 1. Applying pairwise Smith-Waterman on nucleotide sequences? (Danny Yoo)
> 2. Re: Applying pairwise Smith-Waterman on nucleotide
> sequences? (Jason Stajich)
> 3. how to catch exception error (Damien Mattei)
> 4. Re: how to catch exception error (Heikki Lehvaslaiho)
> 5. Re: how to catch exception error (Elia Stupka)
> 6. Re: Bio::Variation::SeqDiff, Bio::Variation::VariantI (Heikki Lehvaslaiho)
>
> --__--__--
>
> Message: 1
> Date: Thu, 6 Jun 2002 18:14:42 -0700 (PDT)
> From: Danny Yoo <dyoo@acoma.Stanford.EDU>
> To: bioperl-l@bioperl.org
> cc: curator@acoma.Stanford.EDU
> Subject: [Bioperl-l] Applying pairwise Smith-Waterman on nucleotide sequences?
>
> Hi everyone,
>
> Hope this isn't a silly questions: I've been trying to get Bio::Tools::pSW
> working on some nucleotide sequences I have. I've written a small test
> program:
>
> ###
> use Bio::Tools::pSW;
> use Bio::Seq;
> my $factory = new Bio::Tools::pSW('-gap' => 12,
> '-ext' => 2,
> );
> $factory->align_and_show(Bio::Seq->new(-seq=>"AAAC", -alphabet=>'dna'),
> Bio::Seq->new(-seq=>"AATC", -alphabet=>'dna'),
> STDOUT);
> ###
>
> I get the following error message:
>
> ###
> Warning Error
> Sequence seq1 is not typed as protein... ignoring!
>
> Warning Error
> Sequence seq2 is not typed as protein... ignoring!
>
> Warning Error
> Could not evaluate these sequences Sequence type [66][Dna]
> Evaluation
> type [65][Protein]
> ------------- EXCEPTION -------------
> MSG: Unable to build an alignment
> STACK Bio::Tools::pSW::align_and_show
> /usr/local/lib/perl5/site_perl/5.6.1/Bio/Tools/pSW.pm:339
> STACK toplevel blast_test.pl:6
>
> --------------------------------------
> ###
>
> I'm getting the impression that Smith-Waterman is restricted to align only
> on protein sequences. Doh.
>
> I'd like to do some nucleotide alignments locally --- should I be using
> something like BLAST instead, or is there some variant of Smith-Waterman
> that works on nucleotide sequences?
>
> Thanks for any help!
>
> --__--__--
>
> Message: 2
> Date: Thu, 6 Jun 2002 21:27:33 -0400 (EDT)
> From: Jason Stajich <jason@cgt.mc.duke.edu>
> To: Danny Yoo <dyoo@acoma.stanford.edu>
> cc: <bioperl-l@bioperl.org>, <curator@acoma.stanford.edu>
> Subject: Re: [Bioperl-l] Applying pairwise Smith-Waterman on nucleotide
> sequences?
>
> This definitely need to go into the FAQ.
>
> See:
> http://bioperl.org/pipermail/bioperl-l/2002-February/007281.html
>
> There is a description of how to run EMBOSS's 'water' from within
> Bioperl in the FAQ
> http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/FAQ?rev=1.14&cvsroot=bioperl&content-type=text/vnd.viewcvs-markup
>
> -j
> On Thu, 6 Jun 2002, Danny Yoo wrote:
>
> > Hi everyone,
> >
> > Hope this isn't a silly questions: I've been trying to get Bio::Tools::pSW
> > working on some nucleotide sequences I have. I've written a small test
> > program:
> >
> >
> > ###
> > use Bio::Tools::pSW;
> > use Bio::Seq;
> > my $factory = new Bio::Tools::pSW('-gap' => 12,
> > '-ext' => 2,
> > );
> > $factory->align_and_show(Bio::Seq->new(-seq=>"AAAC", -alphabet=>'dna'),
> > Bio::Seq->new(-seq=>"AATC", -alphabet=>'dna'),
> > STDOUT);
> > ###
> >
> >
> > I get the following error message:
> >
> > ###
> > Warning Error
> > Sequence seq1 is not typed as protein... ignoring!
> >
> > Warning Error
> > Sequence seq2 is not typed as protein... ignoring!
> >
> > Warning Error
> > Could not evaluate these sequences Sequence type [66][Dna]
> > Evaluation
> > type [65][Protein]
> > ------------- EXCEPTION -------------
> > MSG: Unable to build an alignment
> > STACK Bio::Tools::pSW::align_and_show
> > /usr/local/lib/perl5/site_perl/5.6.1/Bio/Tools/pSW.pm:339
> > STACK toplevel blast_test.pl:6
> >
> > --------------------------------------
> > ###
> >
> >
> > I'm getting the impression that Smith-Waterman is restricted to align only
> > on protein sequences. Doh.
> >
> >
> > I'd like to do some nucleotide alignments locally --- should I be using
> > something like BLAST instead, or is there some variant of Smith-Waterman
> > that works on nucleotide sequences?
> >
> >
> > Thanks for any help!
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> >
>
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
>
> --__--__--
>
> Message: 3
> Date: Fri, 07 Jun 2002 11:25:04 +0200
> From: Damien Mattei <Damien.Mattei@unice.fr>
> To: bioperl-l@bioperl.org
> Subject: [Bioperl-l] how to catch exception error
>
> when doing something like this:
>
> use Bio::DB::GenBank;
>
> $gb = new Bio::DB::GenBank();
>
> # this returns a Seq object :
> $seq = $gb->get_Seq_by_acc("AC019220");
>
> i get an exception that stop my program:
> ------------- EXCEPTION -------------
> MSG: WebDBSeqI Request Error
>
> STACK Bio::DB::WebDBSeqI::_request
> /usr/lib/perl5/site_perl/5.6.1/Bio/DB/WebDBSeqI.pm:523
> STACK Bio::DB::WebDBSeqI::get_seq_stream
> /usr/lib/perl5/site_perl/5.6.1/Bio/DB/WebDBSeqI.pm:375
> STACK Bio::DB::NCBIHelper::get_Stream_by_acc
> /usr/lib/perl5/site_perl/5.6.1/Bio/DB/NCBIHelper.pm:466
> STACK Bio::DB::WebDBSeqI::get_Seq_by_acc
> /usr/lib/perl5/site_perl/5.6.1/Bio/DB/WebDBSeqI.pm:161
> STACK main::nxtbac ./gmap.pl:338
> STACK toplevel ./gmap.pl:25
>
> --------------------------------------
>
> is there a way in bioperl to catch exception
> as it is possible in Java or C++ ?
>
> Damien Mattei
> C.N.R.S / U.N.S.A - UMR 6549
> mailto:mattei@unice.fr
> http://www-iag.unice.fr/
>
> --__--__--
>
> Message: 4
> Date: Fri, 07 Jun 2002 10:56:05 +0100
> From: Heikki Lehvaslaiho <heikki@ebi.ac.uk>
> Organization: EMBL - EBI
> To: Damien Mattei <Damien.Mattei@unice.fr>
> CC: bioperl-l@bioperl.org
> Subject: Re: [Bioperl-l] how to catch exception error
>
> Damien,
>
> Write:
>
> eval {
> $seq = $gb->get_Seq_by_acc($acc);
> };
> print "$@ Could not retrieve $acc\n" if $@;
>
> Yours,
> -Heikki
>
> Damien Mattei wrote:
> >
> > when doing something like this:
> >
> > use Bio::DB::GenBank;
> >
> > $gb = new Bio::DB::GenBank();
> >
> > # this returns a Seq object :
> > $seq = $gb->get_Seq_by_acc("AC019220");
> >
> > i get an exception that stop my program:
> > ------------- EXCEPTION -------------
> > MSG: WebDBSeqI Request Error
> >
> > STACK Bio::DB::WebDBSeqI::_request
> > /usr/lib/perl5/site_perl/5.6.1/Bio/DB/WebDBSeqI.pm:523
> > STACK Bio::DB::WebDBSeqI::get_seq_stream
> > /usr/lib/perl5/site_perl/5.6.1/Bio/DB/WebDBSeqI.pm:375
> > STACK Bio::DB::NCBIHelper::get_Stream_by_acc
> > /usr/lib/perl5/site_perl/5.6.1/Bio/DB/NCBIHelper.pm:466
> > STACK Bio::DB::WebDBSeqI::get_Seq_by_acc
> > /usr/lib/perl5/site_perl/5.6.1/Bio/DB/WebDBSeqI.pm:161
> > STACK main::nxtbac ./gmap.pl:338
> > STACK toplevel ./gmap.pl:25
> >
> > --------------------------------------
> >
> >
> > is there a way in bioperl to catch exception
> > as it is possible in Java or C++ ?
> >
> >
> > Damien Mattei
> > C.N.R.S / U.N.S.A - UMR 6549
> > mailto:mattei@unice.fr
> > http://www-iag.unice.fr/
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
>
> --
> ______ _/ _/_____________________________________________________
> _/ _/ 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
> ___ _/_/_/_/_/________________________________________________________
>
> --__--__--
>
> Message: 5
> Date: Fri, 7 Jun 2002 18:03:25 +0800 (SGT)
> From: Elia Stupka <elia@fugu-sg.org>
> To: Damien Mattei <Damien.Mattei@unice.fr>
> cc: bioperl-l@bioperl.org
> Subject: Re: [Bioperl-l] how to catch exception error
>
> > is there a way in bioperl to catch exception
> > as it is possible in Java or C++ ?
>
> Sure, you just need to use the standard perl syntax, which is to wrap the
> code you want to catch with an eval statement like this:
>
> eval {
>
> code code code
>
> };
>
> if ($@) { print "The code threw this exception $@";
>
> Elia
>
> ********************************
> * http://www.fugu-sg.org/~elia *
> * tel: +65 874 1467 *
> * mobile: +65 90307613 *
> * fax: +65 777 0402 *
> ********************************
>
> --__--__--
>
> Message: 6
> Date: Fri, 07 Jun 2002 15:36:05 +0100
> From: Heikki Lehvaslaiho <heikki@ebi.ac.uk>
> Organization: EMBL - EBI
> To: Eckhard Lehmann <ecky@e-lehmann.de>
> CC: Bioperl Liste <bioperl-l@bioperl.org>
> Subject: Re: [Bioperl-l] Bio::Variation::SeqDiff, Bio::Variation::VariantI
>
> Eckhard,
>
> I've cleaned your code a bit (and fixed one one-off error) and put it into
> SeqDiff.pm in CVS HEAD (it changes the behaviour of the method so bug fix
> release 1.01 will not have it). It will not calculate the mutated DNA
> sequence if is has been already set. Is that OK?
>
> -Heikki
>
> Eckhard Lehmann wrote:
> > Heikki,
> >
> > I think the best way is to initiate a private (or public?) method
> > "_set_dnamut()" which sets up the dna_mut in the way described. It can
> > be called in the current "dna_mut()" method and can be changed
> > afterwards by someone else.
> > So I don't need to change too much of the existing methods.
> >
> > The code at the end of this mail works fine for now.
> >
> > Eckhard
> >
> > #------------------------------------------------------------------
> > sub _set_dnamut {
> > my $self = shift;
> >
> > return 0 unless $self->dna_ori && $self->each_Variant;
> >
> > $self->dna_mut($self->dna_ori);
> > foreach ($self->each_Variant) {
> > next unless $_->isMutation;
> >
> > my ($s, $la, $le);
> > #lies the mutation lesser than 25 bases after the start of sequence?
> > if ($_->start < 25) {$s = 0; $la = $_->start;}
> > else {$s = $_->start - 25; $la = 25;}
> >
> > #is the mutation an insertion?
> > $_->end($_->start) unless $_->allele_ori->seq;
> >
> > #does the mutation end greater than 25 bases before the end of
> > #sequence?
> > if (($_->end + 25) > length($self->dna_mut)) {
> > $le = length($self->dna_mut) - $_->end;
> > } else {$le = 25;}
> >
> > $_->dnStreamSeq(substr($self->dna_mut, $s, $la));
> > $_->upStreamSeq(substr($self->dna_mut, $_->end, $le));
> >
> > my $s_ori = $_->dnStreamSeq . $_->allele_ori->seq . $_->upStreamSeq;
> > my $s_mut = $_->dnStreamSeq . $_->allele_mut->seq . $_->upStreamSeq;
> > (my $str = $self->dna_mut) =~ s/$s_ori/$s_mut/;
> > $self->dna_mut($str);
> > }
> > }
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
>
> --
> ______ _/ _/_____________________________________________________
> _/ _/ 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
>
> End of Bioperl-l Digest