[Bioperl-l] Determining strand orientation from bl2seq report

[Dave Arenillas]

Hi Jason,

Thanks for the info. I forgot to mention in my original post that I did try 
using $hsp->query->strand and $hsp->hit->strand and for some reason 
$hsp->hit->strand always returns 0. I also tried the alternate $hsp->hstrand 
to no avail. Is this a bug in bioperl? It is critical to my application that 
I am able to determine weather the blast HSPs are Plus / Plus or Plus / 
Minus. I guess my next step is to try to run blast in such a way as to be 
able to parse with SearchIO and see if that correctly returns strand info. 
This is a bit of a pain though.

Dave


On Friday 24 January 2003 08:27 am, Jason Stajich wrote:
> Searchio can't parse bl2seq (yet), you have to use Bio::Tools::BPbl2seq,
> so StandAloneBlast returns a Bio::Tools::BPbl2seq report.
>
> start is always less than in end in the bioperl world to get strand you
> call $hsp->query->strand or $hsp->hit->strand.
> The HSP object you get back is a FeaturePair object so you can call all
> the methods that are available there, in addition the $hsp->hit and
> $hsp->query methods return objects which are Bio::SeqFeatureI compliant
> so you can call any method available in Bio::SeqFeatureI on them.
>
> perldoc doesn't do a good job with the fact that methods inherit from a
> superclass so you don't see all those methods in the documentation, if you
> use doc.bioperl.org and click through the inheritance that is available
> in the ISA part of a module documentation you will be able to see what
> are all the methods.
>
> -jason
>
> On Thu, 23 Jan 2003, Dave Arenillas wrote:
> > I'm trying to figure out if there is any way to determine the strand
> > orientation (Plus / Plus or Plus / Minus) of an HSP from the blast report
> > created by running bl2seq.
> >
> > ex.
> > my @params = ('program' => 'blastn',
> >                 'outfile' => "$BlastFile");
> > my $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
> > my $report = $factory->bl2seq($seq1, $seq2);
> >
> > while (my $hsp = $report->next_feature) {
> > 	#
> > 	# get orientation info from $hsp???
> > 	#
> > }
> >
> > Apparently Bio::Tools::BPlite::HSP objects have no methods to return this
> > information. I (incorrectly) assumed that I could test
> > $hsp->hit->start > $hsp->hit->end
> > but start is always less than end even for Plus / Minus orientation.
> >
> > I then attempted to create a SearchIO object and use this to parse the
> > blast report, for ex.
> > my $searchio = new Bio::SearchIO( -format => 'blast',
> >                         -file   => "$BlastFile" );
> >
> > while (my $result = $searchio->next_result) {
> > 	#
> > 	# Results in the error below
> > 	#
> >         while (my $hit = $result->next_hit) {
> >                 while (my $hsp = $hit->next_hsp) {
> > 		}
> > 	}
> > }
> >
> > However, this produced the following error:
> >
> > ------------ EXCEPTION  -------------
> > MSG: no data for midline Lambda     K      H
> > STACK Bio::SearchIO::blast::next_result
> > /usr/lib/perl5/site_perl/5.8.0/Bio/SearchIO/blast.pm:566
> >
> > Is the report produced by bl2seq some kind of simplified blast report
> > which SearchIO cannot parse? Is there any other way of determining HSP
> > strand orientation?
> >
> > Thanks,
> > Dave
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l

-- 
David Arenillas

Bioinformatic Software Developer
Wasserman Lab
Centre for Molecular Medicine and Therapeutics
University of British Columbia
Vancouver, BC Canada
E-mail: dave at cmmt.ubc.ca
Phone: (604) 875-2345 ext. 7948