[Bioperl-l] Alternate hit sorting for Bio::Search::Result objects

[Chris Mungall]

oops, hit send by mistake - just musing out loud... maybe we could just
alter the order hits() / next_hit() returns things rather than actually
modifying the objects. doesn't make much difference at the end of the
day...

On Sat, 27 Dec 2003, Chris Mungall wrote:

>
> $result->sort_hits_by_func( { ..custom sort.. } )
>
> On Tue, 23 Dec 2003, Jason Stajich wrote:
>
> > So Don - you want to apply a custom hit sorting routine to the data before
> > it is output with SearchIO::HTMLResultWriter?
> >
> > The simpliest - albeit cheating and prone problems if there are changes
> > in the module - but is pretty easy to do:
> >
> > @{$result->{'_hits'}} = sort { your custom sort here }
> >                         @{$result->{'_hits'}};
> >
> > Perhaps we should add an API method which can get/set the Hits.
> >
> > You can also create a new Result object in an albeit tedious manner:
> >
> > my @hits = sort { #custom hits } $result->hits();
> >
> > my $rewres = $result->new(-query_name  => $result->query_name,
> >                        -query_accession  => $result->query_accession,
> > 	               -query_description => $result->query_description,
> > 	               -query_length     => $result->query_length,
> >                        -database_name    => $result->database_name,
> > 	               ... # lots more things.
> >                        -hits            => \@hits);
> >
> >
> > So you put all of this in to play like this
> > my $in = new Bio::SearchIO(-format => 'blast',
> >                              -file   => shift @ARGV);
> >
> > my $writer = new Bio::SearchIO::Writer::HTMLResultWriter();
> > my $out = new Bio::SearchIO(-writer => $writer);
> > my $result = $in->next_result;
> > # apply the sorting on the hits
> > #
> >
> > # now write the result out
> > $out->write_result($result);
> >
> >
> >
> > -jason
> >
> >
> >
> > On Tue, 23 Dec 2003, Donald G. Jackson wrote:
> >
> > > Hi,
> > >
> > > I'm working on a blast wrapper using Bio::SearchIO.  I'd like to be able
> > > to sort through the hits by something besides score/input order.  For
> > > example, we've crammed the taxid into the FASTA header and would like to
> > > do something like NCBI's taxblast where hits are sorted by source
> > > organism, then by score.  I'd like to use the
> > > Bio::SearchIO::HTMLResultWriter to output my hits, so can't just get all
> > > the hits and sort them myself.
> > >
> > > I thought I'd seen mention of how to do this, but looking over the docs
> > > and (1.2.3) code I can't find it.  Does anyone have thoughts on how to
> > > do this?
> > >
> > > Thanks,
> > >
> > > Don Jackson
> > > BMS Bioinformatics
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at portal.open-bio.org
> > > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> > >
> >
> > --
> > Jason Stajich
> > Duke University
> > jason at cgt.mc.duke.edu
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
>
>
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