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

[Chris Mungall]

$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
> >
> > _______________________________________________
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> > Bioperl-l at portal.open-bio.org
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> >
>
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
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