[Bioperl-l] Alignment Blast parser
jason at cgt.duhs.duke.edu
Fri Jan 23 10:51:36 EST 2004
yes please - thanks Will!!
On Fri, 23 Jan 2004, Will Spooner wrote:
> Hi Jason,
> Having looked at the code, it does seem sensible to split the
> TextResultWriter->to_string method into component parts. This would allow
> users like me, with detached HSPI objects kicking about, to reuse the
> writer code, e.g:
> my $writer = Bio::SearchIO::Writer::TextResultWriter->new();
> my $hsp = Bio::Search::HSP::MyHSP->new(-id=>'foo');
> print $writer->hsp_alignment_string( $hsp );
> This approach would also allow TextResultWriter subclasses to get a bit
> more granularity from the parent.
> I'm happy to do the necessary, and will post a patch to bugzilla once
> On Fri, 23 Jan 2004, Jason Stajich wrote:
> > Currently the code to do this sort of thing is embedded in
> > SearchIO::Writer::TextResultWriter but generates a whole report.
> > Someone can move the code out that part of the code to a separate function
> > so it can be used for situations like what Nathan is asking for. Not sure
> > where it should go at this point other than in TextResultWriter - we don't
> > really have a class of 'HSP consumers' other than in there.
> > Will's code is smarter as it figures out the multiplier from the start/end
> > while we code it up based on the alignment alg (TBLASTN, BLASTX, etc).
jason at cgt.mc.duke.edu
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