[Bioperl-l] Bio::Tools::Blast update

[Chervitz, Steve]

It recently dawned on me that what I was getting at here was exactly what
Aaron's Bio::Search::* modules were intended for. What I've since done is to
re-tool Bio::Search::Processor to employ a SeqIO-like pattern. The only
difference is that the processor is parameterized on both format and
algorithm, instead of just format as in SeqIO. 

I discovered that there's a fair amount of overlap between
Bio::Search::Result::ResultI and Bio::Tools::AnalysisResult, which should be
unified (perhaps AnalysisResult could inherit from ResultI?). 

Also, there's some clunkiness in the fact that AnalysisResult inherits from
SeqAnalysisParserI. I have a need to separate the parsing functionality from
the result-encapsulating functionality, so it's awkward for me to use
AnalysisResult. Perhaps all of the non-parsing, result-encapsulating
behavior that AnalysisResult depends on can be migrated to ResultI, which
would become a superclass of AnalysisResult. Just a thought.

Before I go checking in large modifications within Bio::Search::*, is there
anyone else who has been working on these modules lately that has any input
here? Aaron?

Cheers,
Steve

P.S. Sorry I missed out on BOSC-2001. Was it as fun as last year?

> -----Original Message-----
> From: Steve Chervitz [mailto:Steve_Chervitz@affymetrix.com]
> Sent: Wednesday, June 20, 2001 1:13 AM
> To: bioperl-l@bioperl.org
> Subject: [Bioperl-l] Bio::Tools::Blast update
> 
> 
> Just wanted to give people an update about the status of my 
> overhaul of 
> Bio::Tools::Blast. I've made some good progress on it lately and 
> probably will be ready to check the new code into the main trunk soon 
> for beta testing.
> 
> A design decision came up that I'd like people's opinion on. Here's a 
> snippet of what you can do with my new code to generate a 
> table of Blast 
> results:
> 
> # Analogous to SeqIO but operating on Blast reports/objects.
> # This does not handle running new analyses, just parsing 
> existing ones.
> 
> use Bio::Tools::BlastIO;
> use Bio::Tools::BlastIO::SbjctTableWriter;
> 
> my $in     = Bio::Tools::BlastIO->new();
> my $writer = Bio::Tools::BlastIO::SbjctTableWriter->new();
> my $out    = Bio::Tools::BlastIO->new( -writer => $writer,
>                                         -file   => 
> ">blast-table.txt" );
> 
> while ( my $blast = $in->next_blast() ) {
>      $out->write_blast($blast);
> }
> 
> This works well enough for crunching through Blast results, 
> but as for 
> integrating with SeqAnalysisParserI, it might be better to 
> have a more 
> generic SeqAnalysisIO system that could be adapted for other types of 
> results besides Blast:
> 
> # Analogous to SeqIO but operating on AnalysisResult objects.
> 
> use Bio::SeqAnalysisIO;
> 
> my $in = Bio::SeqAnalysisIO->new('-method' => 'blast');
> 
> while( my $analysis = $in->next_analysis() ) {
>    while( my $feature = $analysis->next_feature() ) {
>       print "Feature from ", $feature->start," to ", 
> $feature->end, "\n";
>    }
> }
> 
> A nice thing about this is that it extends the Bioperl IO pattern to 
> analysis results. However, this would be an alternative to the 
> SeqAnalysisParserFactory system that's in place now. If we have 
> something that works, why create yet another system? Perhaps 
> a full IO 
> system is only appropriate for some analysis results, such as Blast.
> 
> Opinions welcome.
> 
> Steve
> 
> Steve_Chervitz@affymetrix.com
> 
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