[Bioperl-l] Review request: Merged hmmer2/3 parser

[Chris Fields]

On Nov 5, 2010, at 7:56 AM, Kai Blin wrote:

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> On 2010-11-05 13:35, Dave Messina wrote:
>> I may have missed some recent off-list discussion, but I thought we
>> explicitly talked about *not* merging these since it will complicate
>> future maintenance and Hmmer2 will be obsolete in the near future.
> 
> Yes, that's what I thought until about last week. Then I was bitten by
> the fact that Hmmer3 can't do global alignments, so you can't reliably
> use Hmmer3 to extract protein domains using the domain's motif. As this
> seems to be a common use case, I think we'll end up supporting hmmer2
> for quite a while now.
> 
> There's currently no plans by the Hmmer authors to add globlal and
> glocal (whole profile alignments against parts of the sequence)
> alignments to hmmer3. They suggested to keep using hmmer2 for now.
> 
> For this reason I decided to try and merge the two parsers to a point
> where users don't have to care which version of hmmer their file is.
> 
> Cheers,
> Kai

Makes sense to me.  We're tackling some Bio::Tree revisions next week, my guess is we can also get this added in.  I'm really keen on getting 1.6.2 out sometime soon, before things get really crazy for me this spring.

Key things to test: can specify the exact hmmer2/3 parser directly?  

   my $in = Bio::SearchIO->new(-format => 'hmmer3', -file => 'foo')

Can one explicitly specify the hmmer parser variant?

   my $in = Bio::SearchIO->new(-format => 'hmmer', -version => 3, -file => 'foo')

This will more than likely pop up.  I did something with Bio::SeqIO::fastq to allow specifying sanger/illumina/solexa variants, this would be similar in respect.

chris