[Bioperl-l] Bio::DB::GFF modules

[Lincoln Stein]

Hi All,

I'm very sorry for committing a big wad of mostly undocumented code to
the repository.  I'm working to rectify that today.

In case anyone's wondering what it is I'm working on, it's a
lightweight data access layer for sequence annotations.  The idea is
to support both ACeDB databases and relational annotation databases
using a set of adaptors and aggregators.

The synopsis will give you a good idea of what it's all about:

  use Bio::DB::GFF;

  # Open the sequence database
  my $db      = Bio::DB::GFF->new( -adaptor => 'dbi:mysql',
                                   -dsn     => 'dbi:mysql:elegans42');

  # fetch a 1 megabase segment of sequence starting at landmark "ZK909"
  my $segment = $seqfactory->segment('ZK909', 1 => 1000000);

  # pull out all transcript features
  my @transcripts = $segment->features('transcript');

  # for each transcript, total the length of the introns
  my %totals;
  for my $t (@transcripts) {
    my @introns = $t->Intron;
    $totals{$t->name} += $_->length foreach @introns;
  }

  # Sort the exons of the first transcript by position
  my @exons = sort {$a->start <=> $b->start} $transcripts[0]->Exon;

  # Get a region 1000 bp upstream of first exon
  my $upstream = $exons[0]->segment(-1000,0);

  # get its DNA
  my $dna = $upstream->dna;

  # and get all curated polymorphisms inside it
  @polymorphisms = $upstream->contained_features('polymorphism:curated');

  # get all feature types in the database
  my @types = $db->types;

  # last example: count all feature types that overlap the segment
  my %type_counts = $segment->types(-enumerate=>1);


The module started out as a rewrite of Ace::Sequence, so the API still
varies from FeatureI in a few minor ways (using stop() instead of
end() for example).  This will be fixed.

Lincoln

-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
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