view release on metacpan or  search on metacpan

lib/Bio/DB/SeqFeature/Store.pm  view on Meta::CPAN

This method fetches features based on a location range lookup. You
call it using a positional list of arguments, or a list of
(-argument=E<gt>$value) pairs.

The positional form is as follows:

 $db->get_features_by_location($seqid [[,$start,]$end])

The $seqid is the name of the sequence on which the feature resides,
and start and end are optional endpoints for the match. If the
endpoints are missing then any feature on the indicated seqid is
returned.

Examples:

 get_features_by_location('chr1');      # all features on chromosome 1
 get_features_by_location('chr1',5000); # features between 5000 and the end
 get_features_by_location('chr1',5000,8000); # features between 5000 and 8000

Location lookups are overlapping. A feature will be returned if it
partially or completely overlaps the indicated range.

lib/Bio/DB/SeqFeature/Store/GFF3Loader.pm  view on Meta::CPAN

  # contiguous feature, so add a segment
  warn $old_feat if defined $old_feat and !ref $old_feat;
  if (defined $old_feat) {
      # set this to 1 to disable split-location behavior
      if (0 && @parent_ids) {                  # If multiple features are held together by the same ID
	  $feature_id = $ld->{TemporaryID}++;  # AND they have a Parent attribute, this causes an undesirable
      }                                        # additional layer of aggregation. Changing the ID fixes this.
      elsif       (
	  $old_feat->seq_id ne $refname || 
	  $old_feat->start  != $start || 
	  $old_feat->end    != $end # make sure endpoints are distinct
	  )
      {
	  $self->add_segment($old_feat,$self->sfclass->new(@args));
	  return;
      }
  }

  # we get here if this is a new feature
  # first of all, store the current feature if it is there
  $self->store_current_feature() if defined $ld->{CurrentID};