view release on metacpan or  search on metacpan

Ace/Sequence/Feature.pm  view on Meta::CPAN

    # Special cases, hardcoded in Ace GFF code...
    my $db = $self->db;;
    my $class = $db->class;

    # for Notes we just return a text, no database associated
    return $class->new(Text=>$data[0]) if $tag eq 'Note';

    # for homols, we create the indicated Protein or Sequence object
    # then generate a bogus Homology object (for future compatability??)
    if ($tag eq 'Target') {
	my ($objname,$start,$end) = @data;
	my ($classe,$name) = $objname =~ /^(\w+):(.+)/;
	return Ace::Sequence::Homol->new_homol($classe,$name,$db,$start,$end);
    }

    # General case:
    my $obj = $class->new($tag=>$data[0],$self->db);

    return $obj if defined $obj;

    # Last resort, return a Text
    return $class->new(Text=>$data[0]);
}

sub sub_SeqFeature {
  return wantarray ? () : 0;
}

1;

=head1 NAME

Ace::Sequence::Feature - Examine Sequence Feature Tables

=head1 SYNOPSIS

    # open database connection and get an Ace::Object sequence
    use Ace::Sequence;

    # get a megabase from the middle of chromosome I
    $seq = Ace::Sequence->new(-name   => 'CHROMOSOME_I,
                              -db     => $db,
			      -offset => 3_000_000,
			      -length => 1_000_000);

    # get all the homologies (a list of Ace::Sequence::Feature objs)
    @homol = $seq->features('Similarity');

    # Get information about the first one
    $feature = $homol[0];
    $type    = $feature->type;
    $subtype = $feature->subtype;
    $start   = $feature->start;
    $end     = $feature->end;
    $score   = $feature->score;

    # Follow the target
    $target  = $feature->info;

    # print the target's start and end positions
    print $target->start,'-',$target->end, "\n";

=head1 DESCRIPTION

I<Ace::Sequence::Feature> is a subclass of L<Ace::Sequence::Feature>
specialized for returning information about particular features in a
GFF format feature table.

=head1  OBJECT CREATION

You will not ordinarily create an I<Ace::Sequence::Feature> object
directly.  Instead, objects will be created in response to a feature()
call to an I<Ace::Sequence> object.  If you wish to create an
I<Ace::Sequence::Feature> object directly, please consult the source
code for the I<new()> method.

=head1 OBJECT METHODS

Most methods are inherited from I<Ace::Sequence>.  The following
methods are also supported:

=over 4

=item seqname()

  $object = $feature->seqname;

Return the ACeDB Sequence object that this feature is attached to.
The return value is an I<Ace::Object> of the Sequence class.  This
corresponds to the first field of the GFF format and does not
necessarily correspond to the I<Ace::Sequence> object from which the
feature was obtained (use source_seq() for that).

=item source()

=item method()

=item subtype()

  $source = $feature->source;

These three methods are all synonyms for the same thing.  They return
the second field of the GFF format, called "source" in the
documentation.  This is usually the method or algorithm used to
predict the feature, such as "GeneFinder" or "tRNA" scan.  To avoid
ambiguity and enhance readability, the method() and subtype() synonyms
are also recognized.

=item feature()

=item type()

  $type = $feature->type;

These two methods are also synonyms.  They return the type of the
feature, such as "exon", "similarity" or "Predicted_gene".  In the GFF
documentation this is called the "feature" field.  For readability,
you can also use type() to fetch the field.

=item abs_start()