AcePerl

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


  $frame = $feature->frame;

For features that have a frame, such as a predicted coding sequence,
returns the frame, either 0, 1 or 2.  For other features, returns undef.

=item group()

=item info()

=item target()

  $info = $feature->info;

These methods (synonyms for one another) return an Ace::Object
containing other information about the feature derived from the 8th
field of the GFF format, the so-called "group" field.  The type of the
Ace::Object is dependent on the nature of the feature.  The
possibilities are shown in the table below:

  Feature Type           Value of Group Field
  ------------            --------------------
  
  note                   A Text object containing the note.
  
  similarity             An Ace::Sequence::Homology object containing
                         the target and its start/stop positions.

  intron                 An Ace::Object containing the gene from 
  exon                   which the feature is derived.
  misc_feature

  other                  A Text object containing the group data.

=item asString()

  $label = $feature->asString;

Returns a human-readable identifier describing the nature of the
feature.  The format is:

 $type:$name/$start-$end

for example:

 exon:ZK154.3/1-67

This method is also called automatically when the object is treated in
a string context.

=back

=head1 SEE ALSO

L<Ace>, L<Ace::Object>, L<Ace::Sequence>,L<Ace::Sequence::Homol>,
L<Ace::Sequence::FeatureList>, L<GFF>

=head1 AUTHOR

Lincoln Stein <lstein@cshl.org> with extensive help from Jean
Thierry-Mieg <mieg@kaa.crbm.cnrs-mop.fr>

Copyright (c) 1999, Lincoln D. Stein

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.  See DISCLAIMER.txt for
disclaimers of warranty.

=cut


__END__
# SCRAPS
# the new() code done "right"
# sub new {
#    my $pack = shift;
#    my ($ref,$r_offset,$r_strand,$gff_line) = @_;
#    my ($sourceseq,$method,$type,$start,$end,$score,$strand,$frame,$group) = split "\t";
#    ($start,$end) = ($end,$start) if $strand < 0;
#    my $self = $pack->SUPER::new($source,$start,$end);
#    $self->{info} = {
#  				seqname=> $sourceseq,
#  				method => $method,
#  				type   => $type,
#  				score  => $score,
#  				frame  => $frame,
#  				group  => $group,
#  		  };
#    $self->{fstrand} = $strand;
#    return $self;
#  }



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