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;
# }
( run in 0.539 second using v1.01-cache-2.11-cpan-39bf76dae61 )