Manual Reference Pages - ACE::SEQUENCE::GAPPEDALIGNMENT (3)
Ace::Sequence::GappedAlignment - Gapped alignment object
# open database connection and get an Ace::Sequence object
# 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 gapped alignments
@alignments = $seq->alignments(EST_GENOME);
# get the aligned segments from the first one
@segs = $alignments->segments;
# get the position of the first aligned segment on the
# source sequence:
($s_start,$s_end) = ($segs->start,$segs->end);
# get the target position for the first aligned segment
($t_start,$t_end) = ($segs->target->start,$segs->target->end);
Ace::Sequence::GappedAlignment is a subclass of
Ace::Sequence::Feature. It inherits all the methods of
Ace::Sequence::Feature, but adds the ability to retrieve the positions
of the aligned segments. Each segment is an Ace::Sequence::Feature,
from which you can retrieve the source and target coordinates.
You will not ordinarily create an Ace::Sequence::GappedAlignment
object directly. Instead, objects will be created in response to a
alignments() call to an Ace::Sequence object.
Most methods are inherited from Ace::Sequence::Feature. The
following methods are also supported:
@segments = $gene->segments;
Return a list of Ace::Sequence::Feature objects corresponding to
$relative = $gene->relative;
This turns on and off relative coordinates. By default, the exons and
intron features will be returned in the coordinate system used by the
gene. If relative() is set to a true value, then coordinates will be
expressed as relative to the start of the gene. The first exon will
(usually) be 1.
Ace, Ace::Object, Ace::Sequence,Ace::Sequence::Homol,
Ace::Sequence::Feature, Ace::Sequence::FeatureList, GFF
Lincoln Stein <email@example.com> with extensive help from Jean
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.
Hey! <B>The above document had some coding errors, which are explained below:B>
Around line 166:
You forgot a =back before =head1
|perl v5.20.3 ||ACE::SEQUENCE::GAPPEDALIGNMENT (3) ||2001-11-10 |
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