Ace::Sequence::GappedAlignment - Gapped alignment object
# open database connection and get an Ace::Sequence object 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 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 similar segments.
$relative = $gene->relative; $gene->relative(1);
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.
Lincoln Stein <firstname.lastname@example.org> with extensive help from Jean Thierry-Mieg <email@example.com>
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.