02-22-2007
Moreover I want to add "Sequence" column in the file as well after the script is completed.
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LEARN ABOUT DEBIAN
ace::sequence::gappedalignment
Ace::Sequence::GappedAlignment(3pm) User Contributed Perl Documentation Ace::Sequence::GappedAlignment(3pm)
NAME
Ace::Sequence::GappedAlignment - Gapped alignment object
SYNOPSIS
# 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 = $alignments[0]->segments;
# get the position of the first aligned segment on the
# source sequence:
($s_start,$s_end) = ($segs[0]->start,$segs[0]->end);
# get the target position for the first aligned segment
($t_start,$t_end) = ($segs[0]->target->start,$segs[0]->target->end);
DESCRIPTION
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.
OBJECT CREATION
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.
OBJECT METHODS
Most methods are inherited from Ace::Sequence::Feature. The following methods are also supported:
segments()
@segments = $gene->segments;
Return a list of Ace::Sequence::Feature objects corresponding to similar segments.
relative()
$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.
SEE ALSO
Ace, Ace::Object, Ace::Sequence,Ace::Sequence::Homol, Ace::Sequence::Feature, Ace::Sequence::FeatureList, GFF
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.
POD ERRORS
Hey! The above document had some coding errors, which are explained below:
Around line 166:
You forgot a '=back' before '=head1'
perl v5.14.2 2001-11-10 Ace::Sequence::GappedAlignment(3pm)