Ace::Sequence::GappedAlignment(3pm)

1Ace::Sequence::GappedAlUisgenrmeCnotn(t3r)ibuted Perl DoAccuem:e:nSteaqtuieonnce::GappedAlignment(3)
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NAME

6       Ace::Sequence::GappedAlignment - Gapped alignment object
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SYNOPSIS

9           # open database connection and get an Ace::Sequence object
10           use Ace::Sequence;
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12           # get a megabase from the middle of chromosome I
13           $seq = Ace::Sequence->new(-name   => 'CHROMOSOME_I,
14                                     -db     => $db,
15                                     -offset => 3_000_000,
16                                     -length => 1_000_000);
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18           # get all the gapped alignments
19           @alignments = $seq->alignments('EST_GENOME');
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21           # get the aligned segments from the first one
22           @segs = $alignments[0]->segments;
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24           # get the position of the first aligned segment on the
25           # source sequence:
26           ($s_start,$s_end) = ($segs[0]->start,$segs[0]->end);
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28           # get the target position for the first aligned segment
29           ($t_start,$t_end) = ($segs[0]->target->start,$segs[0]->target->end);
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DESCRIPTION

32       Ace::Sequence::GappedAlignment is a subclass of Ace::Sequence::Feature.
33       It inherits all the methods of Ace::Sequence::Feature, but adds the
34       ability to retrieve the positions of the aligned segments.  Each
35       segment is an Ace::Sequence::Feature, from which you can retrieve the
36       source and target coordinates.
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OBJECT CREATION

39       You will not ordinarily create an Ace::Sequence::GappedAlignment object
40       directly.  Instead, objects will be created in response to a
41       alignments() call to an Ace::Sequence object.
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OBJECT METHODS

44       Most methods are inherited from Ace::Sequence::Feature.  The following
45       methods are also supported:
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47       segments()
48             @segments = $gene->segments;
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50           Return a list of Ace::Sequence::Feature objects corresponding to
51           similar segments.
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53       relative()
54             $relative = $gene->relative;
55             $gene->relative(1);
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57           This turns on and off relative coordinates.  By default, the exons
58           and intron features will be returned in the coordinate system used
59           by the gene.  If relative() is set to a true value, then
60           coordinates will be expressed as relative to the start of the gene.
61           The first exon will (usually) be 1.
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AUTHOR

68       Lincoln Stein <lstein@cshl.org> with extensive help from Jean Thierry-
69       Mieg <mieg@kaa.crbm.cnrs-mop.fr>
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71       Copyright (c) 1999, Lincoln D. Stein
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73       This library is free software; you can redistribute it and/or modify it
74       under the same terms as Perl itself.  See DISCLAIMER.txt for
75       disclaimers of warranty.
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POD ERRORS

78       Hey! The above document had some coding errors, which are explained
79       below:
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81       Around line 166:
82           You forgot a '=back' before '=head1'
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86perl v5.34.0                      2022-01-20 Ace::Sequence::GappedAlignment(3)