1Ace::Sequence::TranscriUpste(r3)Contributed Perl DocumenAtcaet:i:oSnequence::Transcript(3)
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NAME

6       Ace::Sequence::Transcript - Simple "Gene" Object
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SYNOPSIS

9           # open database connection and get an Ace::Object sequence
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 transcripts
19           @genes = $seq->transcripts;
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21           # get the exons from the first one
22           @exons = $genes[0]->exons;
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24           # get the introns
25           @introns = $genes[0]->introns
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27           # get the CDSs (NOT IMPLEMENTED YET!)
28           @cds = $genes[0]->cds;
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DESCRIPTION

31       Ace::Sequence::Gene is a subclass of Ace::Sequence::Feature.  It inher‐
32       its all the methods of Ace::Sequence::Feature, but adds the ability to
33       retrieve the annotated introns and exons of the gene.
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OBJECT CREATION

36       You will not ordinarily create an Ace::Sequence::Gene object directly.
37       Instead, objects will be created in response to a transcripts() call to
38       an Ace::Sequence object.
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OBJECT METHODS

41       Most methods are inherited from Ace::Sequence::Feature.  The following
42       methods are also supported:
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44       exons()
45             @exons = $gene->exons;
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47           Return a list of Ace::Sequence::Feature objects corresponding to
48           annotated exons.
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50       introns()
51             @introns = $gene->introns;
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53           Return a list of Ace::Sequence::Feature objects corresponding to
54           annotated introns.
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56       cds()
57             @cds = $gene->cds;
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59           Return a list of Ace::Sequence::Feature objects corresponding to
60           coding sequence.  THIS IS NOT YET IMPLEMENTED.
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62       relative()
63             $relative = $gene->relative;
64             $gene->relative(1);
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66           This turns on and off relative coordinates.  By default, the exons
67           and intron features will be returned in the coordinate system used
68           by the gene.  If relative() is set to a true value, then coordi‐
69           nates will be expressed as relative to the start of the gene.  The
70           first exon will (usually) be 1.
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SEE ALSO

73       Ace, Ace::Object, Ace::Sequence,Ace::Sequence::Homol,
74       Ace::Sequence::Feature, Ace::Sequence::FeatureList, GFF
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AUTHOR

77       Lincoln Stein <lstein@cshl.org> with extensive help from Jean Thierry-
78       Mieg <mieg@kaa.crbm.cnrs-mop.fr>
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80       Copyright (c) 1999, Lincoln D. Stein
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82       This library is free software; you can redistribute it and/or modify it
83       under the same terms as Perl itself.  See DISCLAIMER.txt for dis‐
84       claimers of warranty.
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88perl v5.8.8                       2001-02-20      Ace::Sequence::Transcript(3)
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