SIMPLE SOLUTIONS

ACE::SEQUENCE::TRANSCRIPT(3PM) - Linux man page online | Library functions

Simple "Gene" Object.

Chapter
2017-11-24
Ace::Sequence::Transcript(3pm) User Contributed Perl Documentation Ace::Sequence::Transcript(3pm)

NAME

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

SYNOPSIS

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

DESCRIPTION

Ace::Sequence::Gene is a subclass of Ace::Sequence::Feature. It inherits all the methods of Ace::Sequence::Feature, but adds the ability to retrieve the annotated introns and exons of the gene.

OBJECT CREATION

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

OBJECT METHODS

Most methods are inherited from Ace::Sequence::Feature. The following methods are also supported: exons() @exons = $gene->exons; Return a list of Ace::Sequence::Feature objects corresponding to annotated exons. introns() @introns = $gene->introns; Return a list of Ace::Sequence::Feature objects corresponding to annotated introns. cds() @cds = $gene->cds; Return a list of Ace::Sequence::Feature objects corresponding to coding sequence. THIS IS NOT YET IMPLEMENTED. 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 <@cshl.org> with extensive help from Jean Thierry-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 168: You forgot a '=back' before '=head1'
perl v5.26.1 2017-11-24 Ace::Sequence::Transcript(3pm)
Download raw manual
Main page User Contributed Perl Documentation (+23303) perl v5.26.1 (+10548) № 3 (+68044)
Go top