09-01-2011
Radulov
That's great! The only part that is missing is the headers (>Sequence ID) for each sequence. How can I modify your perl script so it can include the headers for each and every sequence?
Thanks!
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LEARN ABOUT DEBIAN
ace::sequence::transcript
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 <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 168:
You forgot a '=back' before '=head1'
perl v5.14.2 2001-05-22 Ace::Sequence::Transcript(3pm)