ace::sequence::gene(3pm) [debian man page]

Ace::Sequence::Gene(3pm)				User Contributed Perl Documentation				  Ace::Sequence::Gene(3pm)

NAME

       Ace::Sequence::Gene - 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 genes
	   @genes = $seq->genes;

	   # 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 genes() 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 148:
	   You forgot a '=back' before '=head1'

perl v5.14.2							    2001-02-18						  Ace::Sequence::Gene(3pm)

Ace::Sequence::FeatureList(3pm) 			User Contributed Perl Documentation			   Ace::Sequence::FeatureList(3pm)

NAME

       Ace::Sequence::FeatureList - Lightweight Access to Features

SYNOPSIS

	   # 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);

	   # find out what's there
	   $list = $seq->feature_list;

	   # Scalar context: count all the features
	   $feature_count = $list->types;

	   # Array context: list all the feature types
	   @feature_types = $list->types;

	   # Scalar context, 1 argument.  Count this type
	   $gene_cnt = $list->types('Predicted_gene');
	   print "There are $gene_cnt genes here.
";

	   # Array context, 1 argument.  Get list of subtypes
	   @subtypes = $list->types('Predicted_gene');

	   # Two arguments. Count type & subtype
	   $genefinder_cnt = $list->types('Predicted_gene','genefinder');

DESCRIPTION

       Ace::Sequence::FeatureList is a small class that provides statistical information about sequence features.  From it you can obtain summary
       counts of the features and their types within a selected region.

OBJECT CREATION

       You will not ordinarily create an Ace::Sequence::FeatureList object directly.  Instead, objects will be created by calling a Ace::Sequence
       object's feature_list() method.	If you wish to create an Ace::Sequence::FeatureList object directly, please consult the source code for
       the new() method.

OBJECT METHODS

       There are only two methods in Ace::Sequence::FeatureList.

       type()
	   This method has five distinct behaviors, depending on its context and the number of parameters.  Usage should be intuitive

	    Context	  Arguments	  Behavior
	    -------	  ---------	  --------

	    scalar	   -none-	  total count of features in list
	    array	   -none-	  list feature types (e.g. "exon")
	    scalar	    type	  count features of this type
	    array	    type	  list subtypes of this type
	    -any-	type,subtype	  count features of this type & subtype

	   For example, this code fragment will count the number of exons present on the list:

	     $exon_count = $list->type('exon');

	   This code fragment will count the number of exons found by "genefinder":

	     $predicted_exon_count = $list->type('exon','genefinder');

	   This code fragment will print out all subtypes of "exon" and their counts:

	     for my $subtype ($list->type('exon')) {
		 print $subtype,"	",$list->type('exon',$subtype),"
";
	     }

       asString()
	     print $list->asString;

	   This dumps the list out in tab-delimited format.  The order of columns is type, subtype, count.

SEE ALSO

       Ace, Ace::Object, Ace::Sequence, Ace::Sequence::Feature, GFF

AUTHOR

       Lincoln Stein <lstein@w3.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.

perl v5.14.2							    2000-06-11					   Ace::Sequence::FeatureList(3pm)