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Ace::Sequence::FeatureUser Contributed Perl DocumentaAce::Sequence::Feature(3)

NAME
       Ace::Sequence::Feature -	Examine	Sequence Feature Tables

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 homologies (a list of Ace::Sequence::Feature objs)
	   @homol = $seq->features('Similarity');

	   # Get information about the first one
	   $feature = $homol[0];
	   $type    = $feature->type;
	   $subtype = $feature->subtype;
	   $start   = $feature->start;
	   $end	    = $feature->end;
	   $score   = $feature->score;

	   # Follow the	target
	   $target  = $feature->info;

	   # print the target's	start and end positions
	   print $target->start,'-',$target->end, "\n";

DESCRIPTION
       Ace::Sequence::Feature is a subclass of Ace::Sequence::Feature
       specialized for returning information about particular features in a
       GFF format feature table.

OBJECT CREATION
       You will	not ordinarily create an Ace::Sequence::Feature	object
       directly.  Instead, objects will	be created in response to a feature()
       call to an Ace::Sequence	object.	 If you	wish to	create an
       Ace::Sequence::Feature object directly, please consult the source code
       for the new() method.

OBJECT METHODS
       Most methods are	inherited from Ace::Sequence.  The following methods
       are also	supported:

       seqname()
	     $object = $feature->seqname;

	   Return the ACeDB Sequence object that this feature is attached to.
	   The return value is an Ace::Object of the Sequence class.  This
	   corresponds to the first field of the GFF format and	does not
	   necessarily correspond to the Ace::Sequence object from which the
	   feature was obtained	(use source_seq() for that).

       source()
       method()
       subtype()
	     $source = $feature->source;

	   These three methods are all synonyms	for the	same thing.  They
	   return the second field of the GFF format, called "source" in the
	   documentation.  This	is usually the method or algorithm used	to
	   predict the feature,	such as	"GeneFinder" or	"tRNA" scan.  To avoid
	   ambiguity and enhance readability, the method() and subtype()
	   synonyms are	also recognized.

       feature()
       type()
	     $type = $feature->type;

	   These two methods are also synonyms.	 They return the type of the
	   feature, such as "exon", "similarity" or "Predicted_gene".  In the
	   GFF documentation this is called the	"feature" field.  For
	   readability,	you can	also use type()	to fetch the field.

       abs_start()
	     $start = $feature->abs_start;

	   This	method returns the absolute start of the feature within	the
	   sequence segment indicated by seqname().  As	in the Ace::Sequence
	   method, use start() to obtain the start of the feature relative to
	   its source.

       abs_start()
	     $start = $feature->abs_start;

	   This	method returns the start of the	feature	relative to the
	   sequence segment indicated by seqname().  As	in the Ace::Sequence
	   method, you will more usually use the inherited start() method to
	   obtain the start of the feature relative to its source sequence
	   (the	Ace::Sequence from which it was	originally derived).

       abs_end()
	     $start = $feature->abs_end;

	   This	method returns the end of the feature relative to the sequence
	   segment indicated by	seqname().  As in the Ace::Sequence method,
	   you will more usually use the inherited end() method	to obtain the
	   end of the feature relative to the Ace::Sequence from which it was
	   derived.

       score()
	     $score = $feature->score;

	   For features	that are associated with a numeric score, such as
	   similarities, this returns that value.  For other features, this
	   method returns undef.

       strand()
	     $strand = $feature->strand;

	   Returns the strandedness of this feature, either "+1" or "-1".  For
	   features that are not stranded, returns 0.

       reversed()
	     $reversed = $feature->reversed;

	   Returns true	if the feature is reversed relative to its source
	   sequence.

       frame()
	     $frame = $feature->frame;

	   For features	that have a frame, such	as a predicted coding
	   sequence, returns the frame,	either 0, 1 or 2.  For other features,
	   returns undef.

       group()
       info()
       target()
	     $info = $feature->info;

	   These methods (synonyms for one another) return an Ace::Object
	   containing other information	about the feature derived from the 8th
	   field of the	GFF format, the	so-called "group" field.  The type of
	   the Ace::Object is dependent	on the nature of the feature.  The
	   possibilities are shown in the table	below:

	     Feature Type	    Value of Group Field
	     ------------	     --------------------

	     note		    A Text object containing the note.

	     similarity		    An Ace::Sequence::Homology object containing
				    the	target and its start/stop positions.

	     intron		    An Ace::Object containing the gene from
	     exon		    which the feature is derived.
	     misc_feature

	     other		    A Text object containing the group data.

       asString()
	     $label = $feature->asString;

	   Returns a human-readable identifier describing the nature of	the
	   feature.  The format	is:

	    $type:$name/$start-$end

	   for example:

	    exon:ZK154.3/1-67

	   This	method is also called automatically when the object is treated
	   in a	string context.

SEE ALSO
       Ace, Ace::Object, Ace::Sequence,Ace::Sequence::Homol,
       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.

perl v5.24.1			  2001-09-17	     Ace::Sequence::Feature(3)

NAME | SYNOPSIS | DESCRIPTION | OBJECT CREATION | OBJECT METHODS | SEE ALSO | AUTHOR

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