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Bio::SeqFeatureI(3)   User Contributed Perl Documentation  Bio::SeqFeatureI(3)

NAME
       Bio::SeqFeatureI	- Abstract interface of	a Sequence Feature

SYNOPSIS
	   # get a seqfeature somehow, eg, from	a Sequence with	Features attached

	   foreach $feat ( $seq->get_SeqFeatures() ) {
	       print "Feature from ", $feat->start, "to	",
		     $feat->end, " Primary tag	", $feat->primary_tag,
		     ",	produced by ", $feat->source_tag(), "\n";

	       if ( $feat->strand == 0 ) {
		   print "Feature applicable to	either strand\n";
	       }
	       else {
		   print "Feature on strand ", $feat->strand,"\n"; # -1,1
	       }

	       print "feature location is ",$feat->start, "..",
		     $feat->end, " on strand ",	$feat->strand, "\n";
	       print "easy utility to print locations in GenBank/EMBL way ",
		     $feat->location->to_FTstring(), "\n";

	       foreach $tag ( $feat->get_all_tags() ) {
		   print "Feature has tag ", $tag, " with values, ",
			 join('	',$feat->get_tag_values($tag)),	"\n";
	       }
	       print "new feature\n" if	$feat->has_tag('new');
	       # features can have sub features
	       my @subfeat = $feat->get_SeqFeatures();
	   }

DESCRIPTION
       This interface is the functions one can expect for any Sequence
       Feature,	whatever its implementation or whether it is a more complex
       type (eg, a Gene). This object does not actually	provide	any
       implementation, it just provides	the definitions	of what	methods	one
       can call. See Bio::SeqFeature::Generic for a good standard
       implementation of this object

FEEDBACK
       User feedback is	an integral part of the	evolution of this and other
       Bioperl modules.	Send your comments and suggestions preferably to one
       of the Bioperl mailing lists.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About	the mailing lists

   Support
       Please direct usage questions or	support	issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and
       reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the	problem	with code and
       data examples if	at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track
       the bugs	and their resolution.  Bug reports can be submitted via	the
       web:

	 https://github.com/bioperl/bioperl-live/issues

APPENDIX
       The rest	of the documentation details each of the object	methods.
       Internal	methods	are usually preceded with a _

Bio::SeqFeatureI specific methods
       New method interfaces.

   get_SeqFeatures
	Title	: get_SeqFeatures
	Usage	: @feats = $feat->get_SeqFeatures();
	Function: Returns an array of sub Sequence Features
	Returns	: An array
	Args	: none

   display_name
	Title	: display_name
	Usage	: $name	= $feat->display_name()
	Function: Returns the human-readable name of the feature for displays.
	Returns	: a string
	Args	: none

   primary_tag
	Title	: primary_tag
	Usage	: $tag = $feat->primary_tag()
	Function: Returns the primary tag for a	feature,
		  eg 'exon'
	Returns	: a string
	Args	: none

   source_tag
	Title	: source_tag
	Usage	: $tag = $feat->source_tag()
	Function: Returns the source tag for a feature,
		  eg, 'genscan'
	Returns	: a string
	Args	: none

   has_tag
	Title	: has_tag
	Usage	: $tag_exists =	$self->has_tag('some_tag')
	Function:
	Returns	: TRUE if the specified	tag exists, and	FALSE otherwise
	Args	:

   get_tag_values
	Title	: get_tag_values
	Usage	: @values = $self->get_tag_values('some_tag')
	Function:
	Returns	: An array comprising the values of the	specified tag.
	Args	: a string

       throws an exception if there is no such tag

   get_tagset_values
	Title	: get_tagset_values
	Usage	: @values = $self->get_tagset_values(qw(label transcript_id product))
	Function:
	Returns	: An array comprising the values of the	specified tags,	in order of tags
	Args	: An array of strings

       does NOT	throw an exception if none of the tags are not present

       this method is useful for getting a human-readable label	for a
       SeqFeatureI; not	all tags can be	assumed	to be present, so a list of
       possible	tags in	preferential order is provided

   get_all_tags
	Title	: get_all_tags
	Usage	: @tags	= $feat->get_all_tags()
	Function: gives	all tags for this feature
	Returns	: an array of strings
	Args	: none

   attach_seq
	Title	: attach_seq
	Usage	: $sf->attach_seq($seq)
	Function: Attaches a Bio::Seq object to	this feature. This
		  Bio::Seq object is for the *entire* sequence:	ie
		  from 1 to 10000

		  Note that it is not guaranteed that if you obtain a feature from
		  an object in bioperl,	it will	have a sequence	attached. Also,
		  implementors of this interface can choose to provide an empty
		  implementation of this method. I.e., there is	also no	guarantee
		  that if you do attach	a sequence, seq() or entire_seq() will not
		  return undef.

		  The reason that this method is here on the interface is to enable
		  you to call it on every SeqFeatureI compliant	object,	and
		  that it will be implemented in a useful way and set to a useful
		  value	for the	great majority of use cases. Implementors who choose
		  to ignore the	call are encouraged to specifically state this in
		  their	documentation.

	Example	:
	Returns	: TRUE on success
	Args	: a Bio::PrimarySeqI compliant object

   seq
	Title	: seq
	Usage	: $tseq	= $sf->seq()
	Function: returns the truncated	sequence (if there is a	sequence attached)
		  for this feature
	Example	:
	Returns	: sub seq (a Bio::PrimarySeqI compliant	object)	on attached sequence
		  bounded by start & end, or undef if there is no sequence attached.
		  If the strand	is defined and set to -1, the returned sequence	is
		  the reverse-complement of the	region
	Args	: none

   entire_seq
	Title	: entire_seq
	Usage	: $whole_seq = $sf->entire_seq()
	Function: gives	the entire sequence that this seqfeature is attached to
	Example	:
	Returns	: a Bio::PrimarySeqI compliant object, or undef	if there is no
		  sequence attached
	Args	: none

   seq_id
	Title	: seq_id
	Usage	: $obj->seq_id($newval)
	Function: There	are many cases when you	make a feature that you
		  do know the sequence name, but do not	know its actual
		  sequence. This is an attribute such that you can store
		  the ID (e.g.,	display_id) of the sequence.

		  This attribute should	*not* be used in GFF dumping, as
		  that should come from	the collection in which	the seq
		  feature was found.
	Returns	: value	of seq_id
	Args	: newvalue (optional)

   gff_string
	Title	: gff_string
	Usage	: $str = $feat->gff_string;
		  $str = $feat->gff_string($gff_formatter);
	Function: Provides the feature information in GFF format.

		  The implementation provided here returns GFF2	by default. If you
		  want a different version, supply an object implementing a method
		  gff_string() accepting a SeqFeatureI object as argument. E.g., to
		  obtain GFF1 format, do the following:

		       my $gffio = Bio::Tools::GFF->new(-gff_version =>	1);
		       $gff1str	= $feat->gff_string($gff1io);

	Returns	: A string
	Args	: Optionally, an object	implementing gff_string().

   _static_gff_formatter
	Title	: _static_gff_formatter
	Usage	:
	Function:
	Example	:
	Returns	:
	Args	:

Decorating methods
       These methods have an implementation provided by	Bio::SeqFeatureI, but
       can be validly overwritten by subclasses

   spliced_seq
	 Title	 : spliced_seq

	 Usage	 : $seq	= $feature->spliced_seq()
		   $seq	= $feature_with_remote_locations->spliced_seq($db_for_seqs)

	 Function: Provides a sequence of the feature which is the most
		   semantically	"relevant" feature for this sequence. A	default
		   implementation is provided which for	simple cases returns just
		   the sequence, but for split cases, loops over the split location
		   to return the sequence. In the case of split	locations with
		   remote locations, eg

		   join(AB000123:5567-5589,80..1144)

		   in the case when a database object is passed	in, it will attempt
		   to retrieve the sequence from the database object, and "Do the right	thing",
		   however if no database object is provided, it will generate the correct
		   number of N's (DNA) or X's (protein,	though this is unlikely).

		   This	function is deliberately "magical" attempting to second	guess
		   what	a user wants as	"the" sequence for this	feature.

		   Implementing	classes	are free to override this method with their
		   own magic if	they have a better idea	what the user wants.

	 Args	 : [optional]
		   -db	      A	L<Bio::DB::RandomAccessI> compliant object if
			      one needs	to retrieve remote seqs.
		   -nosort    boolean if the locations should not be sorted
			      by start location.  This may occur, for instance,
			      in a circular sequence where a gene span starts
			      before the end of	the sequence and ends after the
			      sequence start. Example :	join(15685..16260,1..207)
			      (default = if sequence is_circular(), 1, otherwise 0)
		   -phase     truncates	the returned sequence based on the
			      intron phase (0,1,2).

	 Returns : A L<Bio::PrimarySeqI> object

   location
	Title	: location
	Usage	: my $location = $seqfeature->location()
	Function: returns a location object suitable for identifying location
		  of feature on	sequence or parent feature
	Returns	: Bio::LocationI object
	Args	: none

   primary_id
	Title	: primary_id
	Usage	: $obj->primary_id($newval)
	Function:
	Example	:
	Returns	: value	of primary_id (a scalar)
	Args	: on set, new value (a scalar or undef,	optional)

       Primary ID is a synonym for the tag 'ID'

   phase
	Title	: phase
	Usage	: $obj->phase($newval)
	Function: get/set this feature's phase.
	Example	:
	Returns	: undef	if no phase is set,
		  otherwise 0, 1, or 2 (the only valid values for phase)
	Args	: on set, the new value

       Most features do	not have or need a defined phase.

       For features representing a CDS,	the phase indicates where the feature
       begins with reference to	the reading frame.  The	phase is one of	the
       integers	0, 1, or 2, indicating the number of bases that	should be
       removed from the	beginning of this feature to reach the first base of
       the next	codon. In other	words, a phase of "0" indicates	that the next
       codon begins at the first base of the region described by the current
       line, a phase of	"1" indicates that the next codon begins at the	second
       base of this region, and	a phase	of "2" indicates that the codon	begins
       at the third base of this region. This is NOT to	be confused with the
       frame, which is simply start modulo 3.

       For forward strand features, phase is counted from the start field. For
       reverse strand features,	phase is counted from the end field.

Bio::RangeI methods
       These methods are inherited from	RangeI and can be used directly	from a
       SeqFeatureI interface. Remember that a SeqFeature is-a RangeI, and so
       wherever	you see	RangeI you can use a feature ($r in the	below
       documentation).

   start()
	See L<Bio::RangeI>

   end()
	See L<Bio::RangeI>

   strand()
	See L<Bio::RangeI>

   overlaps()
	See L<Bio::RangeI>

   contains()
	See L<Bio::RangeI>

   equals()
	See L<Bio::RangeI>

   intersection()
	See L<Bio::RangeI>

   union()
	See L<Bio::RangeI>

perl v5.32.1			  2019-12-07		   Bio::SeqFeatureI(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | APPENDIX | Bio::SeqFeatureI specific methods | Decorating methods | Bio::RangeI methods

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