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Bio::Variation::VarianUser)Contributed Perl DocumenBio::Variation::VariantI(3)

NAME
       Bio::Variation::VariantI	- Sequence Change SeqFeature abstract class

SYNOPSIS
	 #get Bio::Variant::VariantI somehow
	 print $var->restriction_changes, "\n";
	 foreach $allele ($var->each_Allele) {
	     #work on Bio::Variation::Allele objects
	 }

DESCRIPTION
       This superclass defines common methods to basic sequence	changes.  The
       instantiable classes Bio::Variation::DNAMutation,
       Bio::Variation::RNAChange and Bio::Variation::AAChange use them.	 See
       Bio::Variation::DNAMutation, Bio::Variation::RNAChange, and
       Bio::Variation::AAChange	for more information.

       These classes store information,	heavy computation to determine allele
       sequences is done elsewhere.

       The database cross-references are implemented as
       Bio::Annotation::DBLink objects.	The methods to access them are defined
       in Bio::DBLinkContainerI. See Bio::Annotation::DBLink and
       Bio::DBLinkContainerI for details.

       Bio::Variation::VariantI	redifines and extends Bio::SeqFeature::Generic
       for sequence variations.	This class describes specific sequence change
       events. These events are	always from a specific reference sequence to
       something different. See	Bio::SeqFeature::Generic for more information.

       IMPORTANT: The notion of	reference sequence permeates all
       Bio::Variation classes. This is especially important to remember	when
       dealing with Alleles. In	a polymorphic site, there can be a large
       number of alleles. One of then has to be	selected to be the reference
       allele (allele_ori). ALL	the rest has to	be passed to the Variant using
       the method add_Allele, including	the mutated allele in a	canonical
       mutation. The IO	modules	and generated attributes depend	on it. They
       ignore the allele linked	to using allele_mut and	circulate each Allele
       returned	by each_Allele into allele_mut and calculate the changes
       between that and	allele_ori.

FEEDBACK
   Mailing Lists
       User feedback is	an integral part of the	evolution of this and other
       Bioperl modules.	Send your comments and suggestions preferably to 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

AUTHOR - Heikki	Lehvaslaiho
       Email:  heikki-at-bioperl-dot-org

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

   id
	Title	: id
	Usage	: $obj->id
	Function:

		  Read only method. Returns the	id of the variation object.
		  The id is the	id of the first	DBLink object attached to this object.

	Example	:
	Returns	: scalar
	Args	: none

   add_Allele
	Title	: add_Allele
	Usage	: $self->add_Allele($allele)
	Function:

		   Adds	one Bio::Variation::Allele into	the list of alleles.
		   Note	that the method	forces the convention that nucleotide
		   sequence is in lower	case and amino acds are	in upper
		   case.

	Example	:
	Returns	: 1 when succeeds, 0 for failure.
	Args	: Allele object

   each_Allele
	Title	: alleles
	Usage	: $obj->each_Allele();
	Function:

		    Returns a list of Bio::Variation::Allele objects

	Example	:
	Returns	: list of Alleles
	Args	: none

   isMutation
	Title	: isMutation
	Usage	: print	join('/', $obj->each_Allele) if	not $obj->isMutation;
	Function:

		  Returns or sets the boolean value indicating that the
		  variant described is a canonical mutation with two alleles
		  assinged to be the original (wild type) allele and mutated
		  allele, respectively.	If this	value is not set, it is
		  assumed that the Variant describes polymorphisms.

	Returns	: a boolean

   allele_ori
	Title	: allele_ori
	Usage	: $obj->allele_ori();
	Function:

		   Links to and	returns	the Bio::Variation::Allele object.
		   If value is not set,	returns	false. All other Alleles are
		   compared to this.

		   Amino acid sequences	are stored in upper case characters,
		   others in lower case.

	Example	:
	Returns	: string
	Args	: string

       See Bio::Variation::Allele for more.

   allele_mut
	Title	: allele_mut
	Usage	: $obj->allele_mut();
	Function:

		    Links to and returns the Bio::Variation::Allele
		    object.  Sets and returns the mutated allele sequence.
		    If value is	not set, returns false.

		    Amino acid sequences are stored in upper case characters,
		    others in lower case.

	Example	:
	Returns	: string
	Args	: string

       See Bio::Variation::Allele for more.

   length
	Title	: length
	Usage	: $obj->length();
	Function:

		   Sets	and returns the	length of the affected original
		   allele sequence.  If	value is not set, returns false	== 0.

		   Value 0 means that the variant position is before the
		   start=end sequence position.	(Value 1 would denote a	point
		   mutation). This follows the convension to report an
		   insertion (2insT) in	equivalent way to a corresponding
		   deletion (2delT) (Think about indel polymorpism ATC <=> AC
		   where the origianal state is	not known ).

	Example	:
	Returns	: string
	Args	: string

   upStreamSeq
	Title	: upStreamSeq
	Usage	: $obj->upStreamSeq();
	Function:

		   Sets	and returns upstream flanking sequence string.	If
		   value is not	set, returns false. The	sequence should	be
		   >=25	characters long, if possible.

	Example	:
	Returns	: string or false
	Args	: string

   dnStreamSeq
	Title	: dnStreamSeq
	Usage	: $obj->dnStreamSeq();
	Function:

		   Sets	and returns dnstream flanking sequence string.	If
		   value is not	set, returns false. The	sequence should	be
		   >=25	characters long, if possible.

	Example	:
	Returns	: string or false
	Args	: string

   label
	Title	: label
	Usage	: $obj->label();
	Function:

		   Sets	and returns mutation event label(s).  If value is not
		   set,	or no argument is given	returns	false.	Each
		   instantiable	class needs to implement this method. Valid
		   values are listed in	'Mutation event	controlled vocabulary' in
		   http://www.ebi.ac.uk/mutations/recommendations/mutevent.html.

	Example	:
	Returns	: string
	Args	: string

   status
	Title	: status
	Usage	: $obj->status()
	Function:

		  Returns the status of	the sequence change object.
		  Valid	values are: 'suspected'	and 'proven'

	Example	: $obj->status('proven');
	Returns	: scalar
	Args	: valid	string (optional, for setting)

   proof
	Title	: proof
	Usage	: $obj->proof()
	Function:

		  Returns the proof of the sequence change object.
		  Valid	values are: 'computed' and 'experimental'.

	Example	: $obj->proof('computed');
	Returns	: scalar
	Args	: valid	string (optional, for setting)

   region
	Title	: region
	Usage	: $obj->region();
	Function:

		   Sets	and returns the	name of	the sequence region type or
		   protein domain at this location.  If	value is not set,
		   returns false.

	Example	:
	Returns	: string
	Args	: string

   region_value
	Title	: region_value
	Usage	: $obj->region_value();
	Function:

		   Sets	and returns the	name of	the sequence region_value or
		   protein domain at this location.  If	value is not set,
		   returns false.

	Example	:
	Returns	: string
	Args	: string

   region_dist
	Title	: region_dist
	Usage	: $obj->region_dist();
	Function:

		   Sets	and returns the	distance tot the closest region
		   (i.e. intro/exon or domain) boundary. If distance is	not
		   set,	returns	false.

	Example	:
	Returns	: integer
	Args	: integer

   numbering
	Title	: numbering
	Usage	: $obj->numbering()
	Function:

		  Returns the numbering	chema used locating sequnce features.
		  Valid	values are: 'entry' and	'coding'

	Example	: $obj->numbering('coding');
	Returns	: scalar
	Args	: valid	string (optional, for setting)

   mut_number
	Title	: mut_number
	Usage	: $num = $obj->mut_number;
		: $num = $obj->mut_number($number);
	Function:

		  Returns or sets the number identifying the order in which the
		  mutation has been issued. Numbers shouldstart	from 1.
		  If the number	has never been set, the	method will return ''

		  If you want the output from IO modules look nice and,	for
		  multivariant/allele variations, make sense you better	set
		  this attribute.

	Returns	: an integer

   SeqDiff
	Title	: SeqDiff
	Usage	: $mutobj = $obj->SeqDiff;
		: $mutobj = $obj->SeqDiff($objref);
	Function:

		  Returns or sets the link-reference to	the umbrella
		  Bio::Variation::SeqDiff object.  If there is no link,
		  it will return undef

		  Note:	Adding a variant into a	SeqDiff	object will
		  automatically	set this value.

	Returns	: an obj_ref or	undef

       See Bio::Variation::SeqDiff for more information.

   add_DBLink
	Title	: add_DBLink
	Usage	: $self->add_DBLink($ref)
	Function: adds a link object
	Example	:
	Returns	:
	Args	:

   each_DBLink
	Title	: each_DBLink
	Usage	: foreach $ref ( $self->each_DBlink() )
	Function: gets an array	of DBlink of objects
	Example	:
	Returns	:
	Args	:

   restriction_changes
	Title	: restriction_changes
	Usage	: $obj->restriction_changes();
	Function:

		   Returns a string containing a list of restriction
		   enzyme changes of form +EcoRI, separated by
		   commas. Strings need	to be valid restriction	enzyme names
		   as stored in	REBASE.	allele_ori and allele_mut need to be assigned.

	Example	:
	Returns	: string
	Args	: string

perl v5.32.1			  2020-01-06	   Bio::Variation::VariantI(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Heikki Lehvaslaiho | APPENDIX

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