Bio::Variation::VariantI - Sequence Change SeqFeature abstract class #get Bio::Variant::VariantI somehow print $var->restriction_changes, "\n"; foreach $allele ($var->each_Allele) { #work on Bio::Variation::Allele objects } 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 detemine 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.

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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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Email: heikki@ebi.ac.uk Address: EMBL Outstation, European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambs. CB10 1SD, United Kingdom 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 descibed 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 descibes 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