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 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.

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

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

[email protected]

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 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