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 listsSupport
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/issuesAUTHOR - 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 : noneadd_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 objecteach_Allele
Title : alleles
Usage : $obj->each_Allele();
Function:
Returns a list of Bio::Variation::Allele objects
Example :
Returns : list of Alleles
Args : noneisMutation
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 booleanallele_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 : stringSee 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 : stringSee 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 : stringupStreamSeq
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 : stringdnStreamSeq
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 : stringlabel
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 : stringstatus
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 : stringregion_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 : stringregion_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 : integernumbering
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 integerSeqDiff
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 undefSee 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