Bio::Variation::VariantI.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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 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.
   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:
   http://bugzilla.open-bio.org/
 
 

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.

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