Bio::EnsEMBL::AltAlleleGroup Class Reference

Inheritance diagram for Bio::EnsEMBL::AltAlleleGroup:

Public Member Functions
public Bio::EnsEMBL::AltAlleleGroup	new ()
public	add_member ()
public	get_all_members_with_type ()
public HashRef	attribs ()
public	set_attribs ()
public	remove_attribs ()
public	remove_member ()
public Boolean	contains_member ()
public	remove_all_members ()
public Int	rep_Gene_id ()
public	unset_rep_Gene_id ()
public ArrayRef	get_all_Gene_ids ()
public Bio::EnsEMBL::Gene	get_representative_Gene ()
public ArrayRef	get_all_Genes ()
public ArrayRef	get_all_Genes_types ()
public Int	size ()
public ArrayRef	get_all_members ()
Public Member Functions inherited from Bio::EnsEMBL::Storable
public Bio::EnsEMBL::Storable	new ()
public Instance	new_fast ()
public Int	dbID ()
public Bio::EnsEMBL::DBSQL::BaseAdaptor	adaptor ()
public Boolean	is_stored ()
public	get_all_DAS_Features ()

Detailed Description

Synopsis

use Bio::EnsEMBL::AltAlleleGroup;
use Bio::EnsEMBL::DBSQL::AltAlleleGroupAdaptor;
 
my $aag_adaptor = Bio::EnsEMBL::Registry->get_DBAdaptor("Human","core","AltAlleleGroup");
 
# For a known Gene, find the reference alternative allele
my $aag = $aag_adaptor->fetch_Group_by_dbID($gene->dbID);
my $reference_gene = $aag->get_representative_Gene;
 
# Get a list of AltAlleleGroups
my $list = $aag_adaptor->fetch_all_Groups_by_type('HAS_CODING_POTENTIAL');
$list = $aag_adaptor->fetch_all_Groups();
 
while ($aag = shift @$list) {
    $aag->get_all_Genes;
    # Do your important things ...
}
 
# Creating and editing an AltAlleleGroup
 
my %type_flags = ('IS_MOST_COMMON_ALLELE' => '1','AUTOMATICALLY_ASSIGNED' => '1');
 
$aag = Bio::EnsEMBL::AltAlleleGroup->new(
   -MEMBERS => [ [$gene_id,\%type_flags ] ],
);
$aag->remove_all_members;
$aag->add_member($gene_id,\%type_flags);
 
my $dbID = $aag_adaptor->store($aag);

Description

    Alt allele groups keep track of which alleles are tied to a particular Gene
    They allow related genes to be located. This class allows fetching of both
    IDs and fully fledged Gene objects.
    
    AltAlleleGroup members are assigned types to differentiate them by their
    origin. These types are set as flags, allowing you to select the union of
    types as well as by individual ones.
        
    No flags set denotes a situation of no information.
    Valid flags are as follows:
    'IS_REPRESENTATIVE',
    'IS_MOST_COMMON_ALLELE',
    'IN_CORRECTED_ASSEMBLY',
    'HAS_CODING_POTENTIAL',
    'IN_ARTIFICIALLY_DUPLICATED_ASSEMBLY',
    'IN_SYNTENIC_REGION',
    'HAS_SAME_UNDERLYING_DNA_SEQUENCE',
    'IN_BROKEN_ASSEMBLY_REGION',
    'IS_VALID_ALTERNATE',
    'SAME_AS_REPRESENTATIVE',
    'SAME_AS_ANOTHER_ALLELE',
    'MANUALLY_ASSIGNED',
    'AUTOMATICALLY_ASSIGNED'

Definition at line 67 of file AltAlleleGroup.pm.

Member Function Documentation

add_member()

public Bio::EnsEMBL::AltAlleleGroup::add_member

(

)

  Arg [1]     : Gene dbID
  Arg [2]     : Type List, used for assigning type flags of this member, see Description above
  Description : Adds a record of one new member to the AltAlleleGroup. Once a
                change is made, this must be persisted to the database with
                AltAlleleGroupAdaptor->store or ->update
  Example     :

 $aag->add_member(1040032,$types_hash);
                $aaga->update($aag); # updating the whole group is necessary.
\

Code:

attribs()

public HashRef Bio::EnsEMBL::AltAlleleGroup::attribs

(

)

  Arg [1]     : Int gene id to record attributes against
  Description : Returns all known attributes of the given gene id. Attributes
                are returned as a HashRef but is a copy of the interally
                held attribute list
  Returntype  : HashRef copy of all the given id's attributes
  Example     :

 $aag->attribs(10, 'IS_VALID_ALTERNATE');
                $aag->attribs(10, [ 'IS_VALID_ALTERNATE' ]);
                $aag->attribs(10, {IS_VALID_ALTERNATE => 1});
 
\

Code:

contains_member()

public Boolean Bio::EnsEMBL::AltAlleleGroup::contains_member

(

)

  Arg [1]     : Int gene id to retrieve attributes against
  Description : Searches through the members list looking for the
                specified gene id. Returns true if it was found
                or false if not.
  Returntype  : Boolean indicating if the given gene id is held in this group
  Example     :

 $aag->contains_member(10);
 
\

Code:

get_all_Gene_ids()

public ArrayRef Bio::EnsEMBL::AltAlleleGroup::get_all_Gene_ids

(

)

  Arg[1]      : Boolean - Do not include representative gene in list of ids.
  Arg[2]      : ArrayRef - Can contain dbIDs or Gene objects to exclude from the returned list
  Description : fetches all the Gene dbIDs within the allele group. It can also
                be used to list those ids that are not the representative Gene.
  Returntype  : ArrayRef of gene dbIDs

Code:

get_all_Genes()

public ArrayRef Bio::EnsEMBL::AltAlleleGroup::get_all_Genes

(

)

  Arg[1]      : Boolean - Do not include representative gene in list of ids.
  Arg[2]      : ArrayRef - Can contain dbIDs or Gene objects to exclude from the returned list
  Description : Fetches all the Gene objects within the allele group. It can also
                be used to list those Genes that are not the representative Gene.
  Returntype  : ArrayRef of Bio::EnsEMBL::Gene objects

Code:

get_all_Genes_types()

public ArrayRef Bio::EnsEMBL::AltAlleleGroup::get_all_Genes_types

(

)

  Arg[1]      : Boolean - Do not include representative gene in list of ids.
  Arg[2]      : ArrayRef - Can contain dbIDs or Gene objects to exclude from the returned list
  Description : Fetches all the Gene objects within the allele group and their
                associcated attributes. It can also be used to list those 
                Genes that are not the representative Gene.
  Returntype  : ArrayRef. 2 dimensional holding [Bio::EnsEMBL::Gene, {attribute_hash}]

Code:

get_all_members()

public ArrayRef Bio::EnsEMBL::AltAlleleGroup::get_all_members

(

)

  Description : Retrieves all of the information about all members. Be aware
                that this emits the interal data structure so direct modification
                should be done with caution.
  Returntype  : ArrayRef of id and type list: [gene_id,type]
  Caller      : AltAlleleGroupAdaptor->store

Code:

get_all_members_with_type()

public Bio::EnsEMBL::AltAlleleGroup::get_all_members_with_type

(

)

  Arg [1]     : String The type to search members by
  Description : Loops through the internal members array returning all
                attributes of the same type as what has been specified
  Example     :

 my $members = $aag->get_all_members_with_type('IS_VALID_ALTERNATE');
 
\

Code:

get_representative_Gene()

public Bio::EnsEMBL::Gene Bio::EnsEMBL::AltAlleleGroup::get_representative_Gene

(

)

  Description : Used to fetch a Gene object which has been marked as the
                representative Gene for this alt allele group.
  Returntype  : Bio::EnsEMBL::Gene object which is the representative gene

Code:

new()

public Bio::EnsEMBL::AltAlleleGroup Bio::EnsEMBL::AltAlleleGroup::new

(

)

  Arg [-MEMBERS]: A list reference of [gene_id,type_flags]
                : gene_id is a dbID for Gene (consistent only within one release)
                : type_flags is a hash ref of attributes for this member
  Example    :

$aag = Bio::EnsEMBL::AltAlleleGroup->new(
                  -MEMBERS => [ [1,{$type} ], [2,{$other_type}],[3,{$type}],
              );

  Description: Creates a new alt-allele group object
  Returntype : Bio::EnsEMBL::AltAlleleGroup
  Exceptions : none
  Caller     : general

Code:

remove_all_members()

public Bio::EnsEMBL::AltAlleleGroup::remove_all_members

(

)

  Description : Remove members from this object, but NOT the database. See
                AltAlleleGroupAdaptor->remove() to remove the group from the
                database
 

Code:

remove_attribs()

public Bio::EnsEMBL::AltAlleleGroup::remove_attribs

(

)

  Arg [1]     : Int gene id to retrieve attributes against
  Arg [2]     : ArrayRef/HashRef/Scalar The attribute you wish to remove
  Description : Removes the given type from this group against the specified
                gene identifier
  Example     :

 $aag->remove_attribs(10, 'IS_VALID_ALTERNATE');
                $aag->remove_attribs(10, [ 'IS_VALID_ALTERNATE' ]);
                $aag->remove_attribs(10, {IS_VALID_ALTERNATE => 1});
 
\

Code:

remove_member()

public Bio::EnsEMBL::AltAlleleGroup::remove_member

(

)

  Arg [1]     : Int gene id to retrieve attributes against
  Arg [2]     : ArrayRef/HashRef/Scalar The attribute you wish to remove
  Description : Removes the given member from this group. Any changes
                must be persisted back to the database via update() or
                store() methods in Bio::EnsEMBL::DBSQL::AltAlleleGroupAdaptor.
  Example     :

 $aag->remove_member(10);
 
\

Code:

rep_Gene_id()

public Int Bio::EnsEMBL::AltAlleleGroup::rep_Gene_id

(

)

  Arg[1]      : Optional - set a new representative Gene id for the group
  Description : Reports or sets the representative Gene for this AltAlleleGroup
                If you wish to remove the representative status of all genes without
                setting a new one, see unset_rep_Gene_id
  Returntype  : Integer or undef if none set
 

Code:

set_attribs()

public Bio::EnsEMBL::AltAlleleGroup::set_attribs

(

)

  Arg [1]     : Int gene id to set attributes against
  Arg [2]     : ArrayRef/HashRef/Scalar The attribute you wish to record
  Description : Adds the given type to the specified gene id in this group. You
                can specify the type using an ArrayRef, HashRef or a single scalar
  Example     :

 $aag->attribs(10, 'IS_VALID_ALTERNATE');
                $aag->attribs(10, [ 'IS_VALID_ALTERNATE' ]);
                $aag->attribs(10, {IS_VALID_ALTERNATE => 1});
 
\

Code:

size()

public Int Bio::EnsEMBL::AltAlleleGroup::size

(

)

  Description : Returns the current size of this group in members
  Returntype  : Int the size of the current alt allele group

Code:

unset_rep_Gene_id()

public Bio::EnsEMBL::AltAlleleGroup::unset_rep_Gene_id

(

)

  Description : Removes the representative Gene flag from this AltAlleleGroup.
                This action is not possible through rep_Gene_id due to
                validation of inputs.

Code:

---

The documentation for this class was generated from the following file:

• ensembl/modules/Bio/EnsEMBL/AltAlleleGroup.pm