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Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

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NAME

Bio::EnsEMBL::IntronSupportingEvidence

DESCRIPTION

Formalises an Intron with information about why it is a believed Intron. This serves as a parallel object to Bio::EnsEMBL::Intron which you can use to populate values in this field from. They are different objects though due to Intron's non-existence as a DB data structure.

SYNOPSIS

  #Example setups a ISE from the first two Exons
  my ($five_prime_exon, $three_prime_exon) = @{$transcript->get_all_Exons()}[0..1];
  my $intron = Bio::EnsEMBL::Intron->new($five_prime_exon, $three_prime_exon);

METHODS

new

  Arg [-ANALYSIS]     : Bio::EnsEMBL::Analysis The analysis this intron is linked to
  Arg [-START]        : int - start postion of the IntronSupportingEvidence
  Arg [-END]          : int - end position of the IntronSupportingEvidence
  Arg [-STRAND]       : int - strand the IntronSupportingEvidence is on
  Arg [-SLICE]        : Bio::EnsEMBL::Slice - the slice the IntronSupportingEvidence is on
  Arg [-INTRON]       : Bio::EnsEMBL::Intron Intron the evidence is based 
                        on. Useful if you are not specifying the location 
                        parameters as we will take them from this 
  Arg [-HIT_NAME]     : String The name of the hit
  Arg [-SCORE]        : Double The score associated with the supporting evidence
  Arg [-SCORE_TYPE]   : String The type of score we are representing
  Example             : Bio::EnsEMBL::IntronSupportingEvidence->new(
                          -ANALYSIS => $analysis, -INTRON => $intron, 
                          -SCORE => 100, -SCORE_TYPE => 'DEPTH');
  Description         : Returns a new instance of this object
  Returntype          : Bio::EnsEMBL::IntronSupportEvidence
  Exceptions          : Thrown if data is not as requested

set_values_from_Intron

  Arg [1]     : Bio::EnsEMBL::Intron The intron to base this object on
  Example     : $ise->set_values_from_Intron($intron);
  Description : Sets the start, end, strand and slice of this ISE instance
                using values from the given Intron object.
  Returntype  : None
  Exceptions  : Thrown if data is not as requested

is_splice_canonical

  Arg [1]     : Boolean
  Example     : $ise->is_splice_canonical(1);
  Description : Getter/setter for is_splice_canonical. Splice canonical 
                indicates those Introns which have a splice junction which 
                is structured as expected 
  Returntype  : Boolean
  Exceptions  : 

get_Intron

  Arg [1]     : Bio::EnsEMBL::Transcript
  Example     : my $intron = $ise->intron($transcript);
  Description : Provides access to an Intron object by using a given transcript 
                object and its associcated array of Exons.
  Returntype  : Bio::EnsEMBL::Intron
  Exceptions  : None

hit_name

  Arg [1]     : String name of the hit
  Example     : $ise->hit_name('hit');
  Description : Getter/setter for hit name i.e. an identifier for the alignments
  Returntype  : String
  Exceptions  : None

score

  Arg [1]     : Number; the score associated with this feature
  Example     : $ise->score(100);
  Description : Getter/setter for score
  Returntype  : Number
  Exceptions  : None

score_type

  Arg [1]     : String the enum type. Currently only allowed NONE or DEPTH
  Example     : $ise->score_type('DEPTH');
  Description : Gets and sets the type of score this instance represents
  Returntype  : String
  Exceptions  : Thrown if given an unsupported type of data

has_linked_transcripts

  Example     : $ise->has_linked_transcripts();
  Description : Returns true if we have transcripts linked to this ISE
  Returntype  : Boolean
  Exceptions  : Thrown if we do not have an attached adaptor

equals

  Arg [1]     : Bio::EnsEMBL::IntronSupportEvidence Object to compare to
  Example     : $ise->equals($another_ise);
  Description : Asserts if the given IntronSupportEvidence instance was equal to this
  Returntype  : Boolean
  Exceptions  : None

find_previous_Exon

  Arg [1]     : Bio::EnsEMBL::Transcript Transcript to search for the Exons from
  Example     : $ise->find_previous_Exon($transcript);
  Description : Loops through those Exons available from the Transcript and
                attempts to find one which was the 5' flanking exon. If the
                object has already been persisted we will use dbIDs to
                find the Exons
  Returntype  : Bio::EnsEMBL::Exon
  Exceptions  : None

find_next_Exon

  Arg [1]     : Bio::EnsEMBL::Transcript Transcript to search for the Exons from
  Example     : $ise->find_next_Exon($transcript);
  Description : Loops through those Exons available from the Transcript and
                attempts to find one which was the 3' flanking exon. If the
                object has already been persisted we will use dbIDs to
                find the Exons
  Returntype  : Bio::EnsEMBL::Exon
  Exceptions  : None

cpanm Bio::EnsEMBL

perl -MCPAN -e shell
install Bio::EnsEMBL