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Bio-EnsEMBL-113.0.0
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/ Bio::EnsEMBL::IntronSupportingEvidence

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

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

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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