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Bio::EnsEMBL::Utils::TranscriptAlleles Class Reference

List of all members.


Class Summary

Synopsis

  use Bio::EnsEMBL::Utils::TranscriptAlleles;

  # get the peptide variations caused by a set of Alleles

  %variations = %{
    Bio::EnsEMBL::Utils::TranscriptAlleles::get_all_peptide_variations(
      $transcript, $alleles ) };

Description

This is a utility class which can be used to find consequence type of an
AlleleFeature in a transcript, and to determine the amino acid changes
caused by the AlleleFeature in the Transcript
 

Definition at line 27 of file TranscriptAlleles.pm.

Available Methods

public apply_aa_change ()
public calculate_same_codon ()
public Listref get_all_ConsequenceType ()
public type_variation ()

Method Documentation

public Bio::EnsEMBL::Utils::TranscriptAlleles::apply_aa_change ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Utils::TranscriptAlleles::calculate_same_codon ( )

Undocumented method

Code:
click to view
public Listref Bio::EnsEMBL::Utils::TranscriptAlleles::get_all_ConsequenceType ( )
  Arg [1]    : $transcript the transcript to obtain the peptide variations for
  Arg [2]    : $alleles listref of AlleleFeatures
  Example    : $consequence_types = get_all_ConsequenceType($transcript, \@alleles);
               foreach my $ct (@{$consequence_types}){
                  print "Allele : ", $ct->allele_string, " has a consequence type of :",$ct->type;
                  print " and is affecting the transcript with ",@{$ct->aa_alleles}, "in position ", 
		              $ct->aa_start,"-", $ct->aa_end if (defined $ct->aa_alleles);
		  print "\\n";
	      }
  Description: Takes a list of AlleleFeatures and a Transcritpt, and return a list
                     of ConsequenceType of the alleles in the given Transcript
  Returntype : listref of Bio::EnsEMBL::Variation::ConsequenceType
  Exceptions : none
  Caller     : general
 
Code:
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public Bio::EnsEMBL::Utils::TranscriptAlleles::type_variation ( )

Undocumented method

Code:
click to view

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