LICENSE

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

     http://www.apache.org/licenses/LICENSE-2.0

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CONTACT

  Please email comments or questions to the public Ensembl
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  Questions may also be sent to the Ensembl help desk at
  <http://www.ensembl.org/Help/Contact>.

NAME

Bio::EnsEMBL::CDS - Object representing a CDS

SYNOPSIS

  use Bio::EnsEMBL::CDS;

  $feature = Bio::EnsEMBL::CDS->new(
    -start         => 100,
    -end           => 220,
    -strand        => -1,
    -slice         => $slice,
    -phase         => 1,
    -transcript    => $transcript
  );

DESCRIPTION

This is a CDS feature within the Ensembl CDS. It represents the coding regions of a transcript.

METHODS

new

  Arg [...]  : Named arguments passed to superclass
  Example    : $feature = Bio::EnsEMBL::CDS->new
                        (-start   => 1,
                         -end     => 100,
                         -strand  => 1,
                         -slice   => $slice,
                         -dbID    => 10,
                         -transcript  => $transcript,
                         -phase   => 1);
  Description: Constructs a new Bio::EnsEMBL::CDS.
  Returntype : Bio::EnsEMBL::CDS
  Exceptions : Thrown on invalid -SLICE, -STRAND arguments
  Caller     : general, subclass constructors
  Status     : Stable

transcript

  Arg [1]    : (optional) Bio::EnsEMBL::Transcript
  Example    : $transcript = $cds->transcript();
  Description: Getter/Setter for the transcript associated with this
               CDS.
  Returntype : Bio::EnsEMBL::Transcript
  Exceptions : none
  Caller     : general
  Status     : Stable

translation

    Description: Fetch the translation associated with
                 this transcript, if it exists. Return undef
                 if there is no translation, ie. a pseudogene
    Returntype : Bio::EnsEMBL::Translation or undef
    Caller     : general
    Status     : Stable

seq_region_start

  Arg [1]    : (optional) string $seq_region_start
  Example    : $seq_region_start = $cds->seq_region_start();
  Description: Getter/Setter for the seq_region_start for this CDS.
               Overwrite default method from Feature as CDS does not have
               a table
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable

seq_region_end

  Arg [1]    : (optional) string $seq_region_end
  Example    : $seq_region_end = $cds->seq_region_end();
  Description: Getter/Setter for the seq_region_end for this CDS.
               Overwrite default method from Feature as CDS does not have
               a table
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable

get_Gene

  Description: Get the gene associated with the ExonTranscript,
               if a transcript has been set
  Returntype : Bio::EnsEMBL::Gene or undef
  Exceptions : none
  Caller     : general
  Status     : Stable

translation_id

  Arg [1]    : (optional) string $translation_id
  Example    : $translation_id = $cds->translation_id();
  Description: Getter/Setter for the stable_id for the translation
               associated with this CDS.
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable

phase

  Arg [1]    : (optional) string $phase
  Example    : print $cds->phase();
  Description: This method returns an integer that describes
               the phase of the coding feature
  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable

summary_as_hash

  Example    : my $hash = $cds->summary_as_hash();
  Description: Generates a HashRef compatible with GFFSerializer. Adds
               Parent, source and phase to the basic feature hash
  Returntype : Hash
  Exceptions : none
  Caller     : general
  Status     : Stable

cpanm Bio::EnsEMBL

perl -MCPAN -e shell
install Bio::EnsEMBL