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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::Utils::TranscriptSelector - Finds canonical transcripts

SYNOPSIS

  my $selector = Bio::EnsEMBL::Utils::TranscriptSelector->new($ccds_dba);
  my $canonical_transcript = $selector->select_canonical_transcript_for_Gene($gene);

DESCRIPTION

  The decision process for choosing a canonical transcript of a given Gene is
  an involved process. This package converts transcript attributes into
  numeric values, sorts the values and returns the favourite transcript.
  
  The canonical order of precedence is as follows:
    longest translation of transcript present in CCDS that is reference sequence
    longest translation of protein-coding transcript
    longest translation of transcript marked nonsense-mediated-decay
    longest translation of any other transcript (premature stop codon translations have an effective length of 0)
    longest non-coding transcript
    first stable ID in alphabetical order
    
  The last condition is to give consistent behaviour when everything is else is equal.
  It selects the "older" stable ID, thus preventing new IDs supplanting old ones that
  remain correct.

new

  Arg [1]    : Optional - CCDS database adaptor - needed for species with CCDS only
  Arg [2]    : Optional - Boolean verbose flag. Turn on to fill your logs
  Description: Constructor
  Returntype : Bio::EnsEMBL::Utils::TranscriptSelector

select_canonical_transcript_for_Gene

 Arg 1      : Bio::EnsEMBL::Gene 
 Example    : $canonical_transcript = $selector->select_canonical_transcript_for_Gene
 Description: Sorts the Transcripts of this Gene into order of suitability,
              and returns the favourite Transcript.
 Returntype : Bio::EnsEMBL::Transcript
 Exceptions : 

encode_transcript

 Arg 1      : Transcript
 Description: Converts a transcript into a list of encoded values for sorting
              Priorities are defined immediately above
              Unimportant biotypes and sources are classed as 'other'
 Returntype : Listref of encoded attributes

sort_into_canonical_order

  Arg 1      : 2D array reference of numerically encoded values
                        0              1        2         3             4                  5               6
              ( [transcript dbID, translates, source , biotype, translation length, transcript length, stable ID],
                ...
              ) 
  Description: see Schwartzian transform for method in the following madness:
               sort the 6-column array by the last 5 columns, then map the first elements
               into a list of dbIDs, now in canonical order. 
  Returntype : Listref of ensembl dbIDs
  Caller     : select_canonical_transcript_for_Gene

check_Ens_trans_against_CCDS

  Arg 1      : Transcript 
  Description: Attempts to find a matching transcript in CCDS by comparing Exon
               composition. Returns true if one is found, or silently ends. 
  Returntype : Boolean
  Caller     : encode_transcript