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Bio-EnsEMBL-112.0_54
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/ Bio::EnsEMBL::Utils::TranscriptSelector

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

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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