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Summary

Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::ConfigDependent::TranscriptUtils - utilities for transcript objects which depend on config files

Package variables

Included modules

Inherit

Exporter

Synopsis

  use Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::ConfigDependent::TranscriptUtils qw( method );

  or 

  use Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::ConfigDependent::TranscriptUtils 

  to get all methods

Description

All methods in this class should take a Bio::EnsEMBL::Transcript
object as their first argument.
The methods provided should carry out some standard
functionality for said objects such as printing info, and
cloning and checking phase consistency or splice sites etc

Methods

Methods description

  Arg [1]   : Bio::EnsEMBL::Transcript
  Arg [2]   : int, maximum low complexity
  Function  : calculate how much low complexity a
  transcripts translation has and check if it is above
  the specificed threshold
  Returntype: boolean, 1 for pass 0 for fail
  Exceptions: none
  Example   :

Methods code

sub low_complexity_less_than_maximum {

  my ($transcript, $complexity_threshold) = @_;
  my $peptide = $transcript->translate;
  my $seg = Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Seg->new
    (
     -query => $peptide,
     -analysis => Bio::EnsEMBL::Analysis->new
     (
      -logic_name => 'seg',
      -program_file => 'seg',
     )
    );
  $seg->run;
  my $low_complexity = $seg->get_low_complexity_length;
  logger_info(id($transcript)." has ".$low_complexity.
              " low complexity sequence");
  #print_peptide($transcript);
  #print id($transcript)." has ".$low_complexity." low complexity sequence compared to".
  #  " ".$complexity_threshold."\n";
  if($low_complexity >= $complexity_threshold){
    warn(id($transcript)."'s low ".
            "complexity (".$low_complexity.") is above ".
            "the threshold ".$complexity_threshold.
            "\n");
    return 0;
  }
  return 1;
}

1;

}

General documentation

please send any questions to ensembl-dev@ebi.ac.uk