exon_conservation_check.pl

#!/usr/bin/env perl

use strict;
use warnings;

use FindBin qw($Bin);
use lib "$Bin";

#Bring in pipeline as well for their helpers
use lib "$Bin/../../../ensembl-pipeline/scripts/Finished/assembly";
use lib "$Bin/../../../ensembl-analysis/modules";

#runtime include normally
require AssemblyMapper::Support;
use Bio::EnsEMBL::Utils::Exception qw( throw );
use Pod::Usage;
use Bio::EnsEMBL::DBSQL::OntologyDBAdaptor;
use Bio::EnsEMBL::Utils::BiotypeMapper;

#Genebuilder utils
require Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::TranscriptUtils;
Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::TranscriptUtils->import(qw/clone_Transcript/);
require Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::ExonUtils;
Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::ExonUtils->import(qw/clone_Exon/);

my $support = AssemblyMapper::Support->new(
  extra_options => [
    qw/
      check_transcripts!
      check_exons!
      /
  ]
);
unless ($support->parse_arguments(@_)) {
  warn $support->error if $support->error;
  pod2usage(1);
}
$support->connect_dbs;

my $onto_db_adaptor = Bio::EnsEMBL::DBSQL::OntologyDBAdaptor->new(
  -DBNAME => $support->ref_dba->dbc->dbname,
  -DBCONN => $support->ref_dba->dbc,
);
my $biotype_mapper = new Bio::EnsEMBL::Utils::BiotypeMapper($onto_db_adaptor);

$support->log_stamped("Beginning analysis.\n");
$support->log("EXON KEY       : !! = Very bad (pc mismatch), %% = Somewhat bad (mismatch), ?? = No mapping, might be bad\n");
$support->log("TRANSCRIPT KEY : @@ = Very bad (pc translation mismatch),  = Very bad (pc transcript mismatch), ** = Somewhat bad (mismatch), XX = No mapping, might be bad\n");


$support->iterate_chromosomes(
  prev_stage => '40-fix_overlaps',
  this_stage => '41-conservation',
  worker     => \&compare,
);

$support->log_stamped("Finished.\n");

sub compare {
  my ($asp) = @_;
  if ($support->param('check_exons')) {
    compare_exons($asp);
  }
  if ($support->param('check_transcripts')) {
    compare_transcripts($asp);
  }
  return;
}

sub compare_exons {