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#!/usr/bin/env perl
=head1 SUMMARY
This script is intended to highlight issues with an assembly mapping, by inspecting
the equivalent sequence for each exon. The resulting log is grep-suitable and keyed
for severity.
=head1 SYNOPSIS
perl exon_conservation_check.pl <many arguments>
--dbname, db_name=NAME database name NAME
--host, --dbhost, --db_host=HOST database host HOST
--port, --dbport, --db_port=PORT database port PORT
--user, --dbuser, --db_user=USER database username USER
--pass, --dbpass, --db_pass=PASS database passwort PASS
--assembly=ASSEMBLY assembly version ASSEMBLY
--altdbname=NAME alternative database NAME
--altassembly=ASSEMBLY alternative assembly version ASSEMBLY
Optional options
--logfile, --log=FILE log to FILE (default: *STDOUT)
--logpath=PATH write logfile to PATH (default: .)
=cut
use strict;
use warnings;
use FindBin qw($Bin);
use lib "$Bin";
use AssemblyMapper::Support;
use Bio::EnsEMBL::Utils::Exception qw( throw );
use Pod::Usage;
use Bio::EnsEMBL::DBSQL::OntologyDBAdaptor;
use Bio::EnsEMBL::Utils::BiotypeMapper;
my $support = AssemblyMapper::Support->new(
);
unless ($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("!! = Very bad, %% = Somewhat bad, ?? = No mapping, might be bad\n");
my $ok = $support->iterate_chromosomes(
prev_stage => '40-fix_overlaps',
this_stage => '41-exon-conservation',
worker => \&compare_exons,
);
$support->log_stamped("Finished.\n");
sub compare_exons {
my ($asp) = @_;
my $R_chr = $asp->ref_chr;
my $A_chr = $asp->alt_chr;
my $R_slice = $asp->ref_slice;
my $A_slice = $asp->alt_slice;
my $old_exons = $A_slice->get_all_Exons;
while (my $old_exon = shift @$old_exons) {
# Establish equivalent locations on old and new DBs
my $coord_system = $old_exon->slice->coord_system;
my $new_slice = $R_slice->adaptor->fetch_by_region(
$coord_system->name,
$old_exon->seq_region_name,
$old_exon->start,
$old_exon->end,
$old_exon->strand,
$coord_system->version
);
# make a shadow exon for the new database
my $shadow_exon = new Bio::EnsEMBL::Feature (
-start => $old_exon->seq_region_start,
-end => $old_exon->seq_region_end,
-strand => $old_exon->strand,
-slice => $new_slice,
);
# project new exon to new assembly
my $projected_exon = $shadow_exon->transform($A_slice->coord_system->name,$A_slice->coord_system->version,$R_slice);
# Note that Anacode database naming patterns interfere with normal Registry adaptor fetching,
# hence we must go around the houses somewhat when looking for the appropriate source gene.
#warn "!! fetching gene adaptor ".$old_exon->adaptor->species.":".$old_exon->adaptor->dbc->dbname."Gene";
my $old_gene_adaptor = $old_exon->adaptor->db->get_GeneAdaptor();
my $gene_list = $old_gene_adaptor->fetch_nearest_Gene_by_Feature($old_exon, undef, undef);
if (scalar(@$gene_list) >1) {warn "Encountered many possible genes for the exon."}
my $parent_gene = $gene_list->[0];
# compare sequences if a projection exists
if ($projected_exon && $projected_exon->seq ne $old_exon->seq) {
# Now we have a problem - the feature's sequence was not conserved between assemblies.
# Determine severity of the problem
my $group_list = $biotype_mapper->belongs_to_groups($parent_gene->biotype);
my $warned = 0;
foreach my $group (@$group_list) {
if ($group eq 'protein_coding') {
# Maximum badness.
$support->log("!! ".$parent_gene->stable_id." - ".$old_exon->stable_id.
" projected - ".$projected_exon->start.":".$projected_exon->end."\n"
);
$warned = 1;
}
}
unless ($warned) {
# Middle badness.
$support->log("%% ".$parent_gene->stable_id." - ".$old_exon->stable_id."\n");
}
}
if (! $projected_exon) {
# No projection possibly bad news
$support->log("?? ".$parent_gene->stable_id." - ".$old_exon->stable_id."\n");
}
}
}