Commit 71ad155c authored by Ian Longden's avatar Ian Longden
Browse files

simple sanity check for human and mouse to make sure the core/vega links are...

simple sanity check for human and mouse to make sure the core/vega links are up to date with each other
parent 21b8e763
use Bio::EnsEMBL::Registry;
use Bio::SeqIO;
use strict;
my $reg = "Bio::EnsEMBL::Registry";
my $species = shift;
if($species eq "mouse"){
$reg->load_registry_from_db(
-host => 'ens-staging2',
-user => 'ensro');
}
else{
$reg->load_registry_from_db(
-host => 'ens-staging1',
-user => "ensro");
}
my $core_sa = $reg->get_adaptor($species,"core","slice");
my $vega_sa = $reg->get_adaptor($species,"vega","slice");
if(!defined($core_sa)){
die "Could not get core slice adaptor for $species???";
}
if(!defined($vega_sa)){
die "Could not get vega slice adaptor for $species???";
}
my $sql = 'select tsi.stable_id, x.display_label from xref x, object_xref ox , transcript_stable_id tsi, external_db e where e.external_db_id = x.external_db_id and x.xref_id = ox.xref_id and tsi.transcript_id = ox.ensembl_id and e.db_name like ?';
my $sth = $vega_sa->dbc->prepare($sql) || die "Could not prepare $sql for vega";
my %vega_ott_to_enst;
my %core_ott_to_enst;
$sth->execute("ENST_CDS") or croak( $vega_sa->dbc->errstr() );
while ( my @row = $sth->fetchrow_array() ) {
$vega_ott_to_enst{$row[0]} = $row[1];
}
$sth->execute("ENST_ident") or croak( $vega_sa->dbc->errstr() );
while ( my @row = $sth->fetchrow_array() ) {
$vega_ott_to_enst{$row[0]} = $row[1];
}
print "We have from the vega database ".scalar(%vega_ott_to_enst)." ott to enst entries\n ";
$sth = $core_sa->dbc->prepare($sql) || die "Could not prepare $sql for core ";
$sth->execute("OTTT") or croak( $core_sa->dbc->errstr() );
my $core_extra_count = 0;
while ( my @row = $sth->fetchrow_array() ) {
if(!defined($vega_ott_to_enst{$row[1]})){
$core_extra_count++;
if($core_extra_count < 10){
print "core extra ".$row[1]." ". $row[0]."\n";
}
}
$core_ott_to_enst{$row[1]} = $row[0];
}
print "Core extra tags (OTTT) -> $core_extra_count \n";
$core_extra_count = 0;
$sth = $core_sa->dbc->prepare($sql) || die "Could not prepare $sql for core ";
$sth->execute("shares_CDS_and_UTR_with_OTTT") or croak( $core_sa->dbc->errstr() );
my $core_extra_count = 0;
while ( my @row = $sth->fetchrow_array() ) {
if(!defined($vega_ott_to_enst{$row[1]})){
$core_extra_count++;
if($core_extra_count < 10){
print "core extra ".$row[1]." ". $row[0]."\n";
}
}
$core_ott_to_enst{$row[1]} = $row[0];
}
print "Core extra tags (shares_CDS_and_UTR_with_OTTT) -> $core_extra_count \n";
$core_extra_count = 0;
#$sth = $core_sa->dbc->prepare($sql) || die "Could not prepare $sql for core ";
#$sth->execute("shares_CDS_with_ENST") or croak( $core_sa->dbc->errstr() );
#my $core_extra_count = 0;
#while ( my @row = $sth->fetchrow_array() ) {
# if(!defined($vega_ott_to_enst{$row[1]})){
# $core_extra_count++;
# if($core_extra_count < 10){
# print "core extra ".$row[1]." ". $row[0]."\n";
# }
# }
# $core_ott_to_enst{$row[1]} = $row[0];
#}
#print "Core extra tags (shares_CDS_with_ENST) -> $core_extra_count \n";
#$core_extra_count = 0;
#$sth->execute("Vega_transcript") or croak( $core_sa->dbc->errstr() );
#while ( my @row = $sth->fetchrow_array() ) {
# if(!($row[1] =~ /^OTT/)){
# next;
# }
# if(!defined($vega_ott_to_enst{$row[1]})){
# $core_extra_count++;
# if($core_extra_count < 10){
# print "core extra ".$row[1]." ". $row[0]."\n";
# }
# }
# $core_ott_to_enst{$row[1]} = $row[0];
#}
#print "Core extra tags (Vega_transcript) -> $core_extra_count \n";
$core_extra_count = 0;
$sth->execute("shares_CDS_with_OTTT") or croak( $core_sa->dbc->errstr() );
while ( my @row = $sth->fetchrow_array() ) {
if(!($row[1] =~ /^OTT/)){
next;
}
if(!defined($vega_ott_to_enst{$row[1]})){
$core_extra_count++;
if($core_extra_count < 10){
print "core extra ".$row[1]." ". $row[0]."\n";
}
}
$core_ott_to_enst{$row[1]} = $row[0];
}
print "Core extra tags (shares_CDS_with_OTTT) -> $core_extra_count \n";
$core_extra_count = 0;
print "We have from the core database ".scalar(%core_ott_to_enst)." ott to enst entries\n ";
my $vega_extra_count = 0;
foreach my $key (keys %vega_ott_to_enst){
if(!defined($core_ott_to_enst{$key})){
$vega_extra_count++;
if($vega_extra_count < 10){
print "vega extra ".$key." ". $vega_ott_to_enst{$key}."\n";
}
}
}
print "Vega extra tags -> $vega_extra_count \n";
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