Skip to content
Snippets Groups Projects
Commit 9282ef78 authored by Ian Longden's avatar Ian Longden
Browse files

added Vega_transcripts as a way to get vega mapping and fixed but which only...

added Vega_transcripts as a way to get vega mapping and fixed but which only allowed one entry in the objext xref table hence reducing the number of matches for Vega
parent e11223c2
No related branches found
No related tags found
No related merge requests found
......@@ -125,13 +125,12 @@ sub run_script {
my $hgnc_sql = 'select tsi.stable_id, x.dbprimary_acc from xref x, object_xref ox , transcript_stable_id tsi, gene g, external_db e, transcript t where t.gene_id = g.gene_id and g.gene_id = ox.ensembl_id and tsi.transcript_id = t.transcript_id and e.external_db_id = x.external_db_id and x.xref_id = ox.xref_id and ox.ensembl_object_type = "Gene" and e.db_name like "HGNC"';
my %ott_to_hgnc;
my %ott_to_enst;
my $sth = $core_dbc->prepare($sql) || die "Could not prepare for core $sql\n";
foreach my $external_db (qw(OTTT shares_CDS_and_UTR_with_OTTT shares_CDS_with_OTTT)){
foreach my $external_db (qw(OTTT shares_CDS_and_UTR_with_OTTT shares_CDS_with_OTTT Vega_transcript)){
$sth->execute($external_db) or croak( $core_dbc->errstr());
while ( my @row = $sth->fetchrow_array() ) {
$ott_to_enst{$row[1]} = $row[0];
......@@ -225,22 +224,20 @@ sub run_script {
next;
}
if(!defined($acc{$hgnc})){
$acc{$hgnc} = 1;
my $version ="";
$line_count++;
my $xref_id = $self->add_xref($hgnc, $version{$hgnc} , $label{$hgnc}||$hgnc , $description{$hgnc}, $source_id, $species_id, "DIRECT");
$acc{$hgnc} = $xref_id;
$xref_count++;
}
$self->add_direct_xref($xref_id, $stable_id, "transcript", "");
$self->add_direct_xref($acc{$hgnc}, $stable_id, "transcript", "");
if(defined($syn_hash->{$hgnc})){
foreach my $syn (@{$syn_hash->{$hgnc}}){
$add_syn_sth->execute($xref_id, $syn);
}
if(defined($syn_hash->{$hgnc})){
foreach my $syn (@{$syn_hash->{$hgnc}}){
$add_syn_sth->execute($acc{$hgnc}, $syn);
}
}
}
}
......
......@@ -135,7 +135,7 @@ sub run_script {
my $sth = $core_dbc->prepare($sql) || die "Could not prepare for core $sql\n";
foreach my $external_db (qw(OTTT shares_CDS_and_UTR_with_OTTT shares_CDS_with_OTTT)){
foreach my $external_db (qw(OTTT shares_CDS_and_UTR_with_OTTT shares_CDS_with_OTTT Vega_transcript)){
$sth->execute($external_db) or croak( $core_dbc->errstr());
while ( my @row = $sth->fetchrow_array() ) {
$ott_to_enst{$row[1]} = $row[0];
......@@ -226,23 +226,23 @@ sub run_script {
next;
}
if(!defined($acc{$hgnc})){
$acc{$hgnc} = 1;
my $version ="";
$line_count++;
my $xref_id = $self->add_xref($hgnc, $version{$hgnc} , $label{$hgnc}||$hgnc , $description{$hgnc}, $source_id, $species_id, "DIRECT");
my $xref_id = $self->add_xref($hgnc, $version{$hgnc} , $label{$hgnc}||$hgnc , $description{$hgnc}, $source_id, $species_id, "DIRECT");
$acc{$hgnc} = $xref_id;
$xref_count++;
$self->add_direct_xref($xref_id, $stable_id, "transcript", "");
if(defined($syn_hash->{$hgnc})){
foreach my $syn (@{$syn_hash->{$hgnc}}){
$add_syn_sth->execute($xref_id, $syn);
}
}
$self->add_direct_xref($acc{$hgnc}, $stable_id, "transcript", "");
if(defined($syn_hash->{$hgnc})){
foreach my $syn (@{$syn_hash->{$hgnc}}){
$add_syn_sth->execute($acc{$hgnc}, $syn);
}
}
}
}
$add_syn_sth->finish;
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment