Commit c7d87edf authored by Magali Ruffier's avatar Magali Ruffier
Browse files

removed deprecated source RefSeq_dna

parent 888851f0
......@@ -29,8 +29,6 @@ sub run {
my $peptide_source_id =
$self->get_source_id_for_source_name('RefSeq_peptide');
my $dna_source_id =
$self->get_source_id_for_source_name('RefSeq_dna');
my $mrna_source_id =
$self->get_source_id_for_source_name('RefSeq_mRNA','refseq');
my $ncrna_source_id =
......@@ -45,7 +43,6 @@ sub run {
if($verbose){
print "RefSeq_peptide source ID = $peptide_source_id\n";
print "RefSeq_dna source ID = $dna_source_id\n";
print "RefSeq_mRNA source ID = $mrna_source_id\n";
print "RefSeq_ncRNA source ID = $ncrna_source_id\n";
print "RefSeq_peptide_predicted source ID = $pred_peptide_source_id\n";
......@@ -58,7 +55,6 @@ sub run {
my $xrefs =
$self->create_xrefs( $peptide_source_id,
$dna_source_id,
$pred_peptide_source_id,
$mrna_source_id, $ncrna_source_id,
$pred_mrna_source_id, $pred_ncrna_source_id,
......@@ -94,7 +90,6 @@ sub run {
$self->set_release( $source_id, $release );
$self->set_release( $peptide_source_id, $release );
$self->set_release( $dna_source_id, $release );
$self->set_release( $mrna_source_id, $release );
$self->set_release( $ncrna_source_id, $release );
$self->set_release( $pred_peptide_source_id, $release );
......@@ -114,7 +109,7 @@ sub run {
# Slightly different formats
sub create_xrefs {
my ($self, $peptide_source_id, $dna_source_id, $pred_peptide_source_id,
my ($self, $peptide_source_id, $pred_peptide_source_id,
$mrna_source_id, $ncrna_source_id,
$pred_mrna_source_id, $pred_ncrna_source_id, $file, $species_id ) = @_;
......@@ -175,8 +170,6 @@ sub create_xrefs {
$source_id = $mrna_source_id;
} elsif( $acc =~ /^NR/) {
$source_id = $ncrna_source_id;
} else {
$source_id = $dna_source_id;
}
$xref->{SOURCE_ID} = $source_id;
......
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