Commit 086f1662 authored by Arnaud Kerhornou's avatar Arnaud Kerhornou
Browse files

Attach SGD mapping to translation object rather than transcript objects, so GO...

Attach SGD mapping to translation object rather than transcript objects, so GO mapping get also attach to translations. Commented STDERR statements;
parent 45ff6411
......@@ -27,7 +27,8 @@ sub run {
my $file = @{$files}[0];
my $gene_source_id = $self->get_source_id_for_source_name("SGD_GENE");
my $transcript_source_id = $self->get_source_id_for_source_name("SGD_TRANSCRIPT");
#my $transcript_source_id = $self->get_source_id_for_source_name("SGD_TRANSCRIPT");
my $translation_source_id = $self->get_source_id_for_source_name("SGD_TRANSLATION");
my $sgd_io = $self->get_filehandle($file);
......@@ -52,9 +53,9 @@ sub run {
if ($biotype =~ /ORF|.+RNA|transposable_element_gene|pseudogene/) {
if ($verbose) {
print STDERR "parsing line for biotype, $biotype\n";
print STDERR "sgd_id, biotype, status, orf_name, locus_name, alias_name, $sgd_id, $biotype, $status, $orf_name, $locus_name, $alias_name\n";
print STDERR "desc: $desc\n";
#print STDERR "parsing line for biotype, $biotype\n";
#print STDERR "sgd_id, biotype, status, orf_name, locus_name, alias_name, $sgd_id, $biotype, $status, $orf_name, $locus_name, $alias_name\n";
#print STDERR "desc: $desc\n";
}
if (!defined $locus_name || ($locus_name eq "")) {
......@@ -64,7 +65,7 @@ sub run {
}
else {
if ($verbose) {
print STDERR "assigning the orf_name as the locus_name(ie the gene_name)\n";
#print STDERR "assigning the orf_name as the locus_name(ie the gene_name)\n";
}
$locus_name = $orf_name;
}
......@@ -78,23 +79,21 @@ sub run {
source_id => $gene_source_id,
species_id => $species_id,
info_type => "DIRECT"} );
$self->add_direct_xref($gene_xref_id, $orf_name, "Gene", "DIRECT");
my $transcript_xref_id = $self->add_xref({ acc => $sgd_id,
label => $locus_name,
desc => $desc,
source_id => $transcript_source_id,
species_id => $species_id,
info_type => "DIRECT"} );
$self->add_direct_xref($transcript_xref_id, $orf_name, "Transcript", "DIRECT");
my $translation_xref_id = $self->add_xref({ acc => $sgd_id,
label => $locus_name,
desc => $desc,
source_id => $translation_source_id,
species_id => $species_id,
info_type => "DIRECT"} );
$self->add_direct_xref($translation_xref_id, $orf_name, "Translation", "DIRECT");
$xref_count++;
foreach my $synonym (@syn){
if ($verbose) {
print STDERR "adding synonym, $synonym\n";
# print STDERR "adding synonym, $synonym\n";
}
$self->add_to_syn($sgd_id, $gene_source_id, $synonym, $species_id);
$syn_count++;
......@@ -103,7 +102,7 @@ sub run {
}
else {
if ($verbose) {
print STDERR "filtering biotype, $biotype\n";
#print STDERR "filtering biotype, $biotype\n";
}
}
}
......
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