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Commit ce4d8226 authored by Magali Ruffier's avatar Magali Ruffier
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added method transcript_names_from gene, which assigns uses whatever name has... 

added method transcript_names_from gene, which assigns uses whatever name has been assigned to the gene for all of its transcripts, with an extension number (-201, -202...)
for merged species, this method will be skipped as the official naming module does that already

removed ignore for uniprot_genename with low evidence
uniprot_genename assignments are trusted
parent 894e09d5
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misc-scripts/xref_mapping/XrefMapper/DisplayXrefs.pm
+ 74
− 18
View file @ ce4d8226
......@@ -97,22 +97,6 @@ SELECT object_xref_id
WHERE ox_status = 'DUMP_OUT' AND label REGEXP '^LOC[[:digit:]]+'
LOCP
$ignore{'Uniprot_genename'} =<<IEG;
SELECT DISTINCT ox.object_xref_id
FROM object_xref ox, dependent_xref dx,
xref xmas, xref xdep,
source smas, source sdep
WHERE ox.xref_id = dx.dependent_xref_id AND
dx.dependent_xref_id = xdep.xref_id AND
dx.master_xref_id = xmas.xref_id AND
xmas.source_id = smas.source_id AND
xdep.source_id = sdep.source_id AND
smas.name like "Uniprot/SPTREMBL" AND
smas.status = "LOWEVIDENCE" AND
sdep.name like "Uniprot_genename" AND
ox.ox_status = "DUMP_OUT"
IEG
return [\@list,\%ignore];
}
......@@ -171,6 +155,11 @@ sub genes_and_transcripts_attributes_set{
else{
$self->set_display_xrefs();
}
if ($self->mapper->can("transcript_names_from_gene")) {
$self->mapper->transcript_names_from_gene();
} else {
$self->transcript_names_from_gene();
}
my $sth_stat = $self->xref->dbc->prepare("insert into process_status (status, date) values('display_xref_done',now())");
$sth_stat->execute();
$sth_stat->finish;
......@@ -737,6 +726,72 @@ DXS
}
sub transcript_names_from_gene {
my $self = shift;
print "Assigning transcript names from gene names\n" if ($self->verbose);
my $reset_sth = $self->core->dbc->prepare("UPDATE transcript SET display_xref_id = null");
$reset_sth->execute();
$reset_sth->finish;
my $xref_id_sth = $self->core->dbc->prepare("SELECT max(xref_id) FROM xref");
my $ox_id_sth = $self->core->dbc->prepare("SELECT max(object_xref_id) FROM object_xref");
my $del_xref_sth = $self->core->dbc->prepare("DELETE FROM xref WHERE display_label REGEXP '-2[0-9]{2}\$'");
my $reuse_xref_sth = $self->core->dbc->prepare("SELECT xref_id FROM xref x WHERE external_db_id = ? AND display_label = ? AND version = 0 AND description = ? AND info_type = 'MISC' AND info_text = 'via gene name'");
my $del_ox_sth = $self->core->dbc->prepare("DELETE ox FROM object_xref ox LEFT JOIN xref x ON x.xref_id = ox.xref_id WHERE isnull(x.xref_id)");
my $ins_xref_sth = $self->core->dbc->prepare("INSERT into xref (xref_id, external_db_id, dbprimary_acc, display_label, version, description, info_type, info_text) values(?, ?, ?, ?, 0, ?, 'MISC', 'via gene name')");
my $ins_ox_sth = $self->core->dbc->prepare("INSERT into object_xref (object_xref_id, ensembl_id, ensembl_object_type, xref_id) values(?, ?, 'Transcript', ?)");
my $update_tran_sth = $self->core->dbc->prepare("UPDATE transcript t SET t.display_xref_id= ? WHERE t.transcript_id=?");
my $get_genes = $self->core->dbc->prepare("SELECT g.gene_id, x.external_db_id, x.dbprimary_acc, x.display_label, x.description FROM gene g, xref x where g.display_xref_id = x.xref_id");
my $get_transcripts = $self->core->dbc->prepare("SELECT transcript_id FROM transcript WHERE gene_id = ? ORDER BY seq_region_start, seq_region_end");
$get_genes->execute();
my ($gene_id, $external_db_id, $acc, $label, $description, $transcript_id, $xref_id, $ox_id, $ext, $reuse_xref_id);
$get_genes->bind_columns(\$gene_id, \$external_db_id, \$acc, \$label, \$description);
$xref_id_sth->execute();
$xref_id_sth->bind_columns(\$xref_id);
$xref_id_sth->fetch();
$ox_id_sth->execute();
$ox_id_sth->bind_columns(\$ox_id);
$ox_id_sth->fetch();
$del_xref_sth->execute();
while ($get_genes->fetch()) {
$ext = '201';
$get_transcripts->execute($gene_id);
$get_transcripts->bind_columns(\$transcript_id);
while ($get_transcripts->fetch) {
$xref_id++;
$ox_id++;
$reuse_xref_sth->execute($external_db_id, $label . '-' . $ext, $description);
$reuse_xref_sth->bind_columns(\$reuse_xref_id);
if ($reuse_xref_sth->fetch()) {
$ins_ox_sth->execute($ox_id, $transcript_id, $reuse_xref_id);
$update_tran_sth->execute($reuse_xref_id, $transcript_id);
} else {
$ins_xref_sth->execute($xref_id, $external_db_id, $acc. "-" . $ext, $label . "-" . $ext, $description);
$ins_ox_sth->execute($ox_id, $transcript_id, $xref_id);
$update_tran_sth->execute($xref_id, $transcript_id);
}
$ext++;
}
}
$del_xref_sth->finish();
$del_ox_sth->execute();
$del_ox_sth->finish();
$reuse_xref_sth->finish();
$xref_id_sth->finish();
$ox_id_sth->finish();
$get_genes->finish();
$get_transcripts->finish();
$ins_xref_sth->finish();
$ins_ox_sth->finish();
$update_tran_sth->finish();
}
# Remove after sure everything is cool
sub check_label{
my $self = shift;
......@@ -793,6 +848,7 @@ sub set_source_id_to_external_name {
sub set_gene_descriptions{
my $self = shift;
my $only_those_not_set = shift || 0;
my $sql;
my $update_gene_desc_sth = $self->core->dbc->prepare("UPDATE gene SET description = ? where gene_id = ?");
......@@ -805,7 +861,7 @@ sub set_gene_descriptions{
my %ignore;
if($only_those_not_set){
print "Only setting those not already set\n";
my $sql = "select internal_id from gene_stable_id where desc_set = 1";
$sql = "select internal_id from gene_stable_id where desc_set = 1";
my $sql_sth = $self->xref->dbc->prepare($sql);
$sql_sth->execute;
my $id;
......@@ -821,7 +877,7 @@ sub set_gene_descriptions{
##########################################
my %name_to_external_name;
my $sql = "select external_db_id, db_name, db_display_name from external_db";
$sql = "select external_db_id, db_name, db_display_name from external_db";
my $sth = $self->core->dbc->prepare($sql);
$sth->execute();
my ($id, $name, $display_name);
......
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