Skip to content
Snippets Groups Projects
Commit b06256ef authored by Glenn Proctor's avatar Glenn Proctor
Browse files

Added stats 

Now upload by default, unless -print is specified.
parent f30751ea
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
misc-scripts/xref_projection/project_display_xrefs.pl
+ 52
− 41
View file @ b06256ef
......@@ -11,7 +11,7 @@ use Bio::EnsEMBL::DBSQL::GeneAdaptor;
my $method_link_type = "ENSEMBL_ORTHOLOGUES";
my ($conf, $compara, $from_species, @to_multi, $print, $store, $names, $go_terms);
my ($conf, $compara, $from_species, @to_multi, $print, $names, $go_terms);
GetOptions('conf=s' => \$conf,
'compara=s' => \$compara,
......@@ -21,7 +21,6 @@ GetOptions('conf=s' => \$conf,
'names' => \$names,
'go_terms' => \$go_terms,
'print' => \$print,
'store' => \$store,
'help' => sub { usage(); exit(0); });
@to_multi = split(/,/,join(',',@to_multi));
......@@ -52,9 +51,6 @@ my $ma = Bio::EnsEMBL::Registry->get_adaptor($compara, 'compara', 'Member');
my $from_ga = Bio::EnsEMBL::Registry->get_adaptor($from_species, 'core', 'Gene');
my $changed_names = 0;
my $changed_go_xrefs = 0;
foreach my $to_species (@to_multi) {
my $str = "gene display_xrefs and descriptions" if ($names);
......@@ -68,9 +64,10 @@ foreach my $to_species (@to_multi) {
my $mlss = $mlssa->fetch_by_method_link_type_registry_aliases($method_link_type, [$from_species, $to_species]);
print "$to_species, before projection: \n" . &get_stats($to_ga);
# Get all genes, find homologies, set xrefs
foreach my $gene_id (@{$from_ga->list_dbIDs}) {
my $gene = $from_ga->fetch_by_dbID($gene_id);
......@@ -85,8 +82,7 @@ foreach my $to_species (@to_multi) {
}
print "Projected $changed_names gene names, out of a total of " . scalar(@{$from_ga->list_dbIDs}) . "\n" if ($names);
print "Projected $changed_go_xrefs GO terms\n" if ($go_terms);
print "$to_species, after projection: \n" . &get_stats($to_ga);
}
......@@ -97,8 +93,6 @@ sub project_homologies() {
my ($homologies, $to_ga, $to_dbea, $names, $go_terms, $ma) = @_;
my $changed = 0;
foreach my $homology (@{$homologies}) {
my @mas = @{$homology->get_all_Member_Attribute};
......@@ -108,28 +102,18 @@ sub project_homologies() {
# ----------------------------------------
# Display names and descriptions
if ($names) {
$changed_names += project_display_names($to_ga, $to_dbea, $ma, $from_member, $to_member);
}
project_display_names($to_ga, $to_dbea, $ma, $from_member, $to_member) if ($names);
# ----------------------------------------
# GO terms
if ($go_terms) {
$changed_go_xrefs += project_go_terms($to_ga, $to_dbea, $ma, $from_attribute, $to_attribute);
}
project_go_terms($to_ga, $to_dbea, $ma, $from_attribute, $to_attribute) if ($go_terms);
# ----------------------------------------
}
return $changed;
}
# --------------------------------------------------------------------------------
......@@ -140,8 +124,6 @@ sub project_display_names {
my $to_gene = $to_ga->fetch_by_stable_id($to_member->stable_id());
my $changed = 0;
# if no display name set, do the projection
if (!$to_gene->external_name()) {
......@@ -165,19 +147,15 @@ sub project_display_names {
print $to_gene->stable_id() . " --> " . $dbEntry->display_id() . "\n" if ($print);
# store - need to add the DBEntry and also update the gene display xref id
if ($store) {
if (!$print) {
$to_dbea->store($dbEntry, $to_gene, 'Gene');
$to_ga->update($to_gene);
}
$changed++;
}
}
return $changed;
}
# --------------------------------------------------------------------------------
......@@ -186,8 +164,6 @@ sub project_go_terms {
my ($to_ga, $to_dbea, $ma, $from_attribute, $to_attribute) = @_;
my $changed = 0;
# GO xrefs are linked to translations, not genes
my $from_translation = $ma->fetch_by_dbID($from_attribute->peptide_member_id())->get_Translation();
my $to_translation = $ma->fetch_by_dbID($to_attribute->peptide_member_id())->get_Translation();
......@@ -199,7 +175,9 @@ sub project_go_terms {
next if $dbEntry->dbname() ne "GO";
# only project GO terms with non-IEA evidence codes
next if ($dbEntry->linkage_type() eq "IEA");
foreach my $et (@{$dbEntry->get_all_linkage_types}){
next if ($et eq "IEA");
}
# check that each from GO term isn't already projected
next if go_xref_exists($dbEntry, $to_go_xrefs);
......@@ -216,14 +194,10 @@ sub project_go_terms {
print $to_translation->stable_id() . " --> " . $dbEntry->display_id() . "\n" if ($print);
$to_dbea->store($dbEntry, $to_translation, 'Translation') if ($store);
$changed++;
$to_dbea->store($dbEntry, $to_translation, 'Translation') if (!$print);
}
return $changed;
}
# --------------------------------------------------------------------------------
......@@ -247,6 +221,45 @@ sub go_xref_exists {
# ----------------------------------------------------------------------
sub get_stats {
my ($to_ga) = @_;
my $str = "Gene names: total ";
$str .= &count_rows($to_ga, "SELECT COUNT(*) FROM gene g WHERE g.display_xref_id IS NOT NULL");
$str .= " projected ";
$str .= &count_rows($to_ga, "SELECT COUNT(*) FROM gene g, xref x WHERE g.display_xref_id=x.xref_id AND x.display_label LIKE '%[from%'");
$str .= "\nGO xrefs: total ";
$str .= &count_rows($to_ga, "SELECT COUNT(*) FROM xref x, external_db e WHERE e.external_db_id=x.external_db_id AND e.db_name='GO'");
$str .= " projected ";
$str .= &count_rows($to_ga, "SELECT COUNT(*) FROM xref x, external_db e WHERE e.external_db_id=x.external_db_id AND e.db_name='GO' AND x.display_label LIKE '%[from%'");
$str .= "\n";
return $str;
}
# ----------------------------------------------------------------------
sub count_rows {
my ($adaptor, $sql) = @_;
my $sth = $adaptor->dbc->prepare($sql);
$sth->execute();
return ($sth->fetchrow_array())[0];
}
# ----------------------------------------------------------------------
sub usage {
print << "EOF";
......@@ -257,7 +270,7 @@ sub usage {
perl project_display_xrefs.pl {options}
Options ([..] indcicates optional):
Options ([..] indicates optional):
[--conf filepath] the Bio::EnsEMBL::Registry configuration file. If none
is given, the one set in ENSEMBL_REGISTRY will be used
......@@ -279,9 +292,7 @@ sub usage {
--go_terms Project GO terms.
[--print] Print details of projection
[--store] Upload projections to target databases
[--print] Print details of projection only, don't store in database
[--method] Type of homologs (default: ENSEMBL_ORTHOLOGUES)
......
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