Commit 13e51acd authored by Kieron Taylor's avatar Kieron Taylor 😠
Browse files

Missed the multiple mapping behaviour. Moved code inside the loop.

parent 64e00f69
......@@ -173,30 +173,15 @@ if ($compara) {
}
# Determine if source and target species are both mammals or not: class Mammalia in meta
# table, meaning full GO projection is allowable
# Platypus is not treated as a mammal here, but "is_therian" doesn't mean anything.
my $from_mammal = is_mammal($from_species);
my $to_mammal = is_mammal($to_species);
my %forbidden_terms;
if ($from_mammal && !$to_mammal) {
# Determine GO terms that are not applicable for the present non-mammalian species.
# Consult ontology for list of descendent terms.
# Using a temporary list of general forbidden terms. Presently consists of four GO terms
# recommended by GOA. e.g. "walks on legs" should not be projected to fish
%forbidden_terms = get_ontology_terms('GO:0032501','GO:0007610','GO:0048856','GO:0051704');
# The forbidden_terms list is used in unwanted_go_term();
}
#######
my $from_ga = Bio::EnsEMBL::Registry->get_adaptor($from_species, 'core', 'Gene');
my %projections_by_evidence_type;
my %projections_by_source;
my %forbidden_terms;
my $from_mammal;
my $to_mammal;
foreach my $local_to_species (@to_multi) {
......@@ -205,6 +190,26 @@ foreach my $local_to_species (@to_multi) {
die("Can't get gene adaptor for $to_species - check database connection details; make sure meta table contains the correct species alias\n") if (!$to_ga);
my $to_dbea = Bio::EnsEMBL::Registry->get_adaptor($to_species, 'core', 'DBEntry');
# Determine if source and target species are both mammals or not: class Mammalia in meta
# table, meaning full GO projection is allowable
# Platypus is not treated as a mammal here, but "is_therian" doesn't mean anything.
$from_mammal = is_mammal($from_species);
$to_mammal = is_mammal($to_species);
if ($from_mammal && !$to_mammal) {
# Determine GO terms that are not applicable for the present non-mammalian species.
# Consult ontology for list of descendent terms.
# Using a temporary list of general forbidden terms. Presently consists of four GO terms
# recommended by GOA. e.g. "walks on legs" should not be projected to fish
%forbidden_terms = get_ontology_terms('GO:0032501','GO:0007610','GO:0048856','GO:0051704');
# The forbidden_terms list is used in unwanted_go_term();
}
#######
write_to_projection_db($to_ga->dbc(), $release, $from_species, $from_ga->dbc(), $to_species) unless ($no_database);
backup($to_ga) if (!$no_backup);
......
......@@ -233,6 +233,9 @@ $go_terms{'xenopus'} = [qw(zebrafish)];
# order to run projections in, just in case they are order-sensitive.
my @execution_order = ( 'human', 'mouse', 'rat', 'zebrafish');
# except of course order is irrelevant to the job queue. Consider provisional for when
# someone desires jobs that wait for others to finish.
# ----------------------------------------
# Display names
......
Markdown is supported
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