From 13e51acda7ad4f96aa620c0d87dc47f549a20de2 Mon Sep 17 00:00:00 2001
From: Kieron Taylor <ktaylor@ebi.ac.uk>
Date: Fri, 15 Jun 2012 13:38:14 +0000
Subject: [PATCH] Missed the multiple mapping behaviour. Moved code inside the
loop.
---
.../xref_projection/project_display_xrefs.pl | 43 +++++++++++--------
.../xref_projection/submit_projections.pl | 3 ++
2 files changed, 27 insertions(+), 19 deletions(-)
diff --git a/misc-scripts/xref_projection/project_display_xrefs.pl b/misc-scripts/xref_projection/project_display_xrefs.pl
index 5a9251e298..03cfb19eaf 100644
--- a/misc-scripts/xref_projection/project_display_xrefs.pl
+++ b/misc-scripts/xref_projection/project_display_xrefs.pl
@@ -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);
diff --git a/misc-scripts/xref_projection/submit_projections.pl b/misc-scripts/xref_projection/submit_projections.pl
index b3718b7b87..2ef7d93dc9 100644
--- a/misc-scripts/xref_projection/submit_projections.pl
+++ b/misc-scripts/xref_projection/submit_projections.pl
@@ -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
--
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