From 8396a2619aad2bca33a9f0d2093862105ada217b Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Fri, 29 Jun 2007 14:05:46 +0000
Subject: [PATCH] Don't project if a GO term with the same accession, but IEA
evidence code, exists, as this will lead to duplicates when the projected
term has its evidence code changed to IEA after projection
---
.../xref_projection/project_display_xrefs.pl | 21 +++++++++++++++++--
1 file changed, 19 insertions(+), 2 deletions(-)
diff --git a/misc-scripts/xref_projection/project_display_xrefs.pl b/misc-scripts/xref_projection/project_display_xrefs.pl
index 98f2371358..4c28c5907c 100644
--- a/misc-scripts/xref_projection/project_display_xrefs.pl
+++ b/misc-scripts/xref_projection/project_display_xrefs.pl
@@ -355,6 +355,10 @@ sub go_xref_exists {
foreach my $xref (@{$to_go_xrefs}) {
+# if ($dbEntry->primary_id() eq "GO:0005515" && $xref->primary_id() eq "GO:0005515") {
+# print $xref->dbname() . " " . $xref->primary_id() . " " . join("", @{$xref->get_all_linkage_types()}) . " -> " . $dbEntry->dbname() . " " . $dbEntry->primary_id() . " " . join("", @{$dbEntry->get_all_linkage_types()}) . "\n";
+# }
+
next if (ref($dbEntry) ne "Bio::EnsEMBL::GoXref" || ref($xref) ne "Bio::EnsEMBL::GoXref");
if ($xref->dbname() eq $dbEntry->dbname() &&
@@ -363,6 +367,14 @@ sub go_xref_exists {
return 1;
}
+ # if a GO term with the same accession, but IEA evidence code, exists, also don't project, as this
+ # will lead to duplicates when the projected term has its evidence code changed to IEA after projection
+ if ($xref->primary_id() eq $dbEntry->primary_id()) {
+ foreach my $evidence_code (@{$xref->get_all_linkage_types()}) {
+ return 1 if ($evidence_code eq "IEA");
+ }
+ }
+
}
return 0;
@@ -384,8 +396,8 @@ sub print_stats {
$count = count_rows($to_ga, "SELECT COUNT(*) FROM gene g, xref x WHERE g.display_xref_id=x.xref_id AND g.display_xref_id IS NOT NULL AND (x.info_type != 'PROJECTION' || x.info_type IS NULL)");
printf("Gene names: unprojected %d (%3.1f\%)" , $count, (100 * $count / $total_genes));
- $count = count_rows($to_ga, "SELECT COUNT(*) FROM gene g, xref x WHERE g.display_xref_id=x.xref_id AND x.info_type='PROJECTION'");
- printf(" projected %d (%3.1f\%)" , $count, (100 * $count / $total_genes));
+ my $projected = count_rows($to_ga, "SELECT COUNT(*) FROM gene g, xref x WHERE g.display_xref_id=x.xref_id AND x.info_type='PROJECTION'");
+ printf(" projected %d (%3.1f\%)" , $projected, (100 * $projected / $total_genes));
$count = count_rows($to_ga, "SELECT COUNT(*) FROM gene g, xref x, external_db e WHERE g.display_xref_id=x.xref_id AND x.external_db_id=e.external_db_id AND e.db_name IN ('RefSeq_dna_predicted', 'RefSeq_peptide_predicted')");
printf(" predicted %d (%3.1f\%)" , $count, (100 * $count / $total_genes));
@@ -393,6 +405,11 @@ sub print_stats {
$count = count_rows($to_ga, "SELECT COUNT(*) FROM gene g WHERE display_xref_id IS NOT NULL");
printf(" total genes with names %d (%3.1f\%)\n" , $count, (100 * $count / $total_genes));
+ if ($projected > 0) {
+ my $one2many = count_rows($to_ga, "SELECT COUNT(*) FROM gene g, xref x WHERE g.display_xref_id=x.xref_id AND x.info_type='PROJECTION' AND x.display_label LIKE '%(% of %)%'");
+ my $one2one = $projected - $one2many;
+ printf("Of the %d projected genes, %d (%3.1f\%) are from one-one mappings, %d (%3.1f\%) from one-many mappings\n", $projected, $one2one, (100 * $one2one/$projected), $one2many, (100 * $one2many / $projected));
+ }
}
if ($go_terms) {
--
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