From a7720235ba33cdc5eb7bf0f23bcc822d6d3c44ea Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Wed, 27 May 2009 12:49:00 +0000
Subject: [PATCH] Use the translations of the _canonical_ transcripts of the
source and target genes as the source of GO terms to project, rather than
simply the longest translation in each, which was a bit arbitrary and didn't
alway work.
Also make the print option for GO term projection a bit more verbose - aids debugging.
---
.../xref_projection/project_display_xrefs.pl | 33 ++++++++-----------
1 file changed, 13 insertions(+), 20 deletions(-)
diff --git a/misc-scripts/xref_projection/project_display_xrefs.pl b/misc-scripts/xref_projection/project_display_xrefs.pl
index 40b9aa847e..4e05ad3c98 100644
--- a/misc-scripts/xref_projection/project_display_xrefs.pl
+++ b/misc-scripts/xref_projection/project_display_xrefs.pl
@@ -346,12 +346,11 @@ sub project_go_terms {
my ($to_ga, $to_dbea, $ma, $from_gene, $to_gene) = @_;
# GO xrefs are linked to translations, not genes
- # For historical reasons we only project GO terms between the longest translations of each gene
- # TODO - consider projecting *all* GO terms from *all* source translations to one translation of target?
- # TODO - getting the translation's length seem to involve lots of database accesses - some way to do
- # this quicker? Via SQL?
- my $from_translation = get_longest_translation($from_gene);
- my $to_translation = get_longest_translation($to_gene);
+ # Project GO terms between the translations of the canonical transcripts of each gene
+ my $from_translation = get_canonical_translation($from_gene);
+ my $to_translation = get_canonical_translation($to_gene);
+
+ return if (!$from_translation || !$to_translation);
my $from_latin_species = ucfirst(Bio::EnsEMBL::Registry->get_alias($from_species));
@@ -384,7 +383,7 @@ sub project_go_terms {
$to_translation->add_DBEntry($dbEntry);
- print $to_translation->stable_id() . " --> " . $dbEntry->display_id() . "\n" if ($print);
+ print $from_gene->stable_id() . " " . $from_translation->stable_id() . " " . $dbEntry->display_id() . " --> " . $to_gene->stable_id() . " " . $to_translation->stable_id() . "\n" if ($print);
$to_dbea->store($dbEntry, $to_translation->dbID(), 'Translation', 1) if (!$print);
@@ -735,26 +734,20 @@ sub homology_type_allowed {
}
# ----------------------------------------------------------------------
+# Get the translation associated with the gene's canonical transcript
-sub get_longest_translation {
+sub get_canonical_translation {
my $gene = shift;
- my $longest_translation;
- my $max_length = -1;
-
- foreach my $transcript (@{$gene->get_all_Transcripts()}) {
-
- my $translation = $transcript->translation();
- if ($translation && $translation->length() > $max_length) {
- $longest_translation = $translation;
- }
+ my $canonical_transcript = $gene->canonical_transcript();
+ if (!$canonical_transcript) {
+ warn("Can't get canonical transcript for " . $gene->stable_id() . ", skipping this homology");
+ return undef;
}
- warn("Can't find longest translation for " . $gene->stable_id()) if (!$longest_translation);
-
- return $longest_translation;
+ return $canonical_transcript->translation();;
}
--
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