From d8456c97fa80dcc7519fc52de7de517c3bc06e9d Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Thu, 2 Sep 2004 16:14:18 +0000
Subject: [PATCH] go retrieval
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@1854 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
etc/go_associations.pl | 31 ++++++++++++++++++++++++++-----
1 file changed, 26 insertions(+), 5 deletions(-)
diff --git a/etc/go_associations.pl b/etc/go_associations.pl
index a1559f905..c4020a1c2 100755
--- a/etc/go_associations.pl
+++ b/etc/go_associations.pl
@@ -59,21 +59,42 @@ my $term_l = $apph->get_terms({products=>[@pqlist]});
foreach my $term (@$term_l)
{
- printf "%s; %s; ", $term->acc, $term->name;
+ my $type = $term->term_type;
+ if($type =~ m/_component/i)
+ {
+ printf "/GO_component=\"";
+ }
+ elsif($type =~ m/_function/i)
+ {
+ printf "/GO_function=\"";
+ }
+ elsif($type =~ m/_process/i)
+ {
+ printf "/GO_process=\"";
+ }
+
+ printf "%s (%s);", $term->acc, $term->name;
if($associations)
{
foreach my $assoc (@{$term->selected_association_list || []})
{
my $gp = $assoc->gene_product;
my $ev_l = $assoc->evidence_list || [];
- printf "%s; %s; %s; evidence=%s; %s;",
- $gp->full_name, $gp->acc, $gp->symbol,
- join('; ', map {$_->code} @$ev_l), $gp->as_str;
+ printf " %s; %s:%s", $assoc->evidence_as_str, $gp->speciesdb, $gp->acc;
foreach my $syn (@{$gp->synonym_list || []})
{
- print " Synonym: $syn;";
+ print " ($syn)";
+ }
+ printf ";";
+ printf "%s",$assoc->assocdate;
+
+ printf " db_xref=";
+ foreach my $ref (@{$term->dbxref_list || []})
+ {
+ printf "%s", $ref->as_str;
}
+ printf ";";
}
}
--
GitLab