From 73599cd810e97f22d01d651416468e34dd6c9dde Mon Sep 17 00:00:00 2001
From: elserj <elserj@localhost>
Date: Wed, 13 Mar 2013 21:10:53 +0000
Subject: [PATCH] Added script that can take an obo file and tell you how many
 non-obsolete terms exist

svn path=/; revision=434
---
 .../obo_count_non_obolete_terms.pl            | 54 +++++++++++++++++++
 1 file changed, 54 insertions(+)
 create mode 100755 interactome_scripts/obo_count_non_obolete_terms.pl

diff --git a/interactome_scripts/obo_count_non_obolete_terms.pl b/interactome_scripts/obo_count_non_obolete_terms.pl
new file mode 100755
index 0000000..e03006f
--- /dev/null
+++ b/interactome_scripts/obo_count_non_obolete_terms.pl
@@ -0,0 +1,54 @@
+#!/usr/bin/perl
+
+use strict;
+use warnings;
+
+# use this to get filename, without the rest of the directory structure
+use File::Basename;
+
+##########################################################################
+#   po_obsolete_check.pl                                                 #
+#    Version 0.1                                                         #
+#                                                                        #
+#  Written by Justin Elser, Dept. of BPP, OSU 2011                       #
+#                                                                        #
+#  Program will check the current po obo file for terms that have        #
+#    been obsoleted.  It will then check all association files for       #
+#    annotations linked with those terms and create output files for     #
+#    used for manual intervention by annotation curators.                #
+#                                                                        #
+#  Program should be made part of the SOP when loading new DBs           #
+#                                                                        #
+##########################################################################
+
+#  Use Chris Mungall's GO::Parser to do the searching for is_obsoletes
+use GO::Parser;
+
+
+my $obo_file = $ARGV[0];
+
+# init GO parser
+my $parser = GO::Parser->new({handler=>'obj'});
+$parser->parse($obo_file);
+
+my $ont = $parser->handler->graph;
+
+
+my $obo_terms = $ont->get_all_nodes;
+
+# hash to store obsolete terms
+my %obs_terms_hash;
+my $good_terms_count = 0;
+
+
+foreach my $term (@$obo_terms) {
+	if ($term->is_obsolete){
+		my $id = $term->acc;
+		my $name = $term->name;
+		$obs_terms_hash{$id} = $name;
+	}else{
+			$good_terms_count++;
+	}
+}
+
+print "Good terms count = $good_terms_count\n";
-- 
2.34.1