From ef4ea53607632cfe44f32e3448ee59951acc49b8 Mon Sep 17 00:00:00 2001
From: Michael Paulini <michael.paulini@wormbase.org>
Date: Fri, 1 Nov 2019 13:59:59 +0000
Subject: [PATCH] hopefully last iteration of AGM/allele for 2.3

---
 scripts/AGR/make_agr_AGM.pl         | 2 ++
 scripts/AGR/make_agr_allele_json.pl | 2 +-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/scripts/AGR/make_agr_AGM.pl b/scripts/AGR/make_agr_AGM.pl
index 669a85353..d37f23940 100644
--- a/scripts/AGR/make_agr_AGM.pl
+++ b/scripts/AGR/make_agr_AGM.pl
@@ -30,6 +30,8 @@
 	my @strains = $aceVar->Strain;
 	next unless @strains; # for the alleles without curated strain data
 	foreach my $strain(@strains){
+		# skip the ones without disease annotation
+                next unless $strain->Disease_info;
 	        $strains{"$strain"}||=[];
 		push @{$strains{"$strain"}},"$id";
 	}
diff --git a/scripts/AGR/make_agr_allele_json.pl b/scripts/AGR/make_agr_allele_json.pl
index 9e854920d..26848d4fc 100755
--- a/scripts/AGR/make_agr_allele_json.pl
+++ b/scripts/AGR/make_agr_allele_json.pl
@@ -54,7 +54,7 @@
 
 my $db = Ace->connect(-path => $acedbpath,  -program => $tace) or die("Connection failure: ". Ace->error);
 
-$it = $db->fetch_many(-query => 'find Variation WHERE Live AND COUNT(Gene) == 1 AND (Description OR Interactor OR Disease_info) AND NOT Natural_variant');
+$it = $db->fetch_many(-query => 'find Variation WHERE Live AND COUNT(Gene) == 1 AND (Phenotype OR Disease_info) AND NOT Natural_variant');
 
 while (my $obj = $it->next) {
   next unless $obj->isObject();