From 1d43f38bd5f05da5616cc90eff0903d26d29ec76 Mon Sep 17 00:00:00 2001
From: Jennifer Chang <jennifer.chang.bioinform@gmail.com>
Date: Wed, 5 Jun 2024 10:05:27 -0700
Subject: [PATCH] All genes works on real data, not on example data.

All genes works on real data, for example see:

* https://next.nextstrain.org/staging/zika/trials/Egene20240604/zika/ENV
* https://next.nextstrain.org/staging/zika/trials/Egene20240604/zika/PRO
* https://next.nextstrain.org/staging/zika/trials/Egene20240604/zika/CA
* https://next.nextstrain.org/staging/zika/trials/Egene20240604/zika/MP
* https://next.nextstrain.org/staging/zika/trials/Egene20240604/zika/NS1
* https://next.nextstrain.org/staging/zika/trials/Egene20240604/zika/NS2A
* https://next.nextstrain.org/staging/zika/trials/Egene20240604/zika/NS2B
* https://next.nextstrain.org/staging/zika/trials/Egene20240604/zika/NS3
* https://next.nextstrain.org/staging/zika/trials/Egene20240604/zika/NS4A
* https://next.nextstrain.org/staging/zika/trials/Egene20240604/zika/2K
* https://next.nextstrain.org/staging/zika/trials/Egene20240604/zika/NS4B
* https://next.nextstrain.org/staging/zika/trials/Egene20240604/zika/NS5

But fail on the example data, possibly because not enough sequences cover the full genome.

Dropping the other genes for now, and focusing on the E gene.
---
 phylogenetic/Snakefile                 |  2 +-
 phylogenetic/defaults/config_zika.yaml | 11 -----------
 2 files changed, 1 insertion(+), 12 deletions(-)

diff --git a/phylogenetic/Snakefile b/phylogenetic/Snakefile
index 483e5ef..a2263e5 100644
--- a/phylogenetic/Snakefile
+++ b/phylogenetic/Snakefile
@@ -1,6 +1,6 @@
 configfile: "defaults/config_zika.yaml"
 
-genes = ['genome', 'ENV', 'CA', 'PRO', 'MP', 'NS1', 'NS2A', 'NS2B', 'NS3', 'NS4A', '2K', 'NS4B', 'NS5']
+genes = ['genome', 'ENV']
 
 wildcard_constraints:
     gene = "|".join(genes)
diff --git a/phylogenetic/defaults/config_zika.yaml b/phylogenetic/defaults/config_zika.yaml
index 873a627..7a08ec9 100644
--- a/phylogenetic/defaults/config_zika.yaml
+++ b/phylogenetic/defaults/config_zika.yaml
@@ -13,17 +13,6 @@ filter:
   min_length:
     genome: 5385
     ENV: 1000
-    CA: 120
-    PRO: 90
-    MP: 70
-    NS1: 350
-    NS2A: 220
-    NS2B: 130
-    NS3: 610
-    NS4A: 120
-    2K: 20
-    NS4B: 250
-    NS5: 903
 
 refine:
   coalescent: "opt"