Permalink
Browse files

Update H3N2 outliers.

  • Loading branch information...
1 parent d903bcb commit c5d0b3a70deb369927a34d021a14318455304b85 @trvrb trvrb committed Dec 26, 2016
Showing with 22 additions and 21 deletions.
  1. +22 −21 augur/src/H3N2_process.py
@@ -175,27 +175,28 @@ def clean_outliers(self):
"A/HongKong/HK2MA21-3/2008", "A/HongKong/HK4/2008", "A/HongKong/HK5/2008",
"A/HongKong/HK5MA21-1/2008", "A/HongKong/HK5MA21-3/2008", "A/HongKong/HK6/2008",
"A/HongKong/HK6MA21-2/2008", "A/HongKong/HK6MA21-3/2008", "A/HongKong/HK7/2008",
- "A/HongKong/HK8/2008", "A/HongKong/HK8MA21-2/2008", "A/HongKong/HK8MA21-3/2008",
- "A/HongKong/HK8MA21-4/2008", "A/HongKong/HK9/2008", "A/HongKong/HK9MA21-1/2008",
- "A/HongKong/HK9MA21-2/2008", "A/HongKong/HK9MA21-3/2008", "A/HongKong/HK10/2008",
- "A/HongKong/HK10MA21-1/2008", "A/HongKong/HK10MA21-2/2008", "A/HongKong/HK10MA21-4/2008",
- "A/HongKong/HK11MA21-1/2008", "A/HongKong/HK11MA21-3/2008", "A/HongKong/HK11MA21-4/2008",
- "A/HongKong/HK12/2008", "A/HongKong/HK12MA21-2/2008", "A/HongKong/HKMA12/2008",
- "A/HongKong/HKMA12A/2008", "A/HongKong/HKMA12B/2008", "A/HongKong/HKMA12D/2008",
- "A/HongKong/HKMA12E/2008", "A/HongKong/HKMA20B/2008", "A/HongKong/HKMA20E/2008",
- "A/Busan/15453/2009", "A/Pennsylvania/14/2010", "A/Pennsylvania/40/2010", "A/Guam/AF2771/2011",
- "A/Indiana/8/2011", "A/Kenya/155/2011", "A/Kenya/168/2011", "A/Kenya/170/2011", "A/Nepal/142/2011",
- "A/Pennsylvania/09/2011", "A/Pennsylvania/9/2011", "A/Quebec/167936/2011", "A/Quebec/170658/2011",
- "A/India/6352/2012", "A/Indiana/08/2012", "A/Indiana/13/2012", "A/Ohio/34/2012",
- "A/Helsinki/942/2013", "A/Indiana/06/2013", "A/Indiana/11/2013", "A/Indiana/21/2013",
- "A/Jiangsu-Tianning/1707/2013", "A/HuNan/01/2014", "A/Jiangsu-Chongchuan/1830/2014",
- "A/Jiangsu-Chongchuan/12179/2014", "A/Ohio/2/2014", "A/Ohio/4319/2014", "A/SaoPaulo/3-34891/2014",
- "A/NewJersey/53/2015", "A/SaoPaulo/36178/2015", "A/SaoPaulo/61282/2015", "A/SaoPaulo/65194/2015",
- "A/Michigan/39/2015", "A/Sydney/53/2015", "A/Michigan/82/2016", "A/Michigan/83/2016",
- "A/Michigan/84/2016", "A/Michigan/87/2016", "A/Michigan/89/2016", "A/Michigan/90/2016",
- "A/Michigan/91/2016", "A/Michigan/93/2016", "A/Michigan/94/2016", "A/Michigan/95/2016",
- "A/Michigan/96/2016", "A/Ohio/27/2016", "A/Ohio/28/2016", "A/Ohio/32/2016", "A/Ohio/33/2016",
- "A/Ohio/35/2016", "A/Zhejiang-Wuxin/1300/2016"]
+ "A/HongKong/HK8/2008", "A/HongKong/HK8MA21-1/2008", "A/HongKong/HK8MA21-2/2008",
+ "A/HongKong/HK8MA21-3/2008", "A/HongKong/HK8MA21-4/2008", "A/HongKong/HK9/2008",
+ "A/HongKong/HK9MA21-1/2008", "A/HongKong/HK9MA21-2/2008", "A/HongKong/HK9MA21-3/2008",
+ "A/HongKong/HK10/2008", "A/HongKong/HK10MA21-1/2008", "A/HongKong/HK10MA21-2/2008",
+ "A/HongKong/HK10MA21-4/2008", "A/HongKong/HK11MA21-1/2008", "A/HongKong/HK11MA21-3/2008",
+ "A/HongKong/HK11MA21-4/2008", "A/HongKong/HK12/2008", "A/HongKong/HK12MA21-2/2008",
+ "A/HongKong/HKMA12/2008", "A/HongKong/HKMA12A/2008", "A/HongKong/HKMA12B/2008",
+ "A/HongKong/HKMA12D/2008", "A/HongKong/HKMA12E/2008", "A/HongKong/HKMA20B/2008",
+ "A/HongKong/HKMA20E/2008", "A/Busan/15453/2009", "A/Pennsylvania/14/2010", "A/Pennsylvania/40/2010",
+ "A/Guam/AF2771/2011", "A/Indiana/8/2011", "A/Kenya/155/2011", "A/Kenya/168/2011",
+ "A/Kenya/170/2011", "A/Nepal/142/2011", "A/Pennsylvania/09/2011", "A/Pennsylvania/9/2011",
+ "A/Quebec/167936/2011", "A/Quebec/170658/2011", "A/India/6352/2012", "A/Indiana/08/2012",
+ "A/Indiana/13/2012", "A/Ohio/34/2012", "A/Helsinki/942/2013", "A/Indiana/06/2013",
+ "A/Indiana/11/2013", "A/Indiana/21/2013", "A/Jiangsu-Tianning/1707/2013", "A/HuNan/01/2014",
+ "A/Jiangsu-Chongchuan/1830/2014", "A/Jiangsu-Chongchuan/12179/2014", "A/Ohio/2/2014",
+ "A/Ohio/4319/2014", "A/SaoPaulo/3-34891/2014", "A/NewJersey/53/2015", "A/SaoPaulo/36178/2015",
+ "A/SaoPaulo/61282/2015", "A/SaoPaulo/65194/2015", "A/Michigan/39/2015", "A/Sydney/53/2015",
+ "A/Michigan/82/2016", "A/Michigan/83/2016", "A/Michigan/84/2016", "A/Michigan/87/2016",
+ "A/Michigan/89/2016", "A/Michigan/90/2016", "A/Michigan/91/2016", "A/Michigan/93/2016",
+ "A/Michigan/94/2016", "A/Michigan/95/2016", "A/Michigan/96/2016", "A/Ohio/27/2016",
+ "A/Ohio/28/2016", "A/Ohio/32/2016", "A/Ohio/33/2016", "A/Ohio/35/2016",
+ "A/Zhejiang-Wuxin/1300/2016"]
for v in self.viruses:
if v.strain in outlier_strains:
if self.verbose > 1:

0 comments on commit c5d0b3a

Please sign in to comment.