Skip to content
Permalink
Browse files

Update avian flu parsing

* H5N1 had an extra host to convert to "avian"
* H7N9 had strains with division "china" that are obviously from particular provinces
  • Loading branch information
trvrb committed Nov 10, 2019
1 parent 988ee6c commit e3bd1315eb599babfd608ae0730ca67097843892
Showing with 18 additions and 0 deletions.
  1. +17 −0 source-data/flu_location_fix.tsv
  2. +1 −0 vdb/avian_flu_upload.py
@@ -310,3 +310,20 @@ A/Environment/InnerMongolia/28667/2017 neimenggu
A/Environment/InnerMongolia/28668/2017 neimenggu
A/Environment/InnerMongolia/28669/2017 neimenggu
A/Environment/InnerMongolia/28670/2017 neimenggu
A/Chicken/Guangdong/416 guangdong
A/Chicken/Guangdong/422 guangdong
A/Enviroemnt/Guangdong/423 guangdong
A/Environment/GD-SZ_296/2013 guangdong
A/Environment/GD-SZ_1/2013 guangdong
A/Environment/GD-ST_100/2014 guangdong
A/Environment/GD-ST_101/2014 guangdong
A/Env/GD-YJ370/2017 guangdong
A/GD-ZS029/2017-03-28 guangdong
A/GD-ZS029/2017-03-28 guangdong
A/GD-ST018/2017-01-24 guangdong
A/Env/GD-MZ073/2017 guangdong
A/Environment/Yunnan/315 yunnan
A/Duck/Sichuan/408 sichuan
A/Chicken/Hunan/207 hunan
A/chicken/Jiangsu/JS/02/71/2017 jiangsu
A/Chicken/Hubei/306 hubei
@@ -371,6 +371,7 @@ def format_host(self, v):
"american__wigeon", "anasboschas", "anasacuta", "anasamericana",
"anascarolinensis", "anasclypeata", "anascrecca", "anascyanoptera",
"anasdiscors", "anasformosa", "anasplatyrhynchos", "anaspoecilorhyncha",
"anasplatyrhynchosvar.domesticus",
"anasrubripes", "anassp.", "anasstrepera", "anasstrepera", "anasundalata",
"anseranser", "anserfabalis", "anseralbifrons", "anserindicus",
"arenariainterpres", "avian", "bar__headed__goose", "bird", "barn__swallow",

0 comments on commit e3bd131

Please sign in to comment.
You can’t perform that action at this time.