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Merge branch 'master' of https://github.com/nextstrain/fauna

* 'master' of https://github.com/nextstrain/fauna:
  Fix fiji strain ID, add additional Smith viruses.
  Fix pandas indexing bug.
  Hack a fix for preformatted reference and Smith virus strains.
  Remove lab strains, fix reference strain names.
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2 parents 3d9b0f0 + 4ab147b commit 2ae58531a2d806705463e19353340dc0b9963922 @trvrb trvrb committed Dec 20, 2016
Showing with 339 additions and 286 deletions.
  1. +39 −0 source-data/dengue_strain_name_fix.tsv
  2. +300 −286 vdb/dengue_upload.py
@@ -0,0 +1,39 @@
+NC_001477 DENV1/NAURUISLAND/REFERENCE/1997
+NC_001474 DENV2/THAILAND/REFERENCE/1964
+NC_001475 DENV3/SRI_LANKA/REFERENCE/2000
+NC_002640 DENV4/NA/REFERENCE/2003
+KT452802 DENV4/CAMBODIA/V0624301AC33/2011
+KT452803 DENV4/NICARAGUA/703/1999
+KT452800 DENV3/PUERTORICO/PRS228762AC27/1963
+KT452801 DENV4/INDONESIA/M30153AC36/1973
+L11422 DENV3/FIJI/29472/1992
+KT452792 DENV3/MYANMAR/80931/2008
+KT452793 DENV4/MYANMAR/81087/2008
+KT452791 DENV1/MYANMAR/61117/2005
+KT452796 DENV2/VIETNAM/AC21/2003
+KT452797 DENV2/VIETNAM/DF670AC20/2003
+KT452794 DENV4/BRAZIL/BR12/2012
+KT452795 DENV2/CAMBODIA/D2T0601085KH09KSP/2009
+KT452798 DENV3/INDONESIA/SLEMAN1280AC25/1978
+KT452799 DENV3/CAMBODIA/V0907330AC23/2011
+FJ538920 DENV2/INDIA/POONA742295/1974
+AY145121 DENV1/NAURU/WESTPAC/1974
+JN022608 DENV4/INDONESIA/S1228/1978
+KT382189 DENV2/BRAZIL/BR161/2004
+KT382188 DENV2/GUYANA/CAREC0008221/2000
+KT382187 DENV1/BOLIVIA/FSB3363/2010
+KT382186 DENV1/VENEZUELA/OBT1298/2000
+AY780643 DENV1/PERU/IQT6152/2000
+KF543272 DENV4/CAMBODIA/U0811386/2010
+AY780644 DENV4/THAILAND/D85052/1985
+AY158339 DENV2/PERU/IQT2913/1996
+AY145123 DENV1/NA/WESTERNPACIFICDELTA30/NA
+U88535 DENV1/NAURU/WESTERNPACIFIC/1974
+AF038403 DENV2/PAPUANEWGUINEA/NEWGUINEAC/1944
+KM204118 DENV2/PAPUANEWGUINEA/NEWGUINEAC/1944
+AF038403 DENV2/PAPUANEWGUINEA/NEWGUINEAC/1944
+M29095 DENV2/PapuaNewGuinea/NEWGUINEAC/1944
+AY376438 DENV3/NA/SLEMANDELTA30/NA
+AF326826 DENV4/NA/81669DELTA30/NA
+AF375822 DENV4/DOMINICA/81669/1981
+AF326573 DENV4/DOMINICA/81669/1981
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