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Exclude sylvatic strains

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sidneymbell committed Nov 18, 2017
1 parent 8fd42ac commit 1456d318c83183e666693daa717e80ca35435c0c
Showing with 6 additions and 1 deletion.
  1. +6 −1 builds/dengue/dengue.prepare.py
@@ -28,7 +28,12 @@ def collect_args():
dropped_strains = [
'DENV1/VIETNAM/BIDV992/2006', 'DENV1/FRANCE/00475/2008', 'DENV1/VIETNAM/BIDV3990/2008', 'DENV2/HAITI/DENGUEVIRUS2HOMOSAPIENS1/2016', # Probable recombinants
'DENV2/AUSTRALIA/QML22/2015' # Suspiciously far diverged
'DENV2/AUSTRALIA/QML22/2015', # Suspiciously far diverged
'DENV2/MALAYSIA/DKD811/2008', 'DENV2/MALAYSIA/P81407/1970', 'DENV2/SENEGAL/0674/1970', 'DENV2/SENEGAL/DAKAR0761/1974', # Sylvatic
'DENV2/NIGERIA/IBH11234/1966', 'DENV2/NIGERIA/IBH11664/1966', 'DENV2/NIGERIA/IBH11208/1966', 'DENV2/SENEGAL/DAKARD75505/1999', # Sylvatic
'DENV2/SENEGAL/DAKAR141069/1999', 'DENV2/SENEGAL/DAKAR141070/1999', 'DENV2/GUINEA/PM33974/1981', 'DENV2/BURKINA_FASO/DAKAR2039/1980', # Sylvatic
'DENV2/COTE_D_IVOIRE/DAKAR578/1980', 'DENV2/COTE_D_IVOIRE/DAKAR510/1980', # Sylvatic
'DENV4/MALAYSIA/P731120/1973', 'DENV4/MALAYSIA/P215/1975'# Sylvatic
]
genotype_references = ['AB074760', 'EU848545', 'D10513', 'JF297570', 'JQ922547', 'JF297572', 'JQ922544', 'AF425629', 'AF180817', 'AF425625', 'JQ922546', 'AY713473', 'EF457905', 'U88535', 'AY722801', 'JN379478', 'AY732476', 'AY732474', 'AF425630', 'AY732483', 'AF425611', 'GQ868601', 'AF425620', 'AF425628', 'AB600923', 'AF226687', 'M87512', 'JN638342', 'AF226685', 'AY732477', 'AF425626', 'AY732413', 'FJ196845', 'DQ285562', 'AY153757', 'AY762084', 'AY732461', 'AB608789', 'AM746218', 'AY732480', 'FJ196846', 'JN638344', 'AF425632', 'JN379486', 'DQ855297', 'AY722802', 'JN638340', 'AF311956', 'AB189121', 'AF309641', 'AF298808', 'GQ868559', 'AY726555', 'AB189121', 'AF298807', 'AY422785', 'AF514883', 'AF514889', 'AY620951', 'JN415515', 'JN415499', 'DQ672564', 'AY713476', 'AY732479', 'AY732464', 'AY630407', 'DQ672564', 'KF559254', 'JN415503', 'EU863650', 'FJ196842', 'JN379472', 'JN415488', 'AB195673', 'EU596501', 'JN415524', 'FR666922', 'AM746216', 'AY835999', 'AY858983', 'AB204803', 'EU081258', 'EU081226', 'FN825674', 'EU179860', 'JF297581', 'JN415516', 'JQ922548', 'FJ196844', 'HQ332182', 'JN415533', 'JN415523', 'GU131962', 'KC172829', 'AB608787', 'JN415506', 'GU131863', 'JN903579', 'GQ357692', 'GU131792', 'JN415521', 'JN415527', 'JN415534', 'KR919821', 'KC692495', 'JN903581', 'JF960211', 'JN415519', 'GU131895', 'HQ891316', 'JQ915080', 'HG316481', 'HG316482', 'KC692512', 'KC182084', 'KR919811', 'JN415492', 'JN415494', 'JN415513', 'KJ189367', 'JQ675358', 'KJ649286', 'KR919805', 'KC848576', 'KR919815', 'JX298570', 'KF289072', 'KJ933413', 'KJ726662', 'KR919808', 'KR919819', 'KR919813', 'KF973455', 'KF864667', 'KR919806', 'KR919807', 'KR919809', 'KR919817', 'KF184975', 'KM458188', 'LC002828', 'KR919816', 'KR919812', 'KR919818', 'KR919814', 'KR919820', 'KR919810', 'AF038403', 'U87411', 'EF105387', 'EU003591', 'EF105388', 'EF105384', 'EF105379', 'DQ181806', 'EF105385', 'EU056812', 'EF105382', 'EF105380', 'EF105383', 'EF105386', 'EF105381', 'EF105378', 'M20558', 'AY037116', 'JX966379', 'DQ181799', 'AF208496', 'AF359579', 'EF105389', 'EF105390', 'EF457904', 'EU179858', 'FJ467493', 'JF260983', 'KC294207', 'M93130', 'AF317645', 'AY676353', 'JQ411814', 'AY744685', 'AY923865', 'DQ675519', 'JN406514', 'AY099337', 'AY099336', 'EF629367', 'EU081198', 'HQ332171', 'JN406515', 'HG316484', 'JF262783', 'JF262780', 'EF457906', 'JF262779', 'AF326573', 'JF262782', 'JF262781', 'AY618989', 'AY618993', 'AY618992', 'KF041260', 'JQ822247', 'JN983813', 'JX024758']

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