def __init__(self,min_length = 987, **kwargs):
'''
parameters
min_length -- minimal length for a sequence to be acceptable
'''
flu_filter.__init__(self, **kwargs)
self.min_length = min_length
self.vaccine_strains =[{
'strain':'A/California/07/2009',
'isolate_id':'EPI_ISL_31553',
'date':'2009-04-09',
'lab':'Naval Health Research Center',
'country':'USA',
'region':'NorthAmerica',
'seq':'ATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACACATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAACAGTAACACACTCTGTTAACCTTCTAGAAGACAAGCATAACGGGAAACTATGCAAACTAAGAGGGGTAGCCCCATTGCATTTGGGTAAATGTAACATTGCTGGCTGGATCCTGGGAAATCCAGAGTGTGAATCACTCTCCACAGCAAGCTCATGGTCCTACATTGTGGAAACACCTAGTTCAGACAATGGAACGTGTTACCCAGGAGATTTCATCGATTATGAGGAGCTAAGAGAGCAATTGAGCTCAGTGTCATCATTTGAAAGGTTTGAGATATTCCCCAAGACAAGTTCATGGCCCAATCATGACTCGAACAAAGGTGTAACGGCAGCATGTCCTCATGCTGGAGCAAAAAGCTTCTACAAAAATTTAATATGGCTAGTTAAAAAAGGAAATTCATACCCAAAGCTCAGCAAATCCTACATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTAGTGCTGACCAACAAAGTCTCTATCAGAATGCAGATGCATATGTTTTTGTGGGGTCATCAAGATACAGCAAGAAGTTCAAGCCGGAAATAGCAATAAGACCCAAAGTGAGGGATCAAGAAGGGAGAATGAACTATTACTGGACACTAGTAGAGCCGGGAGACAAAATAACATTCGAAGCAACTGGAAATCTAGTGGTACCGAGATATGCATTCGCAATGGAAAGAAATGCTGGATCTGGTATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCAAACACCCAAGGGTGCTATAAACACCAGCCTCCCATTTCAGAATATACATCCGATCACAATTGGAAAATGTCCAAAATATGTAAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATATCCCGTCTATTCAATCTAGAGGCCTATTTGGGGCCATTGCCGGTTTCATTGAAGGGGGGTGGACAGGGATGGTAGATGGATGGTACGGTTATCACCATCAAAATGAGCAGGGGTCAGGATATGCAGCCGACCTGAAGAGCACACAGAATGCCATTGACGAGATTACTAACAAAGTAAATTCTGTTATTGAAAAGATGAATACACAGTTCACAGCAGTAGGTAAAGAGTTCAACCACCTGGAAAAAAGAATAGAGAATTTAAATAAAAAAGTTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCAAATGTGAAGAACTTATATGAAAAGGTAAGAAGCCAGCTAAAAAACAATGCCAAGGAAATTGGAAACGGCTGCTTTGAATTTTACCACAAATGCGATAACACGTGCATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGTTTCTGGATGTGCTCTAATGGGTCTCTACAGTGTAGAATATGTATTTAA',
}]
self.outgroup = {
'strain': 'A/Swine/Indiana/P12439/00',
'db': 'IRD',
'accession': 'AF455680',
'date': '2002-03-14',
'country': 'USA',
'region': 'NorthAmerica',
'seq': 'ATGAAGGCAATACTAGTAGTCCTGCTATATACATTTACAACCGCAAATGCAGACACATTATGTATAGGTTATCATGCGAACAATTCAACTGACACTGTAGACACAGTACTAGAAAAGAATGTAACAGTAACACACTCTGTTAACCTTCTAGAAGACAGGCATAACGGGAAACTATGTAAACTAAGAGGGGTAGCCCCATTGCATTTGGGTAAATGTAACATTGCTGGCTGGCTCCTGGGAAATCCAGAGTGTGAATCACTCTTCACAGCAAGCTCATGGTCCTACATTGTGGAAACATCTAGTTCAGATAATGGGACGTGTTACCCAGGAGATTTCATCAATTATGAAGAGCTAAGAGAGCAATTGAGCTCAGTGTCATCATTTGAAAGATTTGAGATATTCCCCAAGACAAGTTCATGGCCCAATCATGACACGAACAGAGGTGTGACGGCAGCATGTCCTTATGCTGGAGCAAAAAGCTTCTACAGAAATTTAATATGGCTGGTCAAAAAAGAAAATTCATACCCAAAGCTCAGCAAATCCTATATTAACAATAAGGGGAAGGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACCAGTGCCGACCAACAAAGTCTCTACCAGAATGCAGATGCATATGTTTTTGTGGGGTCATCAAGATACAGCAAGAAGTTCAAGCCAGAAATAGCAGCCAGACCCAAGGTGAGGGACCAAGCAGGGAGAATAAACTATTACTGGACACTAGTAGAGCCTGGAGACAAAATAACATTCGAAGCAACTGGAAATCTAGTGGTACCGAGATATGCCTTCGCAATGGAAAGAAATTCTGGATCTGGTATTATCATTTCAGATACATCAGTCCACGATTGTAATACGACTTGTCAGACACCCAAGGGTGCTATAAACACCAGCCTCCCATTTCAGAATATACATCCAGTCACAATTGGAGAATGTCCAAAATATGTAAAAAGCACAAAATTGAGAATGGCCACAGGATTAAGGAATGTCCCGTCTATTCAATCTAGAGGCCTGTTTGGGGCCATTGCCGGCTTTATTGAGGGGGGATGGACAGGAATGATAGATGGATGGTACGGTTATCACCATCAAAATGAGCAGGGATCAGGATATGCAGCCGACCTGAAGAGCACACAGAATGCCATTGACGGGATCACTAACAAAGTAAATTCTGTTATTGAAAAGATGAACACACAATTCATAGCAGTAGGTAAAGAGTTCAACCACCTGGAAAAAAGAATAGAGAATTTAAATAAAAAGGTTGATGATGGTTTTCTGGATATTTGGACTTACAATGCCGAACTGTTGATTCTGTTGGAAAATGAAAGAACTTTGGATTACCACGATTCAAATGTGAAGAACTTATATGAAAAGGTAAGAAGCCAGCTAAAAAACAATGCCAGGGAAATTGGGAATGGCTGCTTTGAATTTTACCACAAATGTGATGACAAGTGCATGGAAAGCGTCAAAAATGGGACTTATGATTACCCAAAATACTCAGAGGAAGCAAAACTAAACAGAGAGGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGTTTCTGGATGTGCTCTAATGGGTCTCTACAGTGTAGAATATGTATTTAA'
}
def __init__(self,min_length = 987, **kwargs):
'''
parameters
min_length -- minimal length for a sequence to be acceptable
'''
flu_filter.__init__(self, **kwargs)
self.min_length = min_length
self.vaccine_strains =[{
'strain':'A/California/07/2009',
'isolate_id':'EPI_ISL_31553',
'date':'2009-04-09',
'lab':'Naval Health Research Center',
'country':'USA',
'region':'NorthAmerica',
'seq':'ATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACACATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAACAGTAACACACTCTGTTAACCTTCTAGAAGACAAGCATAACGGGAAACTATGCAAACTAAGAGGGGTAGCCCCATTGCATTTGGGTAAATGTAACATTGCTGGCTGGATCCTGGGAAATCCAGAGTGTGAATCACTCTCCACAGCAAGCTCATGGTCCTACATTGTGGAAACACCTAGTTCAGACAATGGAACGTGTTACCCAGGAGATTTCATCGATTATGAGGAGCTAAGAGAGCAATTGAGCTCAGTGTCATCATTTGAAAGGTTTGAGATATTCCCCAAGACAAGTTCATGGCCCAATCATGACTCGAACAAAGGTGTAACGGCAGCATGTCCTCATGCTGGAGCAAAAAGCTTCTACAAAAATTTAATATGGCTAGTTAAAAAAGGAAATTCATACCCAAAGCTCAGCAAATCCTACATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTAGTGCTGACCAACAAAGTCTCTATCAGAATGCAGATGCATATGTTTTTGTGGGGTCATCAAGATACAGCAAGAAGTTCAAGCCGGAAATAGCAATAAGACCCAAAGTGAGGGATCAAGAAGGGAGAATGAACTATTACTGGACACTAGTAGAGCCGGGAGACAAAATAACATTCGAAGCAACTGGAAATCTAGTGGTACCGAGATATGCATTCGCAATGGAAAGAAATGCTGGATCTGGTATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCAAACACCCAAGGGTGCTATAAACACCAGCCTCCCATTTCAGAATATACATCCGATCACAATTGGAAAATGTCCAAAATATGTAAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATATCCCGTCTATTCAATCTAGAGGCCTATTTGGGGCCATTGCCGGTTTCATTGAAGGGGGGTGGACAGGGATGGTAGATGGATGGTACGGTTATCACCATCAAAATGAGCAGGGGTCAGGATATGCAGCCGACCTGAAGAGCACACAGAATGCCATTGACGAGATTACTAACAAAGTAAATTCTGTTATTGAAAAGATGAATACACAGTTCACAGCAGTAGGTAAAGAGTTCAACCACCTGGAAAAAAGAATAGAGAATTTAAATAAAAAAGTTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCAAATGTGAAGAACTTATATGAAAAGGTAAGAAGCCAGCTAAAAAACAATGCCAAGGAAATTGGAAACGGCTGCTTTGAATTTTACCACAAATGCGATAACACGTGCATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGTTTCTGGATGTGCTCTAATGGGTCTCTACAGTGTAGAATATGTATTTAA',
}]
tmp_outgroup = SeqIO.read('source-data/H1N1pdm_outgroup.gb', 'genbank')
genome_annotation = tmp_outgroup.features
self.cds = {x.qualifiers['gene'][0]:x for x in genome_annotation
if 'gene' in x.qualifiers and x.type=='CDS' and
x.qualifiers['gene'][0] in ['SigPep', 'HA1', 'HA2']}
self.outgroup = {
'strain': 'A/Swine/Indiana/P12439/00',
'db': 'IRD',
'accession': 'AF455680',
'date': '2002-03-14',
'country': 'USA',
'region': 'NorthAmerica',
'seq': str(tmp_outgroup.seq).upper()
}
def __init__(self,min_length = 987, **kwargs):
'''
parameters
min_length -- minimal length for a sequence to be acceptable
'''
flu_filter.__init__(self, **kwargs)
self.min_length = min_length
self.vaccine_strains =[
{
"strain": "A/Wisconsin/67/2005",
"db": "IRD",
"accession": "CY163984",
"date": "2005-08-31",
"seq": "ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAACTTCCCGGAAATGACAACAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAATGACCAAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAGTTCCTCAACAGGTGGAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTCCAAAATAAGAAATGGGACCTTTTTGTTGAACGCAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACGATGAAAGCTTCAATTGGACTGGAGTCACTCAAAATGGAACAAGCTCTTCTTGCAAAAGGAGATCTAATAACAGTTTCTTTAGTAGATTGAATTGGTTGACCCACTTAAAATTCAAATACCCAGCATTGAACGTGACTATGCCAAACAATGAAAAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGTTACGGACAATGACCAAATCTTCCTGTATGCTCAAGCATCAGGAAGAATCACAGTCTCTACCAAAAGAAGCCAACAAACTGTAATCCCGAATATCGGATCTAGACCCAGAATAAGGAATATCCCCAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAAATGCAATTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCATTTCAAAATGTAAACAGGATCACATATGGGGCCTGTCCCAGATATGTTAAGCAAAACACTCTGAAATTGGCAACAGGGATGCGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATCGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGTGGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAATAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCAATCAAATCAATGGGAAGCTGAATAGGTTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTAGAAGGGAGAATTCAGGACCTCGAGAAATATGTTGAGGACACTAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAGAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCATGATGTATACAGAGATGAAGCATTAAACAACCGGTTCCAGATCAAAGGCGTTGAGCTGAAGTCAGGATACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAAGGCAACATTAGGTGCAACATTTGCATTTGA"
}, {
"strain": "A/Brisbane/10/2007",
"db": "IRD",
"accession": "CY113005",
"date": "2007-02-06",
"seq": "ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCACTCAAAAACTTCCCGGAAATGACAACAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAATGACCAAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAGTTCCTCAACAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTCCAAAATAAGAAATGGGACCTTTTTGTTGAACGCAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGACTGGAGTCACTCAAAACGGAACAAGCTCTGCTTGCATAAGGAGATCTAATAACAGTTTCTTTAGTAGATTGAATTGGTTGACCCACTTAAAATTCAAATACCCAGCATTGAACGTGACTATGCCAAACAATGAAAAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTACGGACAATGACCAAATCTTCCCGTATGCTCAAGCATCAGGAAGAATCACAGTCTCTACCAAAAGAAGCCAACAAACTGTAATCCCGAATATCGGATCTAGACCCAGAGTAAGGAATATCCCCAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAAATGCAATTCTGAATGCATCACTCCAAACGGAAGCATTCCCAATGACAAACCATTCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCAAAACACTCTGAAATTGGCAACAGGGATGCGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATCGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGTGGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAATAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGATCAAATCAATGGGAAGCTGAATAGGTTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTCGAAGGGAGAATTCAGGACCTTGAGAAATATGTTGAGGACACCAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCACAATGTATACAGAGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGCGTTGAGCTGAAGTCAGGATACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAAGGCAACATTAGGTGCAACATTTGCATTTGA"
}, {
"strain": "A/Perth/16/2009",
"db": "IRD",
"accession": "GQ293081",
"date": "2009-04-07",
"seq": "ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAACTTCCTGGAAATGACAACAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAATGACCAAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAGTTCCTCAACAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAAAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTCCAAAATAAGAAATGGGACCTTTTTGTTGAACGCAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGACTGGAGTCACTCAAAACGGAACAAGCTCTGCTTGCATAAGGAGATCTAAAAACAGTTTCTTTAGTAGATTGAATTGGTTGACCCACTTAAACTTCAAATACCCAGCATTGAACGTGACTATGCCAAACAATGAACAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTACGGACAAAGACCAAATCTTCCTGTATGCTCAAGCATCAGGAAGAATCACAGTCTCTACCAAAAGAAGCCAACAAACCGTAAGCCCGAATATCGGATCTAGACCCAGAGTAAGGAATATCCCTAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAAATGCAATTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCATTCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCAAAACACTCTGAAATTGGCAACAGGGATGCGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATCGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGTGGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAAGAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGATCAAATCAATGGGAAGCTGAATAGATTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTCGAAGGGAGAATTCAGGACCTTGAGAAATATGTTGAGGACACTAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCACGATGTATACAGAGATGAAGCATTAAACAACCGGTTTCAGATCAAGGGAGTTGAGCTGAAGTCAGGGTACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAAGGCAACATTAGGTGCAACATTTGCATTTGA"
}, {
"strain": "A/Victoria/361/2011",
"db": "IRD",
"accession": "GQ293081",
"date": "2011-10-24",
"seq": "ATGAAGACTATCATTGCTTTGAGCCACATTCTATGTCTGGTTTTCGCTCAAAAACTTCCTGGAAATGACAACAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAATGACCAAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAATTCCTCAATAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTCCAAAATAAGAAATGGGACCTTTTTGTTGAACGAAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGACTGGAGTCACTCAAAACGGAACAAGTTCTGCTTGCATAAGGAGATCTAATAATAGTTTCTTTAGTAGATTAAATTGGTTGACCCGCTTAAACTTCAAATACCCAGCATTGAACGTGACTATGCCAAACAATGAACAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGTTACGGACAAGGAACAAATCTTCCTGTATGCTCAATCATCAGGAAGAATCACAGTATCTACCAAAAGAAGCCAACAAGCTGTAATCCCGAATATCGGATATAGACCCAGAATAAGGAATATCCCTAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAAATGCAATTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCATTCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCAAAGCACTCTGAAATTGGCAACAGGAATGCGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATAGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGTGGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAAGAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGATCAAATCAATGGGAAGCTGAATCGATTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTCGAAGGGAGAATTCAGGACCTTGAGAAATATGTTGAGGACACTAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGCAACTAAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCACGATGTATACAGAGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGAGTTGAGCTGAAGTCAGGGTACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAGGGCAACATTAGGTGCAACATTTGCATTTGA"
}, {
"strain": "A/Texas/50/2012",
"db": "GISAID",
"isolate_id": "EPI_ISL_129858",
"date": "2012-04-15",
"seq": "ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAACTTCCTGGAAATGACAATAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAATGACCGAATTGAAGTTACTAATGCTACTGAACTGGTTCAGAATTCCTCAATAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTCCAAAATAAGAAATGGGACCTTTTTGTTGAACGAAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGAATGGAGTCACTCAAAACGGAACAAGTTCTGCTTGCATAAGGAGATCTAATAATAGTTTCTTTAGTAGATTAAATTGGTTGACCCACTTAAACTTCAAATACCCAGCATTGAACGTGACTATGCCAAACAATGAACAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTACGGACAAGGACCAAATCTTCCTGTATGCTCAACCATCAGGAAGAATCACAGTATCTACCAAAAGAAGCCAACAAGCTGTAATCCCGAATATCGGATCTAGACCCAGAATAAGGAATATCCCTAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAAATGCAAGTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCATTCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCAAAGCACTCTGAAATTGGCAACAGGAATGCGGAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATAGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGTGGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAAGAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGATCAAATCAATGGGAAGCTGAATCGATTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTAGAAGGGAGAATTCAGGACCTTGAGAAATATGTTGAGGACACTAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCACGATGTATACAGAGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGAGTTGAGCTGAAGTCAGGGTACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAGGGCAACATTAGGTGCAACATTTGCATTTGA",
}, {
"strain": "A/Switzerland/9715293/2013",
"db": "GISAID",
"isolate_id": "EPI_ISL_162149",
"date": "2013-12-06",
"seq": "ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAACTTCCTGGAAATGACAATAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAATGACCGAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAATTCCTCAATAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTTCAAAATAAGAAATGGGACCTTTTTGTTGAACGAAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGGCTGGAGTCACTCAAAACGGAACAAGTTCTTCTTGCATAAGGGGATCTAATAGTAGTTTCTTTAGTAGATTAAATTGGTTGACCCACTTAAACTCCAAATACCCAGCATTAAACGTGACTATGCCAAACAATGAACAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTACGGACAAGGACCAAATCTTCCTGTATGCACAATCATCAGGAAGAATCACAGTATCTACCAAAAGAAGCCAACAAGCTGTAATCCCGAATATCGGATCTAGACCCAGAATAAGGGATATCCCTAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAAATGCAAGTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCATTCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCAAAGCACTCTGAAATTGGCAACAGGAATGCGAAATGTACCAGAGAGACAAACTAGAGGCATATTTGGCGCAATAGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGTGGATGGTTGGTACGGCTTCAGGCATCAAAATTCTGAGGGAAGAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGATCAAATCAATGGGAAGCTGAATCGATTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTAGAAGGGAGAATTCAGGACCTTGAGAAATATGTTGAGGACACAAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCACGATGTATACAGGGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGAGTTGAGCTGAAGTCAGGGTACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAGGGCAACATTAGGTGCAACATTTGCATTTGA",
}
]
tmp_outgroup = SeqIO.read('source-data/H3N2_outgroup.gb', 'genbank')
genome_annotation = tmp_outgroup.features
self.cds = {x.qualifiers['gene'][0]:x for x in genome_annotation
if 'gene' in x.qualifiers and x.type=='CDS' and
x.qualifiers['gene'][0] in ['SigPep', 'HA1', 'HA2']}
self.outgroup = {
'strain': 'A/Beijing/32/1992',
'db': 'IRD',
'accession': 'U26830',
'date': '1992-01-01',
'country': 'China',
'region': 'China',
'seq': str(tmp_outgroup.seq).upper()
}
def __init__(self,min_length = 0, **kwargs):
'''
parameters
min_length -- minimal length for a sequence to be acceptable
'''
flu_filter.__init__(self, **kwargs)
self.min_length = min_length
self.vaccine_strains =[
{
"strain": "A/Chicken/HongKong/G9/97",
"db": "GISAID",
"accession": "EPI_ISL_1263",
"date": "1997-07-01",
"seq": "ATGGAAATAATAGCACTAATAGCTATACTGGTAGTGACAAAAACAAGCAATGCAGATAAAATTTGCATTGGCTACCAGTCAACAAACTCCACAGAAACTGTTGATACACTAGTAGAAAACAATGTCCCTGTGACACATACCAAAGAATTGCTCCACACAGAGCACAATGGAATGCTATGTGCAACAAACCTGGGGCACCCTCTCATCCTAGACACCTGCACCATCGAAGGGTTGGTGTACGGCAACCCTTCCTGTGATTTGCTACTGGGAGGGAAAGAATGGTCTTACATTGTCGAAAGATCATCAGCTGTCAATGGGATGTGTTACCCTGGAAGGGTAGAGAACCTGGAAGAACTCAGGTCTTTTTTCAGCTCCGCTCGCTCCTACAAAAGACTCCTGCTCTTTCCAGACAGAACTTGGAATGTGACTTACACTGGGACAAGCAAAGCATGTTCAAACTCATTCTACAGAAGTATGAGATGGCTGACACACAAGAGCGATTCTTACCCTATTCAAGACGCCCAATATACTAACGATTGGGGAAAGAATATTCTCTTCATGTGGGGCATACACCACCCACCTACTGATACTGAGCAAATAAATCTATACAAAAAAGCTGATACAACAACAAGTATAACAACGGAAGATATCAATCGAACTTTCAAACCAGTGATAGGGCCAAGGCCTCTTGTCAATGGTCAACAAGGGAGAATTGATTATTATTGGTCAGTACTAAAGCCAGGCCAGACACTGCGAGTGAGATCCAATGGGAATCTAATTGCCCCATGGTATGGACACATTCTTTCAGGAGAAAGCCATGGAAGAATCTTGAAGACCGATTTGAGTAGTGGCAACTGCGTAGTACAATGCCAAACTGAGAAAGGTGGTTTGAACACGACCTTGCCATTCCACAATGTCAGCAAGTATGCATTTGGGAACTGCCCCAAATATGTTGGAGTGAAGAGTCTCAAACTGGCAGTTGGTCTAAGGAATGTTCCTGCTGCATCATATAGAGGGCTCTTCGGTGCCATAGCTGGATTCATAGAAGGCGGTTGGCCAGGACTAGTTGCAGGCTGGTACGGGTTTCAGCATTCAAATGATCAAGGGGTTGGAATGGCCGCAGATAGGGAATCAACTCAAGAAGCAGTTGACAAGATAACATCCAAAGTAAATAACATAATCGACAAAATGAACAAGCAGTATGGA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T--------------------------------------------------------------------------------------"}
]
tmp_outgroup = SeqIO.read('/Users/yujiazhou/Documents/FluProject/augur/source-data/H9_outgroup.gb', 'genbank')
genome_annotation = tmp_outgroup.features
self.cds = {x.qualifiers['gene'][0]:x for x in genome_annotation
if 'gene' in x.qualifiers and x.type=='CDS' and
x.qualifiers['gene'][0] in ['SigPep', 'HA1', 'HA2']}
self.outgroup = {
'strain': 'A/duck/HongKong/147/1977',
'db': 'IRD',
'accession': 'AY206671',
'date': '2003-03-03',
'country': 'HongKong',
'region': 'EastAsia',
'seq': str(tmp_outgroup.seq).upper()
}
def __init__(self,min_length = 0, **kwargs):
'''
parameters
min_length -- minimal length for a sequence to be acceptable
'''
flu_filter.__init__(self, **kwargs)
self.min_length = min_length
self.vaccine_strains =[
{
'strain': 'A/ruddyshelduck/Mongolia/1626/2010',
'isolate_id': 'EPI-ISL-149888',
'date': '2010-09-11',
'lab': 'Other Database Import',
'region': 'NorthAsia',
'seq': 'ATGCTATCAATTGTGATTTTGTTTCTGCTTGTTGCAGAGAGCTCTTCTCAAAACTACACAGGAAACCCTGTGATATGCATGGGACATCATGCTGTGGCCAATGGGACTATGGTAAAGACCCTTACTGATGATCAAGTGGAAGTGGTCACTGCACAAGAATTGGTGGAATCACAGAACCTCCCGGAACTATGCCCGAGTCCTCTAAGACTAGTCGATGGCCAGACCTGTGATATCATCAATGGAGCCTTAGGAAGCCCAGGATGTGACCATTTGAATGGTGCTGAATGGGACATTTTCATAGAAAGGCCCAATGCAGTGGACACTTGCTATCCATTTGATGTGCCAGATTATCAGAGCCTAAGGAGCATACTCGCCAACAATGGGAAATTCGAATTCATTGCTGAAGAATTCCAATGGAGCACCGTGAAGCAAAATGGCAAGTCCGGGGCCTGCAAGAGGGCAAATGTGAACGATTTCTTTAATAAACTGAATTGGCTCGTGAAGTCAGACGGGAATGCATACCCTCTCCAGAATTTGACAAAAGTAAACAACGGTGATTACGCGAGGCTTTACATCTGGGGAGTTCACCACCCTTCGACGGATACCGAGCAAACCGATCTGTACAAGAACAATCCTGGTAGGGTCACTGTATCTACCAAAATCAGTCAAACAAGTGTAGTGCCCAACATTGGCAGCAGACCTTGGGTGAGAGGACAAAGTGGCAGAATCAGCTTCTATTGGACTATTGTAGAGCCTGGAGATTTGATAGTCTTCAACACAATAGGAAATTTAATTGCCCCAAGAGGACATTACAAATTAAACAGTCAGAAGAAGAGCACAATTCTGAACACTGCGACTCCCATAGGCTCATGTGTCAGTAAATGTCATACAGACAAAGGTTCTCTCTCTACCACCAAGCCCTTTCAAAATATCTCAAGGATAGCAGTTGGAGATTGTCCCAAATATGTTAAACAAGGCTCCCTAAAACTTGCAACTGGGATGAGAAATATCCCTGAAAAGGCATCAAGAGGGCTTTTTGGGGCAATAGCTGGGTTCATAGAGAATGGATGGCAAGGTCTGATTGATGGTTGGTATGGCTTCAGACACCAAAATGCAGAAGGAACAGGAACAGCTGTTGATCTAAAATCCACTCAGGCAGCCATCGATCAAATCAATGGAAAACTCAATCGTCTTATTGAGAAAACAAACGAGAAATACCATCAAATCGAAAAAGAATTCGAACAAGTTGAAGGAAGAATCCAAGACCTGGAGAAGTATGTTGAAGACACAAAGATTGATCTATGGTCATATAATGCAGAGCTATTAGTCGCTCTGGAAAACCAGCATACTATAGATGTGACTGACTCGGAGATGAACAAGCTCTTTGAAAGAGTAAGGCGACAACTCAGGGAGAATGCTGAAGACAGAGGAAATGGGTGTTTTGAAATATTCCACAAATGTGACAACAACTGCATTGAAAGCATTCGGAATGGGACCTATGATCATGATGTTTATAGAGATGAAGCGATCAACAATCGATTCCAAATACAGGGAGTCAAATTGACCCAGGGATACAAGGACATCATCCTTTGGATTTCGTTCTCCATATCATGCTTTTTGCTCGTAGCACTGCTTTTGGCCTTCATTTTGTGGGCTTGTCAGAACGGAAACATCCGGTGCCAGATT---TGCATTTGA',
}
]
tmp_outgroup = SeqIO.read('/Users/yujiazhou/Documents/nextflu/H9_nextflu-master/augur/source-data/H4_outgroup.gb', 'genbank')
genome_annotation = tmp_outgroup.features
self.cds = {x.qualifiers['gene'][0]:x for x in genome_annotation
if 'gene' in x.qualifiers and x.type=='CDS' and
x.qualifiers['gene'][0] in ['SigPep', 'HA1', 'HA2']}
self.outgroup = {
'strain': 'A/Duck/Czechoslovakia/1956',
'db': 'OtherDatabaseImport',
'accession': 'EPI-ISL-70104',
'date': '1956-01-01',
'country': 'Czech Republic',
'region': 'Europe',
'seq': str(tmp_outgroup.seq).upper()
}
def __init__(self, aln_fname, outgroup, include_ref_strains = True, outdir = './', formats = ['pdf','png'], verbose = 0, **kwargs):
process.__init__(self, **kwargs)
flu_filter.__init__(self, alignment_file = aln_fname, **kwargs)
tree_refine.__init__(self, **kwargs)
virus_clean.__init__(self, **kwargs)
self.midpoint_rooting = False
self.include_ref_strains = include_ref_strains
self.verbose = verbose
self.formats = formats
self.outdir = outdir.rstrip('/')+'/'
self.auspice_tree_fname = self.outdir + 'tree.json'
self.auspice_align_fname = self.outdir + 'aln.fasta'
self.auspice_aa_align_fname = self.outdir + 'aa_aln.fasta'
self.auspice_sequences_fname = self.outdir + 'sequences.json'
self.auspice_frequencies_fname = None
self.auspice_meta_fname = self.outdir + 'meta.json'
self.path_to_augur = path_to_augur
if os.path.isfile(outgroup):
tmp = [{'strain':seq.name, 'seq':str(record.seq).upper(), 'desc':seq.description}
for seq in SeqIO.parse(outgroup, 'fasta') ]
if len(tmp):
self.outgroup = tmp[0]
if len(tmp)>1:
print "More than one sequence in ", outgroup, "taking first"
if self.verbose:
print "using outgroup found in file ", outgroup
elif outgroup=='auto':
print "automatically determine outgroup"
self.auto_outgroup_blast()
elif isinstance(outgroup, basestring):
seq_names = [x['strain'] for x in self.viruses]
if outgroup in seq_names:
self.outgroup = self.viruses.pop(seq_names.index(outgroup))
if self.verbose:
print "using outgroup found in alignment", outgroup
else:
standard_outgroups = self.load_standard_outgroups()
if outgroup in standard_outgroups:
self.outgroup = standard_outgroups[outgroup]
if self.verbose:
print "using standard outgroup", outgroup
else:
raise ValueError("outgroup %s not found" % outgroup)
return
if "anno:" in self.outgroup['desc']:
anno = [x for x in self.outgroup['desc'].split() if "anno:" in x][0]
anno = (anno.split(':')[1]).split('_')
tmp = [(anno[2*i], int(anno[2*i+1])) for i in range(len(anno)/2)]
self.anno = sorted(tmp, key=lambda x:x[1])
print("Using annotation",self.anno)
else:
self.anno = None
print("No annotation found")
#self.anno = sorted((('SP',0), ('HA1',16), ('HA2',329+16)), key=lambda x:x[1])
self.viruses.append(self.outgroup)
self.filter_geo(prune=False)
self.make_strain_names_unique()
def __init__(self,min_length = 0, **kwargs):
'''
parameters
min_length -- minimal length for a sequence to be acceptable
'''
flu_filter.__init__(self, **kwargs)
self.min_length = min_length
self.vaccine_strains =[
{
'strain': 'A/turkey/Italy/3889/99',
'isolate_id': 'EPI-ISL-2746',
'date': '1990-07-01', #(Month and day unknown)
'region': 'Europe',
'seq': 'ATGAACACTCAAATCCTGGTATTCGCTCTGGTGGCGATCATTCCGACAAATGCAGACAAAATCTGCCTTGGGCATCATGCCGTGTCAAACGGGACTAAAGTAAACACATTAACTGAAAGAGGAGTGGAAGTCGTTAATGCAACTGAAACGGTGGAACGAACAAACGTCCCCAGGATCTGCTCAAAAGGGAAAAGGACAGTTGACCTCGGTCAATGTGGACTTCTGGGAACAATCACTGGGCCACCCCAATGTGACCAATTCCTAGAATTTTCAGCCGATCTAATTATTGAGAGGCGAGAAGGAAGTGGTGTCTGTTATCCTGGGAAATTCGTGAATGAAGAAGCTCTGAGGCAAATTCTCAGGGAGTCAGGCGGAATTGACAAGGAGACAATGGGATTCACATACAGCGGAATAAGAACTAATGGAACAACCAGTGCATGTAGGAGATTAGGATCTTCATTCTATGCAGAGATGAAATGGCTCCTGTCAAACACAGACAATGCTGCTTTCCCGCAGATGACTAAGTCATACAAAAACACAAGGAAAGACCCAGCTCTGATAATATGGGGGATCCACCATTCCGGATCAACTACAGAACAGACCAAGCTATATGGGAGTGGAAACAAACTGATAACAGTTGGGAGTTCTAATTACCAACAGTCCTTTGTACCGAGTCCAGGAGCGAGACCACAAGTGAATGGCCAATCTGGAAGAATTGACTTTCATTGGCTGATGCTAAACCCCAATGACACAGTCACTTTCAGTTTCAATGGGGCCTTCATAGCTCCAGACCGTGCAAGTTTTCTGAGAGGGAAGTCTATGGGGATTCAGAGTGGAGTACAGGTTGATGCCAATTGTGAAGGAGATTGCTATCACAGTGGAGGGACAATAATAAGTAATTTGCCCTTTCAGAACATAAATAGCAGGGCAGTAGGGAAATGTCCGAGATATGTTAAGCAAGAGAGTCTGCTGCTGGCAACAGGGATGAAGAATGTTCCCGAAGTTCCAAAGGGA------------------------------AGAGGCCTATTTGGTGCTATAGCGGGTTTCATTGAAAATGGATGGGAAGGTCTGATTGATGGGTGGTATGGCTTCAGGCATCAAAATGCACAAGGGGAGGGAACTGCTGCAGATTACAAAAGCACCCAATCAGCAATTGATCAAGTAACAGGAAAATTGAACCGGCTTATAGAAAAAACTAACCAACAATTTGAGTTAATAGACAATGAATTCACTGAGGTTGAAAAGCAAATTGGCAATGTGATAAATTGGACCAGAGATTCCATGACAGAAGTGTGGTCCTATAACGCTGAACTCTTGGTAGCAATGGAGAACCAGCACACAATTGATCTGGCCGACTCAGAAATGAACAAACTATACGAACGAGTGAAGAGACAACTGAGAGAGAATGCTGAAGAAGATGGCACTGGTTGCTTCGAAATATTTCACAAGTGTGATGACGACTGTATGGCCAGTATTAGAAACAACACCTATGATCACAGCAAGTACAGGGAAGAGGCAATGCAAAATAGAATACAGATTGACCCAGTCAAACTAAGCAGCGGCTACAAAGATGTGATACTTTGGTTTAGCTTCGGGGCATCATGTTTCATACTTCTGGCCATTGCAATGGGCCTTGTCTTCATATGTGTGAAGAATGGAAACATGCGGTGCACTATTTGTATATAA',
},
{
'strain': 'A/mallard/Netherlands/12/00',
'isolate_id': 'EPI-ISL-3548',
'date': '2000-07-01', # (Month and day unknown)
'region': 'Europe',
'seq': 'ATGAACACTCAAATCCTGGTATTCGCTCTGATGGCGATCATTCCGACAAATGCAGACAAGATCTGCCTTGGGCATCATGCCGTGTCAAACGGGACTAAAGTAAACACATTAACTGAAAGAGGAGTGGAAGTCGTTAATGCAACTGAAACGGTGGAACGAACAAACGTCCCCAGGATCTGCTCAAAAGGGAAAAGGACAGTTGACCTTGGTCAATGTGGACTTCTGGGAACAATCACTGGGCCGCCCCAATGTGACCAATTCCTAGAATTTTCAGCCGATTTAATTATTGAGAGGCGAGAAGGAAGTGATGTCTGTTATCCTGGGAAATTCGTGAATGAAGAAGCTCTGAGGCAAATTCTCAGGGAGTCAGGCGGAATTGACAAGGAGACAATGGGATTCACCTACAGCGGAATAAGAACTAATGGAGCAACCAGTGCATGTAGGAGATCAGGATCTTCATTCTATGCAGAGATGAAATGGCTCCTGTCAAACACAGACAATGCTGCTTTCCCGCAGATGACTAAGTCATACAAAAACACAAGGAAAGACCCAGCTCTGATAATATGGGGGATCCACCATTCCGGATCAACTACAGAACAGACCAAGCTATATGGGAGTGGAAACAAACTGATAACAGTTGGGAGTTCTAATTACCAACAGTCCTTTGTACCGAGTCCAGGAGCGAGACCACAAGTAAATGGCCAATCTGGAAGAATTGACTTTCATTGGCTGATACTAAACCCCAATGACACAGTTACTTTCAGTTTCAATGGGGCCTTCATAGCTCCAGACCGTGCAAGCTTTCTGAGAGGGAAGTCTATGGGAATTCAGAGTGGAGTACAGGTTGATGCCAATTGTGAAGGAGATTGCTATCATAGTGGAGGGACAATAATAAGTAATTTGCCCTTTCAGAACATAAATAGCAGGGCAGTAGGAAAATGTCCGAGATATGTTAAGCAAGAGAGTCTGCTGCTGGCAACAGGAATGAAGAATGTTCCCGAAATCCCAAAGGGA------------------------------AGAGGCCTATTTGGTGCTATAGCGGGTTTCATTGAAAATGGATGGGAAGGTCTGATTGATGGGTGGTATGGCTTCAGGCATCAAAATGCACAAGGGGAGGGAACTGCTGCAGATTACAAAAGCACCCAATCAGCAATTGATCAAATAACAGGAAAATTAAACCGGCTTATAGAAAAAACTAACCAACAATTTGAGTTAATAGACAATGAATTCACTGAGGTTGAAAAGCAAATTGGCAATGTGATAAATTGGACCAGAGATTCCATGACAGAAGTGTGGTCCTATAACGCTGAACTCTTGGTAGCAATGGAGAATCAGCACACAATTGATCTGGCCGACTCAGAAATGAACAAACTGTACGAACGAGTGAAGAGACAACTGAGAGAGAATGCTGAAGAAGATGGCACTGGTTGCTTCGAAATATTTCACAAGTGTGATGACGACTGTATGGCCAGTATTAGAAACAACACCTATGATCACAGCAAGTACAGGGAAGAGGCAATGCAAAATAGAATACAGATTGACCCAGTCAAACTAAGCAGCGGCTACAAAGATGTGATACTTTGGTTTAGCTTCGGGGCATCATGTTTCATACTTCTGGCCATTGCAATGGGCCTTGTCTTCATATGTGTGAAGAATGGAAACATGCGGTGCACTATTTGTATATAA',
},
{
'strain': 'A/human/New-York/107/2003',
'isolate_id': 'EPI-ISL-16424',
'date': '2003-07-01',
'region': 'NorthAmerica',
'seq': 'ATGAACACTCAAATTCTGGCATTCATTGCTTGTGTGCTGACTGGAGTTAAAGGAGACAAAATATGTCTTGGGCACCATGCTGTGGCAAATGGAACAAAAGTGAACACATTAACAGAGAGGGGGATTGAAGTAGTGAATGCCACAGAGACAGTGGAAACTACGAATATCAAGAAAATATGTACCCAGGGGAAAAGGCCAACAGATCTGGGACAATGTGGACTTCTAGGAACCCTAATAGGACCTCCCCAATGTGATCAATTCCTGGAGTTTTCCTCTGATTTGATAATTGAGCGAAGAGAAGGAACCGATATATGCTATCCCGGTAGATTCACAAACGAAGAATCACTGAGGCAGATCCTTCGAAGATCAGGAGGAATTGGTAAGGAGTCAATGGGCTTCACCTATAGTGGAATAAGAACCAATGGAGCGACAAGTGCCTGCACAAGATCAGGTTCTTCTTTCTATGCAGAGATGAAGTGGTTGCTGTCGAATTCAGATAATGCAGCATTCCCACAGATGACAAAGGCGTATAGAAATCCCAGAAACAAACCAGCTCTGATAATTTGGGGAGTTCATCACTCTGAATCGGTTAGCGAGCAGACCAAACTCTATGGAAGTGGAAACAAGTTGATAACAGTAAGAAGCTCAAAATACCAGCAATCATTCACCCCAAATCCGGGAGCACGA------------------------AGAATCGATTTCCACTGGCTACTCCTTGATCCCAATGACACAGTGACCTTCACTTTCAATGGAGCATTCATAGCCCCTGACAGGACAAGTTTCTTTAGGGGAGAATCACTAGGAGTCCAGAGTGATGCTCCTTTGGATTCAAGTTGTAGAGGAGATTGCTTTCACAGTGGGGGTACGATAGTCAGTTCCCTGCCATTCCAAAACATCAACTCTAGAACTGTGGGGAAATGCCCTCGGTATGTCAAACAGAAAAGCCTCCTTCTGGCTACAGGAATGAGAAATGTTCCAGAGAAACCAAAGCCC------------------------------AGAGGCCTTTTTGGAGCAATTGCTGGATTCATAGAGAATGGATGGGAGGGTCTCATCAATGGATGGTATGGTTTCAGACATCAAAATGCACAAGGAGAGGGAACTGCAGCTGACTACAAAAGCACCCAGTCTGCAATAGATCAGATCACAGGCAAATTGAATCGTTTAATTGGCAAAACAAATCAGCAGTTTGAGCTGATAGACAATGAGTTCAATGAGATAGAACAACAAATAGGAAATGTCATTAATTGGACAAGAGACGCAATGACTGAGATATGGTCGTATAATGCTGAGCTGTTGGTGGCAATGGAAAATCAGCATACAATAGATCTTGCGGACTCAGAAATGAGCAAACTTTATGAGCGTGTCAAAAAACAACTAAGGGAGAATGCTGAAGAAGATGGAACTGGATGTTTTGAGATATTTCATAAATGTGACGATCAGTGTATGGAGAGCATAAGGAACAACACGTATGACCATACTCAATACAGAACAGAGTCATTGCAGAATAGAATACAGATAGACCCAGTGAAGTTGAGTAGTGGGTACAAAGACATAATCTTATGGTTTAGCTTCGGGGCATCATGTTTTCTTCTTCTAGCCATTGCAATGGGACTGGTTTTCATTTGCATAAAGAATGGAAACATGCAGTGCACTATTTGTATATAG',
},
{
'strain': 'A/human/Shanghai/2/2013',
'isolate_id': 'EPI-ISL-138738',
'date': '2013-03-05',
'region': 'China',
'seq': 'ATGAACACTCAAATCCTGGTATTCGCTCTGATTGCGATCATTCCAACAAATGCAGACAAAATCTGCCTCGGACATCATGCCGTGTCAAACGGAACCAAAGTAAACACATTAACTGAAAGAGGAGTGGAAGTCGTCAATGCAACTGAAACAGTGGAACGAACAAACATCCCCAGGATCTGCTCAAAAGGGAAAAGGACAGTTGACCTCGGTCAATGTGGACTCCTGGGGACAATCACTGGACCACCTCAATGTGACCAATTCCTAGAATTTTCAGCCGATTTAATTATTGAGAGGCGAGAAGGAAGTGATGTCTGTTATCCTGGGAAATTCGTGAATGAAGAAGCTCTGAGGCAAATTCTCAGAGAATCAGGCGGAATTGACAAGGAAGCAATGGGATTCACATACAGTGGAATAAGAACTAATGGAGCAACCAGTGCATGTAGGAGATCAGGATCTTCATTCTATGCAGAAATGAAATGGCTCCTGTCAAACACAGATAATGCTGCATTCCCGCAGATGACTAAGTCATATAAAAATACAAGAAAAAGCCCAGCTCTAATAGTATGGGGGATCCATCATTCCGTATCAACTGCAGAGCAAACCAAGCTATATGGGAGTGGAAACAAACTGGTGACAGTTGGGAGTTCTAATTATCAACAATCTTTTGTACCGAGTCCAGGAGCGAGACCACAAGTTAATGGTCTATCTGGAAGAATTGACTTTCATTGGCTAATGCTAAATCCCAATGATACAGTCACTTTCAGTTTCAATGGGGCTTTCATAGCTCCAGACCGTGCAAGCTTCCTGAGAGGAAAATCTATGGGAATCCAGAGTGGAGTACAGGTTGATGCCAATTGTGAAGGGGACTGCTATCATAGTGGAGGGACAATAATAAGTAACTTGCCATTTCAGAACATAGATAGCAGGGCAGTTGGAAAATGTCCGAGATATGTTAAGCAAAGGAGTCTGCTGCTAGCAACAGGGATGAAGAATGTTCCTGAGATTCCAAAAGGA------------------------------AGAGGCCTATTTGGTGCTATAGCGGGTTTCATTGAAAATGGATGGGAAGGCCTAATTGATGGTTGGTATGGTTTCAGACACCAGAATGCACAGGGAGAGGGAACTGCTGCAGATTACAAAAGCACTCAATCGGCAATTGATCAAATAACAGGAAAATTAAACCGGCTTATAGAAAAAACCAACCAACAATTTGAGTTGATAGACAATGAATTCAATGAGGTAGAGAAGCAAATCGGTAATGTGATAAATTGGACCAGAGATTCTATAACAGAAGTGTGGTCATACAATGCTGAACTCTTGGTAGCAATGGAGAACCAGCATACAATTGATCTGGCTGATTCAGAAATGGACAAACTGTACGAACGAGTGAAAAGACAGCTGAGAGAGAATGCTGAAGAAGATGGCACTGGTTGCTTTGAAATATTTCACAAGTGTGATGATGACTGTATGGCCAGTATTAGAAATAACACCTATGATCACAGCAAATACAGGGAAGAGGCAATGCAAAATAGAATACAGATTGACCCAGTCAAACTAAGCAGCGGCTACAAAGATGTGATACTTTGGTTTAGCTTCGGGGCATCATGTTTCATACTTCTAGCCATTGTAATGGGCCTTGTCTTCATATGTGTAAAGAATGGAAACATGCGGTGCACTATTTGTATATAA',
},
{
'strain': 'A/human/Anhui/1/2013',
'isolate_id': 'EPI-ISL-138739',
'date': '2013-03-20',
'region': 'China',
'seq': 'ATGAACACTCAAATCCTGGTATTCGCTCTGATTGCGATCATTCCAACAAATGCAGACAAAATCTGCCTCGGACATCATGCCGTGTCAAACGGAACCAAAGTAAACACATTAACTGAAAGAGGAGTGGAAGTCGTCAATGCAACTGAAACAGTGGAACGAACAAACATCCCCAGGATCTGCTCAAAAGGGAAAAGGACAGTTGACCTCGGTCAATGTGGACTCCTGGGGACAATCACTGGACCACCTCAATGTGACCAATTCCTAGAATTTTCAGCCGATTTAATTATTGAGAGGCGAGAAGGAAGTGATGTCTGTTATCCTGGGAAATTCGTGAATGAAGAAGCTCTGAGGCAAATTCTCAGAGAATCAGGCGGAATTGACAAGGAAGCAATGGGATTCACATACAGTGGAATAAGAACTAATGGAGCAACCAGTGCATGTAGGAGATCAGGATCTTCATTCTATGCAGAAATGAAATGGCTCCTGTCAAACACAGATAATGCTGCATTCCCGCAGATGACTAAGTCATATAAAAATACAAGAAAAAGCCCAGCTCTAATAGTATGGGGGATCCATCATTCCGTATCAACTGCAGAGCAAACCAAGCTATATGGGAGTGGAAACAAACTGGTGACAGTTGGGAGTTCTAATTATCAACAATCTTTTGTACCGAGTCCAGGAGCGAGACCACAAGTTAATGGTCTATCTGGAAGAATTGACTTTCATTGGCTAATGCTAAATCCCAATGATACAGTCACTTTCAGTTTCAATGGGGCTTTCATAGCTCCAGACCGTGCAAGCTTCCTGAGAGGAAAATCTATGGGAATCCAGAGTGGAGTACAGGTTGATGCCAATTGTGAAGGGGACTGCTATCATAGTGGAGGGACAATAATAAGTAACTTGCCATTTCAGAACATAGATAGCAGGGCAGTTGGAAAATGTCCGAGATATGTTAAGCAAAGGAGTCTGCTGCTAGCAACAGGGATGAAGAATGTTCCTGAGATTCCAAAGGGA------------------------------AGAGGCCTATTTGGTGCTATAGCGGGTTTCATTGAAAATGGATGGGAAGGCCTAATTGATGGTTGGTATGGTTTCAGACACCAGAATGCACAGGGAGAGGGAACTGCTGCAGATTACAAAAGCACTCAATCGGCAATTGATCAAATAACAGGAAAATTAAACCGGCTTATAGAAAAAACCAACCAACAATTTGAGTTGATAGACAATGAATTCAATGAGGTAGAGAAGCAAATCGGTAATGTGATAAATTGGACCAGAGATTCTATAACAGAAGTGTGGTCATACAATGCTGAACTCTTGGTAGCAATGGAGAACCAGCATACAATTGATCTGGCTGATTCAGAAATGGACAAACTGTACGAACGAGTGAAAAGACAGCTGAGAGAGAATGCTGAAGAAGATGGCACTGGTTGCTTTGAAATATTTCACAAGTGTGATGATGACTGTATGGCCAGTATTAGAAATAACACCTATGATCACAGCAAATACAGGGAAGAGGCAATGCAAAATAGAATACAGATTGACCCAGTCAAACTAAGCAGCGGCTACAAAGATGTGATACTTTGGTTTAGCTTCGGGGCATCATGTTTCATACTTCTAGCCATTGTAATGGGCCTTGTCTTCATATGTGTAAAGAATGGAAACATGCGGTGCACTATTTGTATATAA',
}
]
tmp_outgroup = SeqIO.read('/Users/yujiazhou/Documents/nextflu/H9_nextflu-master/augur/source-data/H7_outgroup.gb', 'genbank')
genome_annotation = tmp_outgroup.features
self.cds = {x.qualifiers['gene'][0]:x for x in genome_annotation
if 'gene' in x.qualifiers and x.type=='CDS' and
x.qualifiers['gene'][0] in ['SigPep', 'HA1', 'HA2']}
self.outgroup = {
'strain':'A/equine/Prague/2/1956',
'db': 'Other-Database-Import',
'isolate_id':'EPI-ISL-89157',
'date':'1956-06-11',
'country': 'CzechRepublic',
'region':'Europe',
'seq':str(tmp_outgroup.seq).upper()
}
def __init__(self,
aln_fname,
outgroup,
outdir='./',
formats=['pdf', 'svg', 'png'],
verbose=0,
**kwargs):
process.__init__(self, **kwargs)
flu_filter.__init__(self, alignment_file=aln_fname, **kwargs)
tree_refine.__init__(self, **kwargs)
virus_clean.__init__(self, **kwargs)
self.verbose = verbose
self.formats = formats
self.outdir = outdir.rstrip('/') + '/'
self.auspice_tree_fname = self.outdir + 'tree.json'
self.auspice_sequences_fname = self.outdir + 'sequences.json'
self.auspice_frequencies_fname = None
self.auspice_meta_fname = self.outdir + 'meta.json'
if os.path.isfile(outgroup):
tmp = [{
'strain': seq.name,
'seq': str(record.seq).upper(),
'desc': seq.description
} for seq in SeqIO.parse(outgroup, 'fasta')]
if len(tmp):
self.outgroup = tmp[0]
if len(tmp) > 1:
print "More than one sequence in ", outgroup, "taking first"
if self.verbose:
print "using outgroup found in file ", outgroup
elif isinstance(outgroup, basestring):
seq_names = [x['strain'] for x in self.viruses]
if outgroup in seq_names:
self.outgroup = self.viruses.pop(seq_names.index(outgroup))
if self.verbose:
print "using outgroup found in alignment", outgroup
else:
standard_outgroups = [{
'strain': seq.name,
'seq': str(seq.seq).upper(),
'desc': seq.description
} for seq in SeqIO.parse(std_outgroup_file, 'fasta')]
outgroup_names = [x['strain'] for x in standard_outgroups]
if outgroup in outgroup_names:
self.outgroup = standard_outgroups[outgroup_names.index(
outgroup)]
if self.verbose:
print "using standard outgroup", outgroup
else:
raise ValueError("outgroup %s not found" % outgroup)
return
self.viruses.append(self.outgroup)
self.filter_geo(prune=False)
#self.filter_host(prune=False)
self.make_strain_names_unique()
def __init__(self,min_length = 987, **kwargs):
'''
parameters
min_length -- minimal length for a sequence to be acceptable
'''
flu_filter.__init__(self, **kwargs)
self.min_length = min_length
self.vaccine_strains =[
{
"strain": "A/Wisconsin/67/2005",
"db": "IRD",
"accession": "CY163984",
"date": "2005-08-31",
"seq": "ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAACTTCCCGGAAATGACAACAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAATGACCAAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAGTTCCTCAACAGGTGGAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTCCAAAATAAGAAATGGGACCTTTTTGTTGAACGCAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACGATGAAAGCTTCAATTGGACTGGAGTCACTCAAAATGGAACAAGCTCTTCTTGCAAAAGGAGATCTAATAACAGTTTCTTTAGTAGATTGAATTGGTTGACCCACTTAAAATTCAAATACCCAGCATTGAACGTGACTATGCCAAACAATGAAAAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGTTACGGACAATGACCAAATCTTCCTGTATGCTCAAGCATCAGGAAGAATCACAGTCTCTACCAAAAGAAGCCAACAAACTGTAATCCCGAATATCGGATCTAGACCCAGAATAAGGAATATCCCCAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAAATGCAATTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCATTTCAAAATGTAAACAGGATCACATATGGGGCCTGTCCCAGATATGTTAAGCAAAACACTCTGAAATTGGCAACAGGGATGCGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATCGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGTGGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAATAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCAATCAAATCAATGGGAAGCTGAATAGGTTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTAGAAGGGAGAATTCAGGACCTCGAGAAATATGTTGAGGACACTAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAGAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCATGATGTATACAGAGATGAAGCATTAAACAACCGGTTCCAGATCAAAGGCGTTGAGCTGAAGTCAGGATACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAAGGCAACATTAGGTGCAACATTTGCATTTGA"
}, {
"strain": "A/Brisbane/10/2007",
"db": "IRD",
"accession": "CY113005",
"date": "2007-02-06",
"seq": "ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCACTCAAAAACTTCCCGGAAATGACAACAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAATGACCAAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAGTTCCTCAACAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTCCAAAATAAGAAATGGGACCTTTTTGTTGAACGCAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGACTGGAGTCACTCAAAACGGAACAAGCTCTGCTTGCATAAGGAGATCTAATAACAGTTTCTTTAGTAGATTGAATTGGTTGACCCACTTAAAATTCAAATACCCAGCATTGAACGTGACTATGCCAAACAATGAAAAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTACGGACAATGACCAAATCTTCCCGTATGCTCAAGCATCAGGAAGAATCACAGTCTCTACCAAAAGAAGCCAACAAACTGTAATCCCGAATATCGGATCTAGACCCAGAGTAAGGAATATCCCCAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAAATGCAATTCTGAATGCATCACTCCAAACGGAAGCATTCCCAATGACAAACCATTCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCAAAACACTCTGAAATTGGCAACAGGGATGCGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATCGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGTGGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAATAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGATCAAATCAATGGGAAGCTGAATAGGTTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTCGAAGGGAGAATTCAGGACCTTGAGAAATATGTTGAGGACACCAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCACAATGTATACAGAGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGCGTTGAGCTGAAGTCAGGATACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAAGGCAACATTAGGTGCAACATTTGCATTTGA"
}, {
"strain": "A/Perth/16/2009",
"db": "IRD",
"accession": "GQ293081",
"date": "2009-04-07",
"seq": "ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAACTTCCTGGAAATGACAACAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAATGACCAAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAGTTCCTCAACAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAAAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTCCAAAATAAGAAATGGGACCTTTTTGTTGAACGCAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGACTGGAGTCACTCAAAACGGAACAAGCTCTGCTTGCATAAGGAGATCTAAAAACAGTTTCTTTAGTAGATTGAATTGGTTGACCCACTTAAACTTCAAATACCCAGCATTGAACGTGACTATGCCAAACAATGAACAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTACGGACAAAGACCAAATCTTCCTGTATGCTCAAGCATCAGGAAGAATCACAGTCTCTACCAAAAGAAGCCAACAAACCGTAAGCCCGAATATCGGATCTAGACCCAGAGTAAGGAATATCCCTAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAAATGCAATTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCATTCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCAAAACACTCTGAAATTGGCAACAGGGATGCGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATCGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGTGGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAAGAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGATCAAATCAATGGGAAGCTGAATAGATTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTCGAAGGGAGAATTCAGGACCTTGAGAAATATGTTGAGGACACTAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCACGATGTATACAGAGATGAAGCATTAAACAACCGGTTTCAGATCAAGGGAGTTGAGCTGAAGTCAGGGTACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAAGGCAACATTAGGTGCAACATTTGCATTTGA"
}, {
"strain": "A/Victoria/361/2011",
"db": "IRD",
"accession": "GQ293081",
"date": "2011-10-24",
"seq": "ATGAAGACTATCATTGCTTTGAGCCACATTCTATGTCTGGTTTTCGCTCAAAAACTTCCTGGAAATGACAACAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAATGACCAAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAATTCCTCAATAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTCCAAAATAAGAAATGGGACCTTTTTGTTGAACGAAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGACTGGAGTCACTCAAAACGGAACAAGTTCTGCTTGCATAAGGAGATCTAATAATAGTTTCTTTAGTAGATTAAATTGGTTGACCCGCTTAAACTTCAAATACCCAGCATTGAACGTGACTATGCCAAACAATGAACAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGTTACGGACAAGGAACAAATCTTCCTGTATGCTCAATCATCAGGAAGAATCACAGTATCTACCAAAAGAAGCCAACAAGCTGTAATCCCGAATATCGGATATAGACCCAGAATAAGGAATATCCCTAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAAATGCAATTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCATTCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCAAAGCACTCTGAAATTGGCAACAGGAATGCGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATAGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGTGGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAAGAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGATCAAATCAATGGGAAGCTGAATCGATTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTCGAAGGGAGAATTCAGGACCTTGAGAAATATGTTGAGGACACTAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGCAACTAAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCACGATGTATACAGAGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGAGTTGAGCTGAAGTCAGGGTACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAGGGCAACATTAGGTGCAACATTTGCATTTGA"
}, {
"strain": "A/Texas/50/2012",
"db": "GISAID",
"isolate_id": "EPI_ISL_129858",
"date": "2012-04-15",
"seq": "ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAACTTCCTGGAAATGACAATAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAATGACCGAATTGAAGTTACTAATGCTACTGAACTGGTTCAGAATTCCTCAATAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTCCAAAATAAGAAATGGGACCTTTTTGTTGAACGAAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGAATGGAGTCACTCAAAACGGAACAAGTTCTGCTTGCATAAGGAGATCTAATAATAGTTTCTTTAGTAGATTAAATTGGTTGACCCACTTAAACTTCAAATACCCAGCATTGAACGTGACTATGCCAAACAATGAACAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTACGGACAAGGACCAAATCTTCCTGTATGCTCAACCATCAGGAAGAATCACAGTATCTACCAAAAGAAGCCAACAAGCTGTAATCCCGAATATCGGATCTAGACCCAGAATAAGGAATATCCCTAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAAATGCAAGTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCATTCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCAAAGCACTCTGAAATTGGCAACAGGAATGCGGAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATAGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGTGGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAAGAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGATCAAATCAATGGGAAGCTGAATCGATTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTAGAAGGGAGAATTCAGGACCTTGAGAAATATGTTGAGGACACTAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCACGATGTATACAGAGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGAGTTGAGCTGAAGTCAGGGTACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAGGGCAACATTAGGTGCAACATTTGCATTTGA",
}, {
"strain": "A/Switzerland/9715293/2013",
"db": "GISAID",
"isolate_id": "EPI_ISL_162149",
"date": "2013-12-06",
"seq": "ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAACTTCCTGGAAATGACAATAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAATGACCGAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAATTCCTCAATAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTTCAAAATAAGAAATGGGACCTTTTTGTTGAACGAAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGGCTGGAGTCACTCAAAACGGAACAAGTTCTTCTTGCATAAGGGGATCTAATAGTAGTTTCTTTAGTAGATTAAATTGGTTGACCCACTTAAACTCCAAATACCCAGCATTAAACGTGACTATGCCAAACAATGAACAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTACGGACAAGGACCAAATCTTCCTGTATGCACAATCATCAGGAAGAATCACAGTATCTACCAAAAGAAGCCAACAAGCTGTAATCCCGAATATCGGATCTAGACCCAGAATAAGGGATATCCCTAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAAATGCAAGTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCATTCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCAAAGCACTCTGAAATTGGCAACAGGAATGCGAAATGTACCAGAGAGACAAACTAGAGGCATATTTGGCGCAATAGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGTGGATGGTTGGTACGGCTTCAGGCATCAAAATTCTGAGGGAAGAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGATCAAATCAATGGGAAGCTGAATCGATTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTAGAAGGGAGAATTCAGGACCTTGAGAAATATGTTGAGGACACAAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCACGATGTATACAGGGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGAGTTGAGCTGAAGTCAGGGTACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAGGGCAACATTAGGTGCAACATTTGCATTTGA",
}
]
self.outgroup = {
'strain': 'A/Beijing/32/1992',
'db': 'IRD',
'accession': 'U26830',
'date': '1992-01-01',
'country': 'China',
'region': 'China',
'seq': 'ATGAAGACTATCATTGCTTTGAGCTACATTTTATGTCTGGTTTTCGCTCAAAAACTTCCCGGAAATGACAACAGCACAGCAACGCTGTGCCTGGGACATCATGCAGTGCCAAACGGAACGCTAGTGAAAACAATCACGAATGATCAAATTGAAGTGACTAATGCTACTGAGCTGGTTCAGAGTTCCTCAACAGGTAGAATATGCGACAGTCCTCACCGAATCCTTGATGGAAAAAACTGCACACTGATAGATGCTCTATTGGGAGACCCTCATTGTGATGGCTTCCAAAATAAGGAATGGGACCTTTTTGTTGAACGCAGCAAAGCTTACAGCAACTGTTACCCTTATGATGTACCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCAGGCACCCTGGAGTTTATCAATGAAGACTTCAATTGGACTGGAGTCGCTCAGGATGGGGGAAGCTATGCTTGCAAAAGGGGATCTGTTAACAGTTTCTTTAGTAGATTGAATTGGTTGCACAAATCAGAATACAAATATCCAGCGCTGAACGTGACTATGCCAAACAATGGCAAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGAGCACGGACAGAGACCAAACCAGCCTATATGTTCGAGCATCAGGGAGAGTCACAGTCTCTACCAAAAGAAGCCAACAAACTGTAACCCCGAATATCGGGTCTAGACCCTGGGTAAGGGGTCAGTCCAGTAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAATAGCACAGGGAATCTAATTGCTCCTCGGGGTTACTTCAAAATACGAAATGGGAAAAGCTCAATAATGAGGTCAGATGCACCCATTGGCACCTGCAGTTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCTTTTCAAAATGTAAACAGGATCACATATGGGGCCTGCCCCAGATATGTTAAGCAAAACACTCTGAAATTGGCAACAGGGATGCGGAATGTACCAGAGAAACAAACTAGAGGCATATTCGGCGCAATCGCAGGTTTCATAGAAAATGGTTGGGAGGGAATGGTAGACGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGCACAGGACAAGCAGCAGATCTTAAAAGCACTCAAGCAGCAATCGACCAAATCAACGGGAAACTGAATAGGTTAATCGAGAAAACGAACGAGAAATTCCATCAAATCGAAAAAGAATTCTCAGAAGTAGAAGGGAGAATTCAGGACCTCGAGAAATATGTTGAAGACACTAAAATAGATCTCTGGTCTTACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTTACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAGGAAGCAACTGAGGGAAAATGCTGAGGACATGGGCAATGGTTGCTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGGTCAATCAGAAATGGAACTTATGACCATGATGTATACAGAGACGAAGCATTAAACAACCGGTTCCAGATCAAAGGTGTTGAGCTGAAGTCAGGATACAAAGATTGGATCCTGTGGATTTCCTTTGCCATATCATGCTTTTTGCTTTGTGTTGTTTTGCTGGGGTTCATCATGTGGGCCTGCCAAAAAGGCAACATTAGGTGTAACATTTGCATTTGA'
}
def __init__(self,min_length = 987, **kwargs):
'''
parameters
min_length -- minimal length for a sequence to be acceptable
'''
flu_filter.__init__(self, **kwargs)
self.min_length = min_length
self.vaccine_strains =[
{
'strain': 'B/Shangdong/7/97',
'isolate_id': 'EPI_ISL_1790',
'date': '1997-07-01', #(Month and day unknown)
'region': 'china',
'country': 'china',
'seq':'GATCGAATCTGCACTGGGATAACATCGTCAAACTCACCCCATGTGGTCAAAACTGCTACTCAAGGGGAGGTCAATGTGACTGGTGTGATACCACTGACAACAACACCCACCAAATCTCATTTTGCAAATCTCAAAGGAACAAAAACCAGAGGGAAACTATGCCCAAAATGCCTCAACTGTACAGATCTGGACGTGGCCTTGGGCAGACCAAAATGCACGGGGAACATACCTTCGGCAAAAGTTTCAATACTCCATGAAGTCAGACCTGTTACATCTGGGTGCTTTCCTATAATGCACGACAGAACAAAAATTAGACAGCTGCCCAATCTTCTCAGAGGATACGAACATATCAGGTTATCAATTCATAACGTTATCAATGCAGAAAAGGCACCAGGAGGACCCTACAAAATTGGAACCTCAGGGTCTTGCCCTAACGTTACCAATGGAAACGGATTCTTCGCAACAATGGCTTGGGCCGTCCCAAAAAACGACAACAACAAAACAGCAACAAATTCATTAACAATAGAAGTACCATACATTTGTACAGAAGGAGAAGACCAAATTACCGTTTGGGGGTTCCACTCTGATAACGAAAACCAAATGGCAAAACTCTATGGGGACTCAAAGCCCCAGAAGTTCACCTCATCTGCCAACGGAGTGACCACACATTACGTTTCACAGATTGGTGGCTTCCCAAATCAAACAGAAGACGGAGGACTACCACAAAGTGGTAGAATTGTTGTTGATTACATGGTGCAAAAATCTGGGAAAACAGGAACAATTACCTATCAAAGAGGTATTTTATTGCCTCAAAAAGTGTGGTGCGCAAGTGGCAGGAGCAAGGTAATAAAAGGGTCCTTGCCTTTAATTGGAGAAGCAGATTGCCTCCACGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTATTACACAGGGGAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTGAAAACACCCTTGAAGCTGGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGGGGTTTCTTCGGAGCTATTGCTGGTTTCTTAGAAGGAGGATGGGAAGGAATGATTGCAGGTTGGCACGGATACACATCCCATGGAGCACATGGAGTAGCAGTGGCAGCAGACCTTAAGAGTACTCAAGAAGCCATAAACAAGATAACAAAAAATCTCAACTCTTTGAGTGAGCTGGAAGTAAAGAATCTTCAAAGACTAAGCGGTGCCATGGATGAACTCCACAACGAAATACTAGAACTAGACGAGAAAGTGGATGATCTCAGAGCTGATACAATAAGCTCGCAAATAGAACTCGCAGTCTTGCTTTCCAAT',
},
{
'strain': 'B/HongKong/330/2001',
'isolate_id': 'EPI_ISL_2342',
'date': '2001-07-01', #(Month and day unknown)
'region': 'china',
'country': 'hong_kong',
'seq': 'GATCGAATCTGCACTGGAATAACATCGTCAAACTCACCCCATGTGGTCAAAACTGCTACTCAAGGGGAAGTCAATGTGACTGGTGTGATACCACTGACAACAACACCCACCAAATCTCATTTTGCAAATCTCAAAGGAACAAAAACCAGAGGGAAACTATGCCCAAAATGTCTCAACTGCACAGATCTGGACGTGGCCTTGGGCAGACCAAAATGCACGGGGAACATACCTTCGGCAAAAGTTTCAATACTCCATGAAGTAAGACCTGTTACATCTGGGTGCTTTCCTATAATGCACGACAGAACAAAAATTAGACAGCTGCCCAATCTTCTCAGAGGATACGAACGTATCAGGTTATCAAACCATAACGTTATCAATGCAGAAAAAGCACCAGGAGGACCCTACAAAATTGGAACCTCAGGGTCTTGCCCTAACGTTACCAATGGAAACGGATTCTTCGCAACAATGGCTTGGGCTGTCCCAAAAAACGAAAACAACAAAACAGCAACAAATTCATTAACAATAGAAGTACCATACATTTGTACAGAAGGAGAAGACCAAATTACCGTTTGGGGGTTCCACTCTGATAGCGAAACCCAAATGGCAAAACTCTATGGAGACTCAAAGCCTCAGAAGTTCACTTCATCTGCCAACGGAGTGACCACACATTACGTTTCACAGATTGGTGGCTTCCCAAATCAAACAGAAGACGGAGGACTACCACAAAGTGGTAGAATTGTTGTTGATTACATGGTGCAAAAATCTGGAAAAACAGGAACAATTACCTATCAAAGAGGTATTTTATTGCCTCAAAAAGTGTGGTGCGCAAGTGGCAGGAGCAAGGTAATAAAAGGATCCTTGCCTTTAATTGGAGAAGCAGATTGCCTCCACGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTACTATACAGGGGAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTGAAAACACCCTTGAAGCTGGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGGGGTTTCTTCGGAGCTTTGGGCTG',
},
{
'strain': 'B/Malaysia/2506/2004',
'isolate_id': 'EPI_ISL_21142',
'date': '2004-07-01', # (Month and day unknown) | |
'region': 'southeast_asia',
'country': 'malaysia',
'seq': 'ATTGTACTACTCATGGTAGTAACATCCAATGCAGATCGAATCTGCACTGGGATAACATCGTCAAACTCACCACATGTTGTCAAAACTGCTACTCAAGGGGAGGTCAATGTGACTGGTGTAATACCACTGACAACAACACCCACCAAATCTCATTTTGCAAATCTCAAAGGAACAGAAACCAGAGGGAAACTATGCCCAAAATGTCTCAACTGCACAGATCTGGACGTGGCCTTGGGCAGACCAAAATGCACGGGGAACATACCCTCGGCAAGAGTTTCAATACTCCATGAAGTCAGACCTGTTACATCTGGGTGCTTTCCTATAATGCACGACAGAACAAAAATTAGACAGCTGCCTAACCTTCTCAGAGGATACGAACATATCAGGTTATCAACTCATAACGTTATCAATGCAGAAAATGCACCAGGAGGATCCTACAAAATTGGAACCTCAGGGTCTTGCCCTAACGTTACCAATGGAAACGGATTTTTCGCAACAATGGCTTGGGCCGTCCCAAAAAACGACAACAACAAAACAGCAACAAATTCATTAACAATAGAAGTACCATACATTTGTACAGAAGGAGAAGACCAAATTACCGTTTGGGGGTTCCACTCTGATAACGAAGCCCAAATGGCAAAGCTCTATGGGGACTCAAAGCCCCAGAAGTTCACCTCATCTGCCAACGGAGTGACCACACATTACGTTTCACAGATTGGTGGCTTCCCAAATCAAACAGAAGACGGAGGACTACCACAAAGTGGTAGAATTGTTGTTGATTACATGGTGCAAAAATCTGGGAAAACAGGAACAATTACCTATCAAAGAGGTATTTTATTGCCTCAAAAAGTGTGGTGCGCAAGTGGCAGGAGCAAGGTAATAAAAGGATCCTTGCCTTTAATTGGAGAAGCAGATTGCCTCCACGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGGGAACATGCAAAGGCCATAGGAAATTGCCCAATATGGGTGAAAACACCCTTGAAGCTGGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGGGGTTTCTTCGGAGCTATTGCTGGTTTCTTAGAAGGAGGATGGGAAGGAATGATTGCAGGTTGGCACGGATACACATCCCATGGGGCACATGGAGTAGCGGTGGCAGCAGACCTTAAGAGCACTCAAGAGGCCATAAACAAGATAACAAAAAATCTCAACTCTTTGAGTGAGCTGGAAGTAAAGAATCTTCAAAGACTAAGCGGTGCCATGGATGAACTCCACAACGAAATACTAGAACTAGACGAGAAAGTGGATGATCTCAGAGCTGATACAATAAGCTCACAAATAGAACTCGCAGTCCTGCTTTCCAATGAAGGAATAATAAACAGTGAAGATGAGCATCTCTTGGCGCTTGAAAGAAAGCTGAAGAAAATGCTGGGCCCCTCTGCTGTAGAGATAGGGAATGGATGCTTTGAAACCAAACACAAGTGCAACCAGACCTGTCTCGACAGAATAGCTGCTGGTACCTTTGATGCAGGAGAATTTTCTCTCCCCACTTTTGATTCACTGAATATTACTGCTGCATCTTTAAATGACGATGGATTGGATAATCATACTATACTGCTTTACTACTCAACTGCTGCCTCCAGTTTGGCTGTAACATTGATGATAGCTATCTTTGTTGTTTATATGGTCTCCAGAGACAATGTTTCTTGCTCCATCTGTCTATAAGGAAAGTTAAACCCTGTATTTTCCTTTATTGTAGTGCTTGTTTGCTTGTTACCATTACAAAAAACGGTTATTGAAAAATGCTCTTGTTACTACTAATA',
},
{
'strain': 'B/Brisbane/60/2008',
'isolate_id': 'EPI_ISL_24365',
'date': '2008-08-04',
'lab': 'Queensland Health Scientific Services',
'region': 'oceania',
'country': 'australia',
'seq': 'AGCAGAAGCAGAGCATTTTCTAATATCCACAAAATGAAGGCAATAATTGTACTACTCATGGTAGTAACATCCAATGCAGATCGAATCTGCACTGGGATAACATCGTCAAACTCACCACATGTCGTCAAAACTGCTACTCAAGGGGAGGTCAATGTGACTGGTGTAATACCACTGACAACAACACCCACCAAATCTCATTTTGCAAATCTCAAAGGAACAGAAACCAGGGGGAAACTATGCCCAAAATGCCTCAACTGCACAGATCTGGACGTAGCCTTGGGCAGACCAAAATGCACGGGGAAAATACCCTCGGCAAGAGTTTCAATACTCCATGAAGTCAGACCTGTTACATCTGGGTGCTTTCCTATAATGCACGACAGAACAAAAATTAGACAGCTGCCTAACCTTCTCCGAGGATACGAACATATCAGGTTATCAACCCATAACGTTATCAATGCAGAAAATGCACCAGGAGGACCCTACAAAATTGGAACCTCAGGGTCTTGCCCTAACATTACCAATGGAAACGGATTTTTCGCAACAATGGCTTGGGCCGTCCCAAAAAACGACAAAAACAAAACAGCAACAAATCCATTAACAATAGAAGTACCATACATTTGTACAGAAGGAGAAGACCAAATTACCGTTTGGGGGTTCCACTCTGACAACGAGACCCAAATGGCAAAGCTCTATGGGGACTCAAAGCCCCAGAAGTTCACCTCATCTGCCAACGGAGTGACCACACATTACGTTTCACAGATTGGTGGCTTCCCAAATCAAACAGAAGACGGAGGACTACCACAAAGTGGTAGAATTGTTGTTGATTACATGGTGCAAAAATCTGGGAAAACAGGAACAATTACCTATCAAAGGGGTATTTTATTGCCTCAAAAGGTGTGGTGCGCAAGTGGCAGGAGCAAGGTAATAAAAGGATCCTTGCCTTTAATTGGAGAAGCAGATTGCCTCCACGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGGGAACATGCAAAGGCCATAGGAAATTGCCCAATATGGGTGAAAACACCCTTGAAGCTGGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGGGGTTTCTTCGGAGCTATTGCTGGTTTCTTAGAAGGAGGATGGGAAGGAATGATTGCAGGTTGGCACGGATACACATCCCATGGGGCACATGGAGTAGCGGTGGCAGCAGACCTTAAGAGCACTCAAGAGGCCATAAACAAGATAACAAAAAATCTCAACTCTTTGAGTGAGCTGGAAGTAAAGAATCTTCAAAGACTAAGCGGTGCCATGGATGAACTCCACAACGAAATACTAGAACTAGATGAGAAAGTGGATGATCTCAGAGCTGATACAATAAGCTCACAAATAGAACTCGCAGTCCTGCTTTCCAATGAAGGAATAATAAACAGTGAAGATGAACATCTCTTGGCGCTTGAAAGAAAGCTGAAGAAAATGCTGGGCCCCTCTGCTGTAGAGATAGGGAATGGATGCTTTGAAACCAAACACAAGTGCAACCAGACCTGTCTCGACAGAATAGCTGCTGGTACCTTTGATGCAGGAGAATTTTCTCTCCCCACCTTTGATTCACTGAATATTACTGCTGCATCTTTAAATGACGATGGATTGGATAATCATACTATACTGCTTTACTACTCAACTGCTGCCTCCAGT',
}
]
tmp_outgroup = SeqIO.read('source-data/Vic_outgroup.gb', 'genbank')
genome_annotation = tmp_outgroup.features
self.cds = {x.qualifiers['gene'][0]:x for x in genome_annotation
if 'gene' in x.qualifiers and x.type=='CDS' and
x.qualifiers['gene'][0] in ['SigPep', 'HA1', 'HA2']}
self.outgroup = {
'strain':'B/HongKong/02/1993',
'region':'China',
'isolate_id':'EPI_ISL_6617',
'date':'1993-02-15', #(Month and day unknown)
'seq': str(tmp_outgroup.seq).upper()
}
def __init__(self, min_length=987, **kwargs):
'''
parameters
min_length -- minimal length for a sequence to be acceptable
'''
flu_filter.__init__(self, **kwargs)
self.min_length = min_length
self.vaccine_strains = [{
'strain':
'A/California/07/2009',
'isolate_id':
'EPI_ISL_31553',
'date':
'2009-04-09',
'lab':
'Naval Health Research Center',
'region':
'north_america',
'country':
'usa',
'seq':
'ATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACACATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAACAGTAACACACTCTGTTAACCTTCTAGAAGACAAGCATAACGGGAAACTATGCAAACTAAGAGGGGTAGCCCCATTGCATTTGGGTAAATGTAACATTGCTGGCTGGATCCTGGGAAATCCAGAGTGTGAATCACTCTCCACAGCAAGCTCATGGTCCTACATTGTGGAAACACCTAGTTCAGACAATGGAACGTGTTACCCAGGAGATTTCATCGATTATGAGGAGCTAAGAGAGCAATTGAGCTCAGTGTCATCATTTGAAAGGTTTGAGATATTCCCCAAGACAAGTTCATGGCCCAATCATGACTCGAACAAAGGTGTAACGGCAGCATGTCCTCATGCTGGAGCAAAAAGCTTCTACAAAAATTTAATATGGCTAGTTAAAAAAGGAAATTCATACCCAAAGCTCAGCAAATCCTACATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTAGTGCTGACCAACAAAGTCTCTATCAGAATGCAGATGCATATGTTTTTGTGGGGTCATCAAGATACAGCAAGAAGTTCAAGCCGGAAATAGCAATAAGACCCAAAGTGAGGGATCAAGAAGGGAGAATGAACTATTACTGGACACTAGTAGAGCCGGGAGACAAAATAACATTCGAAGCAACTGGAAATCTAGTGGTACCGAGATATGCATTCGCAATGGAAAGAAATGCTGGATCTGGTATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCAAACACCCAAGGGTGCTATAAACACCAGCCTCCCATTTCAGAATATACATCCGATCACAATTGGAAAATGTCCAAAATATGTAAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATATCCCGTCTATTCAATCTAGAGGCCTATTTGGGGCCATTGCCGGTTTCATTGAAGGGGGGTGGACAGGGATGGTAGATGGATGGTACGGTTATCACCATCAAAATGAGCAGGGGTCAGGATATGCAGCCGACCTGAAGAGCACACAGAATGCCATTGACGAGATTACTAACAAAGTAAATTCTGTTATTGAAAAGATGAATACACAGTTCACAGCAGTAGGTAAAGAGTTCAACCACCTGGAAAAAAGAATAGAGAATTTAAATAAAAAAGTTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCAAATGTGAAGAACTTATATGAAAAGGTAAGAAGCCAGCTAAAAAACAATGCCAAGGAAATTGGAAACGGCTGCTTTGAATTTTACCACAAATGCGATAACACGTGCATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGTTTCTGGATGTGCTCTAATGGGTCTCTACAGTGTAGAATATGTATTTAA',
}, {
"strain":
"A/Michigan/45/2015",
'isolate_id':
'EPI699812',
"date":
"2015-09-07",
"region":
"north_america",
"country":
"usa",
"seq":
"GGAAAAACAAAAGCAACAAAAATGAAGGCAATACTAGTAGTTCTGCTATATACATTTACAACCGCAAATGCAGACACATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAACAGTAACACACTCTGTTAACCTTCTGGAAGACAAGCATAACGGAAAACTATGCAAACTAAGAGGGGTAGCCCCATTGCATTTGGGTAAATGTAACATTGCTGGCTGGATCCTGGGAAATCCAGAGTGTGAATCACTCTCCACAGCAAGTTCATGGTCCTACATTGTGGAAACATCTAATTCAGACAATGGAACGTGTTACCCAGGAGATTTCATCAATTATGAGGAGCTAAGAGAGCAATTGAGCTCAGTGTCATCATTTGAAAGGTTTGAGATATTCCCCAAGACAAGTTCATGGCCCAATCATGACTCGAACAAAGGTGTAACGGCAGCATGTCCTCACGCTGGAGCAAAAAGCTTCTACAAAAACTTGATATGGCTAGTTAAAAAAGGAAATTCATACCCAAAGCTTAACCAATCCTACATTAATGATAAAGGGAAAGAAGTCCTCGTGCTGTGGGGCATTCACCATCCATCTACTACTGCTGACCAACAAAGTCTCTATCAGAATGCAGATGCATATGTTTTTGTGGGGACATCAAGATACAGCAAGAAGTTCAAGCCGGAAATAGCAACAAGACCCAAAGTGAGGGATCAAGAAGGGAGAATGAACTATTACTGGACACTAGTAGAGCCGGGAGACAAAATAACATTCGAAGCAACTGGAAATCTAGTGGTACCGAGATATGCATTCACAATGGAAAGAAATGCTGGATCTGGTATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCAGACACCCGAGGGTGCTATAAACACCAGCCTCCCATTTCAGAATATACATCCGATCACAATTGGAAAATGTCCAAAGTATGTAAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATGTTCCGTCTATTCAATCTAGAGGCCTATTCGGGGCCATTGCCGGCTTCATTGAAGGGGGGTGGACAGGGATGGTAGATGGATGGTACGGTTATCACCATCAAAATGAGCAGGGGTCAGGATATGCAGCCGACCTGAAGAGCACACAAAATGCCATTGACAAGATTACTAACAAAGTAAATTCTGTTATTGAAAAGATGAATACACAGTTCACAGCAGTGGGTAAAGAGTTCAACCACCTGGAAAAAAGAATAGAGAATCTAAATAAAAAAGTTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTATCACGATTCAAATGTGAAGAACTTGTATGAAAAAGTAAGAAACCAGTTAAAAAACAATGCCAAGGAAATTGGAAACGGCTGCTTTGAATTTTACCACAAATGCGATAACACGTGCATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAAAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGCTTCTGGATGTGCTCTAATGGGTCTCTACAGTGTAGAATATGTATTTAACATTAGGATTTCAGAATCATGAGAAAAACAC"
}]
tmp_outgroup = SeqIO.read('source-data/H1N1pdm_outgroup.gb', 'genbank')
genome_annotation = tmp_outgroup.features
self.cds = {
x.qualifiers['gene'][0]: x
for x in genome_annotation
if 'gene' in x.qualifiers and x.type == 'CDS'
and x.qualifiers['gene'][0] in ['SigPep', 'HA1', 'HA2']
}
self.outgroup = {
'strain': 'A/Swine/Indiana/P12439/00',
'db': 'IRD',
'accession': 'AF455680',
'date': '2002-03-14',
'region': 'north_america',
'country': 'usa',
'seq': str(tmp_outgroup.seq).upper()
}
def __init__(self,min_length = 987, **kwargs):
'''
parameters
min_length -- minimal length for a sequence to be acceptable
'''
flu_filter.__init__(self, **kwargs)
self.min_length = min_length
self.vaccine_strains =[
{
'strain': 'B/Shangdong/7/97',
'isolate_id': 'EPI_ISL_1790',
'date': '1997-07-01', #(Month and day unknown)
'region': 'China',
'seq':'GATCGAATCTGCACTGGGATAACATCGTCAAACTCACCCCATGTGGTCAAAACTGCTACTCAAGGGGAGGTCAATGTGACTGGTGTGATACCACTGACAACAACACCCACCAAATCTCATTTTGCAAATCTCAAAGGAACAAAAACCAGAGGGAAACTATGCCCAAAATGCCTCAACTGTACAGATCTGGACGTGGCCTTGGGCAGACCAAAATGCACGGGGAACATACCTTCGGCAAAAGTTTCAATACTCCATGAAGTCAGACCTGTTACATCTGGGTGCTTTCCTATAATGCACGACAGAACAAAAATTAGACAGCTGCCCAATCTTCTCAGAGGATACGAACATATCAGGTTATCAATTCATAACGTTATCAATGCAGAAAAGGCACCAGGAGGACCCTACAAAATTGGAACCTCAGGGTCTTGCCCTAACGTTACCAATGGAAACGGATTCTTCGCAACAATGGCTTGGGCCGTCCCAAAAAACGACAACAACAAAACAGCAACAAATTCATTAACAATAGAAGTACCATACATTTGTACAGAAGGAGAAGACCAAATTACCGTTTGGGGGTTCCACTCTGATAACGAAAACCAAATGGCAAAACTCTATGGGGACTCAAAGCCCCAGAAGTTCACCTCATCTGCCAACGGAGTGACCACACATTACGTTTCACAGATTGGTGGCTTCCCAAATCAAACAGAAGACGGAGGACTACCACAAAGTGGTAGAATTGTTGTTGATTACATGGTGCAAAAATCTGGGAAAACAGGAACAATTACCTATCAAAGAGGTATTTTATTGCCTCAAAAAGTGTGGTGCGCAAGTGGCAGGAGCAAGGTAATAAAAGGGTCCTTGCCTTTAATTGGAGAAGCAGATTGCCTCCACGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTATTACACAGGGGAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTGAAAACACCCTTGAAGCTGGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGGGGTTTCTTCGGAGCTATTGCTGGTTTCTTAGAAGGAGGATGGGAAGGAATGATTGCAGGTTGGCACGGATACACATCCCATGGAGCACATGGAGTAGCAGTGGCAGCAGACCTTAAGAGTACTCAAGAAGCCATAAACAAGATAACAAAAAATCTCAACTCTTTGAGTGAGCTGGAAGTAAAGAATCTTCAAAGACTAAGCGGTGCCATGGATGAACTCCACAACGAAATACTAGAACTAGACGAGAAAGTGGATGATCTCAGAGCTGATACAATAAGCTCGCAAATAGAACTCGCAGTCTTGCTTTCCAAT',
},
{
'strain': 'B/HongKong/330/2001',
'isolate_id': 'EPI_ISL_2342',
'date': '2001-07-01', #(Month and day unknown)
'region': 'China',
'seq': 'GATCGAATCTGCACTGGAATAACATCGTCAAACTCACCCCATGTGGTCAAAACTGCTACTCAAGGGGAAGTCAATGTGACTGGTGTGATACCACTGACAACAACACCCACCAAATCTCATTTTGCAAATCTCAAAGGAACAAAAACCAGAGGGAAACTATGCCCAAAATGTCTCAACTGCACAGATCTGGACGTGGCCTTGGGCAGACCAAAATGCACGGGGAACATACCTTCGGCAAAAGTTTCAATACTCCATGAAGTAAGACCTGTTACATCTGGGTGCTTTCCTATAATGCACGACAGAACAAAAATTAGACAGCTGCCCAATCTTCTCAGAGGATACGAACGTATCAGGTTATCAAACCATAACGTTATCAATGCAGAAAAAGCACCAGGAGGACCCTACAAAATTGGAACCTCAGGGTCTTGCCCTAACGTTACCAATGGAAACGGATTCTTCGCAACAATGGCTTGGGCTGTCCCAAAAAACGAAAACAACAAAACAGCAACAAATTCATTAACAATAGAAGTACCATACATTTGTACAGAAGGAGAAGACCAAATTACCGTTTGGGGGTTCCACTCTGATAGCGAAACCCAAATGGCAAAACTCTATGGAGACTCAAAGCCTCAGAAGTTCACTTCATCTGCCAACGGAGTGACCACACATTACGTTTCACAGATTGGTGGCTTCCCAAATCAAACAGAAGACGGAGGACTACCACAAAGTGGTAGAATTGTTGTTGATTACATGGTGCAAAAATCTGGAAAAACAGGAACAATTACCTATCAAAGAGGTATTTTATTGCCTCAAAAAGTGTGGTGCGCAAGTGGCAGGAGCAAGGTAATAAAAGGATCCTTGCCTTTAATTGGAGAAGCAGATTGCCTCCACGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTACTATACAGGGGAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTGAAAACACCCTTGAAGCTGGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGGGGTTTCTTCGGAGCTTTGGGCTG',
},
{
'strain': 'B/Malaysia/2506/2004',
'isolate_id': 'EPI_ISL_21142',
'date':'2004-07-01', # (Month and day unknown) | |
'region':'SouthEast Asia',
'seq':'ATTGTACTACTCATGGTAGTAACATCCAATGCAGATCGAATCTGCACTGGGATAACATCGTCAAACTCACCACATGTTGTCAAAACTGCTACTCAAGGGGAGGTCAATGTGACTGGTGTAATACCACTGACAACAACACCCACCAAATCTCATTTTGCAAATCTCAAAGGAACAGAAACCAGAGGGAAACTATGCCCAAAATGTCTCAACTGCACAGATCTGGACGTGGCCTTGGGCAGACCAAAATGCACGGGGAACATACCCTCGGCAAGAGTTTCAATACTCCATGAAGTCAGACCTGTTACATCTGGGTGCTTTCCTATAATGCACGACAGAACAAAAATTAGACAGCTGCCTAACCTTCTCAGAGGATACGAACATATCAGGTTATCAACTCATAACGTTATCAATGCAGAAAATGCACCAGGAGGATCCTACAAAATTGGAACCTCAGGGTCTTGCCCTAACGTTACCAATGGAAACGGATTTTTCGCAACAATGGCTTGGGCCGTCCCAAAAAACGACAACAACAAAACAGCAACAAATTCATTAACAATAGAAGTACCATACATTTGTACAGAAGGAGAAGACCAAATTACCGTTTGGGGGTTCCACTCTGATAACGAAGCCCAAATGGCAAAGCTCTATGGGGACTCAAAGCCCCAGAAGTTCACCTCATCTGCCAACGGAGTGACCACACATTACGTTTCACAGATTGGTGGCTTCCCAAATCAAACAGAAGACGGAGGACTACCACAAAGTGGTAGAATTGTTGTTGATTACATGGTGCAAAAATCTGGGAAAACAGGAACAATTACCTATCAAAGAGGTATTTTATTGCCTCAAAAAGTGTGGTGCGCAAGTGGCAGGAGCAAGGTAATAAAAGGATCCTTGCCTTTAATTGGAGAAGCAGATTGCCTCCACGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGGGAACATGCAAAGGCCATAGGAAATTGCCCAATATGGGTGAAAACACCCTTGAAGCTGGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGGGGTTTCTTCGGAGCTATTGCTGGTTTCTTAGAAGGAGGATGGGAAGGAATGATTGCAGGTTGGCACGGATACACATCCCATGGGGCACATGGAGTAGCGGTGGCAGCAGACCTTAAGAGCACTCAAGAGGCCATAAACAAGATAACAAAAAATCTCAACTCTTTGAGTGAGCTGGAAGTAAAGAATCTTCAAAGACTAAGCGGTGCCATGGATGAACTCCACAACGAAATACTAGAACTAGACGAGAAAGTGGATGATCTCAGAGCTGATACAATAAGCTCACAAATAGAACTCGCAGTCCTGCTTTCCAATGAAGGAATAATAAACAGTGAAGATGAGCATCTCTTGGCGCTTGAAAGAAAGCTGAAGAAAATGCTGGGCCCCTCTGCTGTAGAGATAGGGAATGGATGCTTTGAAACCAAACACAAGTGCAACCAGACCTGTCTCGACAGAATAGCTGCTGGTACCTTTGATGCAGGAGAATTTTCTCTCCCCACTTTTGATTCACTGAATATTACTGCTGCATCTTTAAATGACGATGGATTGGATAATCATACTATACTGCTTTACTACTCAACTGCTGCCTCCAGTTTGGCTGTAACATTGATGATAGCTATCTTTGTTGTTTATATGGTCTCCAGAGACAATGTTTCTTGCTCCATCTGTCTATAAGGAAAGTTAAACCCTGTATTTTCCTTTATTGTAGTGCTTGTTTGCTTGTTACCATTACAAAAAACGGTTATTGAAAAATGCTCTTGTTACTACTAATA',
},
{
'strain':'B/Brisbane/60/2008',
'isolate_id':'EPI_ISL_24365',
'date': '2008-08-04',
'lab':'Queensland Health Scientific Services',
'region':'Oceania',
'seq':'AGCAGAAGCAGAGCATTTTCTAATATCCACAAAATGAAGGCAATAATTGTACTACTCATGGTAGTAACATCCAATGCAGATCGAATCTGCACTGGGATAACATCGTCAAACTCACCACATGTCGTCAAAACTGCTACTCAAGGGGAGGTCAATGTGACTGGTGTAATACCACTGACAACAACACCCACCAAATCTCATTTTGCAAATCTCAAAGGAACAGAAACCAGGGGGAAACTATGCCCAAAATGCCTCAACTGCACAGATCTGGACGTAGCCTTGGGCAGACCAAAATGCACGGGGAAAATACCCTCGGCAAGAGTTTCAATACTCCATGAAGTCAGACCTGTTACATCTGGGTGCTTTCCTATAATGCACGACAGAACAAAAATTAGACAGCTGCCTAACCTTCTCCGAGGATACGAACATATCAGGTTATCAACCCATAACGTTATCAATGCAGAAAATGCACCAGGAGGACCCTACAAAATTGGAACCTCAGGGTCTTGCCCTAACATTACCAATGGAAACGGATTTTTCGCAACAATGGCTTGGGCCGTCCCAAAAAACGACAAAAACAAAACAGCAACAAATCCATTAACAATAGAAGTACCATACATTTGTACAGAAGGAGAAGACCAAATTACCGTTTGGGGGTTCCACTCTGACAACGAGACCCAAATGGCAAAGCTCTATGGGGACTCAAAGCCCCAGAAGTTCACCTCATCTGCCAACGGAGTGACCACACATTACGTTTCACAGATTGGTGGCTTCCCAAATCAAACAGAAGACGGAGGACTACCACAAAGTGGTAGAATTGTTGTTGATTACATGGTGCAAAAATCTGGGAAAACAGGAACAATTACCTATCAAAGGGGTATTTTATTGCCTCAAAAGGTGTGGTGCGCAAGTGGCAGGAGCAAGGTAATAAAAGGATCCTTGCCTTTAATTGGAGAAGCAGATTGCCTCCACGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGGGAACATGCAAAGGCCATAGGAAATTGCCCAATATGGGTGAAAACACCCTTGAAGCTGGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGGGGTTTCTTCGGAGCTATTGCTGGTTTCTTAGAAGGAGGATGGGAAGGAATGATTGCAGGTTGGCACGGATACACATCCCATGGGGCACATGGAGTAGCGGTGGCAGCAGACCTTAAGAGCACTCAAGAGGCCATAAACAAGATAACAAAAAATCTCAACTCTTTGAGTGAGCTGGAAGTAAAGAATCTTCAAAGACTAAGCGGTGCCATGGATGAACTCCACAACGAAATACTAGAACTAGATGAGAAAGTGGATGATCTCAGAGCTGATACAATAAGCTCACAAATAGAACTCGCAGTCCTGCTTTCCAATGAAGGAATAATAAACAGTGAAGATGAACATCTCTTGGCGCTTGAAAGAAAGCTGAAGAAAATGCTGGGCCCCTCTGCTGTAGAGATAGGGAATGGATGCTTTGAAACCAAACACAAGTGCAACCAGACCTGTCTCGACAGAATAGCTGCTGGTACCTTTGATGCAGGAGAATTTTCTCTCCCCACCTTTGATTCACTGAATATTACTGCTGCATCTTTAAATGACGATGGATTGGATAATCATACTATACTGCTTTACTACTCAACTGCTGCCTCCAGT',
}
]
tmp_outgroup = SeqIO.read('source-data/Vic_outgroup.gb', 'genbank')
genome_annotation = tmp_outgroup.features
self.cds = {x.qualifiers['gene'][0]:x for x in genome_annotation
if 'gene' in x.qualifiers and x.type=='CDS' and
x.qualifiers['gene'][0] in ['SigPep', 'HA1', 'HA2']}
self.outgroup = {
'strain':'B/HongKong/02/1993',
'region':'China',
'isolate_id':'EPI_ISL_6617',
'date':'1993-02-15', #(Month and day unknown)
'seq': str(tmp_outgroup.seq).upper()
}
def __init__(self,min_length = 987, **kwargs):
'''
parameters
min_length -- minimal length for a sequence to be acceptable
'''
flu_filter.__init__(self, **kwargs)
self.min_length = min_length
self.vaccine_strains =[
{
'strain': 'B/Shangdong/7/97',
'isolate_id': 'EPI_ISL_1790',
'date': '1997-07-01', #(Month and day unknown)
'region': 'China',
'seq':'GATCGAATCTGCACTGGGATAACATCGTCAAACTCACCCCATGTGGTCAAAACTGCTACTCAAGGGGAGGTCAATGTGACTGGTGTGATACCACTGACAACAACACCCACCAAATCTCATTTTGCAAATCTCAAAGGAACAAAAACCAGAGGGAAACTATGCCCAAAATGCCTCAACTGTACAGATCTGGACGTGGCCTTGGGCAGACCAAAATGCACGGGGAACATACCTTCGGCAAAAGTTTCAATACTCCATGAAGTCAGACCTGTTACATCTGGGTGCTTTCCTATAATGCACGACAGAACAAAAATTAGACAGCTGCCCAATCTTCTCAGAGGATACGAACATATCAGGTTATCAATTCATAACGTTATCAATGCAGAAAAGGCACCAGGAGGACCCTACAAAATTGGAACCTCAGGGTCTTGCCCTAACGTTACCAATGGAAACGGATTCTTCGCAACAATGGCTTGGGCCGTCCCAAAAAACGACAACAACAAAACAGCAACAAATTCATTAACAATAGAAGTACCATACATTTGTACAGAAGGAGAAGACCAAATTACCGTTTGGGGGTTCCACTCTGATAACGAAAACCAAATGGCAAAACTCTATGGGGACTCAAAGCCCCAGAAGTTCACCTCATCTGCCAACGGAGTGACCACACATTACGTTTCACAGATTGGTGGCTTCCCAAATCAAACAGAAGACGGAGGACTACCACAAAGTGGTAGAATTGTTGTTGATTACATGGTGCAAAAATCTGGGAAAACAGGAACAATTACCTATCAAAGAGGTATTTTATTGCCTCAAAAAGTGTGGTGCGCAAGTGGCAGGAGCAAGGTAATAAAAGGGTCCTTGCCTTTAATTGGAGAAGCAGATTGCCTCCACGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTATTACACAGGGGAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTGAAAACACCCTTGAAGCTGGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGGGGTTTCTTCGGAGCTATTGCTGGTTTCTTAGAAGGAGGATGGGAAGGAATGATTGCAGGTTGGCACGGATACACATCCCATGGAGCACATGGAGTAGCAGTGGCAGCAGACCTTAAGAGTACTCAAGAAGCCATAAACAAGATAACAAAAAATCTCAACTCTTTGAGTGAGCTGGAAGTAAAGAATCTTCAAAGACTAAGCGGTGCCATGGATGAACTCCACAACGAAATACTAGAACTAGACGAGAAAGTGGATGATCTCAGAGCTGATACAATAAGCTCGCAAATAGAACTCGCAGTCTTGCTTTCCAAT',
},
{
'strain': 'B/HongKong/330/2001',
'isolate_id': 'EPI_ISL_2342',
'date': '2001-07-01', #(Month and day unknown)
'region': 'China',
'seq': 'GATCGAATCTGCACTGGAATAACATCGTCAAACTCACCCCATGTGGTCAAAACTGCTACTCAAGGGGAAGTCAATGTGACTGGTGTGATACCACTGACAACAACACCCACCAAATCTCATTTTGCAAATCTCAAAGGAACAAAAACCAGAGGGAAACTATGCCCAAAATGTCTCAACTGCACAGATCTGGACGTGGCCTTGGGCAGACCAAAATGCACGGGGAACATACCTTCGGCAAAAGTTTCAATACTCCATGAAGTAAGACCTGTTACATCTGGGTGCTTTCCTATAATGCACGACAGAACAAAAATTAGACAGCTGCCCAATCTTCTCAGAGGATACGAACGTATCAGGTTATCAAACCATAACGTTATCAATGCAGAAAAAGCACCAGGAGGACCCTACAAAATTGGAACCTCAGGGTCTTGCCCTAACGTTACCAATGGAAACGGATTCTTCGCAACAATGGCTTGGGCTGTCCCAAAAAACGAAAACAACAAAACAGCAACAAATTCATTAACAATAGAAGTACCATACATTTGTACAGAAGGAGAAGACCAAATTACCGTTTGGGGGTTCCACTCTGATAGCGAAACCCAAATGGCAAAACTCTATGGAGACTCAAAGCCTCAGAAGTTCACTTCATCTGCCAACGGAGTGACCACACATTACGTTTCACAGATTGGTGGCTTCCCAAATCAAACAGAAGACGGAGGACTACCACAAAGTGGTAGAATTGTTGTTGATTACATGGTGCAAAAATCTGGAAAAACAGGAACAATTACCTATCAAAGAGGTATTTTATTGCCTCAAAAAGTGTGGTGCGCAAGTGGCAGGAGCAAGGTAATAAAAGGATCCTTGCCTTTAATTGGAGAAGCAGATTGCCTCCACGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTACTATACAGGGGAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTGAAAACACCCTTGAAGCTGGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGGGGTTTCTTCGGAGCTTTGGGCTG',
},
{
'strain': 'B/Malaysia/2506/2004',
'isolate_id': 'EPI_ISL_21142',
'date':'2004-07-01', # (Month and day unknown) | |
'region':'SouthEast Asia',
'seq':'ATTGTACTACTCATGGTAGTAACATCCAATGCAGATCGAATCTGCACTGGGATAACATCGTCAAACTCACCACATGTTGTCAAAACTGCTACTCAAGGGGAGGTCAATGTGACTGGTGTAATACCACTGACAACAACACCCACCAAATCTCATTTTGCAAATCTCAAAGGAACAGAAACCAGAGGGAAACTATGCCCAAAATGTCTCAACTGCACAGATCTGGACGTGGCCTTGGGCAGACCAAAATGCACGGGGAACATACCCTCGGCAAGAGTTTCAATACTCCATGAAGTCAGACCTGTTACATCTGGGTGCTTTCCTATAATGCACGACAGAACAAAAATTAGACAGCTGCCTAACCTTCTCAGAGGATACGAACATATCAGGTTATCAACTCATAACGTTATCAATGCAGAAAATGCACCAGGAGGATCCTACAAAATTGGAACCTCAGGGTCTTGCCCTAACGTTACCAATGGAAACGGATTTTTCGCAACAATGGCTTGGGCCGTCCCAAAAAACGACAACAACAAAACAGCAACAAATTCATTAACAATAGAAGTACCATACATTTGTACAGAAGGAGAAGACCAAATTACCGTTTGGGGGTTCCACTCTGATAACGAAGCCCAAATGGCAAAGCTCTATGGGGACTCAAAGCCCCAGAAGTTCACCTCATCTGCCAACGGAGTGACCACACATTACGTTTCACAGATTGGTGGCTTCCCAAATCAAACAGAAGACGGAGGACTACCACAAAGTGGTAGAATTGTTGTTGATTACATGGTGCAAAAATCTGGGAAAACAGGAACAATTACCTATCAAAGAGGTATTTTATTGCCTCAAAAAGTGTGGTGCGCAAGTGGCAGGAGCAAGGTAATAAAAGGATCCTTGCCTTTAATTGGAGAAGCAGATTGCCTCCACGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGGGAACATGCAAAGGCCATAGGAAATTGCCCAATATGGGTGAAAACACCCTTGAAGCTGGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGGGGTTTCTTCGGAGCTATTGCTGGTTTCTTAGAAGGAGGATGGGAAGGAATGATTGCAGGTTGGCACGGATACACATCCCATGGGGCACATGGAGTAGCGGTGGCAGCAGACCTTAAGAGCACTCAAGAGGCCATAAACAAGATAACAAAAAATCTCAACTCTTTGAGTGAGCTGGAAGTAAAGAATCTTCAAAGACTAAGCGGTGCCATGGATGAACTCCACAACGAAATACTAGAACTAGACGAGAAAGTGGATGATCTCAGAGCTGATACAATAAGCTCACAAATAGAACTCGCAGTCCTGCTTTCCAATGAAGGAATAATAAACAGTGAAGATGAGCATCTCTTGGCGCTTGAAAGAAAGCTGAAGAAAATGCTGGGCCCCTCTGCTGTAGAGATAGGGAATGGATGCTTTGAAACCAAACACAAGTGCAACCAGACCTGTCTCGACAGAATAGCTGCTGGTACCTTTGATGCAGGAGAATTTTCTCTCCCCACTTTTGATTCACTGAATATTACTGCTGCATCTTTAAATGACGATGGATTGGATAATCATACTATACTGCTTTACTACTCAACTGCTGCCTCCAGTTTGGCTGTAACATTGATGATAGCTATCTTTGTTGTTTATATGGTCTCCAGAGACAATGTTTCTTGCTCCATCTGTCTATAAGGAAAGTTAAACCCTGTATTTTCCTTTATTGTAGTGCTTGTTTGCTTGTTACCATTACAAAAAACGGTTATTGAAAAATGCTCTTGTTACTACTAATA',
},
{
'strain':'B/Brisbane/60/2008',
'isolate_id':'EPI_ISL_24365',
'date': '2008-08-04',
'lab':'Queensland Health Scientific Services',
'region':'Oceania',
'seq':'AGCAGAAGCAGAGCATTTTCTAATATCCACAAAATGAAGGCAATAATTGTACTACTCATGGTAGTAACATCCAATGCAGATCGAATCTGCACTGGGATAACATCGTCAAACTCACCACATGTCGTCAAAACTGCTACTCAAGGGGAGGTCAATGTGACTGGTGTAATACCACTGACAACAACACCCACCAAATCTCATTTTGCAAATCTCAAAGGAACAGAAACCAGGGGGAAACTATGCCCAAAATGCCTCAACTGCACAGATCTGGACGTAGCCTTGGGCAGACCAAAATGCACGGGGAAAATACCCTCGGCAAGAGTTTCAATACTCCATGAAGTCAGACCTGTTACATCTGGGTGCTTTCCTATAATGCACGACAGAACAAAAATTAGACAGCTGCCTAACCTTCTCCGAGGATACGAACATATCAGGTTATCAACCCATAACGTTATCAATGCAGAAAATGCACCAGGAGGACCCTACAAAATTGGAACCTCAGGGTCTTGCCCTAACATTACCAATGGAAACGGATTTTTCGCAACAATGGCTTGGGCCGTCCCAAAAAACGACAAAAACAAAACAGCAACAAATCCATTAACAATAGAAGTACCATACATTTGTACAGAAGGAGAAGACCAAATTACCGTTTGGGGGTTCCACTCTGACAACGAGACCCAAATGGCAAAGCTCTATGGGGACTCAAAGCCCCAGAAGTTCACCTCATCTGCCAACGGAGTGACCACACATTACGTTTCACAGATTGGTGGCTTCCCAAATCAAACAGAAGACGGAGGACTACCACAAAGTGGTAGAATTGTTGTTGATTACATGGTGCAAAAATCTGGGAAAACAGGAACAATTACCTATCAAAGGGGTATTTTATTGCCTCAAAAGGTGTGGTGCGCAAGTGGCAGGAGCAAGGTAATAAAAGGATCCTTGCCTTTAATTGGAGAAGCAGATTGCCTCCACGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGGGAACATGCAAAGGCCATAGGAAATTGCCCAATATGGGTGAAAACACCCTTGAAGCTGGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGGGGTTTCTTCGGAGCTATTGCTGGTTTCTTAGAAGGAGGATGGGAAGGAATGATTGCAGGTTGGCACGGATACACATCCCATGGGGCACATGGAGTAGCGGTGGCAGCAGACCTTAAGAGCACTCAAGAGGCCATAAACAAGATAACAAAAAATCTCAACTCTTTGAGTGAGCTGGAAGTAAAGAATCTTCAAAGACTAAGCGGTGCCATGGATGAACTCCACAACGAAATACTAGAACTAGATGAGAAAGTGGATGATCTCAGAGCTGATACAATAAGCTCACAAATAGAACTCGCAGTCCTGCTTTCCAATGAAGGAATAATAAACAGTGAAGATGAACATCTCTTGGCGCTTGAAAGAAAGCTGAAGAAAATGCTGGGCCCCTCTGCTGTAGAGATAGGGAATGGATGCTTTGAAACCAAACACAAGTGCAACCAGACCTGTCTCGACAGAATAGCTGCTGGTACCTTTGATGCAGGAGAATTTTCTCTCCCCACCTTTGATTCACTGAATATTACTGCTGCATCTTTAAATGACGATGGATTGGATAATCATACTATACTGCTTTACTACTCAACTGCTGCCTCCAGT',
}
]
self.outgroup = {
'strain':'B/HongKong/02/1993',
'region':'China',
'isolate_id':'EPI_ISL_6617',
'date':'1993-02-15', #(Month and day unknown)
'seq': 'ATATCCACAAAATGAAGGCAATAATTGTACTACTCATGGTAGTAACATCCAATGCAGATCGAATCTGCACTGGGATAACATCGTCAAACTCACCCCATGTGGTCAAAACTGCTACTCAAGGGGAAGTCAATGTGACTGGTGTGATACCACTGACAACAACACCCACCAAATCTCATTTTGCAAATCTCAAAGGAACAAAAACCAGAGGGAAACTATGCCCAAAGTGTCTCAACTGCACAGATCTGGACGTGGCCTTGGGCAGACCAAAATGCACGGGGACCATACCTTCGGCAAAAGTTTCAATACTCCACGAAGTCAAACCTGTTACATCTGGGTGCTTTCCTATAATGCACGACAGAACAAAAATTAGACAGCTGCCCAATCTTCTCAGAGGATACGAACATATCAGGTTATCAACCCATAACGTTATCAACGCAGAAAAGGCACCAGGAGGACCCTACAAAATTGGAACCTCAGGGTCTTGCCCTAACATTACCAATGGAAACGGATTCTTCGCAACAATGGCTTGGGCTGTCCCAAAAAACGACAACAACAAAACAGCAACAAATTCATTAACAGTAGAAGTACCATACATTTGTACAGAAGGAGAAGACCAAATTACCGTTTGGGGGTTCCACTCTGATAACGAAACCCAAATGGCAAAACTCTATGGAGACTCAAAACCTCAGAAGTTCACCTCATCTGCCAACGGAGTGACCACACATTACGTTTCACAGATTGGTGGCTTCCCAAATCAAGCAGAAGACGGAGGGCTACCACAAAGTGGTAGAATTGTTGTTGATTACATGGTGCAAAAATCTGGAAAAACAGGAACAATTACCTACCAAAGAGGTATTTTATTGCCTCAAAAAGTGTGGTGCGCAAGTGGCAGGAGCAAGGTAATAAAAGGATCCTTGCCTTTAATTGGCGAAGCAGATTGCCTCCACGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGGGAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTGAAAACACCCTTGAATCTGGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAAGAAAGGGGTTTCTTCGGAGCTATTGCTGGTTTCTTAGAAGGAGGATGGGAAGGAATGATTGCAGGTTGGCACGGATACACATCCCATGGAGCACATGGAGTAGCAGTGGCAGCAGACCTTAAGAGTACACAAGAAGCCATAAACAAGATAACAAAAAATCTCAACTCTTTGAGTGAGCTTGAAGTAAAGAATCTTCAAAGACTAAGCGGTGCCATGGATGAACTCCACAACGAAATACTCGAACTGGATGAGAAAGTGGATGATCTCAGAGCTGACACAATAAGCTCGCAAATAGAGCTCGCAGTCTTGCTTTCCAATGAAGGAATAATAAACAGCGAAGATGAGCATCTCTTGGCACTTGAAAGAAAACTGAAGAAAATGCTGGGCCCCTCTGCTGTAGAGATAGGGAATGGATGCTTCGAAACCAAACACAAGTGCAACCAGACCTGCCTCGACAGAATAGCTGCTGGCACCTTTAATGCAGGAGAATTTTCTCTCCCCACCTTTGATTCATTAAATATTACTGCTGCATCTTTAAATGATGATGGATTGGATAATCATACTATACTGCTTTACTACTCAACTGCTGCTTCCAGTTTGGCTGTAACATTGATGATAGCTATCTTTATTGTTTATATGGTCTCCAGAGACAATGTTTCTTGCTCCATCTGTCTATAAGGAAAGTTAAGCCCTGTATTTTCCTTTATTGTAGTGCTTGTTTGCTTGTTACCATTACAAAAAACGTTATTGA'
}
def __init__(self, min_length=987, **kwargs):
"""
parameters
min_length -- minimal length for a sequence to be acceptable
"""
flu_filter.__init__(self, **kwargs)
self.min_length = min_length
self.vaccine_strains = [
{
"strain": "B/Shangdong/7/97",
"isolate_id": "EPI_ISL_1790",
"date": "1997-07-01", # (Month and day unknown)
"region": "China",
"seq": "GATCGAATCTGCACTGGGATAACATCGTCAAACTCACCCCATGTGGTCAAAACTGCTACTCAAGGGGAGGTCAATGTGACTGGTGTGATACCACTGACAACAACACCCACCAAATCTCATTTTGCAAATCTCAAAGGAACAAAAACCAGAGGGAAACTATGCCCAAAATGCCTCAACTGTACAGATCTGGACGTGGCCTTGGGCAGACCAAAATGCACGGGGAACATACCTTCGGCAAAAGTTTCAATACTCCATGAAGTCAGACCTGTTACATCTGGGTGCTTTCCTATAATGCACGACAGAACAAAAATTAGACAGCTGCCCAATCTTCTCAGAGGATACGAACATATCAGGTTATCAATTCATAACGTTATCAATGCAGAAAAGGCACCAGGAGGACCCTACAAAATTGGAACCTCAGGGTCTTGCCCTAACGTTACCAATGGAAACGGATTCTTCGCAACAATGGCTTGGGCCGTCCCAAAAAACGACAACAACAAAACAGCAACAAATTCATTAACAATAGAAGTACCATACATTTGTACAGAAGGAGAAGACCAAATTACCGTTTGGGGGTTCCACTCTGATAACGAAAACCAAATGGCAAAACTCTATGGGGACTCAAAGCCCCAGAAGTTCACCTCATCTGCCAACGGAGTGACCACACATTACGTTTCACAGATTGGTGGCTTCCCAAATCAAACAGAAGACGGAGGACTACCACAAAGTGGTAGAATTGTTGTTGATTACATGGTGCAAAAATCTGGGAAAACAGGAACAATTACCTATCAAAGAGGTATTTTATTGCCTCAAAAAGTGTGGTGCGCAAGTGGCAGGAGCAAGGTAATAAAAGGGTCCTTGCCTTTAATTGGAGAAGCAGATTGCCTCCACGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTATTACACAGGGGAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTGAAAACACCCTTGAAGCTGGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGGGGTTTCTTCGGAGCTATTGCTGGTTTCTTAGAAGGAGGATGGGAAGGAATGATTGCAGGTTGGCACGGATACACATCCCATGGAGCACATGGAGTAGCAGTGGCAGCAGACCTTAAGAGTACTCAAGAAGCCATAAACAAGATAACAAAAAATCTCAACTCTTTGAGTGAGCTGGAAGTAAAGAATCTTCAAAGACTAAGCGGTGCCATGGATGAACTCCACAACGAAATACTAGAACTAGACGAGAAAGTGGATGATCTCAGAGCTGATACAATAAGCTCGCAAATAGAACTCGCAGTCTTGCTTTCCAAT",
},
{
"strain": "B/HongKong/330/2001",
"isolate_id": "EPI_ISL_2342",
"date": "2001-07-01", # (Month and day unknown)
"region": "China",
"seq": "GATCGAATCTGCACTGGAATAACATCGTCAAACTCACCCCATGTGGTCAAAACTGCTACTCAAGGGGAAGTCAATGTGACTGGTGTGATACCACTGACAACAACACCCACCAAATCTCATTTTGCAAATCTCAAAGGAACAAAAACCAGAGGGAAACTATGCCCAAAATGTCTCAACTGCACAGATCTGGACGTGGCCTTGGGCAGACCAAAATGCACGGGGAACATACCTTCGGCAAAAGTTTCAATACTCCATGAAGTAAGACCTGTTACATCTGGGTGCTTTCCTATAATGCACGACAGAACAAAAATTAGACAGCTGCCCAATCTTCTCAGAGGATACGAACGTATCAGGTTATCAAACCATAACGTTATCAATGCAGAAAAAGCACCAGGAGGACCCTACAAAATTGGAACCTCAGGGTCTTGCCCTAACGTTACCAATGGAAACGGATTCTTCGCAACAATGGCTTGGGCTGTCCCAAAAAACGAAAACAACAAAACAGCAACAAATTCATTAACAATAGAAGTACCATACATTTGTACAGAAGGAGAAGACCAAATTACCGTTTGGGGGTTCCACTCTGATAGCGAAACCCAAATGGCAAAACTCTATGGAGACTCAAAGCCTCAGAAGTTCACTTCATCTGCCAACGGAGTGACCACACATTACGTTTCACAGATTGGTGGCTTCCCAAATCAAACAGAAGACGGAGGACTACCACAAAGTGGTAGAATTGTTGTTGATTACATGGTGCAAAAATCTGGAAAAACAGGAACAATTACCTATCAAAGAGGTATTTTATTGCCTCAAAAAGTGTGGTGCGCAAGTGGCAGGAGCAAGGTAATAAAAGGATCCTTGCCTTTAATTGGAGAAGCAGATTGCCTCCACGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTACTATACAGGGGAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTGAAAACACCCTTGAAGCTGGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGGGGTTTCTTCGGAGCTTTGGGCTG",
},
{
"strain": "B/Malaysia/2506/2004",
"isolate_id": "EPI_ISL_21142",
"date": "2004-07-01", # (Month and day unknown) | |
"region": "SouthEast Asia",
"seq": "ATTGTACTACTCATGGTAGTAACATCCAATGCAGATCGAATCTGCACTGGGATAACATCGTCAAACTCACCACATGTTGTCAAAACTGCTACTCAAGGGGAGGTCAATGTGACTGGTGTAATACCACTGACAACAACACCCACCAAATCTCATTTTGCAAATCTCAAAGGAACAGAAACCAGAGGGAAACTATGCCCAAAATGTCTCAACTGCACAGATCTGGACGTGGCCTTGGGCAGACCAAAATGCACGGGGAACATACCCTCGGCAAGAGTTTCAATACTCCATGAAGTCAGACCTGTTACATCTGGGTGCTTTCCTATAATGCACGACAGAACAAAAATTAGACAGCTGCCTAACCTTCTCAGAGGATACGAACATATCAGGTTATCAACTCATAACGTTATCAATGCAGAAAATGCACCAGGAGGATCCTACAAAATTGGAACCTCAGGGTCTTGCCCTAACGTTACCAATGGAAACGGATTTTTCGCAACAATGGCTTGGGCCGTCCCAAAAAACGACAACAACAAAACAGCAACAAATTCATTAACAATAGAAGTACCATACATTTGTACAGAAGGAGAAGACCAAATTACCGTTTGGGGGTTCCACTCTGATAACGAAGCCCAAATGGCAAAGCTCTATGGGGACTCAAAGCCCCAGAAGTTCACCTCATCTGCCAACGGAGTGACCACACATTACGTTTCACAGATTGGTGGCTTCCCAAATCAAACAGAAGACGGAGGACTACCACAAAGTGGTAGAATTGTTGTTGATTACATGGTGCAAAAATCTGGGAAAACAGGAACAATTACCTATCAAAGAGGTATTTTATTGCCTCAAAAAGTGTGGTGCGCAAGTGGCAGGAGCAAGGTAATAAAAGGATCCTTGCCTTTAATTGGAGAAGCAGATTGCCTCCACGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGGGAACATGCAAAGGCCATAGGAAATTGCCCAATATGGGTGAAAACACCCTTGAAGCTGGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGGGGTTTCTTCGGAGCTATTGCTGGTTTCTTAGAAGGAGGATGGGAAGGAATGATTGCAGGTTGGCACGGATACACATCCCATGGGGCACATGGAGTAGCGGTGGCAGCAGACCTTAAGAGCACTCAAGAGGCCATAAACAAGATAACAAAAAATCTCAACTCTTTGAGTGAGCTGGAAGTAAAGAATCTTCAAAGACTAAGCGGTGCCATGGATGAACTCCACAACGAAATACTAGAACTAGACGAGAAAGTGGATGATCTCAGAGCTGATACAATAAGCTCACAAATAGAACTCGCAGTCCTGCTTTCCAATGAAGGAATAATAAACAGTGAAGATGAGCATCTCTTGGCGCTTGAAAGAAAGCTGAAGAAAATGCTGGGCCCCTCTGCTGTAGAGATAGGGAATGGATGCTTTGAAACCAAACACAAGTGCAACCAGACCTGTCTCGACAGAATAGCTGCTGGTACCTTTGATGCAGGAGAATTTTCTCTCCCCACTTTTGATTCACTGAATATTACTGCTGCATCTTTAAATGACGATGGATTGGATAATCATACTATACTGCTTTACTACTCAACTGCTGCCTCCAGTTTGGCTGTAACATTGATGATAGCTATCTTTGTTGTTTATATGGTCTCCAGAGACAATGTTTCTTGCTCCATCTGTCTATAAGGAAAGTTAAACCCTGTATTTTCCTTTATTGTAGTGCTTGTTTGCTTGTTACCATTACAAAAAACGGTTATTGAAAAATGCTCTTGTTACTACTAATA",
},
{
"strain": "B/Brisbane/60/2008",
"isolate_id": "EPI_ISL_24365",
"date": "2008-08-04",
"lab": "Queensland Health Scientific Services",
"region": "Oceania",
"seq": "AGCAGAAGCAGAGCATTTTCTAATATCCACAAAATGAAGGCAATAATTGTACTACTCATGGTAGTAACATCCAATGCAGATCGAATCTGCACTGGGATAACATCGTCAAACTCACCACATGTCGTCAAAACTGCTACTCAAGGGGAGGTCAATGTGACTGGTGTAATACCACTGACAACAACACCCACCAAATCTCATTTTGCAAATCTCAAAGGAACAGAAACCAGGGGGAAACTATGCCCAAAATGCCTCAACTGCACAGATCTGGACGTAGCCTTGGGCAGACCAAAATGCACGGGGAAAATACCCTCGGCAAGAGTTTCAATACTCCATGAAGTCAGACCTGTTACATCTGGGTGCTTTCCTATAATGCACGACAGAACAAAAATTAGACAGCTGCCTAACCTTCTCCGAGGATACGAACATATCAGGTTATCAACCCATAACGTTATCAATGCAGAAAATGCACCAGGAGGACCCTACAAAATTGGAACCTCAGGGTCTTGCCCTAACATTACCAATGGAAACGGATTTTTCGCAACAATGGCTTGGGCCGTCCCAAAAAACGACAAAAACAAAACAGCAACAAATCCATTAACAATAGAAGTACCATACATTTGTACAGAAGGAGAAGACCAAATTACCGTTTGGGGGTTCCACTCTGACAACGAGACCCAAATGGCAAAGCTCTATGGGGACTCAAAGCCCCAGAAGTTCACCTCATCTGCCAACGGAGTGACCACACATTACGTTTCACAGATTGGTGGCTTCCCAAATCAAACAGAAGACGGAGGACTACCACAAAGTGGTAGAATTGTTGTTGATTACATGGTGCAAAAATCTGGGAAAACAGGAACAATTACCTATCAAAGGGGTATTTTATTGCCTCAAAAGGTGTGGTGCGCAAGTGGCAGGAGCAAGGTAATAAAAGGATCCTTGCCTTTAATTGGAGAAGCAGATTGCCTCCACGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGGGAACATGCAAAGGCCATAGGAAATTGCCCAATATGGGTGAAAACACCCTTGAAGCTGGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGGGGTTTCTTCGGAGCTATTGCTGGTTTCTTAGAAGGAGGATGGGAAGGAATGATTGCAGGTTGGCACGGATACACATCCCATGGGGCACATGGAGTAGCGGTGGCAGCAGACCTTAAGAGCACTCAAGAGGCCATAAACAAGATAACAAAAAATCTCAACTCTTTGAGTGAGCTGGAAGTAAAGAATCTTCAAAGACTAAGCGGTGCCATGGATGAACTCCACAACGAAATACTAGAACTAGATGAGAAAGTGGATGATCTCAGAGCTGATACAATAAGCTCACAAATAGAACTCGCAGTCCTGCTTTCCAATGAAGGAATAATAAACAGTGAAGATGAACATCTCTTGGCGCTTGAAAGAAAGCTGAAGAAAATGCTGGGCCCCTCTGCTGTAGAGATAGGGAATGGATGCTTTGAAACCAAACACAAGTGCAACCAGACCTGTCTCGACAGAATAGCTGCTGGTACCTTTGATGCAGGAGAATTTTCTCTCCCCACCTTTGATTCACTGAATATTACTGCTGCATCTTTAAATGACGATGGATTGGATAATCATACTATACTGCTTTACTACTCAACTGCTGCCTCCAGT",
},
]
self.outgroup = {
"strain": "B/HongKong/02/1993",
"region": "China",
"isolate_id": "EPI_ISL_6617",
"date": "1993-02-15", # (Month and day unknown)
"seq": "ATATCCACAAAATGAAGGCAATAATTGTACTACTCATGGTAGTAACATCCAATGCAGATCGAATCTGCACTGGGATAACATCGTCAAACTCACCCCATGTGGTCAAAACTGCTACTCAAGGGGAAGTCAATGTGACTGGTGTGATACCACTGACAACAACACCCACCAAATCTCATTTTGCAAATCTCAAAGGAACAAAAACCAGAGGGAAACTATGCCCAAAGTGTCTCAACTGCACAGATCTGGACGTGGCCTTGGGCAGACCAAAATGCACGGGGACCATACCTTCGGCAAAAGTTTCAATACTCCACGAAGTCAAACCTGTTACATCTGGGTGCTTTCCTATAATGCACGACAGAACAAAAATTAGACAGCTGCCCAATCTTCTCAGAGGATACGAACATATCAGGTTATCAACCCATAACGTTATCAACGCAGAAAAGGCACCAGGAGGACCCTACAAAATTGGAACCTCAGGGTCTTGCCCTAACATTACCAATGGAAACGGATTCTTCGCAACAATGGCTTGGGCTGTCCCAAAAAACGACAACAACAAAACAGCAACAAATTCATTAACAGTAGAAGTACCATACATTTGTACAGAAGGAGAAGACCAAATTACCGTTTGGGGGTTCCACTCTGATAACGAAACCCAAATGGCAAAACTCTATGGAGACTCAAAACCTCAGAAGTTCACCTCATCTGCCAACGGAGTGACCACACATTACGTTTCACAGATTGGTGGCTTCCCAAATCAAGCAGAAGACGGAGGGCTACCACAAAGTGGTAGAATTGTTGTTGATTACATGGTGCAAAAATCTGGAAAAACAGGAACAATTACCTACCAAAGAGGTATTTTATTGCCTCAAAAAGTGTGGTGCGCAAGTGGCAGGAGCAAGGTAATAAAAGGATCCTTGCCTTTAATTGGCGAAGCAGATTGCCTCCACGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGGGAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTGAAAACACCCTTGAATCTGGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAAGAAAGGGGTTTCTTCGGAGCTATTGCTGGTTTCTTAGAAGGAGGATGGGAAGGAATGATTGCAGGTTGGCACGGATACACATCCCATGGAGCACATGGAGTAGCAGTGGCAGCAGACCTTAAGAGTACACAAGAAGCCATAAACAAGATAACAAAAAATCTCAACTCTTTGAGTGAGCTTGAAGTAAAGAATCTTCAAAGACTAAGCGGTGCCATGGATGAACTCCACAACGAAATACTCGAACTGGATGAGAAAGTGGATGATCTCAGAGCTGACACAATAAGCTCGCAAATAGAGCTCGCAGTCTTGCTTTCCAATGAAGGAATAATAAACAGCGAAGATGAGCATCTCTTGGCACTTGAAAGAAAACTGAAGAAAATGCTGGGCCCCTCTGCTGTAGAGATAGGGAATGGATGCTTCGAAACCAAACACAAGTGCAACCAGACCTGCCTCGACAGAATAGCTGCTGGCACCTTTAATGCAGGAGAATTTTCTCTCCCCACCTTTGATTCATTAAATATTACTGCTGCATCTTTAAATGATGATGGATTGGATAATCATACTATACTGCTTTACTACTCAACTGCTGCTTCCAGTTTGGCTGTAACATTGATGATAGCTATCTTTATTGTTTATATGGTCTCCAGAGACAATGTTTCTTGCTCCATCTGTCTATAAGGAAAGTTAAGCCCTGTATTTTCCTTTATTGTAGTGCTTGTTTGCTTGTTACCATTACAAAAAACGTTATTGA",
}
def __init__(self,min_length = 987, **kwargs):
'''
parameters
min_length -- minimal length for a sequence to be acceptable
'''
flu_filter.__init__(self, **kwargs)
self.min_length = min_length
self.vaccine_strains =[
{ 'strain':'A/Beijing/262/95',
'isolate_id':'EPI_ISL_2656',
'region':'China',
'db':'GISAID',
'date':'1995-07-01', # (Month and day unknown)
'seq':'AGCAAAAGCAGGGGAAAATAAAAACAACCAAAATGAAAGCAAAACTACTAGTCCTGTTATGTACATTTACAGCTACATATGCAGACACAATATGTATAGGCTACCATGCCAACAACTCAACCGACACTGTTGACACAGTACTTGAGAAGAATGTGACAGTGACACACTCTGTCAACCTACTTGAGGACAGTCACAATGGAAAACTATGTCTACTAAAAGGAATAGCCCCACTACAATTGGGTAATTGCAGCGTTGCCGGATGGATCTTAGGAAACCCAGAATGCGAATCACTGATTTCTAAGGAATCATGGTCCTACATTGTAGAGACACCAAACCCTGAGAATGGAACATGTTACCCAGGGTATTTCGCCGACTATGAGGAACTGAGGGAGCAATTGAGTTCAGTATCATCATTTGAGAGATTCGAAATATTCCCCAAAGAAAGCTCATGGCCCAAACACACCGTAACAGGAGTAACGGCATCATGCTCCCATAATGGGAAAAGCAGTTTTTACAGAAATTTGCTATGGCTGACGGAGAAGAATGGCTTGTACCCAAATCTGAGCAATTCCTATGTGAACAACAAAGAGAAAGAAGTCCTTGTACTATGGGGTGTTCATCACCCATCTAACATAGGGGACCAAAGGGCCATCTATCATACAGAAAACGCTTATGTCTCTGTAGTGTCTTCACATTATAGCAGAAGATTCACCCCAGAAATAGCAAAAAGACCCAAAGTAAGAGGTCAGGAAGGAAGAATCAACTACTACTGGACTCTGCTGGAACCCGGGGACACAATAATATTTGAGGCAAATGGAAATCTAATAGCGCCATGGTATGCTTTCGCACTGAGTAGAGGCTTTGGGTCAGGAATCATCACCTCAAATGCACCAATGAATGAATGTGATGCGAAGTGTCAAACACCTCAGGGAGCTATAAACAGTAGTCTTCCTTTCCAGAATGTACACCCAGTCACAATAGGAGAGTGTCCAAAGTATGTCAGGAGTACAAAATTAAGGATGGTTACAGGACTAAGGAATATCCCATCCATTCAATCCAGAGGTTTGTTTGGAGCCATTGCCGGTTTCATTGAAGGGGGGTGGACTGGAATGATGGATGGGTGGTATGGTTATCATCATCAGAATGAGCAAGGATCTGGCTATGCTGCAGATCAAAAAAGCACACAAAATGCCATTAACGGGATTACAAATAAGGTGAATTCTGTAATTGAGAAAATGAACACTCAATTCACAGCTGTGGGCAAAGAATTCAACAAATTAGAAAGAAGGATGGAAAACTTAAATAAAAAAGTTGATGATGGATTTCTAGACATTTGGACATATAATGCAGAATTGTTGGTTCTACTGGAAAATGAAAGGACTTTGGATTTCCATGACTCAAATGTGAAGAATCTGTATGAGAAAGTGAAAAGCCAATTAAAGAATAATGCCAAAGAAATAGGGAACGGGTGTTTTGAATTCTATCACAAGTGTAACAATGAATGCATGGAAAGTGTGAAAAATGGAACTTATGACTATCCAAAATATTCCGAAGAATCAAAGTTAAACAGGGAGAAAATTGATGGAGTGAAATTGGAATCAATGGGAGTCTATCAGATTCTGGCGATCTACTCAACTGTCGCCAGTTCACTGGTTCTTTTGGTCTCCCTGGGGGCAATCAGCTTCTGGATGTGTTCCAATGGGTCTTTGCAGTGTAGAATATGCATCTGAGACCAGAATTTCAGAAATATAAGAAAAAACACCCTTGTTTCTACT',
},
{ 'strain':'A/NewCaledonia/20/99',
'isolate_id':'EPI_ISL_158137',
'region':'Oceania',
'date':'1999-06-09',
'seq':'GACACAATATGTATAGGCTACCATGCCAACAACTCAACCGACACTGTTGACACAGTACTTGAGAAGAATGTGACAGTGACACACTCTGTCAACCTACTTGAGGACAGTCACAACGGAAAACTATGTCTACTAAAAGGAATAGCCCCACTACAATTGGGTAATTGCAGCGTTGCCGGATGGATCTTAGGAAACCCAGAATGCGAATTACTGATTTCCAAGGAATCATGGTCCTACATTGTAGAAACACCAAATCCTGAGAATGGAACATGTTACCCAGGGTATTTCGCCGACTATGAGGAACTGAGGGAGCAATTGAGTTCAGTATCTTCATTTGAGAGATTCGAAATATTCCCCAAAGAAAGCTCATGGCCCAACCACACCGTAACCGGAGTATCAGCATCATGCTCCCATAATGGGAAAAGCAGTTTTTACAGAAATTTGCTATGGCTGACGGGGAAGAATGGTTTGTACCCAAACCTGAGCAAGTCCTATGTAAACAACAAAGAGAAAGAAGTCCTTGTACTATGGGGTGTTCATCACCCGCCTAACATAGGGGACCAAAGGGCCCTCTATCATACAGAAAATGCTTATGTCTCTGTAGTGTCTTCACATTATAGCAGAAGATTCACCCCAGAAATAGCCAAAAGACCCAAAGTAAGAGATCAGGAAGGAAGAATCAACTACTACTGGACTCTGCTGGAACCTGGGGATACAATAATATTTGAGGCAAATGGAAATCTAATAGCGCCATGGTATGCTTTTGCACTGAGTAGAGGCTTTGGATCAGGAATCATCACCTCAAATGCACCAATGGATGAATGTGATGCGAAGTGTCAAACACCTCAGGGAGCTATAAACAGCAGTCTTCCTTTCCAGAATGTACACCCAGTCACAATAGGAGAGTGTCCAAAGTATGTCAGGAGTGCAAAATTAAGGATGGTTACAGGACTAAGGAACATCCCATCCATTCAATCCAGAGGTTTGTTTGGAGCCATTGCCGGTTTCATTGAAGGGGGGTGGACTGGAATGGTAGATGGGTGGTATGGTTATCATCATCAGAATGAGCAAGGATCTGGCTATGCTGCAGATCAAAAAAGTACACAAAATGCCATTAACGGGATTACAAACAAGGTGAATTCTGTAATTGAGAAAATGAACACTCAATTCACAGCTGTGGGCAAAGAATTCAACAAATTGGAAAGAAGGATGGAAAACTTAAATAAAAAAGTTGATGATGGGTTTCTAGACATTTGGACATATAATGCAGAATTGTTGGTTCTACTGGAAAATGAAAGGACTTTGGATTTCCATGACTCCAATGTGAAGAATCTGTATGAGAAAGTAAAAAGCCAATTAAAGAATAATGCCAAAGAAATAGGAAACGGGTGTTTTGAATTCTATCACAAGTGTAACAATGAATGCATGGAGAGTGTGAAAAATGGAACTTATGACTATCCAAAATATTCCGAAGAATCAAAGTTAAACAGGGAGAAAATTGATGGAGTGAAATTGGAATCAATGGGAGTCTATCAGATTCTGGCGATCTACTCAACTGTCGCCAGTTCCCTGGTTCTTTTGGTCTCCCTGGGGGCAATCAGCTTCTGGATGTGTTCCAATGGGTCTTTGCAGTGCAGAATATGC',
},
{'strain': 'A/SolomonIslands/3/2006',
'isolate_id':'EPI_ISL_157458',
'region':'Oceania',
'date':'2006-08-21',
'lab':'WHO Centre for Reference & Research on Influenza',
'seq': 'GACACAATATGTATAGGCTACCATGCCAACAACTCAACCGACACTGTTGACACAGTACTTGAGAAGAATGTGACAGTGACACACTCTGTCAACCTGCTTGAGGACAGTCACAATGGAAAATTATGTCTATTAAAAGGAATAGCCCCACTACAATTGGGTAATTGCAGCGTTGCCGGATGGATCTTAGGAAACCCAGAATGCGAATTACTGATTTCCAGGGAATCATGGTCCTACATTGTAGAAAAACCAAATCCTGAGAATGGAACATGTTACCCAGGGCATTTCGCCGACTATGAGGAACTGAGGGAGCAATTGAGTTCAGTATCTTCATTTGAGAGATTCGAAATATTCCCCAAAGAAAGCTCATGGCCCAACCACACCACAACCGGAGTATCAGCATCATGCTCCCATAATGGGGAAAGCAGTTTTTACAAAAATTTGCTATGGCTGACGGGGAAGAATGGTTTGTACCCAAACCTGAGCAAGTCCTATGCAAACAACAAAGAGAAAGAAGTCCTTGTACTATGGGGTGTTCATCACCCGCCTAACATAGGTGACCAAAGGGCTCTCTATCATACAGAAAATGCTTATGTCTCTGTAGTGTCTTCACATTATAGCAGAAAATTCACCCCAGAAATAGCCAAAAGACCCAAAGTAAGAGATCGAGAAGGAAGAATCAACTACTACTGGACTCTACTTGAACCCGGGGATACAATAATATTTGAGGCAAATGGAAATCTAATAGCGCCAAGATATGCTTTCGCACTGAGTAGAGGCTTTGGATCAGGAATCATCAACTCAAATGCACCAATGGATGAATGTGATGCGAAGTGCCAAACACCTCAGGGAGCTATAAACAGCAGTCTTCCTTTCCAGAATGTACACCCTGTCACAATAGGAGAGTGTCCAAAGTATGTCAGGAGTGCAAAATTAAGGATGGTTACAGGACTAAGGAACATCCCATCCATTCAATCCAGAGGTTTGTTTGGAGCCATTGCCGGTTTCATTGAAGGGGGGTGGACTGGAATGGTAGATGGTTGGTATGGTTATCATCATCAGAATGAGCAAGGATCTGGCTATGCTGCAGATCAAAAAAGCACACAAAATGCCATTAATGGGATTACAAACAAGGTGAATTCTGTAATTGAGAAAATGAACACTCAATTCACAGCTGTGGGCAAAGAATTCAACAAATTGGAAAGAAGGATGGAAAACTTAAATAAAAAAGTTGATGATGGGTTTATAGACATTTGGACATATAATGCAGAATTGTTGGTTCTACTGGAAAATGAAAGGACTTTGGATTTCCATGACTCCAATGTGAAGAATCTGTATGAGAAAGTAAAAAGCCAATTAAAGAATAATGCCAAAGAAATAGGAAATGGGTGTTTTGAATTCTATCACAAGTGTAACGATGAATGCATGGAGAGTGTAAAAAATGGAACTTATGACTATCCAAAATATTCCGAAGAATCAAAGTTAAACAGGGAGAAAATTGATGGAGTGAAATTGGAATCAATGGGAGTCTATCAGATTCTGGCGATCTACTCAACAGTCGCCAGTTCTCTGGTCCTTTTGGTCTCCCTGGGGGCAATCAGATTCG',
},
{'strain':'A/Brisbane/59/2007',
'isolate_id':'EPI_ISL_23344',
'region':'Oceania',
'date':'2007-07-01', # (Month and day unknown)
'seq': 'ATGAAAGTAAAACTACTGGTCCTGTTATGCACATTTACAGCTACATATGCAGACACAATATGTATAGGCTACCATGCTAACAACTCGACCGACACTGTTGACACAGTACTTGAAAAGAATGTGACAGTGACACACTCTGTCAACCTGCTTGAGAACAGTCACAATGGAAAACTATGTCTATTAAAAGGAATAGCCCCACTACAATTGGGTAATTGCAGCGTTGCCGGGTGGATCTTAGGAAACCCAGAATGCGAATTACTGATTTCCAAGGAGTCATGGTCCTACATTGTAGAAAAACCAAATCCTGAGAATGGAACATGTTACCCAGGGCATTTCGCTGACTATGAGGAACTGAGGGAGCAATTGAGTTCAGTATCTTCATTTGAGAGGTTCGAAATATTCCCCAAAGAAAGCTCATGGCCCAACCACACCGTAACCGGAGTGTCAGCATCATGCTCCCATAATGGGGAAAGCAGTTTTTACAGAAATTTGCTATGGCTGACGGGGAAGAATGGTTTGTACCCAAACCTGAGCAAGTCCTATGCAAACAACAAAGAAAAAGAAGTCCTTGTACTATGGGGTGTTCATCACCCGCCAAACATAGGTRWCCAAAAGGCCCTCTATCATACAGAAAATGCTTATGTCTCTGTAGTGTCTTCACATTATAGCAGAAAATTCACCCCAGAAATAGCCAAAAGACCCAAAGTAAGAGATCAAGAAGGAAGAATCAATTACTACTGGACTCTGCTTGAACCCGGGGATACAATAATATTTGAGGCAAATGGAAATCTAATAGCGCCAAGATATGCTTTCGCACTGAGTAGAGGCTTTGGATCAGGAATCATCAACTCAAATGCACCAATGGATAAATGTGATGCGAAGTGCCAAACACCTCAGGGAGCTATAAACAGCAGTCTTCCTTTCCAGAACGTACACCCAGTCACAATAGGAGAGTGTCCAAAGTATGTCAGGAGTGCAAAATTAAGGATGGTTACAGGACTAAGGAACATCCCATCCATTCAATCCAGAGGTTTGTTTGGAGCCATTGCCGGTTTCATTGAAGGGGGGTGGACTGGAATGGTAGATGGTTGGTATGGTTATCATCATCAGAATGAGCAAGGATCTGGCTATGCTGCAGATCAAAAAAGCACACAAAATGCCATTAATGGGATTACAAACAAGGTGAATTCTGTAATTGAGAAAATGAACACTCAATTCACAGCAGTGGGCAAAGAATTCAACAAATTGGAAAGAAGGATGGAAAACTTGAATAAAAAAGTTGATGATGGGTTTATAGACATTTGGACATATAATGCAGAACTGTTGGTTCTACTGGAAAATGAAAGGACTTTGGATTTCCATGACTCCAATGTGAAGAATCTGTATGAGAAAGTAAAAAGCCAGTTAAAGAATAATGCTAAAGAAATAGGAAATGGGTGTTTTGAATTCTATCACAAGTGTAACGATGAATGCATGGAGAGTGTAAAGAATGGAACTTATGACTATCCAAAATATTCCGAAGAATCAAAGTTAAACAGGGAGAAAATTGATGGAGTGAAATTGGAATCAATGGGAGTCTATCAGATTCTGGCGATCTACTCAACAGTCGCCAGTTCTCTGGTTCTTTTGGTCTCCCTGGGGGCAATCAGCTTCTGGATGTGTTCCAATGGGTCTTTACAGTGTAGAATATGCATCTAA',
}
]
self.outgroup = {
'strain': 'A/Tokyo/1/51',
'db': 'GISAID',
'accession': 'EPI_ISL_101',
'date': '1951-07-01',
'country': 'Japan',
'region': 'JapanKorea',
'seq': 'ATGAAAGCAAAACTACTGATCCTGTTATGTGCACTTTCAGCTACAGATGCAGACACAATATGTATAGGCTACCATGCTAACAATTCAACCGACACTGTTGACACAGTACTCGAAAAGAATGTGACAGTGACACACTCTGTAAACCTACTCGAAGACAGCCACAACGGGAAATTATGCAGATTAAAAGGAATAGCCCCACTACAATTGGGGAAATGTAACATTGCCGGATGGATCTTGGGAACCCCAGAATGCGAATCATTGCTCTCTAATAGATCATGGTCCTACATTGCAGAAACACCAAACTGTGAGAATGGAACATGTTACCCAGGAGATTTCGCCGACTATGAGGAACTGAGGGAGCAATTGAGCTCAGTATCATCATTCGAGAGATTCGAAATATTCCCCAAGGAAAGATCATGGCCCAAACACAACATAACCAGAGGAGTAACGGCAGCATGCTCCCACGCGAAGAAAAGCAGTTTTTACAAAAATTTGCTCTGGCTGACGGAGGCAAATGGCTCATACCCAAATCTGAGCAAGTCCTATGTGAACAATAAAGAGAAAGAAGTCCTTGTGCTGTGGGGTGTTCATCACCCGTCTAACATAGAGGATCAAAGGACCCTCTATCGGAAAGAAAATGCTTATGTCTCTGTGGTGTCTTCAAATTATAACAGGAGATTCACCCCGGAAATAGCAGAAAGACCCAAAGTAAGAGGTCAAGCAGGGAGAATAAACTATTACTGGACTTTGCTAGAACCCGGAGACAAAATAATATTTGAGGCAAATGGAAACCTAATAGCGCCATGGTATGCTTTCGCACTGAGTAGAGGCCTTGGATCAGGAATCATCACCTCAAACGCATCAATGGATGAATGTGACACGAAGTGTCAGACACCCCAGGGAGCTATAAACAGTAGTCTCCCTTTTCAGAACATACACCCAGTCACAATAGGAGAGTGCCCAAAATACGTCAGGAGTACCAAATTGAGGATGGTTACAGGACTAAGGAACATCCCATCCATTCAATCCAGA',
}
def __init__(self,min_length = 987, **kwargs):
'''
parameters
min_length -- minimal length for a sequence to be acceptable
'''
flu_filter.__init__(self, **kwargs)
self.min_length = min_length
self.vaccine_strains =[
{ 'strain':'A/Beijing/262/95',
'isolate_id':'EPI_ISL_2656',
'region':'China',
'db':'GISAID',
'date':'1995-07-01', # (Month and day unknown)
'seq':'AGCAAAAGCAGGGGAAAATAAAAACAACCAAAATGAAAGCAAAACTACTAGTCCTGTTATGTACATTTACAGCTACATATGCAGACACAATATGTATAGGCTACCATGCCAACAACTCAACCGACACTGTTGACACAGTACTTGAGAAGAATGTGACAGTGACACACTCTGTCAACCTACTTGAGGACAGTCACAATGGAAAACTATGTCTACTAAAAGGAATAGCCCCACTACAATTGGGTAATTGCAGCGTTGCCGGATGGATCTTAGGAAACCCAGAATGCGAATCACTGATTTCTAAGGAATCATGGTCCTACATTGTAGAGACACCAAACCCTGAGAATGGAACATGTTACCCAGGGTATTTCGCCGACTATGAGGAACTGAGGGAGCAATTGAGTTCAGTATCATCATTTGAGAGATTCGAAATATTCCCCAAAGAAAGCTCATGGCCCAAACACACCGTAACAGGAGTAACGGCATCATGCTCCCATAATGGGAAAAGCAGTTTTTACAGAAATTTGCTATGGCTGACGGAGAAGAATGGCTTGTACCCAAATCTGAGCAATTCCTATGTGAACAACAAAGAGAAAGAAGTCCTTGTACTATGGGGTGTTCATCACCCATCTAACATAGGGGACCAAAGGGCCATCTATCATACAGAAAACGCTTATGTCTCTGTAGTGTCTTCACATTATAGCAGAAGATTCACCCCAGAAATAGCAAAAAGACCCAAAGTAAGAGGTCAGGAAGGAAGAATCAACTACTACTGGACTCTGCTGGAACCCGGGGACACAATAATATTTGAGGCAAATGGAAATCTAATAGCGCCATGGTATGCTTTCGCACTGAGTAGAGGCTTTGGGTCAGGAATCATCACCTCAAATGCACCAATGAATGAATGTGATGCGAAGTGTCAAACACCTCAGGGAGCTATAAACAGTAGTCTTCCTTTCCAGAATGTACACCCAGTCACAATAGGAGAGTGTCCAAAGTATGTCAGGAGTACAAAATTAAGGATGGTTACAGGACTAAGGAATATCCCATCCATTCAATCCAGAGGTTTGTTTGGAGCCATTGCCGGTTTCATTGAAGGGGGGTGGACTGGAATGATGGATGGGTGGTATGGTTATCATCATCAGAATGAGCAAGGATCTGGCTATGCTGCAGATCAAAAAAGCACACAAAATGCCATTAACGGGATTACAAATAAGGTGAATTCTGTAATTGAGAAAATGAACACTCAATTCACAGCTGTGGGCAAAGAATTCAACAAATTAGAAAGAAGGATGGAAAACTTAAATAAAAAAGTTGATGATGGATTTCTAGACATTTGGACATATAATGCAGAATTGTTGGTTCTACTGGAAAATGAAAGGACTTTGGATTTCCATGACTCAAATGTGAAGAATCTGTATGAGAAAGTGAAAAGCCAATTAAAGAATAATGCCAAAGAAATAGGGAACGGGTGTTTTGAATTCTATCACAAGTGTAACAATGAATGCATGGAAAGTGTGAAAAATGGAACTTATGACTATCCAAAATATTCCGAAGAATCAAAGTTAAACAGGGAGAAAATTGATGGAGTGAAATTGGAATCAATGGGAGTCTATCAGATTCTGGCGATCTACTCAACTGTCGCCAGTTCACTGGTTCTTTTGGTCTCCCTGGGGGCAATCAGCTTCTGGATGTGTTCCAATGGGTCTTTGCAGTGTAGAATATGCATCTGAGACCAGAATTTCAGAAATATAAGAAAAAACACCCTTGTTTCTACT',
},
{ 'strain':'A/NewCaledonia/20/99',
'isolate_id':'EPI_ISL_158137',
'region':'Oceania',
'date':'1999-06-09',
'seq':'GACACAATATGTATAGGCTACCATGCCAACAACTCAACCGACACTGTTGACACAGTACTTGAGAAGAATGTGACAGTGACACACTCTGTCAACCTACTTGAGGACAGTCACAACGGAAAACTATGTCTACTAAAAGGAATAGCCCCACTACAATTGGGTAATTGCAGCGTTGCCGGATGGATCTTAGGAAACCCAGAATGCGAATTACTGATTTCCAAGGAATCATGGTCCTACATTGTAGAAACACCAAATCCTGAGAATGGAACATGTTACCCAGGGTATTTCGCCGACTATGAGGAACTGAGGGAGCAATTGAGTTCAGTATCTTCATTTGAGAGATTCGAAATATTCCCCAAAGAAAGCTCATGGCCCAACCACACCGTAACCGGAGTATCAGCATCATGCTCCCATAATGGGAAAAGCAGTTTTTACAGAAATTTGCTATGGCTGACGGGGAAGAATGGTTTGTACCCAAACCTGAGCAAGTCCTATGTAAACAACAAAGAGAAAGAAGTCCTTGTACTATGGGGTGTTCATCACCCGCCTAACATAGGGGACCAAAGGGCCCTCTATCATACAGAAAATGCTTATGTCTCTGTAGTGTCTTCACATTATAGCAGAAGATTCACCCCAGAAATAGCCAAAAGACCCAAAGTAAGAGATCAGGAAGGAAGAATCAACTACTACTGGACTCTGCTGGAACCTGGGGATACAATAATATTTGAGGCAAATGGAAATCTAATAGCGCCATGGTATGCTTTTGCACTGAGTAGAGGCTTTGGATCAGGAATCATCACCTCAAATGCACCAATGGATGAATGTGATGCGAAGTGTCAAACACCTCAGGGAGCTATAAACAGCAGTCTTCCTTTCCAGAATGTACACCCAGTCACAATAGGAGAGTGTCCAAAGTATGTCAGGAGTGCAAAATTAAGGATGGTTACAGGACTAAGGAACATCCCATCCATTCAATCCAGAGGTTTGTTTGGAGCCATTGCCGGTTTCATTGAAGGGGGGTGGACTGGAATGGTAGATGGGTGGTATGGTTATCATCATCAGAATGAGCAAGGATCTGGCTATGCTGCAGATCAAAAAAGTACACAAAATGCCATTAACGGGATTACAAACAAGGTGAATTCTGTAATTGAGAAAATGAACACTCAATTCACAGCTGTGGGCAAAGAATTCAACAAATTGGAAAGAAGGATGGAAAACTTAAATAAAAAAGTTGATGATGGGTTTCTAGACATTTGGACATATAATGCAGAATTGTTGGTTCTACTGGAAAATGAAAGGACTTTGGATTTCCATGACTCCAATGTGAAGAATCTGTATGAGAAAGTAAAAAGCCAATTAAAGAATAATGCCAAAGAAATAGGAAACGGGTGTTTTGAATTCTATCACAAGTGTAACAATGAATGCATGGAGAGTGTGAAAAATGGAACTTATGACTATCCAAAATATTCCGAAGAATCAAAGTTAAACAGGGAGAAAATTGATGGAGTGAAATTGGAATCAATGGGAGTCTATCAGATTCTGGCGATCTACTCAACTGTCGCCAGTTCCCTGGTTCTTTTGGTCTCCCTGGGGGCAATCAGCTTCTGGATGTGTTCCAATGGGTCTTTGCAGTGCAGAATATGC',
},
{'strain': 'A/SolomonIslands/3/2006',
'isolate_id':'EPI_ISL_157458',
'region':'Oceania',
'date':'2006-08-21',
'lab':'WHO Centre for Reference & Research on Influenza',
'seq': 'GACACAATATGTATAGGCTACCATGCCAACAACTCAACCGACACTGTTGACACAGTACTTGAGAAGAATGTGACAGTGACACACTCTGTCAACCTGCTTGAGGACAGTCACAATGGAAAATTATGTCTATTAAAAGGAATAGCCCCACTACAATTGGGTAATTGCAGCGTTGCCGGATGGATCTTAGGAAACCCAGAATGCGAATTACTGATTTCCAGGGAATCATGGTCCTACATTGTAGAAAAACCAAATCCTGAGAATGGAACATGTTACCCAGGGCATTTCGCCGACTATGAGGAACTGAGGGAGCAATTGAGTTCAGTATCTTCATTTGAGAGATTCGAAATATTCCCCAAAGAAAGCTCATGGCCCAACCACACCACAACCGGAGTATCAGCATCATGCTCCCATAATGGGGAAAGCAGTTTTTACAAAAATTTGCTATGGCTGACGGGGAAGAATGGTTTGTACCCAAACCTGAGCAAGTCCTATGCAAACAACAAAGAGAAAGAAGTCCTTGTACTATGGGGTGTTCATCACCCGCCTAACATAGGTGACCAAAGGGCTCTCTATCATACAGAAAATGCTTATGTCTCTGTAGTGTCTTCACATTATAGCAGAAAATTCACCCCAGAAATAGCCAAAAGACCCAAAGTAAGAGATCGAGAAGGAAGAATCAACTACTACTGGACTCTACTTGAACCCGGGGATACAATAATATTTGAGGCAAATGGAAATCTAATAGCGCCAAGATATGCTTTCGCACTGAGTAGAGGCTTTGGATCAGGAATCATCAACTCAAATGCACCAATGGATGAATGTGATGCGAAGTGCCAAACACCTCAGGGAGCTATAAACAGCAGTCTTCCTTTCCAGAATGTACACCCTGTCACAATAGGAGAGTGTCCAAAGTATGTCAGGAGTGCAAAATTAAGGATGGTTACAGGACTAAGGAACATCCCATCCATTCAATCCAGAGGTTTGTTTGGAGCCATTGCCGGTTTCATTGAAGGGGGGTGGACTGGAATGGTAGATGGTTGGTATGGTTATCATCATCAGAATGAGCAAGGATCTGGCTATGCTGCAGATCAAAAAAGCACACAAAATGCCATTAATGGGATTACAAACAAGGTGAATTCTGTAATTGAGAAAATGAACACTCAATTCACAGCTGTGGGCAAAGAATTCAACAAATTGGAAAGAAGGATGGAAAACTTAAATAAAAAAGTTGATGATGGGTTTATAGACATTTGGACATATAATGCAGAATTGTTGGTTCTACTGGAAAATGAAAGGACTTTGGATTTCCATGACTCCAATGTGAAGAATCTGTATGAGAAAGTAAAAAGCCAATTAAAGAATAATGCCAAAGAAATAGGAAATGGGTGTTTTGAATTCTATCACAAGTGTAACGATGAATGCATGGAGAGTGTAAAAAATGGAACTTATGACTATCCAAAATATTCCGAAGAATCAAAGTTAAACAGGGAGAAAATTGATGGAGTGAAATTGGAATCAATGGGAGTCTATCAGATTCTGGCGATCTACTCAACAGTCGCCAGTTCTCTGGTCCTTTTGGTCTCCCTGGGGGCAATCAGATTCG',
},
{'strain':'A/Brisbane/59/2007',
'isolate_id':'EPI_ISL_23344',
'region':'Oceania',
'date':'2007-07-01', # (Month and day unknown)
'seq': 'ATGAAAGTAAAACTACTGGTCCTGTTATGCACATTTACAGCTACATATGCAGACACAATATGTATAGGCTACCATGCTAACAACTCGACCGACACTGTTGACACAGTACTTGAAAAGAATGTGACAGTGACACACTCTGTCAACCTGCTTGAGAACAGTCACAATGGAAAACTATGTCTATTAAAAGGAATAGCCCCACTACAATTGGGTAATTGCAGCGTTGCCGGGTGGATCTTAGGAAACCCAGAATGCGAATTACTGATTTCCAAGGAGTCATGGTCCTACATTGTAGAAAAACCAAATCCTGAGAATGGAACATGTTACCCAGGGCATTTCGCTGACTATGAGGAACTGAGGGAGCAATTGAGTTCAGTATCTTCATTTGAGAGGTTCGAAATATTCCCCAAAGAAAGCTCATGGCCCAACCACACCGTAACCGGAGTGTCAGCATCATGCTCCCATAATGGGGAAAGCAGTTTTTACAGAAATTTGCTATGGCTGACGGGGAAGAATGGTTTGTACCCAAACCTGAGCAAGTCCTATGCAAACAACAAAGAAAAAGAAGTCCTTGTACTATGGGGTGTTCATCACCCGCCAAACATAGGTRWCCAAAAGGCCCTCTATCATACAGAAAATGCTTATGTCTCTGTAGTGTCTTCACATTATAGCAGAAAATTCACCCCAGAAATAGCCAAAAGACCCAAAGTAAGAGATCAAGAAGGAAGAATCAATTACTACTGGACTCTGCTTGAACCCGGGGATACAATAATATTTGAGGCAAATGGAAATCTAATAGCGCCAAGATATGCTTTCGCACTGAGTAGAGGCTTTGGATCAGGAATCATCAACTCAAATGCACCAATGGATAAATGTGATGCGAAGTGCCAAACACCTCAGGGAGCTATAAACAGCAGTCTTCCTTTCCAGAACGTACACCCAGTCACAATAGGAGAGTGTCCAAAGTATGTCAGGAGTGCAAAATTAAGGATGGTTACAGGACTAAGGAACATCCCATCCATTCAATCCAGAGGTTTGTTTGGAGCCATTGCCGGTTTCATTGAAGGGGGGTGGACTGGAATGGTAGATGGTTGGTATGGTTATCATCATCAGAATGAGCAAGGATCTGGCTATGCTGCAGATCAAAAAAGCACACAAAATGCCATTAATGGGATTACAAACAAGGTGAATTCTGTAATTGAGAAAATGAACACTCAATTCACAGCAGTGGGCAAAGAATTCAACAAATTGGAAAGAAGGATGGAAAACTTGAATAAAAAAGTTGATGATGGGTTTATAGACATTTGGACATATAATGCAGAACTGTTGGTTCTACTGGAAAATGAAAGGACTTTGGATTTCCATGACTCCAATGTGAAGAATCTGTATGAGAAAGTAAAAAGCCAGTTAAAGAATAATGCTAAAGAAATAGGAAATGGGTGTTTTGAATTCTATCACAAGTGTAACGATGAATGCATGGAGAGTGTAAAGAATGGAACTTATGACTATCCAAAATATTCCGAAGAATCAAAGTTAAACAGGGAGAAAATTGATGGAGTGAAATTGGAATCAATGGGAGTCTATCAGATTCTGGCGATCTACTCAACAGTCGCCAGTTCTCTGGTTCTTTTGGTCTCCCTGGGGGCAATCAGCTTCTGGATGTGTTCCAATGGGTCTTTACAGTGTAGAATATGCATCTAA',
}
]
self.outgroup = {
'strain': 'A/Tokyo/1/51',
'db': 'GISAID',
'accession': 'EPI_ISL_101',
'date': '1951-07-01',
'country': 'Japan',
'region': 'JapanKorea',
'seq': 'ATGAAAGCAAAACTACTGATCCTGTTATGTGCACTTTCAGCTACAGATGCAGACACAATATGTATAGGCTACCATGCTAACAATTCAACCGACACTGTTGACACAGTACTCGAAAAGAATGTGACAGTGACACACTCTGTAAACCTACTCGAAGACAGCCACAACGGGAAATTATGCAGATTAAAAGGAATAGCCCCACTACAATTGGGGAAATGTAACATTGCCGGATGGATCTTGGGAACCCCAGAATGCGAATCATTGCTCTCTAATAGATCATGGTCCTACATTGCAGAAACACCAAACTGTGAGAATGGAACATGTTACCCAGGAGATTTCGCCGACTATGAGGAACTGAGGGAGCAATTGAGCTCAGTATCATCATTCGAGAGATTCGAAATATTCCCCAAGGAAAGATCATGGCCCAAACACAACATAACCAGAGGAGTAACGGCAGCATGCTCCCACGCGAAGAAAAGCAGTTTTTACAAAAATTTGCTCTGGCTGACGGAGGCAAATGGCTCATACCCAAATCTGAGCAAGTCCTATGTGAACAATAAAGAGAAAGAAGTCCTTGTGCTGTGGGGTGTTCATCACCCGTCTAACATAGAGGATCAAAGGACCCTCTATCGGAAAGAAAATGCTTATGTCTCTGTGGTGTCTTCAAATTATAACAGGAGATTCACCCCGGAAATAGCAGAAAGACCCAAAGTAAGAGGTCAAGCAGGGAGAATAAACTATTACTGGACTTTGCTAGAACCCGGAGACAAAATAATATTTGAGGCAAATGGAAACCTAATAGCGCCATGGTATGCTTTCGCACTGAGTAGAGGCCTTGGATCAGGAATCATCACCTCAAACGCATCAATGGATGAATGTGACACGAAGTGTCAGACACCCCAGGGAGCTATAAACAGTAGTCTCCCTTTTCAGAACATACACCCAGTCACAATAGGAGAGTGCCCAAAATACGTCAGGAGTACCAAATTGAGGATGGTTACAGGACTAAGGAACATCCCATCCATTCAATCCAGA',
}
def __init__(self, aln_fname, outgroup, outdir = './', formats = ['pdf','svg','png'], verbose = 0, **kwargs):
process.__init__(self, **kwargs)
flu_filter.__init__(self, alignment_file = aln_fname, **kwargs)
tree_refine.__init__(self, **kwargs)
virus_clean.__init__(self, **kwargs)
self.verbose = verbose
self.formats = formats
self.outdir = outdir.rstrip('/')+'/'
self.auspice_tree_fname = self.outdir + 'tree.json'
self.auspice_sequences_fname = self.outdir + 'sequences.json'
self.auspice_frequencies_fname = None
self.auspice_meta_fname = self.outdir + 'meta.json'
if os.path.isfile(outgroup):
tmp = [{'strain':seq.name, 'seq':str(record.seq).upper(), 'desc':seq.description}
for seq in SeqIO.parse(outgroup, 'fasta') ]
if len(tmp):
self.outgroup = tmp[0]
if len(tmp)>1:
print "More than one sequence in ", outgroup, "taking first"
if self.verbose:
print "using outgroup found in file ", outgroup
elif isinstance(outgroup, basestring):
seq_names = [x['strain'] for x in self.viruses]
if outgroup in seq_names:
self.outgroup = self.viruses.pop(seq_names.index(outgroup))
if self.verbose:
print "using outgroup found in alignment", outgroup
else:
standard_outgroups = [{'strain':seq.name, 'seq':str(seq.seq).upper(), 'desc':seq.description}
for seq in SeqIO.parse(std_outgroup_file, 'fasta') ]
outgroup_names = [x['strain'] for x in standard_outgroups]
if outgroup in outgroup_names:
self.outgroup = standard_outgroups[outgroup_names.index(outgroup)]
if self.verbose:
print "using standard outgroup", outgroup
else:
raise ValueError("outgroup %s not found" % outgroup)
return
self.viruses.append(self.outgroup)
self.filter_geo(prune=False)
#self.filter_host(prune=False)
self.make_strain_names_unique()
def __init__(self, min_length=987, **kwargs):
'''
parameters
min_length -- minimal length for a sequence to be acceptable
'''
flu_filter.__init__(self, **kwargs)
self.min_length = min_length
self.vaccine_strains = [{
'strain':
'A/California/07/2009',
'isolate_id':
'EPI_ISL_31553',
'date':
'2009-04-09',
'lab':
'Naval Health Research Center',
'country':
'USA',
'region':
'NorthAmerica',
'seq':
'ATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACACATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAACAGTAACACACTCTGTTAACCTTCTAGAAGACAAGCATAACGGGAAACTATGCAAACTAAGAGGGGTAGCCCCATTGCATTTGGGTAAATGTAACATTGCTGGCTGGATCCTGGGAAATCCAGAGTGTGAATCACTCTCCACAGCAAGCTCATGGTCCTACATTGTGGAAACACCTAGTTCAGACAATGGAACGTGTTACCCAGGAGATTTCATCGATTATGAGGAGCTAAGAGAGCAATTGAGCTCAGTGTCATCATTTGAAAGGTTTGAGATATTCCCCAAGACAAGTTCATGGCCCAATCATGACTCGAACAAAGGTGTAACGGCAGCATGTCCTCATGCTGGAGCAAAAAGCTTCTACAAAAATTTAATATGGCTAGTTAAAAAAGGAAATTCATACCCAAAGCTCAGCAAATCCTACATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTAGTGCTGACCAACAAAGTCTCTATCAGAATGCAGATGCATATGTTTTTGTGGGGTCATCAAGATACAGCAAGAAGTTCAAGCCGGAAATAGCAATAAGACCCAAAGTGAGGGATCAAGAAGGGAGAATGAACTATTACTGGACACTAGTAGAGCCGGGAGACAAAATAACATTCGAAGCAACTGGAAATCTAGTGGTACCGAGATATGCATTCGCAATGGAAAGAAATGCTGGATCTGGTATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCAAACACCCAAGGGTGCTATAAACACCAGCCTCCCATTTCAGAATATACATCCGATCACAATTGGAAAATGTCCAAAATATGTAAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATATCCCGTCTATTCAATCTAGAGGCCTATTTGGGGCCATTGCCGGTTTCATTGAAGGGGGGTGGACAGGGATGGTAGATGGATGGTACGGTTATCACCATCAAAATGAGCAGGGGTCAGGATATGCAGCCGACCTGAAGAGCACACAGAATGCCATTGACGAGATTACTAACAAAGTAAATTCTGTTATTGAAAAGATGAATACACAGTTCACAGCAGTAGGTAAAGAGTTCAACCACCTGGAAAAAAGAATAGAGAATTTAAATAAAAAAGTTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCAAATGTGAAGAACTTATATGAAAAGGTAAGAAGCCAGCTAAAAAACAATGCCAAGGAAATTGGAAACGGCTGCTTTGAATTTTACCACAAATGCGATAACACGTGCATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGTTTCTGGATGTGCTCTAATGGGTCTCTACAGTGTAGAATATGTATTTAA',
}]
tmp_outgroup = SeqIO.read(
'/Users/yujia_zhou/Documents/Work/H9_nextflu-master/augur/source-data/H1N1pdm_outgroup.gb',
'genbank')
genome_annotation = tmp_outgroup.features
self.cds = {
x.qualifiers['gene'][0]: x
for x in genome_annotation
if 'gene' in x.qualifiers and x.type == 'CDS'
and x.qualifiers['gene'][0] in ['SigPep', 'HA1', 'HA2']
}
self.outgroup = {
'strain': 'A/Swine/Indiana/P12439/00',
'db': 'IRD',
'accession': 'AF455680',
'date': '2002-03-14',
'country': 'USA',
'region': 'NorthAmerica',
'seq': str(tmp_outgroup.seq).upper()
}
def __init__(self, min_length=0, **kwargs):
'''
parameters
min_length -- minimal length for a sequence to be acceptable
'''
flu_filter.__init__(self, **kwargs)
self.min_length = min_length
self.vaccine_strains = [{
"strain":
"A/Chicken/HongKong/G9/97",
"db":
"GISAID",
"accession":
"EPI_ISL_1263",
"date":
"1997-07-01",
"seq":
"ATGGAAATAATAGCACTAATAGCTATACTGGTAGTGACAAAAACAAGCAATGCAGATAAAATTTGCATTGGCTACCAGTCAACAAACTCCACAGAAACTGTTGATACACTAGTAGAAAACAATGTCCCTGTGACACATACCAAAGAATTGCTCCACACAGAGCACAATGGAATGCTATGTGCAACAAACCTGGGGCACCCTCTCATCCTAGACACCTGCACCATCGAAGGGTTGGTGTACGGCAACCCTTCCTGTGATTTGCTACTGGGAGGGAAAGAATGGTCTTACATTGTCGAAAGATCATCAGCTGTCAATGGGATGTGTTACCCTGGAAGGGTAGAGAACCTGGAAGAACTCAGGTCTTTTTTCAGCTCCGCTCGCTCCTACAAAAGACTCCTGCTCTTTCCAGACAGAACTTGGAATGTGACTTACACTGGGACAAGCAAAGCATGTTCAAACTCATTCTACAGAAGTATGAGATGGCTGACACACAAGAGCGATTCTTACCCTATTCAAGACGCCCAATATACTAACGATTGGGGAAAGAATATTCTCTTCATGTGGGGCATACACCACCCACCTACTGATACTGAGCAAATAAATCTATACAAAAAAGCTGATACAACAACAAGTATAACAACGGAAGATATCAATCGAACTTTCAAACCAGTGATAGGGCCAAGGCCTCTTGTCAATGGTCAACAAGGGAGAATTGATTATTATTGGTCAGTACTAAAGCCAGGCCAGACACTGCGAGTGAGATCCAATGGGAATCTAATTGCCCCATGGTATGGACACATTCTTTCAGGAGAAAGCCATGGAAGAATCTTGAAGACCGATTTGAGTAGTGGCAACTGCGTAGTACAATGCCAAACTGAGAAAGGTGGTTTGAACACGACCTTGCCATTCCACAATGTCAGCAAGTATGCATTTGGGAACTGCCCCAAATATGTTGGAGTGAAGAGTCTCAAACTGGCAGTTGGTCTAAGGAATGTTCCTGCTGCATCATATAGAGGGCTCTTCGGTGCCATAGCTGGATTCATAGAAGGCGGTTGGCCAGGACTAGTTGCAGGCTGGTACGGGTTTCAGCATTCAAATGATCAAGGGGTTGGAATGGCCGCAGATAGGGAATCAACTCAAGAAGCAGTTGACAAGATAACATCCAAAGTAAATAACATAATCGACAAAATGAACAAGCAGTATGGA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T--------------------------------------------------------------------------------------"
}]
tmp_outgroup = SeqIO.read(
'/Users/yujiazhou/Documents/FluProject/augur/source-data/H9_outgroup.gb',
'genbank')
genome_annotation = tmp_outgroup.features
self.cds = {
x.qualifiers['gene'][0]: x
for x in genome_annotation
if 'gene' in x.qualifiers and x.type == 'CDS'
and x.qualifiers['gene'][0] in ['SigPep', 'HA1', 'HA2']
}
self.outgroup = {
'strain': 'A/duck/HongKong/147/1977',
'db': 'IRD',
'accession': 'AY206671',
'date': '2003-03-03',
'country': 'HongKong',
'region': 'EastAsia',
'seq': str(tmp_outgroup.seq).upper()
}
def __init__(self, min_length=987, **kwargs):
"""
parameters
min_length -- minimal length for a sequence to be acceptable
"""
flu_filter.__init__(self, **kwargs)
self.min_length = min_length
self.vaccine_strains = [
{
"strain": "B/Beijing/184/93",
"isolate_id": "EPI_ISL_969",
"date": "1993-07-01", # (Month and day unknown)
"region": "China",
"seq": "GATCGAATCTGTACTGGGATAACATCTTCAAACTCACCTCATGTGGTCAAAACAGCTACTCAAGGGGAGGTCAATGTGACTGGTGTGATACCACTGACAACAACACCAACAAAATCTCATTTTGGAAATCTCAAAGGAACAAAGACCAGAGGGAAACTATGCCCAAACTGTCTCAACTGCACAGATCTGGATGTGGCCTTGGGCAGACCAATGTGTGTGGGGACCACACCTTCGGCAAAAGCTTCAATACTCCACGAAGTCAGACCTGTTACATCCGGGTGCTTTCCTATAATGCACGACAGAACAAAAATCAGACAGCTACCCAATCTTCTCAGAGGATATGAAAATATCAGATTATCAACCCAAAACGTTATCAACGCAGAAAAGGCACCAGGAGGACCCTACAGGCTTGGAACCTCAGGATCTTGCCCTAACGCTACCAGTAGAAGCGGATTTTTCGCAACAATGGCTTGGGCTGTCCCAAGGGACAACAACAAAACAGCAACAAATCCACTAACAGTAGAAGTACCATACATTTGTACAAAAGGAGAAGACCAAATTACTGTTTGGGGGTTCCATTCTGATAACAAAATCCAAATGAAAAACCTCTATGGAGACTCAAATCCTCAAAAGTTCACCTCATCTGCTAATGGAGTAACCACACATTATGTTTCTCAGATTGGCGGCTTCCCAGATCAAACAGAAGACGGAGGGCTACCACAAAGCGGCAGAATTGTTGTTGATTACATGGTGCAAAAACCTGGGAAAACAGGAACAATTGTCTATCAAAGAGGTGTTTTGTTGCCTCAAAAGGTGTGGTGCGCGAGTGGCAGGAGCAAAGTAATAAAAGGGTCCTTGCCTTTAATTGGTGAAGCAGATTGCCTTCACGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGAGAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTGAAAACACCTTTGAAGCTTGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGG",
},
{
"strain": "B/Sichuan/379/99",
"isolate_id": "EPI_ISL_21113",
"date": "1999-07-01", # (Month and day unknown)
"region": "China",
"seq": "GAGGCAATAATTGTACTACTCATGGTAGTAACATCCAATGCAGATCGAATCTGCACTGGGATAACATCGTCAAACTCACCTCATGTGGTCAAAACAGCTACTCAAGGGGAGGTCAATGTAACTGGTGCGATACCACTGACAACAACACCAACAAAATCTCATTTTGCAAATCTCAAAGGAACAAAGACCAGAGGGAAACTATGCCCAACCTGTCTCAACTGCACAGATCTGGATGTGGCCTTGGGCAGACCAATGTGTGTGGGGATCACACCTTCGGCAAAAGCTTCAATACTCCACGAAATCAAACCTGTTACATCCGGATGCTTTCCTATAATGCACGACAGAACAAAAATCAGACAGCTACCCAATCTTCTCAGAGGATATGAAAAAATCAGATTATCAACCCAAAACGTTATCAACGCAGAAAAGGCACCAGGAGGACCTTACAGACTTGGAACTTCAGGATCTTGCCCTAACGCTACCAGTAAAAGCGGATTTTTCGCAACAATGGCTTGGGCTGTCCCAAGGGACAACAACAAAACAGCAACGAATCCACTAACAGTAGAAGTACCACACATCTGTACAAAAGAAGAAGACCAAATTACTGTTTGGGGGTTCCATTCTGATGACAAAACCCAAATGAAAAACCTCTATGGAGACTCAAATCCTCAAAAGTTCACCTCATCTGCTAATGGAATAACCACACATTATGTTTCTCAGATTGGCGGCTTCCCGGACCAAACAGAGGACGGAGGGCTACCACAAAGCGGCAGAATTGTTGTTGATTACATGGTGCAAAAACCTGGGAAAACAGGAACAATTGTCTATCAAAGAGGGATTTTGTTGCCTCAAAAGGTGTGGTGCGCGAGTGGTAGGAGCAAAGTAATAAAAGGGTCCTTGCCTTTAATTGGTGAAGCAGATTGCCTTCATGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGAGAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTGAAAACACCTTTGAAGCTTGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGGGGTTTCT",
},
{
"strain": "B/Shanghai/361/2002",
"isolate_id": "EPI_ISL_2842",
"date": "2002-06-12",
"region": "China",
"seq": "AATGCAGATCGAATCTGCACTGGGATAACATCTTCAAACTCACCTCATGTGGTCAAAACAGCTACTCAAGGGGAGGTCAATGTGACTGGTGTGATACCACTGACAACAACTCCAATAAAATCTCATTTTGCAAATCTCAAAGGAACAAGGACTAGAGGGAAACTATGCCCAGATTGTCTCAACTGCACAGATCTGGATGTGGCCTTGGGCAGACCAATGTGTGTGGGGACCACACCTTCGGCAAAAGCTTCAATACTCCACGAAGTCAGACCTGTTACATCCGGGTGCTTTCCTATAATGCACGACAGAACAAAAATCAGACAACTACCCAATCTTCTCAGAGGATATGAAAATATCAGGTTATCAACCCAAAACGTTATCGATGCAGAAAAGGCCCTAGGAGGACCCTACAGACTTGGAACCTCAGGATCTTGCCCTAACGCCACCAGTAAAAGCGGATTTTTCGCAACAATGGCTTGGGCTGTCCCAAAGGACAACAACAAAAATGCAACGAACCCACTAACAGTAGAAGTACCATACATCTGTACAGAAGGGGAAGACCAAATTACTGTTTGGGGGTTCCATTCAGATGACAAAACCCAAATGAAAAACCTCTATGGAGACTCAAATCCTCAAAAGTTCACCTCATCTGCTAATGGAGTAACCACACATTATGTTTCTCAGATTGGCGGCTTCCCAGATCAAACAGAAGACGGAGGACTACCACAAAGCGGCAGAATTGTTGTTGATTACATGGTGCAAAAACCTGGGAAAACAGGAACAATTGTCTATCAAAGAGGTGTTTTGTTGCCTCAAAAGGTGTGGTGCGCGAGTGGCAGGAGCAAAGTAATAAAAGGGTCCTTGCCTTTAATTGGTGAAGCAGATTGCCTTCATGAAAAATACGGTGGGTTAAACAAAAGCAAGCCTTACTACACAGGAGAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTGAAAACACCTTTGAAGCTTGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGGGGTTTC",
},
{
"strain": "B/Florida/4/2006",
"isolate_id": "EPI_ISL_21307",
"date": "2006-11-01",
"region": "NorthAmerica",
"seq": "ATGAAGGCAATAATTGTACTACTCATGGTAGTAACATCCAATGCAGATCGAATCTGCACTGGAATAACATCTTCAAACTCACCTCATGTGGTCAAAACAGCCACTCAAGGGGAGGTCAATGTGACTGGTGTGATACCACTAACAACAACACCAACAAAATCTTATTTTGCAAATCTCAAAGGAACAAGGACCAGAGGGAAACTATGCCCAGACTGTCTCAACTGCACAGATCTGGATGTGGCTTTGGGCAGACCAATGTGTGTGGGGACCACACCTTCGGCGAAAGCTTCAATACTCCACGAAGTCAAACCTGTTACATCCGGGTGCTTTCCTATAATGCACGACAGAACAAAAATCAGGCAACTACCCAATCTTCTCAGAGGATATGAAAATATCAGGCTATCAACCCAAAACGTCATCGATGCGGAAAAGGCACCAGGAGGACCCTACAGACTTGGAACCTCAGGATCTTGCCCTAACGCTACCAGTAAGAGCGGATTTTTCGCAACAATGGCTTGGGCTGTCCCAAAGGACAACAACAAAAATGCAACGAACCCACTAACAGTAGAAGTACCATACATTTGTACAGAAGGGGAAGACCAAATCACTGTTTGGGGGTTCCATTCAGATGACAAAACCCAAATGAAGAACCTCTATGGAGACTCAAATCCTCAAAAGTTCACCTCATCTGCTAATGGAGTAACCACACACTATGTTTCTCAGATTGGCAGCTTCCCAGATCAAACAGAAGACGGAGGACTACCACAAAGCGGCAGGATTGTTGTTGATTACATGATGCAAAAACCTGGGAAAACAGGAACAATTGTCTACCAAAGAGGTGTTTTGTTGCCTCAAAAGGTGTGGTGCGCGAGTGGCAGGAGCAAAGTAATAAAAGGGTCCTTGCCTTTAATTGGTGAAGCAGATTGCCTTCATGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGAGAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTGAAAACACCTTTGAAGCTTGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGGGGTTTCTTCGGAGCTATTGCTGGTTTCCTAGAAGGAGGATGGGAAGGAATGATTGCAGGCTGGCACGGATACACATCTCACGGAGCACATGGAGTGGCAGTGGCGGCGGACCTTAAGAGTACGCAAGAAGCTATAAACAAGATAACAAAAAATCTCAATTCTTTGAGTGAGCTAGAAGTAAAGAATCTTCAAAGACTAAGTGGTGCCATGGATGAACTCCACAACGAAATACTCGAGCTGGATGAGAAAGTGGATGATCTCAGAGCTGACACTATAAGCTCGCAAATAGAACTTGCAGTCTTGCTTTCCAACGAAGGAATAATAAACAGTGAAGATGAGCATCTATTGGCACTTGAGAGAAAACTAAAGAAAATGCTGGGTCCCTCTGCTGTAGAGATAGGAAATGGATGCTTCGAAACCAAACACAAGTGCAACCAGACCTGCTTAGACAGGATAGCTGCTGGCACCTTTAATGCAGGAGAATTTTCTCTCCCCACTTTTGATTCACTGAACATTACTGCTGCATCTTTAAATGATGATGGATTGGATAACCATACTATACTGCTCTATTACTCAACTGCTGCTTCTAGTTTGGCTGTAACATTGATGCTAGCTATTTTTATTGTTTATATGGTCTCCAGAGACAACGTTTCATGCTCCATCTGTCTATAA",
},
{
"strain": "B/Wisconsin/01/2010",
"isolate_id": "EPI_ISL_76940",
"date": "2010-02-20",
"region": "NorthAmerica",
"seq": "ATGAAGGCAATAATTGTACTACTCATGGTAGTAACATCCAATGCAGATCGAATCTGCACTGGGATAACATCTTCAAACTCACCTCATGTGGTCAAAACAGCTACTCAAGGGGAGGTCAATGTGACTGGCGTGATACCACTGACAACAACACCAACAAAATCTTATTTTGCAAATCTCAAAGGAACAAGGACCAGAGGGAAACTATGCCCGGACTGTCTCAACTGTACAGATCTGGATGTGGCCTTGGGCAGGCCAATGTGTGTGGGGACCACACCTTCTGCTAAAGCTTCAATACTCCACGAGGTCAGACCTGTTACATCCGGGTGCTTTCCTATAATGCACGACAGAACAAAAATCAGGCAACTACCCAATCTTCTCAGAGGATATGAAAATATCAGGTTATCAACCCAAAACGTTATCGATGCAGAAAAAGCACCAGGAGGACCCTACAGACTTGGAACCTCAGGATCTTGCCCTAACGCTACCAGTAAAATCGGATTTTTTGCAACAATGGCTTGGGCTGTCCCAAAGGACAACTACAAAAATGCAACGAACCCACTAACAGTAGAAGTACCATACATTTGTACAGAAGGGGAAGACCAAATTACTGTTTGGGGGTTCCATTCAGATAACAAAACCCAAATGAAGAGCCTCTATGGAGACTCAAATCCTCAAAAGTTCACCTCATCTGCTAATGGAGTAACCACACATTATGTTTCTCAGATTGGCGACTTCCCAGATCAAACAGAAGACGGAGGACTACCACAAAGCGGCAGAATTGTTGTTGATTACATGATGCAAAAACCTGGGAAAACAGGAACAATTGTCTATCAAAGAGGTGTTTTGTTGCCTCAAAAGGTGTGGTGCGCGAGTGGCAGGAGCAAAGTAATAAAAGGGTCATTGCCTTTAATTGGTGAAGCAGATTGCCTTCATGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGAGAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTAAAAACACCTTTGAAGCTTGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTGAAGGAAAGGGGTTTCTTCGGAGCTATTGCTGGTTTCCTAGAAGGAGGATGGGAAGGAATGATTGCAGGTTGGCACGGATACACATCTCACGGAGCACATGGAGTGGCAGTGGCGGCAGACCTTAAGAGTACACAAGAAGCTATAAATAAGATAACAAAAAATCTCAATTCTTTGAGTGAGCTAGAAGTAAAGAACCTTCAAAGACTAAGTGGTGCCATGGATGAACTCCACAACGAAATACTCGAGCTGGATGAGAAAGTGGATGATCTCAGAGCTGACACTATAAGCTCACAAATAGAACTTGCAGTCTTGCTTTCCAACGAAGGAATAATAAACAGTGAAGACGAGCATCTATTGGCACTTGAGAGAAAACTAAAGAAAATGCTGGGTCCCTCTGCTGTAGACATAGGAAACGGATGCTTCGAAACCAAACACAAATGCAACCAGACCTGCTTAGACAGGATAGCTGCTGGCACCTTTAATGCAGGAGAATTTTCTCTCCCCACTTTTGATTCATTGAACATTACTGCTGCATCTTTAAATGATGATGGATTGGATAACCATACTATACTGCTCTATTACTCAACTGCTGCTTCTAGTTTGGCTGTAACATTAATGCTAGCTATTTTTATTGTTTATATGGTCTCCAGAGACAACGTTTCATGCTCCATCTGTCTATAA",
},
{
"strain": "B/Massachusetts/02/2012",
"isolate_id": "EPI_ISL_121434",
"date": "2012-03-13",
"region": "NorthAmerica",
"seq": "ATGAAGGCAATAATTGTACTACTAATGGTAGTAACATCCAATGCAGATCGAATCTGCACTGGGATAACATCTTCAAACTCACCTCATGTGGTCAAAACAGCTACTCAAGGGGAGGTCAATGTGACTGGTGTGATACCACTAACAACAACACCAACAAAATCTTATTTTGCAAATCTCAAAGGAACAAAGACCAGAGGGAAACTATGCCCAGACTGTCTCAACTGTACAGATCTGGATGTGGCCCTGGGCAGGCCAATGTGTGTGGGAACTACACCTTCTGCGAAAGCTTCAATACTTCACGAAGTCAGACCTGTTACATCCGGGTGCTTCCCTATAATGCACGACAGAACAAAAATCAGGCAACTAGCCAATCTTCTCAGAGGATATGAAAATATCAGGTTATCAACCCAAAACGTTATCGATGCAGAAAAGGCACCAGGAGGACCCTACAGACTTGGAACCTCAGGATCTTGCCCTAACGCTACCAGTAAAAGCGGATTTTTCGCAACAATGGCTTGGGCTGTCCCAAAGGACAACAACAAAAATGCAACGAACCCATTAACAGTAGAAGTACCATACATTTGTGCAGAAGGGGAAGACCAAATTACTGTTTGGGGGTTCCATTCAGATAACAAAACCCAAATGAAGAACCTCTATGGAGACTCAAATCCTCAAAAGTTCACCTCATCTGCTAATGGAGTAACCACACATTATGTTTCTCAGATTGGCGGCTTCCCAGATCAAACAGAAGACGGAGGACTACCACAAAGCGGCAGAATTGTCGTTGATTACATGATGCAAAAACCTGGGAAAACAGGAACAATTGTCTATCAAAGAGGTGTTTTGTTGCCTCAAAAGGTGTGGTGCGCGAGTGGCAGGAGCAAAGTAATAAAAGGGTCCTTGCCTTTAATTGGTGAAGCAGATTGCCTTCATGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGAGAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTGAAAACACCTTTGAAGCTTGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGGGGTTTCTTCGGAGCTATTGCTGGTTTCCTAGAAGGAGGATGGGAAGGAATGATTGCAGGTTGGCACGGATACACATCTCACGGAGCACATGGAGTGGCAGTTGCTGCAGACCTTAAGAGCACACAAGAAGCTATAAACAAGATAACAAAAAATCTCAACTCTTTGAGTGAGCTAGAAGTAAAGAATCTTCAAAGGCTAAGTGGTGCCATGGATGAACTCCACAACGAAATACTCGAGCTGGATGAGAAAGTGGATGACCTCAGAGCTGACACTATAAGTTCACAAATAGAACTTGCAGTCTTGCTTTCCAACGAAGGAATAATAAACAGTGAAGACGAGCATCTATTGGCACTTGAGAGAAAACTAAAGAAAATGCTGGGTCCCTCTGCTGTAGACATAGGAAATGGATGCTTCGAAACCAAACACAAATGCAACCAGACCTGCTTAGACAGGATAGCTGCTGGCACCTTTAATGCAGGAGAGTTTTCTCTCCCCACTTTTGATTCATTGAACATTACTGCTGCATCTTTAAATGATGATGGATTGGATAACCATACTATACTGCTCTATTACTCAACTGCTGCTTCTAGTTTGGCTGTAACATTGATGCTAGCTATTTTTATTGTTTATATGGTCTCCAGAGACAACGTTTCATGCTCCATCTGTCTATAA",
},
{
"strain": "B/PHUKET/3073/2013",
"isolate_id": "EPI_ISL_161843",
"date": "2013-11-21",
"region": "SoutheastAsia",
"seq": "ATGAAGGCAATAATTGTACTACTCATGGTAGTAACATCCAACGCAGATCGAATCTGCACTGGGATAACATCTTCAAACTCACCTCATGTGGTCAAAACAGCTACTCAAGGGGAGGTCAATGTGACTGGCGTGATACCACTGACAACAACACCAACAAAATCTTATTTTGCAAATCTCAAAGGAACAAGGACCAGAGGGAAACTATGCCCGGACTGTCTCAACTGTACAGATCTGGATGTGGCCTTGGGCAGGCCAATGTGTGTGGGGACCACACCTTCTGCTAAAGCTTCAATACTCCATGAGGTCAGACCTGTTACATCCGGGTGCTTTCCTATAATGCACGACAGAACAAAAATCAGGCAACTACCCAATCTTCTCAGAGGATATGAAAAGATCAGGTTATCAACCCAAAACGTTATCGATGCAGAAAAAGCACCAGGAGGACCCTACAGACTTGGAACCTCAGGATCTTGCCCTAACGCTACCAGTAAAATCGGATTTTTTGCAACAATGGCTTGGGCTGTCCCAAAGGACAACTACAAAAATGCAACGAACCCACTAACAGTGGAAGTACCATACATTTGTACAGAAGGGGAAGACCAAATTACTGTTTGGGGGTTCCATTCGGATAACAAAACCCAAATGAAGAGCCTCTATGGAGACTCAAATCCTCAAAAGTTCACCTCATCTGCTAATGGAGTAACCACGCATTATGTTTCTCAGATTGGCGACTTCCCAGATCAAACAGAAGACGGAGGACTACCACAAAGCGGCAGAATTGTTGTTGATTACATGATGCAAAAACCTGGGAAAACAGGAACAATTGTCTATCAAAGGGGTGTTTTGTTGCCTCAAAAGGTGTGGTGCGCGAGTGGCAGGAGCAAAGTAATAAAAGGGTCATTGCCTTTAATTGGTGAAGCAGATTGCCTTCATGAAGAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGAAAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTAAAAACACCTTTGAAGCTTGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTGAAGGAAAGGGGTTTCTTCGGAGCTATTGCTGGTTTCCTAGAAGGAGGATGGGAAGGAATGATTGCAGGTTGGCACGGATACACATCTCACGGAGCACATGGAGTGGCAGTGGCGGCAGACCTTAAGAGTACACAAGAAGCTATAAATAAGATAACAAAAAATCTCAATTCTTTGAGTGAACTAGAAGTAAAGAACCTTCAAAGACTAAGTGGTGCCATGGATGAACTCCACAACGAAATACTCGAGCTGGATGAAAAAGTGGATGATCTCAGAGCTGACACTATAAGCTCACAAATAGAACTTGCAGTCTTGCTTTCCAACGAAGGAATAATAAACAGTGAAGACGAGCATCTATTGGCACTTGAGAGAAAACTAAAGAAAATGCTGGGTCCCTCTGCTGTAGACATAGGAAACGGATGCTTCGAAACCAAACACAAATGCAACCAGACCTGCTTAGACAGGATAGCTGCTGGCACCTTTAATGCAGGAGAATTTTCTCTCCCCACTTTTGATTCATTGAACATTACTGCTGCATCTTTAAATGATGATGGATTGGATAACCATACTATACTGCTCTATTACTCAACTGCTGCTTCTAGTTTGGCTGTAACATTAATGCTAGCTATTTTTATTGTTTATATGGTCTCCAGAGACAACGTTTCATGCTCCATCTGTCTATAAAGAAGGTTAGGCCTTGTATTTTCCTTTATTGTAGTGCTTGTTTGCTTGTCATCATTACAAAGAAAC",
},
]
tmp_outgroup = SeqIO.read("source-data/Yam_outgroup.gb", "genbank")
genome_annotation = tmp_outgroup.features
self.cds = {
x.qualifiers["gene"][0]: x
for x in genome_annotation
if "gene" in x.qualifiers and x.type == "CDS" and x.qualifiers["gene"][0] in ["SigPep", "HA1", "HA2"]
}
self.outgroup = {
"strain": "B/Singapore/11/94",
"isolate_id": "EPI_ISL_20980",
"date": "1994-05-10",
"region": "China",
"seq": str(tmp_outgroup.seq).upper(),
}
def __init__(self,min_length = 987, **kwargs):
'''
parameters
min_length -- minimal length for a sequence to be acceptable
'''
flu_filter.__init__(self, **kwargs)
self.min_length = min_length
self.vaccine_strains =[
{
'strain': 'B/Beijing/184/93',
'isolate_id': 'EPI_ISL_969',
'date': '1993-07-01', #(Month and day unknown)
'region': 'China',
'seq': 'GATCGAATCTGTACTGGGATAACATCTTCAAACTCACCTCATGTGGTCAAAACAGCTACTCAAGGGGAGGTCAATGTGACTGGTGTGATACCACTGACAACAACACCAACAAAATCTCATTTTGGAAATCTCAAAGGAACAAAGACCAGAGGGAAACTATGCCCAAACTGTCTCAACTGCACAGATCTGGATGTGGCCTTGGGCAGACCAATGTGTGTGGGGACCACACCTTCGGCAAAAGCTTCAATACTCCACGAAGTCAGACCTGTTACATCCGGGTGCTTTCCTATAATGCACGACAGAACAAAAATCAGACAGCTACCCAATCTTCTCAGAGGATATGAAAATATCAGATTATCAACCCAAAACGTTATCAACGCAGAAAAGGCACCAGGAGGACCCTACAGGCTTGGAACCTCAGGATCTTGCCCTAACGCTACCAGTAGAAGCGGATTTTTCGCAACAATGGCTTGGGCTGTCCCAAGGGACAACAACAAAACAGCAACAAATCCACTAACAGTAGAAGTACCATACATTTGTACAAAAGGAGAAGACCAAATTACTGTTTGGGGGTTCCATTCTGATAACAAAATCCAAATGAAAAACCTCTATGGAGACTCAAATCCTCAAAAGTTCACCTCATCTGCTAATGGAGTAACCACACATTATGTTTCTCAGATTGGCGGCTTCCCAGATCAAACAGAAGACGGAGGGCTACCACAAAGCGGCAGAATTGTTGTTGATTACATGGTGCAAAAACCTGGGAAAACAGGAACAATTGTCTATCAAAGAGGTGTTTTGTTGCCTCAAAAGGTGTGGTGCGCGAGTGGCAGGAGCAAAGTAATAAAAGGGTCCTTGCCTTTAATTGGTGAAGCAGATTGCCTTCACGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGAGAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTGAAAACACCTTTGAAGCTTGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGG',
},
{
'strain': 'B/Sichuan/379/99',
'isolate_id': 'EPI_ISL_21113',
'date': '1999-07-01', # (Month and day unknown)
'region': 'China',
'seq': 'GAGGCAATAATTGTACTACTCATGGTAGTAACATCCAATGCAGATCGAATCTGCACTGGGATAACATCGTCAAACTCACCTCATGTGGTCAAAACAGCTACTCAAGGGGAGGTCAATGTAACTGGTGCGATACCACTGACAACAACACCAACAAAATCTCATTTTGCAAATCTCAAAGGAACAAAGACCAGAGGGAAACTATGCCCAACCTGTCTCAACTGCACAGATCTGGATGTGGCCTTGGGCAGACCAATGTGTGTGGGGATCACACCTTCGGCAAAAGCTTCAATACTCCACGAAATCAAACCTGTTACATCCGGATGCTTTCCTATAATGCACGACAGAACAAAAATCAGACAGCTACCCAATCTTCTCAGAGGATATGAAAAAATCAGATTATCAACCCAAAACGTTATCAACGCAGAAAAGGCACCAGGAGGACCTTACAGACTTGGAACTTCAGGATCTTGCCCTAACGCTACCAGTAAAAGCGGATTTTTCGCAACAATGGCTTGGGCTGTCCCAAGGGACAACAACAAAACAGCAACGAATCCACTAACAGTAGAAGTACCACACATCTGTACAAAAGAAGAAGACCAAATTACTGTTTGGGGGTTCCATTCTGATGACAAAACCCAAATGAAAAACCTCTATGGAGACTCAAATCCTCAAAAGTTCACCTCATCTGCTAATGGAATAACCACACATTATGTTTCTCAGATTGGCGGCTTCCCGGACCAAACAGAGGACGGAGGGCTACCACAAAGCGGCAGAATTGTTGTTGATTACATGGTGCAAAAACCTGGGAAAACAGGAACAATTGTCTATCAAAGAGGGATTTTGTTGCCTCAAAAGGTGTGGTGCGCGAGTGGTAGGAGCAAAGTAATAAAAGGGTCCTTGCCTTTAATTGGTGAAGCAGATTGCCTTCATGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGAGAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTGAAAACACCTTTGAAGCTTGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGGGGTTTCT',
},
{
'strain': 'B/Shanghai/361/2002',
'isolate_id': 'EPI_ISL_2842',
'date': '2002-06-12',
'region': 'China',
'seq': 'AATGCAGATCGAATCTGCACTGGGATAACATCTTCAAACTCACCTCATGTGGTCAAAACAGCTACTCAAGGGGAGGTCAATGTGACTGGTGTGATACCACTGACAACAACTCCAATAAAATCTCATTTTGCAAATCTCAAAGGAACAAGGACTAGAGGGAAACTATGCCCAGATTGTCTCAACTGCACAGATCTGGATGTGGCCTTGGGCAGACCAATGTGTGTGGGGACCACACCTTCGGCAAAAGCTTCAATACTCCACGAAGTCAGACCTGTTACATCCGGGTGCTTTCCTATAATGCACGACAGAACAAAAATCAGACAACTACCCAATCTTCTCAGAGGATATGAAAATATCAGGTTATCAACCCAAAACGTTATCGATGCAGAAAAGGCCCTAGGAGGACCCTACAGACTTGGAACCTCAGGATCTTGCCCTAACGCCACCAGTAAAAGCGGATTTTTCGCAACAATGGCTTGGGCTGTCCCAAAGGACAACAACAAAAATGCAACGAACCCACTAACAGTAGAAGTACCATACATCTGTACAGAAGGGGAAGACCAAATTACTGTTTGGGGGTTCCATTCAGATGACAAAACCCAAATGAAAAACCTCTATGGAGACTCAAATCCTCAAAAGTTCACCTCATCTGCTAATGGAGTAACCACACATTATGTTTCTCAGATTGGCGGCTTCCCAGATCAAACAGAAGACGGAGGACTACCACAAAGCGGCAGAATTGTTGTTGATTACATGGTGCAAAAACCTGGGAAAACAGGAACAATTGTCTATCAAAGAGGTGTTTTGTTGCCTCAAAAGGTGTGGTGCGCGAGTGGCAGGAGCAAAGTAATAAAAGGGTCCTTGCCTTTAATTGGTGAAGCAGATTGCCTTCATGAAAAATACGGTGGGTTAAACAAAAGCAAGCCTTACTACACAGGAGAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTGAAAACACCTTTGAAGCTTGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGGGGTTTC',
},
{
'strain': 'B/Florida/4/2006',
'isolate_id': 'EPI_ISL_21307',
'date': '2006-11-01',
'region': 'NorthAmerica',
'seq': 'ATGAAGGCAATAATTGTACTACTCATGGTAGTAACATCCAATGCAGATCGAATCTGCACTGGAATAACATCTTCAAACTCACCTCATGTGGTCAAAACAGCCACTCAAGGGGAGGTCAATGTGACTGGTGTGATACCACTAACAACAACACCAACAAAATCTTATTTTGCAAATCTCAAAGGAACAAGGACCAGAGGGAAACTATGCCCAGACTGTCTCAACTGCACAGATCTGGATGTGGCTTTGGGCAGACCAATGTGTGTGGGGACCACACCTTCGGCGAAAGCTTCAATACTCCACGAAGTCAAACCTGTTACATCCGGGTGCTTTCCTATAATGCACGACAGAACAAAAATCAGGCAACTACCCAATCTTCTCAGAGGATATGAAAATATCAGGCTATCAACCCAAAACGTCATCGATGCGGAAAAGGCACCAGGAGGACCCTACAGACTTGGAACCTCAGGATCTTGCCCTAACGCTACCAGTAAGAGCGGATTTTTCGCAACAATGGCTTGGGCTGTCCCAAAGGACAACAACAAAAATGCAACGAACCCACTAACAGTAGAAGTACCATACATTTGTACAGAAGGGGAAGACCAAATCACTGTTTGGGGGTTCCATTCAGATGACAAAACCCAAATGAAGAACCTCTATGGAGACTCAAATCCTCAAAAGTTCACCTCATCTGCTAATGGAGTAACCACACACTATGTTTCTCAGATTGGCAGCTTCCCAGATCAAACAGAAGACGGAGGACTACCACAAAGCGGCAGGATTGTTGTTGATTACATGATGCAAAAACCTGGGAAAACAGGAACAATTGTCTACCAAAGAGGTGTTTTGTTGCCTCAAAAGGTGTGGTGCGCGAGTGGCAGGAGCAAAGTAATAAAAGGGTCCTTGCCTTTAATTGGTGAAGCAGATTGCCTTCATGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGAGAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTGAAAACACCTTTGAAGCTTGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGGGGTTTCTTCGGAGCTATTGCTGGTTTCCTAGAAGGAGGATGGGAAGGAATGATTGCAGGCTGGCACGGATACACATCTCACGGAGCACATGGAGTGGCAGTGGCGGCGGACCTTAAGAGTACGCAAGAAGCTATAAACAAGATAACAAAAAATCTCAATTCTTTGAGTGAGCTAGAAGTAAAGAATCTTCAAAGACTAAGTGGTGCCATGGATGAACTCCACAACGAAATACTCGAGCTGGATGAGAAAGTGGATGATCTCAGAGCTGACACTATAAGCTCGCAAATAGAACTTGCAGTCTTGCTTTCCAACGAAGGAATAATAAACAGTGAAGATGAGCATCTATTGGCACTTGAGAGAAAACTAAAGAAAATGCTGGGTCCCTCTGCTGTAGAGATAGGAAATGGATGCTTCGAAACCAAACACAAGTGCAACCAGACCTGCTTAGACAGGATAGCTGCTGGCACCTTTAATGCAGGAGAATTTTCTCTCCCCACTTTTGATTCACTGAACATTACTGCTGCATCTTTAAATGATGATGGATTGGATAACCATACTATACTGCTCTATTACTCAACTGCTGCTTCTAGTTTGGCTGTAACATTGATGCTAGCTATTTTTATTGTTTATATGGTCTCCAGAGACAACGTTTCATGCTCCATCTGTCTATAA'
},
{
'strain': 'B/Wisconsin/01/2010',
'isolate_id': 'EPI_ISL_76940',
'date': '2010-02-20',
'region': 'NorthAmerica',
'seq': 'ATGAAGGCAATAATTGTACTACTCATGGTAGTAACATCCAATGCAGATCGAATCTGCACTGGGATAACATCTTCAAACTCACCTCATGTGGTCAAAACAGCTACTCAAGGGGAGGTCAATGTGACTGGCGTGATACCACTGACAACAACACCAACAAAATCTTATTTTGCAAATCTCAAAGGAACAAGGACCAGAGGGAAACTATGCCCGGACTGTCTCAACTGTACAGATCTGGATGTGGCCTTGGGCAGGCCAATGTGTGTGGGGACCACACCTTCTGCTAAAGCTTCAATACTCCACGAGGTCAGACCTGTTACATCCGGGTGCTTTCCTATAATGCACGACAGAACAAAAATCAGGCAACTACCCAATCTTCTCAGAGGATATGAAAATATCAGGTTATCAACCCAAAACGTTATCGATGCAGAAAAAGCACCAGGAGGACCCTACAGACTTGGAACCTCAGGATCTTGCCCTAACGCTACCAGTAAAATCGGATTTTTTGCAACAATGGCTTGGGCTGTCCCAAAGGACAACTACAAAAATGCAACGAACCCACTAACAGTAGAAGTACCATACATTTGTACAGAAGGGGAAGACCAAATTACTGTTTGGGGGTTCCATTCAGATAACAAAACCCAAATGAAGAGCCTCTATGGAGACTCAAATCCTCAAAAGTTCACCTCATCTGCTAATGGAGTAACCACACATTATGTTTCTCAGATTGGCGACTTCCCAGATCAAACAGAAGACGGAGGACTACCACAAAGCGGCAGAATTGTTGTTGATTACATGATGCAAAAACCTGGGAAAACAGGAACAATTGTCTATCAAAGAGGTGTTTTGTTGCCTCAAAAGGTGTGGTGCGCGAGTGGCAGGAGCAAAGTAATAAAAGGGTCATTGCCTTTAATTGGTGAAGCAGATTGCCTTCATGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGAGAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTAAAAACACCTTTGAAGCTTGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTGAAGGAAAGGGGTTTCTTCGGAGCTATTGCTGGTTTCCTAGAAGGAGGATGGGAAGGAATGATTGCAGGTTGGCACGGATACACATCTCACGGAGCACATGGAGTGGCAGTGGCGGCAGACCTTAAGAGTACACAAGAAGCTATAAATAAGATAACAAAAAATCTCAATTCTTTGAGTGAGCTAGAAGTAAAGAACCTTCAAAGACTAAGTGGTGCCATGGATGAACTCCACAACGAAATACTCGAGCTGGATGAGAAAGTGGATGATCTCAGAGCTGACACTATAAGCTCACAAATAGAACTTGCAGTCTTGCTTTCCAACGAAGGAATAATAAACAGTGAAGACGAGCATCTATTGGCACTTGAGAGAAAACTAAAGAAAATGCTGGGTCCCTCTGCTGTAGACATAGGAAACGGATGCTTCGAAACCAAACACAAATGCAACCAGACCTGCTTAGACAGGATAGCTGCTGGCACCTTTAATGCAGGAGAATTTTCTCTCCCCACTTTTGATTCATTGAACATTACTGCTGCATCTTTAAATGATGATGGATTGGATAACCATACTATACTGCTCTATTACTCAACTGCTGCTTCTAGTTTGGCTGTAACATTAATGCTAGCTATTTTTATTGTTTATATGGTCTCCAGAGACAACGTTTCATGCTCCATCTGTCTATAA'
},
{
'strain': 'B/Massachusetts/02/2012',
'isolate_id': 'EPI_ISL_121434',
'date': '2012-03-13',
'region': 'NorthAmerica',
'seq': 'ATGAAGGCAATAATTGTACTACTAATGGTAGTAACATCCAATGCAGATCGAATCTGCACTGGGATAACATCTTCAAACTCACCTCATGTGGTCAAAACAGCTACTCAAGGGGAGGTCAATGTGACTGGTGTGATACCACTAACAACAACACCAACAAAATCTTATTTTGCAAATCTCAAAGGAACAAAGACCAGAGGGAAACTATGCCCAGACTGTCTCAACTGTACAGATCTGGATGTGGCCCTGGGCAGGCCAATGTGTGTGGGAACTACACCTTCTGCGAAAGCTTCAATACTTCACGAAGTCAGACCTGTTACATCCGGGTGCTTCCCTATAATGCACGACAGAACAAAAATCAGGCAACTAGCCAATCTTCTCAGAGGATATGAAAATATCAGGTTATCAACCCAAAACGTTATCGATGCAGAAAAGGCACCAGGAGGACCCTACAGACTTGGAACCTCAGGATCTTGCCCTAACGCTACCAGTAAAAGCGGATTTTTCGCAACAATGGCTTGGGCTGTCCCAAAGGACAACAACAAAAATGCAACGAACCCATTAACAGTAGAAGTACCATACATTTGTGCAGAAGGGGAAGACCAAATTACTGTTTGGGGGTTCCATTCAGATAACAAAACCCAAATGAAGAACCTCTATGGAGACTCAAATCCTCAAAAGTTCACCTCATCTGCTAATGGAGTAACCACACATTATGTTTCTCAGATTGGCGGCTTCCCAGATCAAACAGAAGACGGAGGACTACCACAAAGCGGCAGAATTGTCGTTGATTACATGATGCAAAAACCTGGGAAAACAGGAACAATTGTCTATCAAAGAGGTGTTTTGTTGCCTCAAAAGGTGTGGTGCGCGAGTGGCAGGAGCAAAGTAATAAAAGGGTCCTTGCCTTTAATTGGTGAAGCAGATTGCCTTCATGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGAGAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTGAAAACACCTTTGAAGCTTGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGGGGTTTCTTCGGAGCTATTGCTGGTTTCCTAGAAGGAGGATGGGAAGGAATGATTGCAGGTTGGCACGGATACACATCTCACGGAGCACATGGAGTGGCAGTTGCTGCAGACCTTAAGAGCACACAAGAAGCTATAAACAAGATAACAAAAAATCTCAACTCTTTGAGTGAGCTAGAAGTAAAGAATCTTCAAAGGCTAAGTGGTGCCATGGATGAACTCCACAACGAAATACTCGAGCTGGATGAGAAAGTGGATGACCTCAGAGCTGACACTATAAGTTCACAAATAGAACTTGCAGTCTTGCTTTCCAACGAAGGAATAATAAACAGTGAAGACGAGCATCTATTGGCACTTGAGAGAAAACTAAAGAAAATGCTGGGTCCCTCTGCTGTAGACATAGGAAATGGATGCTTCGAAACCAAACACAAATGCAACCAGACCTGCTTAGACAGGATAGCTGCTGGCACCTTTAATGCAGGAGAGTTTTCTCTCCCCACTTTTGATTCATTGAACATTACTGCTGCATCTTTAAATGATGATGGATTGGATAACCATACTATACTGCTCTATTACTCAACTGCTGCTTCTAGTTTGGCTGTAACATTGATGCTAGCTATTTTTATTGTTTATATGGTCTCCAGAGACAACGTTTCATGCTCCATCTGTCTATAA'
},
{
'strain': 'B/PHUKET/3073/2013',
'isolate_id': 'EPI_ISL_161843',
'date': '2013-11-21',
'region': 'SoutheastAsia',
'seq': 'ATGAAGGCAATAATTGTACTACTCATGGTAGTAACATCCAACGCAGATCGAATCTGCACTGGGATAACATCTTCAAACTCACCTCATGTGGTCAAAACAGCTACTCAAGGGGAGGTCAATGTGACTGGCGTGATACCACTGACAACAACACCAACAAAATCTTATTTTGCAAATCTCAAAGGAACAAGGACCAGAGGGAAACTATGCCCGGACTGTCTCAACTGTACAGATCTGGATGTGGCCTTGGGCAGGCCAATGTGTGTGGGGACCACACCTTCTGCTAAAGCTTCAATACTCCATGAGGTCAGACCTGTTACATCCGGGTGCTTTCCTATAATGCACGACAGAACAAAAATCAGGCAACTACCCAATCTTCTCAGAGGATATGAAAAGATCAGGTTATCAACCCAAAACGTTATCGATGCAGAAAAAGCACCAGGAGGACCCTACAGACTTGGAACCTCAGGATCTTGCCCTAACGCTACCAGTAAAATCGGATTTTTTGCAACAATGGCTTGGGCTGTCCCAAAGGACAACTACAAAAATGCAACGAACCCACTAACAGTGGAAGTACCATACATTTGTACAGAAGGGGAAGACCAAATTACTGTTTGGGGGTTCCATTCGGATAACAAAACCCAAATGAAGAGCCTCTATGGAGACTCAAATCCTCAAAAGTTCACCTCATCTGCTAATGGAGTAACCACGCATTATGTTTCTCAGATTGGCGACTTCCCAGATCAAACAGAAGACGGAGGACTACCACAAAGCGGCAGAATTGTTGTTGATTACATGATGCAAAAACCTGGGAAAACAGGAACAATTGTCTATCAAAGGGGTGTTTTGTTGCCTCAAAAGGTGTGGTGCGCGAGTGGCAGGAGCAAAGTAATAAAAGGGTCATTGCCTTTAATTGGTGAAGCAGATTGCCTTCATGAAGAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGAAAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTAAAAACACCTTTGAAGCTTGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTGAAGGAAAGGGGTTTCTTCGGAGCTATTGCTGGTTTCCTAGAAGGAGGATGGGAAGGAATGATTGCAGGTTGGCACGGATACACATCTCACGGAGCACATGGAGTGGCAGTGGCGGCAGACCTTAAGAGTACACAAGAAGCTATAAATAAGATAACAAAAAATCTCAATTCTTTGAGTGAACTAGAAGTAAAGAACCTTCAAAGACTAAGTGGTGCCATGGATGAACTCCACAACGAAATACTCGAGCTGGATGAAAAAGTGGATGATCTCAGAGCTGACACTATAAGCTCACAAATAGAACTTGCAGTCTTGCTTTCCAACGAAGGAATAATAAACAGTGAAGACGAGCATCTATTGGCACTTGAGAGAAAACTAAAGAAAATGCTGGGTCCCTCTGCTGTAGACATAGGAAACGGATGCTTCGAAACCAAACACAAATGCAACCAGACCTGCTTAGACAGGATAGCTGCTGGCACCTTTAATGCAGGAGAATTTTCTCTCCCCACTTTTGATTCATTGAACATTACTGCTGCATCTTTAAATGATGATGGATTGGATAACCATACTATACTGCTCTATTACTCAACTGCTGCTTCTAGTTTGGCTGTAACATTAATGCTAGCTATTTTTATTGTTTATATGGTCTCCAGAGACAACGTTTCATGCTCCATCTGTCTATAAAGAAGGTTAGGCCTTGTATTTTCCTTTATTGTAGTGCTTGTTTGCTTGTCATCATTACAAAGAAAC'
}
]
self.outgroup = {
'strain':'B/Singapore/11/94',
'isolate_id':'EPI_ISL_20980',
'date':'1994-05-10',
'region':'China',
'seq':'ATATCCACAAAATGAAGGCAATAATTGTACTACTCATGGTAGTAACATCCAATGCAGATCGAATCTGCACTGGGATAACATCTTCAAACTCACCTCATGTGGTCAAAACAGCTACTCAAGGGGAGGTCAATGTGACTGGTGTGATACCACTGACAACAACACCAACAAAATCTCATTTTGCAAATCTCAAAGGAACAAAGACCAGAGGGAAACTATGCCCAAACTGTCTCAACTGCACAGATCTGGATGTGGCCTTGGGCAGACCAATGTGTGTGGGGACCACACCTTCGGCAAAAGCTTCAATACTCCACGAAGTCAGACCTGTTACATCCGGGTGCTTTCCTATAATGCACGACAGAACAAAAATCAGACAGCTACCCAATCTTCTCAGAGGATATGAAAATATCAGATTATCAACCCAAAACGTTATCAATGCAGAAAAGGCACCAGGAGGACCCTACAGACTTGGAACCTCAGGATCTTGCCCTAACGCTACCAGTAGAAGCGGATTTTTCGCAACAATGGCTTGGGCTGTCCCAAGGGACAACAACAAAACAGCAACGAATCCACTAACAGTAGAAGTACCATACGTTTGTACAGAAGGAGAAGACCAAATTACTGTTTGGGGGTTCCATTCTGATAACAAAACCCAAATGAAAAACCTCTATGGAGACTCAAATCCTCAAAAGTTCACCTCATCTGCTAATGGAGTAACCACACATTATGTTTCTCAGATTGGCGGCTTCCCAGATCAAACAGAAGACGGAGGGCTACCACAAAGCGGCAGAATTGTTGTTGATTACATGGTGCAAAAACCTGGGAAAACAGGAACAATTGTCTATCAAAGAGGTGTTTTGTTGCCTCAAAAGGTGTGGTGCGCGAGTGGCAGGAGCAAAGTAATAAAAGGGTCCTTGCCTTTAATTGGTGAAGCAGATTGCCTTCACGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGAGAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTGAAAACACCTTTGAAGCTTGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGGGGTTTCTTCGGAGCTATTGCTGGTTTCTTAGAAGGAGGATGGGAAGGAATGATTGCAGGTTGGCACGGATACACATCTCACGGAGCACATGGAGTGGCAGTGGCAGCAGACCTTAAGAGTACGCAAGAAGCCATAAACAAGATAACAAAAAATCTCAATTCTTTGAGTGAGCTAGAAGTAAAGAATCTTCAAAGACTAAGTGGTGCCATGGATGAACTCCACAACGAAATACTCGAGCTGGATGAGAAAGTGGATGATCTCAGAGCTGACACTATAAGCTCGCAAATAGAACTTGCAGTCTTGCTTTCCAACGAAGGAATAATAAACAGTGAAGATGAGCATCTATTGGCACTTGAGAGAAAACTAAAGAAAATGCTGGGTCCCTCTGCTGTAGACATAGGGAATGGATGCTTCGAAACCAAACACAAGTGCAACCAGACCTGCTTAGACAGGATAGCTGCTGGCACCTTTAATGCAGGAGAATTTTCTCTCCCCACTTTTGATTCACTGAATATTACTGCTGCATCTTTAAATGATGATGGATTGGATAACCATACTATACTGCTCTACTACTCAACTGCTGCTTCTAGTTTGGCTGTAACATTGATGATAGCTATTTTTATTGTTTATATGGTCTCCAGAGACAATGTTTCATGCTCCATCTGTCTATAAGGAAAATTAAGCCCTGTATTTTCCTTTATTGTAGTGCTTGTTTGTTTGTTACCATTACAAAGAAACGTTATTGA'
}
def __init__(self, min_length=0, **kwargs):
'''
parameters
min_length -- minimal length for a sequence to be acceptable
'''
flu_filter.__init__(self, **kwargs)
self.min_length = min_length
self.vaccine_strains = [{
'strain':
'A/mallard/Maryland/13OS3318/2014',
'isolate_id':
'EPI-ISL-216765',
'date':
'2014-06-24',
'lab':
'Other Database Import',
'region':
'NorthAmerica',
'seq':
'ATGTACAAAATAGTACTAGTATTCGCGCTCCTTGGAGCGGTGAATGGTCTTGACAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCACAAACGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAGTCGAAATTACAAGGACTTAGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGATCTACACCTTACCGGAACATGGGACACTTTAATAGAGAGAGACAATTCTATTGCCTACTGTTACCCGGGTACCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATCGACAAGATAAGCACTGGGTTTACATATGGATCATCCATCAATTCAGCTGGAACCACTAAAGCATGCATGAGAAATGGAGGAAATAGTTTCTATGCGGAGCTAAAGTGGTTAGTGTCGAAGAGCAAAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTGTAATCTGGGGAATTCATCACCCTTCAAGCACACAAGAAAAGAATGATCTGTATGGAACACAATCACTTTCCATTTCAGTGGGGAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAATGGCCAAAGTGGGCGGATTGATTTCCATTGGACGATGGTACAACCAGGTGATAACATCACTTTCTCGCATAATGGTGGATTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTTGGCATTCAATCAGGAGCTTCAGTAGACAATAACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAATATGTGAACAAAAAGAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGGATGGTAGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCCGCGGATTACAGAAGTACACAGGCAGCTATAGATCAAATAACCGGGAAATTGAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAATGAAATAGAACATCAAATCGGTAATGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGCTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAAATGCTGAATTTATATGAGAGAGTGAGGAAGCAACTAAGGCAAAATGCTGAAGAAGATGGGAAAGGGTGCTTTGAAATATATCACAAATGCAATGACAACTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTTTTCTTCTGCTTGAAAAATGGAAACATGCGCTGCACAATCTGTATTTAG',
}]
self.new_strains = [{
"strain":
"A/Unknown/Unknown/Batch2-1_002_01102017_4_H10N6",
"db":
"Unknown",
"accession":
"Unknown",
"date":
"2017-01-10",
"seq":
"ATGTACAAAATAGTACTAGTATTCGCGCTCCTTGGAGCGGTGCATGGTCTTGACAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCACAAATGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAGTCGAAATTACAAGGACTTAGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGACCTACACCTTACCGGAACATGGGACACTTTAATAGAGAGAGACAATTCTATTGCCTATTGTTACCCGGGTGCCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATTGACAAGATAAGCACCGGGTTCACATATGGATCATCCATCAATTCAGCTGGAACCACTCAAGCATGCATGAGAAATGGAGGGAATAGTTTCTATGCGGAGCTAAAGTGGCTAGTGTCGAAGAACACAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTATAATCTGGGGAATTCATCACCCTTCAAGCACAAAAGAGAAGAATGATCTGTATGGAACACAATCACTTTCCATTTCAGTGGGGAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAAAGGCCAAAGTGGGCGGATTGATTTTCATTGGACGATGGTACAGCCAGGTGATAACATCACTTTCTCGCATAATGGTGGATTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTTGGCATTCAATCAGTAGCTTCAGTAGACAATGACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAGTATGTGAACAAAAGAAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGAATGGTGGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCCGCGGATTACAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTGAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATCAGTAATGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGCTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAAATGCTGAATCTATATGAGAGGGTGAGGAAGCAACTAAGGCAAAATGCTGAAGAAGATGGGAAAGGGTGCTTTGAAATATACCACAAATGCGATGACAATTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTTTTCTTCTGCTTAAAAAATGGAAACATGCGATGCACAATCTGTATTTAG",
}, {
"strain":
"A/Unknown/Unknown/Batch2-1_007_01102017_4_H10N4",
"db":
"Unknown",
"accession":
"Unknown",
"date":
"2017-01-10",
"seq":
"ATGTACAAAATAGTACTAGTATTCGCGCTCCTTGGAGCGGTGCATGGTCTTGACAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCACAAATGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAGTCGAAATTACAAGGACTTAGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGACCTACACCTTACCGGAACATGGGACACTTTAATAGAGAGAGACAATTCTATTGCCTATTGTTACCCAGGTGCCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATTGACAAGATAAGCACCGGGTTCACATATGGATCATCCATCAATTCAGCTGGAACCACTCAAGCATGCATGAGAAATGGAGGGAATAGTTTCTATGCGGAGCTAAAGTGGCTAGTGTCGAAGAACACAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTATAATCTGGGGAATTCATCACCCTTCAAGCACAAAAGAGAAGAATGATCTGTATGGAACGCAATCACTTTCCATTTCAGTGGGGAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAAAGGCCAAAGTGGGCGGATTGATTTTCATTGGACGATGGTACAGCCAGGTGATAACATCACTTTCTCGCATAATGGTGGATTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTTGGCATTCAATCAGTAGCTTCAGTAGACAATGACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAGTATGTGAACAAAAGAAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGAATGGTGGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCCGCGGATTACAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTGAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATCAGTAATGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGCTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAAATGCTGAATCTATATGAGAGGGTGAGGAAGCAACTAAGGCAAAATGCTGAAGAAGATGGGAAAGGGTGCTTTGAAATATACCACAAATGCGATGACAATTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTTTTCTTCTGCTTAAAAAATGGAAACATGCGATGCACAATCTGTATTTAG",
}, {
"strain":
"A/Unknown/Unknown/Batch2-1_008_01102017_4_H10N7",
"db":
"Unknown",
"accession":
"Unknown",
"date":
"2017-01-10",
"seq":
"ATGTACAAAATAGCACTAGTATTCGCGCTCCTTGGAGCGGTGGATGGTCTTGATAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCATAAACGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAATCGAAATTACAAGGACTTAGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGATCTACACCTTACCGGAACATGGGACACCTTAATAGAGAGAGACAATTCTATTGCCTACTGTTACCCGGGTGCCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATCGACAAGATAAGCACTGGGTTTACATATGGATCATCCATCAATTCAGCTGGAACCACTAAAGCATGCATGAGAAATGGAGGAAATAGTTTCTACGCGGAGCTAAAGTGGCTAGTGTCGAAGAGCAAAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTATAATCTGGGGAATTCATCACCCTTCAAGCACACAAGAAAAGAATGATCTGTATGGAACACAATCACTTTCCATTTCAGTGGGAAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAATGGCCAAAGTGGACGGATTGATTTCCATTGGACGATGGTACAACCAGGTGATAACATTACTTTCTCGCATAATGGTGGATTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTGGGCATTCAATCAGGAGCTTCAGTAGACAATGACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAATATGTGAACAAAAAGAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGGATGGTAGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCCGCGGATTACAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTAAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATCGGTAACGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGCTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAGATGCTGAATTTATATGAGAGAGTGAGGAAGCAACTAAGGCAAAATGCTGAAGAAGATGGAAAAGGGTGCTTTGAAATATATCACAAATGCGATGACAACTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTCTTCTTCTGCTTGAAAAATGGAAACATGCGCTGCACAATCTGTATTTAG",
}, {
"strain":
"A/Unknown/Unknown/Batch2-1_010_01102017_4_H10N5",
"db":
"Unknown",
"accession":
"Unknown",
"date":
"2017-01-10",
"seq":
"ATGTACAAAATAGTACTAGTATTCGCGCTCCTTGGAGCGGTGCATGGTCTTGACAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCACAAATGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAGTCGAAATTACAAGGACTTAGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGACCTACACCTTACCGGAACATGGGACACTTTAATAGAGAGAGACAATTCTATTGCCTATTGTTACCCGGGTGCCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATTGACAAGATAAGCACCGGGTTCACATATGGATCATCCATCAATTCAGCTGGAACCACTCAAGCATGCATGAGAAATGGAGGGAATAGTTTCTATGCGGAGCTAAAGTGGCTAGTGTCGAAGAACACAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTATAATCTGGGGAATTCATCACCCTTCAAGCACAAAAGAGAAGAATGATCTGTATGGAACACAATCACTTTCCATTTCAGTGGGGAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAAAGGCCAAAGTGGGCGGATTGATTTTCATTGGACGATGGTACAGCCAGGTGATAACATCACTTTCTCGCATAATGGTGGATTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTTGGCATTCAATCAGTAGCTTCAGTAGACAATGACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAGTATGTGAACAAAAGAAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGAATGGTGGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCCGCGGATTACAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTGAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATCAGTAATGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGCTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAAATGCTGAATCTATATGAGAGRGTGAGGAAGCAACTAAGGCAAAATGCTGAAGAAGATGGGAAAGGGTGCTTTGAAATATACCACAAATGCGATGACAATTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTTTTCTTCTGCTTAAAAAATGGAAACATGCGATGCACAATCTGTATTTAG",
}, {
"strain":
"A/Unknown/Unknown/Batch2-1_013_01102017_4_H10N5",
"db":
"Unknown",
"accession":
"Unknown",
"date":
"2017-01-10",
"seq":
"ATGTACAAAATAGTACTAGTATTCGCGCTCCTTGGAGCGGTGCATGGTCTTGACAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCACAAATGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAGTCGAAATTACAAGGACTTAGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGACCTACACCTTACCGGAACATGGGACACTTTAATAGAGAGAGACAATTCTATTGCCTATTGTTACCCGGGTGCCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATTGACAAGATAAGCACCGGGTTCACATATGGATCATCCATCAATTCAGCTGGAACCACTCAAGCATGCATGAGAAATGGAGGGAATAGTTTCTATGCGGAGCTAAAGTGGCTAGTGTCGAAGAACACAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTATAATCTGGGGAATTCATCACCCTTCAAGCACAAAAGAGAAGAATGATCTGTATGGAACACAATCACTTTCCATTTCAGTGGGGAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAAAGGCCAAAGTGGGCGGATTGATTTTCATTGGACGATGGTACAGCCAGGTGATAACATCACTTTCTCGCATAATGGTGGATTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTTGGCATTCAATCAGTAGCTTCAGTAGACAATGACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAGTATGTGAACAAAAGAAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGAATGGTGGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCTGCGGATTACAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTGAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATCAGTAATGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGTTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAAATGCTGAATCTATATGAGAGGGTGAGGAAGCAACTAAGGCAAAATGCTGAAGAAGATGGGAAAGGGTGCTTTGAAATATACCACAAATGCGATGACAATTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTTTTCTTCTGCTTAAAAAATGGAAACATGCGATGCACAATCTGTATTTAG",
}, {
"strain":
"A/Unknown/Unknown/Batch2-1_021_01102017_4_H10N4",
"db":
"Unknown",
"accession":
"Unknown",
"date":
"2017-01-10",
"seq":
"ATGTACAAAATAGTACTAGTATTCGCGCTCCTTGGAGCGGTGCATGGTCTTGACAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCACAAATGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAGTCGAAATTACAAGGACTTAGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGACCTACACCTTACCGGAACATGGGACACTTTAATAGAGAGAGACAATTCTATTGCCTATTGTTACCCAGGTGCCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATTGACAAGATAAGCACCGGGTTCACATATGGATCATCCATCAATTCAGCTGGAACCACTCAAGCATGCATGAGAAATGGAGGGAATAGTTTCTATGCGGAGCTAAAGTGGCTAGTGTCGAAGAACACAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTATAATCTGGGGAATTCATCACCCTTCAAGCACAAAAGAGAAGAATGATCTGTATGGAACACAATCACTTTCCATTTCAGTGGGGAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAAAGGCCAAAGTGGGCGGATTGATTTTCATTGGACGATGGTACAGCCAGGTGATAACATCACTTTCTCGCATAATGGTGGATTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTTGGCATTCAATCAGTAGCTTCAGTAGACAATGACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAGTATGTGAACAAAAGAAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGAATGGTGGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCCGCGGATTACAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTGAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATCAGTAATGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGCTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAAATGCTGAATCTATATGAGAGGGTGAGGAAGCAACTAAGGCAAAATGCTGAAGAAGATGGGAAAGGGTGCTTTGAAATATACCACAAATGCGATGACAATTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTTTTCTTCTGCTTAAAAAATGGAAACATGCGATGCACAATCTGTATTTAG",
}, {
"strain":
"A/Unknown/Unknown/Batch2-1_027_01102017_4_H10N5",
"db":
"Unknown",
"accession":
"Unknown",
"date":
"2017-01-10",
"seq":
"ATGTACAAAATAGTACTAGTATTCGCGCTCCTTGGAGCGGTGCATGGTCTTGACAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCACAAATGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAGTCGAAATTACAAGGACTTAGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGACCTACACCTTACCGGAACATGGGACACTTTAATAGAGAGAGACAATTCTATTGCCTATTGTTACCCGGGTGCCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATTGACAAGATAAGCACCGGGTTCACATATGGATCATCCATCAATTCAGCTGGAACCACTCAAGCATGCATGAGAAATGGAGGGAATAGTTTCTATGCGGAGCTAAAGTGGCTAGTGTCGAAGAACACAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTATAATCTGGGGAATTCATCACCCTTCAAGCACAAAAGAGAAGAATGATCTGTATGGAACACAATCACTTTCCATTTCAGTGGGGAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAAAGGCCAAAGTGGGCGGATTGATTTTCATTGGACGATGGTACAGCCAGGTGATAACATCACTTTCTCGCATAATGGTGGATTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTTGGCATTCAATCAGTAGCTTCAGTAGACAATGACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAGTATGTGAACAAAAGAAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGAATGGTGGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCCGCGGATTACAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTGAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATCAGTAATGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGCTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAAATGCTGAATTTATATGAGAGGGTGAGGAAGCAACTAAGGCAAAATGCTGAAGAAGATGGGAAAGGGTGCTTTGAAATATACCACAAATGCGATGACAATTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTTTTCTTCTGCTTAAAAAATGGAAACATGCGATGCACAATCTGTATTTAG",
}, {
"strain":
"A/Unknown/Unknown/Batch2-1_028_01102017_4_H10N5",
"db":
"Unknown",
"accession":
"Unknown",
"date":
"2017-01-10",
"seq":
"ATGTACAAAATAGTACTAGTATTCGCGCTCCTTGGAGCGGTGCATGGTCTTGACAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCACAAATGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAGTCGAAATTACAAGGACTTAGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGACCTACACCTTACCGGAACATGGGACACTTTAATAGAGAGAGACAATTCTATTGCCTATTGTTACCCGGGTGCCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATTGACAAGATAAGCACCGGGTTCACATATGGATCATCCATCAATTCAGCTGGAACCACTCAAGCATGCATGAGAAATGGAGGGAATAGTTTCTATGCGGAGCTAAAGTGGCTAGTGTCGAAGAACACAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTATAATCTGGGGAATTCATCACCCTTCAAGCACAAAAGAGAAGAATGATCTGTATGGAACACAATCACTTTCCATTTCAGTGGGGAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAAAGGCCAAAGTGGGCGGATTGATTTTCATTGGACGATGGTACAGCCAGGTGATAACATCACTTTCTCGCATAATGGTGGATTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTTGGCATTCAATCAGTAGCTTCAGTAGACAATGACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAGTATGTGAACAAAAGAAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGAATGGTGGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCCGCGGATTACAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTGAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATCAGTAATGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGCTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAAATGCTGAATCTATATGAGAGGGTGAGGAAGCAACTAAGACAAAATGCTGAAGAAGATGGGAAAGGGTGCTTTGAAATATACCACAAATGCGATGACAATTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTTTTCTTCTGCTTAAAAAATGGAAACATGCGATGCACAATCTGTATTTAG",
}, {
"strain":
"A/Unknown/Unknown/Batch2-1_030_01102017_4_H10N5",
"db":
"Unknown",
"accession":
"Unknown",
"date":
"2017-01-10",
"seq":
"ATGTACAAAATAGTACTAGTATTCGCGCTCCTTGGAGCGGTGCATGGTCTTGACAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCACAAATGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAGTCGAAATTACAAGGACTTAGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGACCTACACCTTACCGGAACATGGGACACTTTAATAGAGAGAGACAATTCTATTGCCTATTGTTACCCGGGTGCCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATTGACAAGATAAGCACCGGGTTCACATATGGATCATCCATCAATTCAGCTGGAACCACTCAAGCATGCATGAGAAATGGAGGGAATAGTTTCTATGCGGAGCTAAAGTGGCTAGTGTCGAAGAACACAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTATAATCTGGGGAATTCATCACCCTTCAAGCACAAAAGAGAAGAATGATCTGTATGGAACACAATCACTTTCCATTTCAGTGGGGAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAAAGGCCAAAGTGGGCGGATTGATTTTCATTGGACGATGGTACAGCCAGGTGATAACATCACTTTCTCGCATAATGGTGGATTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTTGGCATTCAATCAGTAGCTTCAGTAGACAATGACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAGTATGTGAACAAAAGAAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGAATGGTGGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCCGCGGATTACAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTGAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATCAGTAATGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGCTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAAATGCTGAATCTATATGAGAGGGTGAGGAAGCAACTAAGGCAAAATGCTGAAGAAGATGGGAAAGGGTGCTTTGAAATATACCACAAATGCGATGACAATTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTTTTCTTCTGCTTAAAAAATGGAAACATGCGATGCACAATCTGTATTTAG",
}, {
"strain":
"A/Unknown/Unknown/Batch2-1_031_01102017_4_H10N5",
"db":
"Unknown",
"accession":
"Unknown",
"date":
"2017-01-10",
"seq":
"ATGTACAAAATAGTACTAGTATTCGCGCTCCTTGGAGCGGTGCATGGTCTTGACAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCACAAATGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAGTCGAAATTACAAGGACTTAGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGACCTACACCTTACCGGAACATGGGACACTTTAATAGAGAGAGACAATTCTATTGCCTATTGTTACCCGGGTGCCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATTGACAAGATAAGCACCGGGTTCACATATGGATCATCCATCAATTCAGCTGGAACCACTCAAGCATGCATGAGAAATGGAGGGAATAGTTTCTATGCGGAGCTAAAGTGGCTAGTGTCGAAGAACACAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTATAATCTGGGGAATTCATCATCCTTCAAGCACAAAAGAGAAGAATGATCTGTATGGAACACAATCACTTTCCATTTCAGTGGGGAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAAAGGCCAAAGTGGGCGGATTGATTTTCATTGGACGATGGTACAGCCAGGTGATAACATCACTTTCTCGCATAATGGTGGATTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTTGGCATTCAATCAGTAGCTTCAGTAGACAATGACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAGTATGTGAACAAAAGAAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGAATGGTGGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCCGCGGATTACAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTGAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATCAGTAATGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGCTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAAATGCTGAATCTATATGAGAGGGTGAGGAAGCAACTAAGGCAAAATGCTGAAGAAGATGGGAAAGGGTGCTTTGAAATATACCACAAATGCGATGACAATTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTTTTCTTCTGCTTAAAAAATGGAAACATGCGATGCACAATCTGTATTTAG",
}, {
"strain":
"A/Unknown/Unknown/Batch2-1_033_01102017_4_H10N5",
"db":
"Unknown",
"accession":
"Unknown",
"date":
"2017-01-10",
"seq":
"ATGTACAAAATAGTACTAGTATTCGCGCTCCTTGGAGCGGTGCATGGTCTTGACAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCACAAATGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAGTCGAAATTACAAGGACTTAGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGACCTACACCTTACCGGAACATGGGACACTTTAATAGAGAGAGACAATTCTATTGCCTACTGTTACCCGGGTGCCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATTGACAAGATAAGCACCGGGTTCACATATGGATCATCCATCAATTCAGCTGGAACCACTCAAGCATGCATGAGAAATGGAGGGAATAGTTTCTATGCGGAGCTAAAGTGGCTAGTGTCGAAGAACACAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTATAATCTGGGGAATTCATCACCCTTCAAGCACAAAAGAGAAGAATGATCTGTATGGAACACAATCACTTTCCATTTCAGTGGGGAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAAAGGCCAAAGTGGGCGGATTGATTTTCATTGGACGATGGTACAGCCAGGTGATAACATCACTTTCTCGCATAATGGTGGATTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTTGGCATTCAATCAGTAGCTTCAGTAGACAATGACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAGTATGTGAACAAAAGAAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGAATGGTGGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCCGCGGATTACAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTGAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATCAGTAATGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGCTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAAATGCTGAATCTATATGAGAGGGTGAGGAAGCAACTAAGGCAAAATGCTGAAGAAGATGGGAAAGGGTGCTTTGAAATATACCACAAATGCGATGACAATTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTTTTCTTCTGCTTAAAAAATGGAAACATGCGATGCACAATCTGTATTTAG",
}, {
"strain":
"A/Unknown/Unknown/Batch2-1_034_01102017_4_H10N7",
"db":
"Unknown",
"accession":
"Unknown",
"date":
"2017-01-10",
"seq":
"ATGTACAAAATAGCACTAGTATTCGCGCTCCTTGGAGCGGTGGATGGTCTTGATAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCATAAACGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAATCGAAATTACAAGGACTTAGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGATCTACACCTTACCGGAACATGGGACACCTTAATAGAGAGAGACAATTCTATTGCCTACTGTTACCCGGGTGCCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATCGACAAGATAAGCACTGGGTTTACATATGGATCATCCATCAATTCAGCTGGAACCACTAAAGCATGCATGAGAAATGGAGGAAATAGTTTCTACGCGGAGCTAAAGTGGCTAGTGTCGAAGAGCAAAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTATAATCTGGGGAATTCATCACCCTTCAAGCACACAAGAAAAGAATGATCTGTATGGAACACAATCACTTTCCATTTCAGTGGGAAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAATGGCCAAAGTGGACGGATTGATTTCCATTGGACGATGGTACAACCAGGTGATAACATTACTTTCTCGCATAATGGTGGATTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTGGGCATTCAATCAGGAGCTTCAGTAGACAATGACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAATATGTGAACAAAAAGAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGGATGGTAGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCCGCGGATTACAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTAAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATCGGTAACGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGCTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAGATGCTGAATTTATATGAGAGAGTGAGGAAGCAACTAAGGCAAAATGCTGAAGAAGATGGAAAAGGGTGCTTTGAAATATATCACAAATGCGATGACAACTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTCTTCTTCTGCTTGAAAAATGGAAACATGCGCTGCACAATCTGTATTTAG",
}, {
"strain":
"A/Unknown/Unknown/Batch2-1_036_01102017_4_H10N5",
"db":
"Unknown",
"accession":
"Unknown",
"date":
"2017-01-10",
"seq":
"ATGTACAAAATAGTACTAGTATTCGCGCTCCTTGGAGCGGTGCATGGTCTTGACAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCACAAATGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAGTCGAAATTACAAGGACTTAGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGACCTACACCTTACCGGAACATGGGACACTTTAATAGAGAGAGACAATTCTATTGCCTATTGTTACCCGGGTGCCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATTGACAAGATAAGCACCGGGTTCACATATGGATCATCCATCAATTCAGCTGGAACCACTCAAGCATGCATGAGAAATGGAGGGAATAGTTTCTATGCGGAGCTAAAGTGGCTAGTGTCGAAGAACACAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTATAATCTGGGGAATTCATCACCCTTCAAGCACAAAAGAGAAGAATGATCTGTATGGAACACAATCACTTTCCATTTCAGTGGGGAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAAAGGCCAAAGTGGGCGGATTGATTTTCATTGGACGATGGTACAGCCAGGTGATAACATCACTTTCTCGCATAATGGTGGATTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTTGGCATTCAATCAGTAGCTTCAGTAGACAATGACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAGTATGTGAACAAAAGAAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGAATGGTGGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCCGCGGATTACAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTGAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATCAGTAATGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGCTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAAATGCTGAATCTATATGAGAGGGTGAGGAAGCAACTAAGGCAAAATGCTGAAGAAGATGGGAAAGGGTGCTTTGAAATATACCACAAATGCGATGACAATTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTTTTCTTCTGCTTAAAAAATGGAAACATGCGATGCACAATCTGTATTTAG",
}, {
"strain":
"A/Unknown/Unknown/Batch2-1_037_01102017_4_H10N5",
"db":
"Unknown",
"accession":
"Unknown",
"date":
"2017-01-10",
"seq":
"ATGTACAAAATAGTACTAGTATTCGCGCTCCTTGGAGCGGTGCATGGTCTTGACAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCACAAATGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAACCTGGACAAACTTTGCATGAAAAGTCGAAATTACAAGGACTTAGGTGATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGACCTACACCTTACCGGAACATGGGACACTTTAATAGAGAGAGACAATTCTATTGCCTATTGTTACCCGGGTGCCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATTGACAAGATAAGCACCGGGTTCACATATGGATCATCCATCAATTCAGCTGGAACCACTCAAGCATGCATGAGAAATGGAGGGAATAGTTTCTATGCGGAGCTAAAGTGGCTAGTGTCGAAGAACACAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTATAATCTGGGGAATTCATCACCCTTCAAGCACAAAAGAGAAGAATGATCTGTATGGAACACAATCACTTTCCATTTCAGTGGGGAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAAAGGCCAAAGTGGGCGGATTGATTTTCATTGGACGATGGTACAGCCAGGTGATAACATCACTTTCTCGCATAATGGTGGATTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTTGGCATTCAATCAGTAGCTTCAGTAGACAATGACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAGTATGTGAACAAAAGAAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGAATGGTGGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCTGCGGATTACAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTGAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATCAGTAATGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGCTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAAATGCTGAATCTATATGAGAGGGTGAGGAAGCAACTAAGGCAAAATGCTGAAGAAGATGGGAAAGGGTGCTTTGAAATATACCACAAATGCGATGACAATTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTTTTCTTCTGCTTAAAAAATGGAAACATGCGATGCACAATCTGTATTTAG",
}, {
"strain":
"A/Unknown/Unknown/Batch2-1_039_01102017_4_H10N5",
"db":
"Unknown",
"accession":
"Unknown",
"date":
"2017-01-10",
"seq":
"ATGTACAAAATAGTACTAGTATTCGCGCTCCTTGGAGCGGTGCATGGTCTTGACAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCACAAATGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAGTCGAAATTACAAGGACTTAGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGACCTACACCTTACCGGAACATGGGACACTTTAATAGAGAGAGACAATTCTATTGCCTATTGTTACCCGGGTGCCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATTGACAAGATAAGCACCGGGTTCACATATGGATCATCCATCAATTCAGCTGGAACCACTCAAGCATGCATGAGAAATGGAGGGAATAGTTTCTATGCGGAGCTAAAGTGGCTAGTGTCGAAGAACACAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTATAATCTGGGGAATTCATCACCCTTCAAGCACAAAAGAGAAGAATGATCTGTATGGAACACAATCACTTTCCATTTCAGTGGGGAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAAAGGCCAAAGTGGGCGGATTGATTTTCATTGGACGATGGTACAGCCAGGTGATAACATCACTTTCTCGCATAATGGTGGATTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTTGGCATTCAATCAGTAGCTTCAGTAGACAATGACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAGTATGTGAACAAAAGAAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGAATGGTGGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCCGCGGATTACAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTGAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATCAGTAATGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGCTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAAATGCTGAATCTATATGAGAGGGTGAGGAAGCAACTAAGGCAAAATGCTGAAGAAGATGGGAAAGGGTGCTTTGAAATATACCACAAATGCGATGACAATTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTTTTCTTCTGCTTAAAAAATGGAAACATGCGATGCACAATCTGTATTTAG",
}, {
"strain":
"A/Unknown/Unknown/Batch2-1_042_01102017_4_H10N5",
"db":
"Unknown",
"accession":
"Unknown",
"date":
"2017-01-10",
"seq":
"ATGTACAAAATAGTACTAGTATTCGCGCTCCTTGGAGCGGTGCATGGTCTTGACAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCACAAATGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAGTCGAAATTACAAGGACTTAGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGACCTACACCTTACCGGAACATGGGACACTTTAATAGAGAGAGACAATTCTATTGCCTATTGTTACCCGGGTGCCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATTGACAAGATAAGCACCGGGTTCACATATGGATCATCCATCAATTCAGCTGGAACCACTCAAGCATGCATGAGAAATGGAGGGAATAGTTTCTATGCGGAGCTAAAGTGGCTAGTGTCGAAGAACACAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTATAATCTGGGGAATTCATCACCCTTCAAGCACAAAAGAGAAGAATGATCTGTATGGAACACAATCACTTTCCATTTCAGTGGGGAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAAAGGCCAAAGTGGGCGGATTGATTTTCATTGGACGATGGTACAGCCAGGTGATAACATCACTTTCTCGCATAATGGTGGATTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTTGGCATTCAATCAGTAGCTTCAGTAGACAATGACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAGTATGTGAACAAAAGAAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGAATGGTGGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCCGCGGATTACAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTGAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATCAGTAATGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGCTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAAATGCTGAATCTATATGAGAGGGTGAGGAAGCAACTAAGGCAAAATGCTGAAGAAGATGGGAAAGGGTGCTTTGAAATATACCACAAATGCGATGACAATTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTTTTCTTCTGCTTAAAAAATGGAAACATGCGATGCACAATCTGTATTTAG",
}, {
"strain":
"A/Unknown/Unknown/Batch2-1_043_01102017_4_H10N4",
"db":
"Unknown",
"accession":
"Unknown",
"date":
"2017-01-10",
"seq":
"ATGTACAAAATAGTACTAGTATTCGCGCTCCTTGGAGCGGTGCATGGTCTTGACAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCACAAATGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAGTCGAAATTACAAGGACTTAGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGACCTACACCTTACCGGAACATGGGACACTTTAATAGAGAGAGACAATTCTATTGCCTATTGTTACCCGGGTGCCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATTGACAAGATAAGCACCGGGTTCACATATGGATCATCCATCAATTCAGCTGGAACCACTCAAGCATGCATGAGAGATGGAGGGAATAGTTTCTATGCGGAGCTAAAGTGGCTAGTGTCGAAGAACACAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTATAATCTGGGGAATTCATCACCCTTCAAGCACAAAAGAGAAGAATGATCTGTATGGAACACAATCACTTTCCATTTCAGTGGGGAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAAAGGCCAAAGTGGGCGGATTGATTTTCATTGGACGATGGTACAGCCAGGTGATAACATCACTTTCTCGCATAATGGTGGATTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTTGGCATTCAATCGGTAGCTTCAGTAGACAATGACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAGTATGTGAACAAAAGAAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGAATGGTGGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCCGCGGATTACAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTGAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATCAGTAATGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGCTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAAATGCTGAATCTATATGAGAGGGTGAGGAAGCAACTAAGGCAAAATGCTGAAGAAGATGGGAAAGGGTGCTTTGAAATATACCACAAATGCGATGACAATTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTTTTCTTCTGCTTAAAAAATGGAAACATGCGATGCACAATCTGTATTTAG",
}, {
"strain":
"A/Unknown/Unknown/Batch2-1_044_01102017_4_H10N5",
"db":
"Unknown",
"accession":
"Unknown",
"date":
"2017-01-10",
"seq":
"ATGCACAAAATAGTACTAGTATTCGCGCTCCTTGGAGCGGTGCATGGTCTTGACAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCACAAATGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAGTCGAAATTACAAGGACTTAGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGACCTACACCTTACCGGAACATGGGACACTTTAATAGAGAGAGACAATTCTATTGCCTATTGTTACCCGGGTGCCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATTGACAAGATAAGCACCGGGTTCACATATGGATCATCCATCAATTCAGCTGGAACCACTCAAGCATGCATGAGAAATGGAGGGAATAGTTTCTATGCGGAGCTAAAGTGGCTAGTGTCGAAGAACACAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTATAATCTGGGGAATTCATCACCCTTCAAGCACAAAAGAGAAGAATGATCTGTATGGAACACAATCACTTTCCATTTCAGTGGGGAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAAAGGCCAAAGTGGGCGGATTGATTTTCATTGGACGATGGTACAGCCAGGTGATAACATCACTTTCTCGCATAATGGTGGATTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTTGGCATTCAATCAGTAGCTTCAGTAGACAATGACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAGTATGTGAACAAAAGAAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGAATGGTGGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCCGCGGATTACAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTGAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATCAGTAATGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGCTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAAATGCTGAATCTATATGAGAGGGTGAGGAAGCAACTAAGGCAAAATGCTGAAGAAGATGGGAAAGGGTGCTTTGAAATATACCACAAATGCGATGACAATTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTTTTCTTCTGCTTAAAAAATGGAAACATGCGATGCACAATCTGTATTTAG",
}, {
"strain":
"A/Unknown/Unknown/Batch2-1_048_01102017_4_H10N5",
"db":
"Unknown",
"accession":
"Unknown",
"date":
"2017-01-10",
"seq":
"ATGTACAAAATAGTACTAGTATTCGCGCTCCTTGGAGCGGTGCATGGTCTTGACAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCACAAATGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAGTCGAAATTACAAGGACTTAGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGACCTACACCTTACCGGAACATGGGACACTTTAATAGAGAGAGACAATTCTATTGCCTATTGTTACCCGGGTGCCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATTGACAAGATAAGCACCGGGTTCACATATGGATCATCCATCAATTCAGCTGGAACCACTCAAGCATGCATGAGAAATGGAGGGAATAGTTTCTATGCGGAGCTAAAGTGGCTAGTGTCGAAGAACACAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTATAATCTGGGGAATTCATCACCCTTCAAGCACAAAAGAGAAGAATGATCTGTATGGAACACAATCACTTTCCATTTCAGTGGGGAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAAAGGCCAAAGTGGGCGGATTGATTTTCATTGGACGATGGTACAGCCAGGTGATAACATCACTTTCTCGCATAATGGTGGACTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTTGGCATTCAATCAGTAGCTTCAGTAGACAATGACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAGTATGTGAACAAAAGAAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGAATGGTGGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCCGCGGATTACAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTGAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATCAGTAATGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGCTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAAATGCTGAATCTATATGAGAGGGTGAGGAAGCAACTAAGGCAAAATGCTGAAGAAGATGGGAAAGGGTGCTTTGAAATATACCACAAATGCGATGACAATTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTTTTCTTCTGCTTAAAAAATGGAAACATGCGATGCACAATCTGTATTTAG",
}]
tmp_outgroup = SeqIO.read(
'/Users/yujiazhou/Documents/nextflu/H9_nextflu-master/augur/source-data/H10_outgroup.gb',
'genbank')
genome_annotation = tmp_outgroup.features
self.cds = {
x.qualifiers['gene'][0]: x
for x in genome_annotation
if 'gene' in x.qualifiers and x.type == 'CDS'
and x.qualifiers['gene'][0] in ['SigPep', 'HA1', 'HA2']
}
self.outgroup = {
'strain': 'A/mallard-duck/ALB/302/1977',
'region': 'NorthAmerica',
'isolate_id': 'EPI-ISL-8890',
'date': '1977-08-13', #(Month and day unknown)
'seq': str(tmp_outgroup.seq).upper()
}
def __init__(self, min_length=0, **kwargs):
'''
parameters
min_length -- minimal length for a sequence to be acceptable
'''
flu_filter.__init__(self, **kwargs)
self.min_length = min_length
self.vaccine_strains = [
{
'strain':
'A/turkey/Italy/3889/99',
'isolate_id':
'EPI-ISL-2746',
'date':
'1990-07-01', #(Month and day unknown)
'region':
'Europe',
'seq':
'ATGAACACTCAAATCCTGGTATTCGCTCTGGTGGCGATCATTCCGACAAATGCAGACAAAATCTGCCTTGGGCATCATGCCGTGTCAAACGGGACTAAAGTAAACACATTAACTGAAAGAGGAGTGGAAGTCGTTAATGCAACTGAAACGGTGGAACGAACAAACGTCCCCAGGATCTGCTCAAAAGGGAAAAGGACAGTTGACCTCGGTCAATGTGGACTTCTGGGAACAATCACTGGGCCACCCCAATGTGACCAATTCCTAGAATTTTCAGCCGATCTAATTATTGAGAGGCGAGAAGGAAGTGGTGTCTGTTATCCTGGGAAATTCGTGAATGAAGAAGCTCTGAGGCAAATTCTCAGGGAGTCAGGCGGAATTGACAAGGAGACAATGGGATTCACATACAGCGGAATAAGAACTAATGGAACAACCAGTGCATGTAGGAGATTAGGATCTTCATTCTATGCAGAGATGAAATGGCTCCTGTCAAACACAGACAATGCTGCTTTCCCGCAGATGACTAAGTCATACAAAAACACAAGGAAAGACCCAGCTCTGATAATATGGGGGATCCACCATTCCGGATCAACTACAGAACAGACCAAGCTATATGGGAGTGGAAACAAACTGATAACAGTTGGGAGTTCTAATTACCAACAGTCCTTTGTACCGAGTCCAGGAGCGAGACCACAAGTGAATGGCCAATCTGGAAGAATTGACTTTCATTGGCTGATGCTAAACCCCAATGACACAGTCACTTTCAGTTTCAATGGGGCCTTCATAGCTCCAGACCGTGCAAGTTTTCTGAGAGGGAAGTCTATGGGGATTCAGAGTGGAGTACAGGTTGATGCCAATTGTGAAGGAGATTGCTATCACAGTGGAGGGACAATAATAAGTAATTTGCCCTTTCAGAACATAAATAGCAGGGCAGTAGGGAAATGTCCGAGATATGTTAAGCAAGAGAGTCTGCTGCTGGCAACAGGGATGAAGAATGTTCCCGAAGTTCCAAAGGGA------------------------------AGAGGCCTATTTGGTGCTATAGCGGGTTTCATTGAAAATGGATGGGAAGGTCTGATTGATGGGTGGTATGGCTTCAGGCATCAAAATGCACAAGGGGAGGGAACTGCTGCAGATTACAAAAGCACCCAATCAGCAATTGATCAAGTAACAGGAAAATTGAACCGGCTTATAGAAAAAACTAACCAACAATTTGAGTTAATAGACAATGAATTCACTGAGGTTGAAAAGCAAATTGGCAATGTGATAAATTGGACCAGAGATTCCATGACAGAAGTGTGGTCCTATAACGCTGAACTCTTGGTAGCAATGGAGAACCAGCACACAATTGATCTGGCCGACTCAGAAATGAACAAACTATACGAACGAGTGAAGAGACAACTGAGAGAGAATGCTGAAGAAGATGGCACTGGTTGCTTCGAAATATTTCACAAGTGTGATGACGACTGTATGGCCAGTATTAGAAACAACACCTATGATCACAGCAAGTACAGGGAAGAGGCAATGCAAAATAGAATACAGATTGACCCAGTCAAACTAAGCAGCGGCTACAAAGATGTGATACTTTGGTTTAGCTTCGGGGCATCATGTTTCATACTTCTGGCCATTGCAATGGGCCTTGTCTTCATATGTGTGAAGAATGGAAACATGCGGTGCACTATTTGTATATAA',
},
{
'strain':
'A/mallard/Netherlands/12/00',
'isolate_id':
'EPI-ISL-3548',
'date':
'2000-07-01', # (Month and day unknown)
'region':
'Europe',
'seq':
'ATGAACACTCAAATCCTGGTATTCGCTCTGATGGCGATCATTCCGACAAATGCAGACAAGATCTGCCTTGGGCATCATGCCGTGTCAAACGGGACTAAAGTAAACACATTAACTGAAAGAGGAGTGGAAGTCGTTAATGCAACTGAAACGGTGGAACGAACAAACGTCCCCAGGATCTGCTCAAAAGGGAAAAGGACAGTTGACCTTGGTCAATGTGGACTTCTGGGAACAATCACTGGGCCGCCCCAATGTGACCAATTCCTAGAATTTTCAGCCGATTTAATTATTGAGAGGCGAGAAGGAAGTGATGTCTGTTATCCTGGGAAATTCGTGAATGAAGAAGCTCTGAGGCAAATTCTCAGGGAGTCAGGCGGAATTGACAAGGAGACAATGGGATTCACCTACAGCGGAATAAGAACTAATGGAGCAACCAGTGCATGTAGGAGATCAGGATCTTCATTCTATGCAGAGATGAAATGGCTCCTGTCAAACACAGACAATGCTGCTTTCCCGCAGATGACTAAGTCATACAAAAACACAAGGAAAGACCCAGCTCTGATAATATGGGGGATCCACCATTCCGGATCAACTACAGAACAGACCAAGCTATATGGGAGTGGAAACAAACTGATAACAGTTGGGAGTTCTAATTACCAACAGTCCTTTGTACCGAGTCCAGGAGCGAGACCACAAGTAAATGGCCAATCTGGAAGAATTGACTTTCATTGGCTGATACTAAACCCCAATGACACAGTTACTTTCAGTTTCAATGGGGCCTTCATAGCTCCAGACCGTGCAAGCTTTCTGAGAGGGAAGTCTATGGGAATTCAGAGTGGAGTACAGGTTGATGCCAATTGTGAAGGAGATTGCTATCATAGTGGAGGGACAATAATAAGTAATTTGCCCTTTCAGAACATAAATAGCAGGGCAGTAGGAAAATGTCCGAGATATGTTAAGCAAGAGAGTCTGCTGCTGGCAACAGGAATGAAGAATGTTCCCGAAATCCCAAAGGGA------------------------------AGAGGCCTATTTGGTGCTATAGCGGGTTTCATTGAAAATGGATGGGAAGGTCTGATTGATGGGTGGTATGGCTTCAGGCATCAAAATGCACAAGGGGAGGGAACTGCTGCAGATTACAAAAGCACCCAATCAGCAATTGATCAAATAACAGGAAAATTAAACCGGCTTATAGAAAAAACTAACCAACAATTTGAGTTAATAGACAATGAATTCACTGAGGTTGAAAAGCAAATTGGCAATGTGATAAATTGGACCAGAGATTCCATGACAGAAGTGTGGTCCTATAACGCTGAACTCTTGGTAGCAATGGAGAATCAGCACACAATTGATCTGGCCGACTCAGAAATGAACAAACTGTACGAACGAGTGAAGAGACAACTGAGAGAGAATGCTGAAGAAGATGGCACTGGTTGCTTCGAAATATTTCACAAGTGTGATGACGACTGTATGGCCAGTATTAGAAACAACACCTATGATCACAGCAAGTACAGGGAAGAGGCAATGCAAAATAGAATACAGATTGACCCAGTCAAACTAAGCAGCGGCTACAAAGATGTGATACTTTGGTTTAGCTTCGGGGCATCATGTTTCATACTTCTGGCCATTGCAATGGGCCTTGTCTTCATATGTGTGAAGAATGGAAACATGCGGTGCACTATTTGTATATAA',
},
{
'strain':
'A/human/New-York/107/2003',
'isolate_id':
'EPI-ISL-16424',
'date':
'2003-07-01',
'region':
'NorthAmerica',
'seq':
'ATGAACACTCAAATTCTGGCATTCATTGCTTGTGTGCTGACTGGAGTTAAAGGAGACAAAATATGTCTTGGGCACCATGCTGTGGCAAATGGAACAAAAGTGAACACATTAACAGAGAGGGGGATTGAAGTAGTGAATGCCACAGAGACAGTGGAAACTACGAATATCAAGAAAATATGTACCCAGGGGAAAAGGCCAACAGATCTGGGACAATGTGGACTTCTAGGAACCCTAATAGGACCTCCCCAATGTGATCAATTCCTGGAGTTTTCCTCTGATTTGATAATTGAGCGAAGAGAAGGAACCGATATATGCTATCCCGGTAGATTCACAAACGAAGAATCACTGAGGCAGATCCTTCGAAGATCAGGAGGAATTGGTAAGGAGTCAATGGGCTTCACCTATAGTGGAATAAGAACCAATGGAGCGACAAGTGCCTGCACAAGATCAGGTTCTTCTTTCTATGCAGAGATGAAGTGGTTGCTGTCGAATTCAGATAATGCAGCATTCCCACAGATGACAAAGGCGTATAGAAATCCCAGAAACAAACCAGCTCTGATAATTTGGGGAGTTCATCACTCTGAATCGGTTAGCGAGCAGACCAAACTCTATGGAAGTGGAAACAAGTTGATAACAGTAAGAAGCTCAAAATACCAGCAATCATTCACCCCAAATCCGGGAGCACGA------------------------AGAATCGATTTCCACTGGCTACTCCTTGATCCCAATGACACAGTGACCTTCACTTTCAATGGAGCATTCATAGCCCCTGACAGGACAAGTTTCTTTAGGGGAGAATCACTAGGAGTCCAGAGTGATGCTCCTTTGGATTCAAGTTGTAGAGGAGATTGCTTTCACAGTGGGGGTACGATAGTCAGTTCCCTGCCATTCCAAAACATCAACTCTAGAACTGTGGGGAAATGCCCTCGGTATGTCAAACAGAAAAGCCTCCTTCTGGCTACAGGAATGAGAAATGTTCCAGAGAAACCAAAGCCC------------------------------AGAGGCCTTTTTGGAGCAATTGCTGGATTCATAGAGAATGGATGGGAGGGTCTCATCAATGGATGGTATGGTTTCAGACATCAAAATGCACAAGGAGAGGGAACTGCAGCTGACTACAAAAGCACCCAGTCTGCAATAGATCAGATCACAGGCAAATTGAATCGTTTAATTGGCAAAACAAATCAGCAGTTTGAGCTGATAGACAATGAGTTCAATGAGATAGAACAACAAATAGGAAATGTCATTAATTGGACAAGAGACGCAATGACTGAGATATGGTCGTATAATGCTGAGCTGTTGGTGGCAATGGAAAATCAGCATACAATAGATCTTGCGGACTCAGAAATGAGCAAACTTTATGAGCGTGTCAAAAAACAACTAAGGGAGAATGCTGAAGAAGATGGAACTGGATGTTTTGAGATATTTCATAAATGTGACGATCAGTGTATGGAGAGCATAAGGAACAACACGTATGACCATACTCAATACAGAACAGAGTCATTGCAGAATAGAATACAGATAGACCCAGTGAAGTTGAGTAGTGGGTACAAAGACATAATCTTATGGTTTAGCTTCGGGGCATCATGTTTTCTTCTTCTAGCCATTGCAATGGGACTGGTTTTCATTTGCATAAAGAATGGAAACATGCAGTGCACTATTTGTATATAG',
},
{
'strain':
'A/human/Shanghai/2/2013',
'isolate_id':
'EPI-ISL-138738',
'date':
'2013-03-05',
'region':
'China',
'seq':
'ATGAACACTCAAATCCTGGTATTCGCTCTGATTGCGATCATTCCAACAAATGCAGACAAAATCTGCCTCGGACATCATGCCGTGTCAAACGGAACCAAAGTAAACACATTAACTGAAAGAGGAGTGGAAGTCGTCAATGCAACTGAAACAGTGGAACGAACAAACATCCCCAGGATCTGCTCAAAAGGGAAAAGGACAGTTGACCTCGGTCAATGTGGACTCCTGGGGACAATCACTGGACCACCTCAATGTGACCAATTCCTAGAATTTTCAGCCGATTTAATTATTGAGAGGCGAGAAGGAAGTGATGTCTGTTATCCTGGGAAATTCGTGAATGAAGAAGCTCTGAGGCAAATTCTCAGAGAATCAGGCGGAATTGACAAGGAAGCAATGGGATTCACATACAGTGGAATAAGAACTAATGGAGCAACCAGTGCATGTAGGAGATCAGGATCTTCATTCTATGCAGAAATGAAATGGCTCCTGTCAAACACAGATAATGCTGCATTCCCGCAGATGACTAAGTCATATAAAAATACAAGAAAAAGCCCAGCTCTAATAGTATGGGGGATCCATCATTCCGTATCAACTGCAGAGCAAACCAAGCTATATGGGAGTGGAAACAAACTGGTGACAGTTGGGAGTTCTAATTATCAACAATCTTTTGTACCGAGTCCAGGAGCGAGACCACAAGTTAATGGTCTATCTGGAAGAATTGACTTTCATTGGCTAATGCTAAATCCCAATGATACAGTCACTTTCAGTTTCAATGGGGCTTTCATAGCTCCAGACCGTGCAAGCTTCCTGAGAGGAAAATCTATGGGAATCCAGAGTGGAGTACAGGTTGATGCCAATTGTGAAGGGGACTGCTATCATAGTGGAGGGACAATAATAAGTAACTTGCCATTTCAGAACATAGATAGCAGGGCAGTTGGAAAATGTCCGAGATATGTTAAGCAAAGGAGTCTGCTGCTAGCAACAGGGATGAAGAATGTTCCTGAGATTCCAAAAGGA------------------------------AGAGGCCTATTTGGTGCTATAGCGGGTTTCATTGAAAATGGATGGGAAGGCCTAATTGATGGTTGGTATGGTTTCAGACACCAGAATGCACAGGGAGAGGGAACTGCTGCAGATTACAAAAGCACTCAATCGGCAATTGATCAAATAACAGGAAAATTAAACCGGCTTATAGAAAAAACCAACCAACAATTTGAGTTGATAGACAATGAATTCAATGAGGTAGAGAAGCAAATCGGTAATGTGATAAATTGGACCAGAGATTCTATAACAGAAGTGTGGTCATACAATGCTGAACTCTTGGTAGCAATGGAGAACCAGCATACAATTGATCTGGCTGATTCAGAAATGGACAAACTGTACGAACGAGTGAAAAGACAGCTGAGAGAGAATGCTGAAGAAGATGGCACTGGTTGCTTTGAAATATTTCACAAGTGTGATGATGACTGTATGGCCAGTATTAGAAATAACACCTATGATCACAGCAAATACAGGGAAGAGGCAATGCAAAATAGAATACAGATTGACCCAGTCAAACTAAGCAGCGGCTACAAAGATGTGATACTTTGGTTTAGCTTCGGGGCATCATGTTTCATACTTCTAGCCATTGTAATGGGCCTTGTCTTCATATGTGTAAAGAATGGAAACATGCGGTGCACTATTTGTATATAA',
},
{
'strain':
'A/human/Anhui/1/2013',
'isolate_id':
'EPI-ISL-138739',
'date':
'2013-03-20',
'region':
'China',
'seq':
'ATGAACACTCAAATCCTGGTATTCGCTCTGATTGCGATCATTCCAACAAATGCAGACAAAATCTGCCTCGGACATCATGCCGTGTCAAACGGAACCAAAGTAAACACATTAACTGAAAGAGGAGTGGAAGTCGTCAATGCAACTGAAACAGTGGAACGAACAAACATCCCCAGGATCTGCTCAAAAGGGAAAAGGACAGTTGACCTCGGTCAATGTGGACTCCTGGGGACAATCACTGGACCACCTCAATGTGACCAATTCCTAGAATTTTCAGCCGATTTAATTATTGAGAGGCGAGAAGGAAGTGATGTCTGTTATCCTGGGAAATTCGTGAATGAAGAAGCTCTGAGGCAAATTCTCAGAGAATCAGGCGGAATTGACAAGGAAGCAATGGGATTCACATACAGTGGAATAAGAACTAATGGAGCAACCAGTGCATGTAGGAGATCAGGATCTTCATTCTATGCAGAAATGAAATGGCTCCTGTCAAACACAGATAATGCTGCATTCCCGCAGATGACTAAGTCATATAAAAATACAAGAAAAAGCCCAGCTCTAATAGTATGGGGGATCCATCATTCCGTATCAACTGCAGAGCAAACCAAGCTATATGGGAGTGGAAACAAACTGGTGACAGTTGGGAGTTCTAATTATCAACAATCTTTTGTACCGAGTCCAGGAGCGAGACCACAAGTTAATGGTCTATCTGGAAGAATTGACTTTCATTGGCTAATGCTAAATCCCAATGATACAGTCACTTTCAGTTTCAATGGGGCTTTCATAGCTCCAGACCGTGCAAGCTTCCTGAGAGGAAAATCTATGGGAATCCAGAGTGGAGTACAGGTTGATGCCAATTGTGAAGGGGACTGCTATCATAGTGGAGGGACAATAATAAGTAACTTGCCATTTCAGAACATAGATAGCAGGGCAGTTGGAAAATGTCCGAGATATGTTAAGCAAAGGAGTCTGCTGCTAGCAACAGGGATGAAGAATGTTCCTGAGATTCCAAAGGGA------------------------------AGAGGCCTATTTGGTGCTATAGCGGGTTTCATTGAAAATGGATGGGAAGGCCTAATTGATGGTTGGTATGGTTTCAGACACCAGAATGCACAGGGAGAGGGAACTGCTGCAGATTACAAAAGCACTCAATCGGCAATTGATCAAATAACAGGAAAATTAAACCGGCTTATAGAAAAAACCAACCAACAATTTGAGTTGATAGACAATGAATTCAATGAGGTAGAGAAGCAAATCGGTAATGTGATAAATTGGACCAGAGATTCTATAACAGAAGTGTGGTCATACAATGCTGAACTCTTGGTAGCAATGGAGAACCAGCATACAATTGATCTGGCTGATTCAGAAATGGACAAACTGTACGAACGAGTGAAAAGACAGCTGAGAGAGAATGCTGAAGAAGATGGCACTGGTTGCTTTGAAATATTTCACAAGTGTGATGATGACTGTATGGCCAGTATTAGAAATAACACCTATGATCACAGCAAATACAGGGAAGAGGCAATGCAAAATAGAATACAGATTGACCCAGTCAAACTAAGCAGCGGCTACAAAGATGTGATACTTTGGTTTAGCTTCGGGGCATCATGTTTCATACTTCTAGCCATTGTAATGGGCCTTGTCTTCATATGTGTAAAGAATGGAAACATGCGGTGCACTATTTGTATATAA',
}
]
tmp_outgroup = SeqIO.read(
'/Users/yujiazhou/Documents/nextflu/H9_nextflu-master/augur/source-data/H7_outgroup.gb',
'genbank')
genome_annotation = tmp_outgroup.features
self.cds = {
x.qualifiers['gene'][0]: x
for x in genome_annotation
if 'gene' in x.qualifiers and x.type == 'CDS'
and x.qualifiers['gene'][0] in ['SigPep', 'HA1', 'HA2']
}
self.outgroup = {
'strain': 'A/equine/Prague/2/1956',
'db': 'Other-Database-Import',
'isolate_id': 'EPI-ISL-89157',
'date': '1956-06-11',
'country': 'CzechRepublic',
'region': 'Europe',
'seq': str(tmp_outgroup.seq).upper()
}
def __init__(self,min_length = 0, **kwargs):
'''
parameters
min_length -- minimal length for a sequence to be acceptable
'''
flu_filter.__init__(self, **kwargs)
self.min_length = min_length
self.vaccine_strains =[
{
'strain':'A/mallard/Maryland/13OS3318/2014',
'isolate_id':'EPI-ISL-216765',
'date': '2014-06-24',
'lab':'Other Database Import',
'region':'NorthAmerica',
'seq':'ATGTACAAAATAGTACTAGTATTCGCGCTCCTTGGAGCGGTGAATGGTCTTGACAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCACAAACGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAGTCGAAATTACAAGGACTTAGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGATCTACACCTTACCGGAACATGGGACACTTTAATAGAGAGAGACAATTCTATTGCCTACTGTTACCCGGGTACCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATCGACAAGATAAGCACTGGGTTTACATATGGATCATCCATCAATTCAGCTGGAACCACTAAAGCATGCATGAGAAATGGAGGAAATAGTTTCTATGCGGAGCTAAAGTGGTTAGTGTCGAAGAGCAAAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTGTAATCTGGGGAATTCATCACCCTTCAAGCACACAAGAAAAGAATGATCTGTATGGAACACAATCACTTTCCATTTCAGTGGGGAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAATGGCCAAAGTGGGCGGATTGATTTCCATTGGACGATGGTACAACCAGGTGATAACATCACTTTCTCGCATAATGGTGGATTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTTGGCATTCAATCAGGAGCTTCAGTAGACAATAACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAATATGTGAACAAAAAGAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGGATGGTAGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCCGCGGATTACAGAAGTACACAGGCAGCTATAGATCAAATAACCGGGAAATTGAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAATGAAATAGAACATCAAATCGGTAATGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGCTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAAATGCTGAATTTATATGAGAGAGTGAGGAAGCAACTAAGGCAAAATGCTGAAGAAGATGGGAAAGGGTGCTTTGAAATATATCACAAATGCAATGACAACTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTTTTCTTCTGCTTGAAAAATGGAAACATGCGCTGCACAATCTGTATTTAG',
}
]
self.new_strains =[
{
"strain": "A/Unknown/Unknown/Batch2-1_002_01102017_4_H10N6",
"db": "Unknown",
"accession": "Unknown",
"date": "2017-01-10",
"seq": "ATGTACAAAATAGTACTAGTATTCGCGCTCCTTGGAGCGGTGCATGGTCTTGACAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCACAAATGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAGTCGAAATTACAAGGACTTAGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGACCTACACCTTACCGGAACATGGGACACTTTAATAGAGAGAGACAATTCTATTGCCTATTGTTACCCGGGTGCCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATTGACAAGATAAGCACCGGGTTCACATATGGATCATCCATCAATTCAGCTGGAACCACTCAAGCATGCATGAGAAATGGAGGGAATAGTTTCTATGCGGAGCTAAAGTGGCTAGTGTCGAAGAACACAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTATAATCTGGGGAATTCATCACCCTTCAAGCACAAAAGAGAAGAATGATCTGTATGGAACACAATCACTTTCCATTTCAGTGGGGAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAAAGGCCAAAGTGGGCGGATTGATTTTCATTGGACGATGGTACAGCCAGGTGATAACATCACTTTCTCGCATAATGGTGGATTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTTGGCATTCAATCAGTAGCTTCAGTAGACAATGACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAGTATGTGAACAAAAGAAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGAATGGTGGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCCGCGGATTACAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTGAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATCAGTAATGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGCTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAAATGCTGAATCTATATGAGAGGGTGAGGAAGCAACTAAGGCAAAATGCTGAAGAAGATGGGAAAGGGTGCTTTGAAATATACCACAAATGCGATGACAATTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTTTTCTTCTGCTTAAAAAATGGAAACATGCGATGCACAATCTGTATTTAG",
}, {
"strain": "A/Unknown/Unknown/Batch2-1_007_01102017_4_H10N4",
"db": "Unknown",
"accession": "Unknown",
"date": "2017-01-10",
"seq": "ATGTACAAAATAGTACTAGTATTCGCGCTCCTTGGAGCGGTGCATGGTCTTGACAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCACAAATGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAGTCGAAATTACAAGGACTTAGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGACCTACACCTTACCGGAACATGGGACACTTTAATAGAGAGAGACAATTCTATTGCCTATTGTTACCCAGGTGCCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATTGACAAGATAAGCACCGGGTTCACATATGGATCATCCATCAATTCAGCTGGAACCACTCAAGCATGCATGAGAAATGGAGGGAATAGTTTCTATGCGGAGCTAAAGTGGCTAGTGTCGAAGAACACAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTATAATCTGGGGAATTCATCACCCTTCAAGCACAAAAGAGAAGAATGATCTGTATGGAACGCAATCACTTTCCATTTCAGTGGGGAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAAAGGCCAAAGTGGGCGGATTGATTTTCATTGGACGATGGTACAGCCAGGTGATAACATCACTTTCTCGCATAATGGTGGATTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTTGGCATTCAATCAGTAGCTTCAGTAGACAATGACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAGTATGTGAACAAAAGAAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGAATGGTGGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCCGCGGATTACAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTGAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATCAGTAATGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGCTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAAATGCTGAATCTATATGAGAGGGTGAGGAAGCAACTAAGGCAAAATGCTGAAGAAGATGGGAAAGGGTGCTTTGAAATATACCACAAATGCGATGACAATTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTTTTCTTCTGCTTAAAAAATGGAAACATGCGATGCACAATCTGTATTTAG",
}, {
"strain": "A/Unknown/Unknown/Batch2-1_008_01102017_4_H10N7",
"db": "Unknown",
"accession": "Unknown",
"date": "2017-01-10",
"seq": "ATGTACAAAATAGCACTAGTATTCGCGCTCCTTGGAGCGGTGGATGGTCTTGATAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCATAAACGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAATCGAAATTACAAGGACTTAGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGATCTACACCTTACCGGAACATGGGACACCTTAATAGAGAGAGACAATTCTATTGCCTACTGTTACCCGGGTGCCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATCGACAAGATAAGCACTGGGTTTACATATGGATCATCCATCAATTCAGCTGGAACCACTAAAGCATGCATGAGAAATGGAGGAAATAGTTTCTACGCGGAGCTAAAGTGGCTAGTGTCGAAGAGCAAAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTATAATCTGGGGAATTCATCACCCTTCAAGCACACAAGAAAAGAATGATCTGTATGGAACACAATCACTTTCCATTTCAGTGGGAAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAATGGCCAAAGTGGACGGATTGATTTCCATTGGACGATGGTACAACCAGGTGATAACATTACTTTCTCGCATAATGGTGGATTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTGGGCATTCAATCAGGAGCTTCAGTAGACAATGACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAATATGTGAACAAAAAGAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGGATGGTAGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCCGCGGATTACAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTAAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATCGGTAACGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGCTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAGATGCTGAATTTATATGAGAGAGTGAGGAAGCAACTAAGGCAAAATGCTGAAGAAGATGGAAAAGGGTGCTTTGAAATATATCACAAATGCGATGACAACTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTCTTCTTCTGCTTGAAAAATGGAAACATGCGCTGCACAATCTGTATTTAG",
}, {
"strain": "A/Unknown/Unknown/Batch2-1_010_01102017_4_H10N5",
"db": "Unknown",
"accession": "Unknown",
"date": "2017-01-10",
"seq": "ATGTACAAAATAGTACTAGTATTCGCGCTCCTTGGAGCGGTGCATGGTCTTGACAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCACAAATGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAGTCGAAATTACAAGGACTTAGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGACCTACACCTTACCGGAACATGGGACACTTTAATAGAGAGAGACAATTCTATTGCCTATTGTTACCCGGGTGCCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATTGACAAGATAAGCACCGGGTTCACATATGGATCATCCATCAATTCAGCTGGAACCACTCAAGCATGCATGAGAAATGGAGGGAATAGTTTCTATGCGGAGCTAAAGTGGCTAGTGTCGAAGAACACAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTATAATCTGGGGAATTCATCACCCTTCAAGCACAAAAGAGAAGAATGATCTGTATGGAACACAATCACTTTCCATTTCAGTGGGGAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAAAGGCCAAAGTGGGCGGATTGATTTTCATTGGACGATGGTACAGCCAGGTGATAACATCACTTTCTCGCATAATGGTGGATTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTTGGCATTCAATCAGTAGCTTCAGTAGACAATGACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAGTATGTGAACAAAAGAAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGAATGGTGGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCCGCGGATTACAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTGAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATCAGTAATGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGCTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAAATGCTGAATCTATATGAGAGRGTGAGGAAGCAACTAAGGCAAAATGCTGAAGAAGATGGGAAAGGGTGCTTTGAAATATACCACAAATGCGATGACAATTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTTTTCTTCTGCTTAAAAAATGGAAACATGCGATGCACAATCTGTATTTAG",
}, {
"strain": "A/Unknown/Unknown/Batch2-1_013_01102017_4_H10N5",
"db": "Unknown",
"accession": "Unknown",
"date": "2017-01-10",
"seq": "ATGTACAAAATAGTACTAGTATTCGCGCTCCTTGGAGCGGTGCATGGTCTTGACAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCACAAATGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAGTCGAAATTACAAGGACTTAGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGACCTACACCTTACCGGAACATGGGACACTTTAATAGAGAGAGACAATTCTATTGCCTATTGTTACCCGGGTGCCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATTGACAAGATAAGCACCGGGTTCACATATGGATCATCCATCAATTCAGCTGGAACCACTCAAGCATGCATGAGAAATGGAGGGAATAGTTTCTATGCGGAGCTAAAGTGGCTAGTGTCGAAGAACACAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTATAATCTGGGGAATTCATCACCCTTCAAGCACAAAAGAGAAGAATGATCTGTATGGAACACAATCACTTTCCATTTCAGTGGGGAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAAAGGCCAAAGTGGGCGGATTGATTTTCATTGGACGATGGTACAGCCAGGTGATAACATCACTTTCTCGCATAATGGTGGATTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTTGGCATTCAATCAGTAGCTTCAGTAGACAATGACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAGTATGTGAACAAAAGAAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGAATGGTGGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCTGCGGATTACAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTGAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATCAGTAATGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGTTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAAATGCTGAATCTATATGAGAGGGTGAGGAAGCAACTAAGGCAAAATGCTGAAGAAGATGGGAAAGGGTGCTTTGAAATATACCACAAATGCGATGACAATTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTTTTCTTCTGCTTAAAAAATGGAAACATGCGATGCACAATCTGTATTTAG",
}, {
"strain": "A/Unknown/Unknown/Batch2-1_021_01102017_4_H10N4",
"db": "Unknown",
"accession": "Unknown",
"date": "2017-01-10",
"seq": "ATGTACAAAATAGTACTAGTATTCGCGCTCCTTGGAGCGGTGCATGGTCTTGACAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCACAAATGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAGTCGAAATTACAAGGACTTAGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGACCTACACCTTACCGGAACATGGGACACTTTAATAGAGAGAGACAATTCTATTGCCTATTGTTACCCAGGTGCCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATTGACAAGATAAGCACCGGGTTCACATATGGATCATCCATCAATTCAGCTGGAACCACTCAAGCATGCATGAGAAATGGAGGGAATAGTTTCTATGCGGAGCTAAAGTGGCTAGTGTCGAAGAACACAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTATAATCTGGGGAATTCATCACCCTTCAAGCACAAAAGAGAAGAATGATCTGTATGGAACACAATCACTTTCCATTTCAGTGGGGAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAAAGGCCAAAGTGGGCGGATTGATTTTCATTGGACGATGGTACAGCCAGGTGATAACATCACTTTCTCGCATAATGGTGGATTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTTGGCATTCAATCAGTAGCTTCAGTAGACAATGACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAGTATGTGAACAAAAGAAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGAATGGTGGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCCGCGGATTACAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTGAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATCAGTAATGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGCTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAAATGCTGAATCTATATGAGAGGGTGAGGAAGCAACTAAGGCAAAATGCTGAAGAAGATGGGAAAGGGTGCTTTGAAATATACCACAAATGCGATGACAATTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTTTTCTTCTGCTTAAAAAATGGAAACATGCGATGCACAATCTGTATTTAG",
}, {
"strain": "A/Unknown/Unknown/Batch2-1_027_01102017_4_H10N5",
"db": "Unknown",
"accession": "Unknown",
"date": "2017-01-10",
"seq": "ATGTACAAAATAGTACTAGTATTCGCGCTCCTTGGAGCGGTGCATGGTCTTGACAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCACAAATGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAGTCGAAATTACAAGGACTTAGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGACCTACACCTTACCGGAACATGGGACACTTTAATAGAGAGAGACAATTCTATTGCCTATTGTTACCCGGGTGCCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATTGACAAGATAAGCACCGGGTTCACATATGGATCATCCATCAATTCAGCTGGAACCACTCAAGCATGCATGAGAAATGGAGGGAATAGTTTCTATGCGGAGCTAAAGTGGCTAGTGTCGAAGAACACAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTATAATCTGGGGAATTCATCACCCTTCAAGCACAAAAGAGAAGAATGATCTGTATGGAACACAATCACTTTCCATTTCAGTGGGGAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAAAGGCCAAAGTGGGCGGATTGATTTTCATTGGACGATGGTACAGCCAGGTGATAACATCACTTTCTCGCATAATGGTGGATTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTTGGCATTCAATCAGTAGCTTCAGTAGACAATGACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAGTATGTGAACAAAAGAAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGAATGGTGGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCCGCGGATTACAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTGAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATCAGTAATGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGCTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAAATGCTGAATTTATATGAGAGGGTGAGGAAGCAACTAAGGCAAAATGCTGAAGAAGATGGGAAAGGGTGCTTTGAAATATACCACAAATGCGATGACAATTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTTTTCTTCTGCTTAAAAAATGGAAACATGCGATGCACAATCTGTATTTAG",
}, {
"strain": "A/Unknown/Unknown/Batch2-1_028_01102017_4_H10N5",
"db": "Unknown",
"accession": "Unknown",
"date": "2017-01-10",
"seq": "ATGTACAAAATAGTACTAGTATTCGCGCTCCTTGGAGCGGTGCATGGTCTTGACAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCACAAATGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAGTCGAAATTACAAGGACTTAGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGACCTACACCTTACCGGAACATGGGACACTTTAATAGAGAGAGACAATTCTATTGCCTATTGTTACCCGGGTGCCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATTGACAAGATAAGCACCGGGTTCACATATGGATCATCCATCAATTCAGCTGGAACCACTCAAGCATGCATGAGAAATGGAGGGAATAGTTTCTATGCGGAGCTAAAGTGGCTAGTGTCGAAGAACACAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTATAATCTGGGGAATTCATCACCCTTCAAGCACAAAAGAGAAGAATGATCTGTATGGAACACAATCACTTTCCATTTCAGTGGGGAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAAAGGCCAAAGTGGGCGGATTGATTTTCATTGGACGATGGTACAGCCAGGTGATAACATCACTTTCTCGCATAATGGTGGATTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTTGGCATTCAATCAGTAGCTTCAGTAGACAATGACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAGTATGTGAACAAAAGAAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGAATGGTGGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCCGCGGATTACAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTGAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATCAGTAATGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGCTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAAATGCTGAATCTATATGAGAGGGTGAGGAAGCAACTAAGACAAAATGCTGAAGAAGATGGGAAAGGGTGCTTTGAAATATACCACAAATGCGATGACAATTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTTTTCTTCTGCTTAAAAAATGGAAACATGCGATGCACAATCTGTATTTAG",
}, {
"strain": "A/Unknown/Unknown/Batch2-1_030_01102017_4_H10N5",
"db": "Unknown",
"accession": "Unknown",
"date": "2017-01-10",
"seq": "ATGTACAAAATAGTACTAGTATTCGCGCTCCTTGGAGCGGTGCATGGTCTTGACAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCACAAATGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAGTCGAAATTACAAGGACTTAGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGACCTACACCTTACCGGAACATGGGACACTTTAATAGAGAGAGACAATTCTATTGCCTATTGTTACCCGGGTGCCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATTGACAAGATAAGCACCGGGTTCACATATGGATCATCCATCAATTCAGCTGGAACCACTCAAGCATGCATGAGAAATGGAGGGAATAGTTTCTATGCGGAGCTAAAGTGGCTAGTGTCGAAGAACACAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTATAATCTGGGGAATTCATCACCCTTCAAGCACAAAAGAGAAGAATGATCTGTATGGAACACAATCACTTTCCATTTCAGTGGGGAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAAAGGCCAAAGTGGGCGGATTGATTTTCATTGGACGATGGTACAGCCAGGTGATAACATCACTTTCTCGCATAATGGTGGATTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTTGGCATTCAATCAGTAGCTTCAGTAGACAATGACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAGTATGTGAACAAAAGAAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGAATGGTGGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCCGCGGATTACAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTGAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATCAGTAATGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGCTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAAATGCTGAATCTATATGAGAGGGTGAGGAAGCAACTAAGGCAAAATGCTGAAGAAGATGGGAAAGGGTGCTTTGAAATATACCACAAATGCGATGACAATTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTTTTCTTCTGCTTAAAAAATGGAAACATGCGATGCACAATCTGTATTTAG",
}, {
"strain": "A/Unknown/Unknown/Batch2-1_031_01102017_4_H10N5",
"db": "Unknown",
"accession": "Unknown",
"date": "2017-01-10",
"seq": "ATGTACAAAATAGTACTAGTATTCGCGCTCCTTGGAGCGGTGCATGGTCTTGACAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCACAAATGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAGTCGAAATTACAAGGACTTAGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGACCTACACCTTACCGGAACATGGGACACTTTAATAGAGAGAGACAATTCTATTGCCTATTGTTACCCGGGTGCCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATTGACAAGATAAGCACCGGGTTCACATATGGATCATCCATCAATTCAGCTGGAACCACTCAAGCATGCATGAGAAATGGAGGGAATAGTTTCTATGCGGAGCTAAAGTGGCTAGTGTCGAAGAACACAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTATAATCTGGGGAATTCATCATCCTTCAAGCACAAAAGAGAAGAATGATCTGTATGGAACACAATCACTTTCCATTTCAGTGGGGAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAAAGGCCAAAGTGGGCGGATTGATTTTCATTGGACGATGGTACAGCCAGGTGATAACATCACTTTCTCGCATAATGGTGGATTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTTGGCATTCAATCAGTAGCTTCAGTAGACAATGACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAGTATGTGAACAAAAGAAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGAATGGTGGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCCGCGGATTACAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTGAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATCAGTAATGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGCTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAAATGCTGAATCTATATGAGAGGGTGAGGAAGCAACTAAGGCAAAATGCTGAAGAAGATGGGAAAGGGTGCTTTGAAATATACCACAAATGCGATGACAATTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTTTTCTTCTGCTTAAAAAATGGAAACATGCGATGCACAATCTGTATTTAG",
}, {
"strain": "A/Unknown/Unknown/Batch2-1_033_01102017_4_H10N5",
"db": "Unknown",
"accession": "Unknown",
"date": "2017-01-10",
"seq": "ATGTACAAAATAGTACTAGTATTCGCGCTCCTTGGAGCGGTGCATGGTCTTGACAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCACAAATGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAGTCGAAATTACAAGGACTTAGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGACCTACACCTTACCGGAACATGGGACACTTTAATAGAGAGAGACAATTCTATTGCCTACTGTTACCCGGGTGCCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATTGACAAGATAAGCACCGGGTTCACATATGGATCATCCATCAATTCAGCTGGAACCACTCAAGCATGCATGAGAAATGGAGGGAATAGTTTCTATGCGGAGCTAAAGTGGCTAGTGTCGAAGAACACAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTATAATCTGGGGAATTCATCACCCTTCAAGCACAAAAGAGAAGAATGATCTGTATGGAACACAATCACTTTCCATTTCAGTGGGGAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAAAGGCCAAAGTGGGCGGATTGATTTTCATTGGACGATGGTACAGCCAGGTGATAACATCACTTTCTCGCATAATGGTGGATTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTTGGCATTCAATCAGTAGCTTCAGTAGACAATGACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAGTATGTGAACAAAAGAAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGAATGGTGGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCCGCGGATTACAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTGAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATCAGTAATGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGCTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAAATGCTGAATCTATATGAGAGGGTGAGGAAGCAACTAAGGCAAAATGCTGAAGAAGATGGGAAAGGGTGCTTTGAAATATACCACAAATGCGATGACAATTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTTTTCTTCTGCTTAAAAAATGGAAACATGCGATGCACAATCTGTATTTAG",
}, {
"strain": "A/Unknown/Unknown/Batch2-1_034_01102017_4_H10N7",
"db": "Unknown",
"accession": "Unknown",
"date": "2017-01-10",
"seq": "ATGTACAAAATAGCACTAGTATTCGCGCTCCTTGGAGCGGTGGATGGTCTTGATAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCATAAACGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAATCGAAATTACAAGGACTTAGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGATCTACACCTTACCGGAACATGGGACACCTTAATAGAGAGAGACAATTCTATTGCCTACTGTTACCCGGGTGCCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATCGACAAGATAAGCACTGGGTTTACATATGGATCATCCATCAATTCAGCTGGAACCACTAAAGCATGCATGAGAAATGGAGGAAATAGTTTCTACGCGGAGCTAAAGTGGCTAGTGTCGAAGAGCAAAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTATAATCTGGGGAATTCATCACCCTTCAAGCACACAAGAAAAGAATGATCTGTATGGAACACAATCACTTTCCATTTCAGTGGGAAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAATGGCCAAAGTGGACGGATTGATTTCCATTGGACGATGGTACAACCAGGTGATAACATTACTTTCTCGCATAATGGTGGATTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTGGGCATTCAATCAGGAGCTTCAGTAGACAATGACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAATATGTGAACAAAAAGAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGGATGGTAGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCCGCGGATTACAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTAAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATCGGTAACGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGCTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAGATGCTGAATTTATATGAGAGAGTGAGGAAGCAACTAAGGCAAAATGCTGAAGAAGATGGAAAAGGGTGCTTTGAAATATATCACAAATGCGATGACAACTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTCTTCTTCTGCTTGAAAAATGGAAACATGCGCTGCACAATCTGTATTTAG",
}, {
"strain": "A/Unknown/Unknown/Batch2-1_036_01102017_4_H10N5",
"db": "Unknown",
"accession": "Unknown",
"date": "2017-01-10",
"seq": "ATGTACAAAATAGTACTAGTATTCGCGCTCCTTGGAGCGGTGCATGGTCTTGACAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCACAAATGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAGTCGAAATTACAAGGACTTAGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGACCTACACCTTACCGGAACATGGGACACTTTAATAGAGAGAGACAATTCTATTGCCTATTGTTACCCGGGTGCCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATTGACAAGATAAGCACCGGGTTCACATATGGATCATCCATCAATTCAGCTGGAACCACTCAAGCATGCATGAGAAATGGAGGGAATAGTTTCTATGCGGAGCTAAAGTGGCTAGTGTCGAAGAACACAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTATAATCTGGGGAATTCATCACCCTTCAAGCACAAAAGAGAAGAATGATCTGTATGGAACACAATCACTTTCCATTTCAGTGGGGAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAAAGGCCAAAGTGGGCGGATTGATTTTCATTGGACGATGGTACAGCCAGGTGATAACATCACTTTCTCGCATAATGGTGGATTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTTGGCATTCAATCAGTAGCTTCAGTAGACAATGACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAGTATGTGAACAAAAGAAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGAATGGTGGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCCGCGGATTACAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTGAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATCAGTAATGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGCTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAAATGCTGAATCTATATGAGAGGGTGAGGAAGCAACTAAGGCAAAATGCTGAAGAAGATGGGAAAGGGTGCTTTGAAATATACCACAAATGCGATGACAATTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTTTTCTTCTGCTTAAAAAATGGAAACATGCGATGCACAATCTGTATTTAG",
}, {
"strain": "A/Unknown/Unknown/Batch2-1_037_01102017_4_H10N5",
"db": "Unknown",
"accession": "Unknown",
"date": "2017-01-10",
"seq": "ATGTACAAAATAGTACTAGTATTCGCGCTCCTTGGAGCGGTGCATGGTCTTGACAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCACAAATGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAACCTGGACAAACTTTGCATGAAAAGTCGAAATTACAAGGACTTAGGTGATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGACCTACACCTTACCGGAACATGGGACACTTTAATAGAGAGAGACAATTCTATTGCCTATTGTTACCCGGGTGCCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATTGACAAGATAAGCACCGGGTTCACATATGGATCATCCATCAATTCAGCTGGAACCACTCAAGCATGCATGAGAAATGGAGGGAATAGTTTCTATGCGGAGCTAAAGTGGCTAGTGTCGAAGAACACAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTATAATCTGGGGAATTCATCACCCTTCAAGCACAAAAGAGAAGAATGATCTGTATGGAACACAATCACTTTCCATTTCAGTGGGGAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAAAGGCCAAAGTGGGCGGATTGATTTTCATTGGACGATGGTACAGCCAGGTGATAACATCACTTTCTCGCATAATGGTGGATTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTTGGCATTCAATCAGTAGCTTCAGTAGACAATGACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAGTATGTGAACAAAAGAAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGAATGGTGGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCTGCGGATTACAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTGAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATCAGTAATGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGCTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAAATGCTGAATCTATATGAGAGGGTGAGGAAGCAACTAAGGCAAAATGCTGAAGAAGATGGGAAAGGGTGCTTTGAAATATACCACAAATGCGATGACAATTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTTTTCTTCTGCTTAAAAAATGGAAACATGCGATGCACAATCTGTATTTAG",
}, {
"strain": "A/Unknown/Unknown/Batch2-1_039_01102017_4_H10N5",
"db": "Unknown",
"accession": "Unknown",
"date": "2017-01-10",
"seq": "ATGTACAAAATAGTACTAGTATTCGCGCTCCTTGGAGCGGTGCATGGTCTTGACAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCACAAATGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAGTCGAAATTACAAGGACTTAGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGACCTACACCTTACCGGAACATGGGACACTTTAATAGAGAGAGACAATTCTATTGCCTATTGTTACCCGGGTGCCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATTGACAAGATAAGCACCGGGTTCACATATGGATCATCCATCAATTCAGCTGGAACCACTCAAGCATGCATGAGAAATGGAGGGAATAGTTTCTATGCGGAGCTAAAGTGGCTAGTGTCGAAGAACACAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTATAATCTGGGGAATTCATCACCCTTCAAGCACAAAAGAGAAGAATGATCTGTATGGAACACAATCACTTTCCATTTCAGTGGGGAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAAAGGCCAAAGTGGGCGGATTGATTTTCATTGGACGATGGTACAGCCAGGTGATAACATCACTTTCTCGCATAATGGTGGATTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTTGGCATTCAATCAGTAGCTTCAGTAGACAATGACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAGTATGTGAACAAAAGAAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGAATGGTGGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCCGCGGATTACAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTGAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATCAGTAATGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGCTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAAATGCTGAATCTATATGAGAGGGTGAGGAAGCAACTAAGGCAAAATGCTGAAGAAGATGGGAAAGGGTGCTTTGAAATATACCACAAATGCGATGACAATTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTTTTCTTCTGCTTAAAAAATGGAAACATGCGATGCACAATCTGTATTTAG",
}, {
"strain": "A/Unknown/Unknown/Batch2-1_042_01102017_4_H10N5",
"db": "Unknown",
"accession": "Unknown",
"date": "2017-01-10",
"seq": "ATGTACAAAATAGTACTAGTATTCGCGCTCCTTGGAGCGGTGCATGGTCTTGACAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCACAAATGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAGTCGAAATTACAAGGACTTAGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGACCTACACCTTACCGGAACATGGGACACTTTAATAGAGAGAGACAATTCTATTGCCTATTGTTACCCGGGTGCCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATTGACAAGATAAGCACCGGGTTCACATATGGATCATCCATCAATTCAGCTGGAACCACTCAAGCATGCATGAGAAATGGAGGGAATAGTTTCTATGCGGAGCTAAAGTGGCTAGTGTCGAAGAACACAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTATAATCTGGGGAATTCATCACCCTTCAAGCACAAAAGAGAAGAATGATCTGTATGGAACACAATCACTTTCCATTTCAGTGGGGAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAAAGGCCAAAGTGGGCGGATTGATTTTCATTGGACGATGGTACAGCCAGGTGATAACATCACTTTCTCGCATAATGGTGGATTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTTGGCATTCAATCAGTAGCTTCAGTAGACAATGACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAGTATGTGAACAAAAGAAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGAATGGTGGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCCGCGGATTACAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTGAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATCAGTAATGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGCTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAAATGCTGAATCTATATGAGAGGGTGAGGAAGCAACTAAGGCAAAATGCTGAAGAAGATGGGAAAGGGTGCTTTGAAATATACCACAAATGCGATGACAATTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTTTTCTTCTGCTTAAAAAATGGAAACATGCGATGCACAATCTGTATTTAG",
}, {
"strain": "A/Unknown/Unknown/Batch2-1_043_01102017_4_H10N4",
"db": "Unknown",
"accession": "Unknown",
"date": "2017-01-10",
"seq": "ATGTACAAAATAGTACTAGTATTCGCGCTCCTTGGAGCGGTGCATGGTCTTGACAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCACAAATGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAGTCGAAATTACAAGGACTTAGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGACCTACACCTTACCGGAACATGGGACACTTTAATAGAGAGAGACAATTCTATTGCCTATTGTTACCCGGGTGCCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATTGACAAGATAAGCACCGGGTTCACATATGGATCATCCATCAATTCAGCTGGAACCACTCAAGCATGCATGAGAGATGGAGGGAATAGTTTCTATGCGGAGCTAAAGTGGCTAGTGTCGAAGAACACAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTATAATCTGGGGAATTCATCACCCTTCAAGCACAAAAGAGAAGAATGATCTGTATGGAACACAATCACTTTCCATTTCAGTGGGGAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAAAGGCCAAAGTGGGCGGATTGATTTTCATTGGACGATGGTACAGCCAGGTGATAACATCACTTTCTCGCATAATGGTGGATTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTTGGCATTCAATCGGTAGCTTCAGTAGACAATGACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAGTATGTGAACAAAAGAAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGAATGGTGGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCCGCGGATTACAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTGAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATCAGTAATGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGCTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAAATGCTGAATCTATATGAGAGGGTGAGGAAGCAACTAAGGCAAAATGCTGAAGAAGATGGGAAAGGGTGCTTTGAAATATACCACAAATGCGATGACAATTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTTTTCTTCTGCTTAAAAAATGGAAACATGCGATGCACAATCTGTATTTAG",
}, {
"strain": "A/Unknown/Unknown/Batch2-1_044_01102017_4_H10N5",
"db": "Unknown",
"accession": "Unknown",
"date": "2017-01-10",
"seq": "ATGCACAAAATAGTACTAGTATTCGCGCTCCTTGGAGCGGTGCATGGTCTTGACAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCACAAATGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAGTCGAAATTACAAGGACTTAGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGACCTACACCTTACCGGAACATGGGACACTTTAATAGAGAGAGACAATTCTATTGCCTATTGTTACCCGGGTGCCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATTGACAAGATAAGCACCGGGTTCACATATGGATCATCCATCAATTCAGCTGGAACCACTCAAGCATGCATGAGAAATGGAGGGAATAGTTTCTATGCGGAGCTAAAGTGGCTAGTGTCGAAGAACACAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTATAATCTGGGGAATTCATCACCCTTCAAGCACAAAAGAGAAGAATGATCTGTATGGAACACAATCACTTTCCATTTCAGTGGGGAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAAAGGCCAAAGTGGGCGGATTGATTTTCATTGGACGATGGTACAGCCAGGTGATAACATCACTTTCTCGCATAATGGTGGATTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTTGGCATTCAATCAGTAGCTTCAGTAGACAATGACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAGTATGTGAACAAAAGAAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGAATGGTGGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCCGCGGATTACAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTGAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATCAGTAATGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGCTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAAATGCTGAATCTATATGAGAGGGTGAGGAAGCAACTAAGGCAAAATGCTGAAGAAGATGGGAAAGGGTGCTTTGAAATATACCACAAATGCGATGACAATTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTTTTCTTCTGCTTAAAAAATGGAAACATGCGATGCACAATCTGTATTTAG",
}, {
"strain": "A/Unknown/Unknown/Batch2-1_048_01102017_4_H10N5",
"db": "Unknown",
"accession": "Unknown",
"date": "2017-01-10",
"seq": "ATGTACAAAATAGTACTAGTATTCGCGCTCCTTGGAGCGGTGCATGGTCTTGACAAAATATGTCTTGGACATCATGCAGTCTCCAATGGCACCATCGTAAAGACTCTCACAAATGAAAAGGAAGAGGTGACCAATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAGTCGAAATTACAAGGACTTAGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGACCTACACCTTACCGGAACATGGGACACTTTAATAGAGAGAGACAATTCTATTGCCTATTGTTACCCGGGTGCCACTGTGAATGAAGAAGCATTAAGGCAGAAAATTATGGAAAGTGGAGGGATTGACAAGATAAGCACCGGGTTCACATATGGATCATCCATCAATTCAGCTGGAACCACTCAAGCATGCATGAGAAATGGAGGGAATAGTTTCTATGCGGAGCTAAAGTGGCTAGTGTCGAAGAACACAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAGAACACCTTATAATCTGGGGAATTCATCACCCTTCAAGCACAAAAGAGAAGAATGATCTGTATGGAACACAATCACTTTCCATTTCAGTGGGGAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCACAAGTGAAAGGCCAAAGTGGGCGGATTGATTTTCATTGGACGATGGTACAGCCAGGTGATAACATCACTTTCTCGCATAATGGTGGACTAATAGCACCCAGCAGAGTGAGTAAGCTAAAGGGAAGAGGCCTTGGCATTCAATCAGTAGCTTCAGTAGACAATGACTGTGAGTCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAACTCCCTTTTCAGAATCTTTCTCCAAGAACCGTGGGTCAATGCCCCAAGTATGTGAACAAAAGAAGCCTGTTGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGGATTCATAGAAAATGGATGGGAAGGAATGGTGGATGGTTGGTATGGTTTCCGGCACCAAAATGCCCAAGGCACTGGTCAGGCCGCGGATTACAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTGAACAGGCTGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATCAGTAATGTAATAAACTGGACTAAAGATTCTATAACAGACATCTGGACGTATCAAGCTGAATTGCTGGTAGCAATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAAATGCTGAATCTATATGAGAGGGTGAGGAAGCAACTAAGGCAAAATGCTGAAGAAGATGGGAAAGGGTGCTTTGAAATATACCACAAATGCGATGACAATTGTATGGAAAGCATCAGAAACAACACTTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTCAACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCATGCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTTTTCTTCTGCTTAAAAAATGGAAACATGCGATGCACAATCTGTATTTAG",
}
]
tmp_outgroup = SeqIO.read('/Users/yujiazhou/Documents/nextflu/H9_nextflu-master/augur/source-data/H10_outgroup.gb', 'genbank')
genome_annotation = tmp_outgroup.features
self.cds = {x.qualifiers['gene'][0]:x for x in genome_annotation
if 'gene' in x.qualifiers and x.type=='CDS' and
x.qualifiers['gene'][0] in ['SigPep', 'HA1', 'HA2']}
self.outgroup = {
'strain':'A/mallard-duck/ALB/302/1977',
'region':'NorthAmerica',
'isolate_id':'EPI-ISL-8890',
'date':'1977-08-13', #(Month and day unknown)
'seq': str(tmp_outgroup.seq).upper()
}
def __init__(self,
aln_fname,
outgroup,
include_ref_strains=True,
outdir='./',
formats=['pdf', 'png'],
verbose=0,
**kwargs):
process.__init__(self, **kwargs)
flu_filter.__init__(self, alignment_file=aln_fname, **kwargs)
tree_refine.__init__(self, **kwargs)
virus_clean.__init__(self, **kwargs)
self.midpoint_rooting = False
self.include_ref_strains = include_ref_strains
self.verbose = verbose
self.formats = formats
self.outdir = outdir.rstrip('/') + '/'
self.auspice_tree_fname = self.outdir + 'tree.json'
self.auspice_align_fname = self.outdir + 'aln.fasta'
self.auspice_aa_align_fname = self.outdir + 'aa_aln.fasta'
self.auspice_sequences_fname = self.outdir + 'sequences.json'
self.auspice_frequencies_fname = None
self.auspice_meta_fname = self.outdir + 'meta.json'
self.path_to_augur = path_to_augur
if os.path.isfile(outgroup):
tmp = [{
'strain': seq.name,
'seq': str(record.seq).upper(),
'desc': seq.description
} for seq in SeqIO.parse(outgroup, 'fasta')]
if len(tmp):
self.outgroup = tmp[0]
if len(tmp) > 1:
print "More than one sequence in ", outgroup, "taking first"
if self.verbose:
print "using outgroup found in file ", outgroup
elif outgroup == 'auto':
print "automatically determine outgroup"
self.auto_outgroup_blast()
elif isinstance(outgroup, basestring):
seq_names = [x['strain'] for x in self.viruses]
if outgroup in seq_names:
self.outgroup = self.viruses.pop(seq_names.index(outgroup))
if self.verbose:
print "using outgroup found in alignment", outgroup
else:
standard_outgroups = self.load_standard_outgroups()
if outgroup in standard_outgroups:
self.outgroup = standard_outgroups[outgroup]
if self.verbose:
print "using standard outgroup", outgroup
else:
raise ValueError("outgroup %s not found" % outgroup)
return
if "anno:" in self.outgroup['desc']:
anno = [x for x in self.outgroup['desc'].split()
if "anno:" in x][0]
anno = (anno.split(':')[1]).split('_')
tmp = [(anno[2 * i], int(anno[2 * i + 1]))
for i in range(len(anno) / 2)]
self.anno = sorted(tmp, key=lambda x: x[1])
print("Using annotation", self.anno)
else:
self.anno = None
print("No annotation found")
#self.anno = sorted((('SP',0), ('HA1',16), ('HA2',329+16)), key=lambda x:x[1])
self.viruses.append(self.outgroup)
self.filter_geo(prune=False)
self.make_strain_names_unique()
def __init__(self,min_length = 900, **kwargs):
'''
parameters
min_length -- minimal length for a sequence to be acceptable
'''
flu_filter.__init__(self, **kwargs)
self.min_length = min_length
self.vaccine_strains =[
{
"strain": "A/Wisconsin/67/2005",
"db": "IRD",
"accession": "CY163984",
"date": "2005-08-31",
"region": "north_america",
"country": "usa",
"seq": "ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAACTTCCCGGAAATGACAACAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAATGACCAAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAGTTCCTCAACAGGTGGAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTCCAAAATAAGAAATGGGACCTTTTTGTTGAACGCAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACGATGAAAGCTTCAATTGGACTGGAGTCACTCAAAATGGAACAAGCTCTTCTTGCAAAAGGAGATCTAATAACAGTTTCTTTAGTAGATTGAATTGGTTGACCCACTTAAAATTCAAATACCCAGCATTGAACGTGACTATGCCAAACAATGAAAAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGTTACGGACAATGACCAAATCTTCCTGTATGCTCAAGCATCAGGAAGAATCACAGTCTCTACCAAAAGAAGCCAACAAACTGTAATCCCGAATATCGGATCTAGACCCAGAATAAGGAATATCCCCAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAAATGCAATTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCATTTCAAAATGTAAACAGGATCACATATGGGGCCTGTCCCAGATATGTTAAGCAAAACACTCTGAAATTGGCAACAGGGATGCGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATCGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGTGGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAATAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCAATCAAATCAATGGGAAGCTGAATAGGTTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTAGAAGGGAGAATTCAGGACCTCGAGAAATATGTTGAGGACACTAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAGAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCATGATGTATACAGAGATGAAGCATTAAACAACCGGTTCCAGATCAAAGGCGTTGAGCTGAAGTCAGGATACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAAGGCAACATTAGGTGCAACATTTGCATTTGA"
}, {
"strain": "A/Brisbane/10/2007",
"db": "IRD",
"accession": "CY113005",
"date": "2007-02-06",
"region": "oceania",
"country": "australia",
"seq": "ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCACTCAAAAACTTCCCGGAAATGACAACAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAATGACCAAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAGTTCCTCAACAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTCCAAAATAAGAAATGGGACCTTTTTGTTGAACGCAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGACTGGAGTCACTCAAAACGGAACAAGCTCTGCTTGCATAAGGAGATCTAATAACAGTTTCTTTAGTAGATTGAATTGGTTGACCCACTTAAAATTCAAATACCCAGCATTGAACGTGACTATGCCAAACAATGAAAAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTACGGACAATGACCAAATCTTCCCGTATGCTCAAGCATCAGGAAGAATCACAGTCTCTACCAAAAGAAGCCAACAAACTGTAATCCCGAATATCGGATCTAGACCCAGAGTAAGGAATATCCCCAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAAATGCAATTCTGAATGCATCACTCCAAACGGAAGCATTCCCAATGACAAACCATTCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCAAAACACTCTGAAATTGGCAACAGGGATGCGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATCGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGTGGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAATAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGATCAAATCAATGGGAAGCTGAATAGGTTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTCGAAGGGAGAATTCAGGACCTTGAGAAATATGTTGAGGACACCAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCACAATGTATACAGAGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGCGTTGAGCTGAAGTCAGGATACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAAGGCAACATTAGGTGCAACATTTGCATTTGA"
}, {
"strain": "A/Perth/16/2009",
"db": "IRD",
"accession": "GQ293081",
"date": "2009-04-07",
"region": "oceania",
"country": "australia",
"seq": "ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAACTTCCTGGAAATGACAACAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAATGACCAAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAGTTCCTCAACAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAAAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTCCAAAATAAGAAATGGGACCTTTTTGTTGAACGCAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGACTGGAGTCACTCAAAACGGAACAAGCTCTGCTTGCATAAGGAGATCTAAAAACAGTTTCTTTAGTAGATTGAATTGGTTGACCCACTTAAACTTCAAATACCCAGCATTGAACGTGACTATGCCAAACAATGAACAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTACGGACAAAGACCAAATCTTCCTGTATGCTCAAGCATCAGGAAGAATCACAGTCTCTACCAAAAGAAGCCAACAAACCGTAAGCCCGAATATCGGATCTAGACCCAGAGTAAGGAATATCCCTAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAAATGCAATTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCATTCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCAAAACACTCTGAAATTGGCAACAGGGATGCGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATCGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGTGGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAAGAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGATCAAATCAATGGGAAGCTGAATAGATTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTCGAAGGGAGAATTCAGGACCTTGAGAAATATGTTGAGGACACTAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCACGATGTATACAGAGATGAAGCATTAAACAACCGGTTTCAGATCAAGGGAGTTGAGCTGAAGTCAGGGTACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAAGGCAACATTAGGTGCAACATTTGCATTTGA"
}, {
"strain": "A/Victoria/361/2011",
"db": "IRD",
"accession": "GQ293081",
"date": "2011-10-24",
"region": "oceania",
"country": "australia",
"seq": "ATGAAGACTATCATTGCTTTGAGCCACATTCTATGTCTGGTTTTCGCTCAAAAACTTCCTGGAAATGACAACAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAATGACCAAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAATTCCTCAATAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTCCAAAATAAGAAATGGGACCTTTTTGTTGAACGAAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGACTGGAGTCACTCAAAACGGAACAAGTTCTGCTTGCATAAGGAGATCTAATAATAGTTTCTTTAGTAGATTAAATTGGTTGACCCGCTTAAACTTCAAATACCCAGCATTGAACGTGACTATGCCAAACAATGAACAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGTTACGGACAAGGAACAAATCTTCCTGTATGCTCAATCATCAGGAAGAATCACAGTATCTACCAAAAGAAGCCAACAAGCTGTAATCCCGAATATCGGATATAGACCCAGAATAAGGAATATCCCTAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAAATGCAATTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCATTCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCAAAGCACTCTGAAATTGGCAACAGGAATGCGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATAGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGTGGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAAGAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGATCAAATCAATGGGAAGCTGAATCGATTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTCGAAGGGAGAATTCAGGACCTTGAGAAATATGTTGAGGACACTAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGCAACTAAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCACGATGTATACAGAGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGAGTTGAGCTGAAGTCAGGGTACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAGGGCAACATTAGGTGCAACATTTGCATTTGA"
}, {
"strain": "A/Texas/50/2012",
"db": "GISAID",
"isolate_id": "EPI_ISL_129858",
"date": "2012-04-15",
"region": "north_america",
"country": "usa",
"seq": "ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAACTTCCTGGAAATGACAATAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAATGACCGAATTGAAGTTACTAATGCTACTGAACTGGTTCAGAATTCCTCAATAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTCCAAAATAAGAAATGGGACCTTTTTGTTGAACGAAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGAATGGAGTCACTCAAAACGGAACAAGTTCTGCTTGCATAAGGAGATCTAATAATAGTTTCTTTAGTAGATTAAATTGGTTGACCCACTTAAACTTCAAATACCCAGCATTGAACGTGACTATGCCAAACAATGAACAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTACGGACAAGGACCAAATCTTCCTGTATGCTCAACCATCAGGAAGAATCACAGTATCTACCAAAAGAAGCCAACAAGCTGTAATCCCGAATATCGGATCTAGACCCAGAATAAGGAATATCCCTAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAAATGCAAGTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCATTCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCAAAGCACTCTGAAATTGGCAACAGGAATGCGGAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATAGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGTGGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAAGAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGATCAAATCAATGGGAAGCTGAATCGATTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTAGAAGGGAGAATTCAGGACCTTGAGAAATATGTTGAGGACACTAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCACGATGTATACAGAGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGAGTTGAGCTGAAGTCAGGGTACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAGGGCAACATTAGGTGCAACATTTGCATTTGA",
}, {
"strain": "A/Switzerland/9715293/2013",
"db": "GISAID",
"isolate_id": "EPI_ISL_162149",
"date": "2013-12-06",
"region": "europe",
"country": "switzerland",
"seq": "ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAACTTCCTGGAAATGACAATAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAATGACCGAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAATTCCTCAATAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTTCAAAATAAGAAATGGGACCTTTTTGTTGAACGAAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGGCTGGAGTCACTCAAAACGGAACAAGTTCTTCTTGCATAAGGGGATCTAATAGTAGTTTCTTTAGTAGATTAAATTGGTTGACCCACTTAAACTCCAAATACCCAGCATTAAACGTGACTATGCCAAACAATGAACAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTACGGACAAGGACCAAATCTTCCTGTATGCACAATCATCAGGAAGAATCACAGTATCTACCAAAAGAAGCCAACAAGCTGTAATCCCGAATATCGGATCTAGACCCAGAATAAGGGATATCCCTAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAAATGCAAGTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCATTCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCAAAGCACTCTGAAATTGGCAACAGGAATGCGAAATGTACCAGAGAGACAAACTAGAGGCATATTTGGCGCAATAGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGTGGATGGTTGGTACGGCTTCAGGCATCAAAATTCTGAGGGAAGAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGATCAAATCAATGGGAAGCTGAATCGATTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTAGAAGGGAGAATTCAGGACCTTGAGAAATATGTTGAGGACACAAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCACGATGTATACAGGGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGAGTTGAGCTGAAGTCAGGGTACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAGGGCAACATTAGGTGCAACATTTGCATTTGA",
}, {
"strain": "A/HongKong/4801/2014",
"db": "GISAID",
"isolate_id": "EPI_ISL_165554",
"date": "2014-02-26",
"region": "china",
"country": "hong_kong",
"seq": "ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAAATTCCTGGAAATGACAATAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAATGACCGAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAATTCCTCAATAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTTCAAAATAAGAAATGGGACCTTTTTGTTGAACGAAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGACTGGAGTCACTCAAAACGGAACAAGTTCTGCTTGCATAAGGAGATCTAGTAGTAGTTTCTTTAGTAGATTAAATTGGTTGACCCACTTAAACTACACATACCCAGCATTGAACGTGACTATGCCAAACAATGAACAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTACGGACAAGGACCAAATCTTCCTGTATGCTCAATCATCAGGAAGAATCACAGTATCTACCAAAAGAAGCCAACAAGCTGTAATCCCAAATATCGGATCTAGACCCAGAATAAGGGATATCCCTAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAAATGCAAGTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCATTCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCATAGCACTCTGAAATTGGCAACAGGAATGCGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATAGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGTGGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAAGAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGATCAAATCAATGGGAAGCTGAATCGATTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTAGAAGGAAGAATTCAGGACCTTGAGAAATATGTTGAGGACACTAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATAAGAAATGGAACTTATGACCACAATGTGTACAGGGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGAGTTGAGCTGAAGTCAGGGTACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAGGGCAACATTAGGTGCAACATTTGCATTTGA",
}, {
"strain": "A/Alaska/232/2015",
"db": "GISAID",
"isolate_id": "EPI787411",
"date": "2015-09-09",
"region": "north_america",
"country": "usa",
"seq": "GGATAATTCTATTAACCATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAAATTCCTGGAAATGACAATAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACAAATGACCGAATTGAAGTTACTAATGCTACTGAGTTGGTTCAGAATTCCTCAATAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAGAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTTCAAAATAAGAAATGGGACCTTTTTGTTGAACGAAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGACTGGAGTCACTCAAAACGGAACAAGTTCTTCTTGCATAAGGAGATCTAGTAGTAGTTTCTTTAGTAGATTAAATTGGTTGACCCACTTAAACTACAAATATCCAGCATTGAACGTGACTATGCCAAACAAGGAACAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTACGGACAAGGACCAAATCTACCCGTATGCTCAATCATCAGGAAGAATCACAGTATCTACCAAAAGAAGCCAACAAGCTGTAATCCCAAATATCGGATCTAGACCCAGAATAAGGGATATCCCTAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAAATGCAAGTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCATTCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCATAGCACTCTGAAATTGGCAACAGGAATGCGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATAGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGTGGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAAGAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGATCAAATCAATGGGAAGCTGAATCGGTTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTAGAAGGAAGAGTTCAAGACCTTGAGAAATATGTTGAGGACACTAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGAAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATAAGAAATGAAACTTATGACCACAATGTGTACAGGGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGAGTTGAGCTGAAGTCAGGGTACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAGGGCAACATTAGATGCAACATTTGCATTTGAGTGCATTAATTAAAAACAC"
}
]
tmp_outgroup = SeqIO.read('source-data/H3N2_outgroup.gb', 'genbank')
genome_annotation = tmp_outgroup.features
self.cds = {x.qualifiers['gene'][0]:x for x in genome_annotation
if 'gene' in x.qualifiers and x.type=='CDS' and
x.qualifiers['gene'][0] in ['SigPep', 'HA1', 'HA2']}
self.outgroup = {
'strain': 'A/Beijing/32/1992',
'db': 'IRD',
'accession': 'U26830',
'date': '1992-01-01',
'country': 'china',
'region': 'china',
'seq': str(tmp_outgroup.seq).upper()
}
def __init__(self,min_length = 987, **kwargs):
'''
parameters
min_length -- minimal length for a sequence to be acceptable
'''
flu_filter.__init__(self, **kwargs)
self.min_length = min_length
self.vaccine_strains =[
{
'strain': 'B/Beijing/184/93',
'isolate_id': 'EPI_ISL_969',
'date': '1993-07-01', #(Month and day unknown)
'region': 'China',
'seq': 'GATCGAATCTGTACTGGGATAACATCTTCAAACTCACCTCATGTGGTCAAAACAGCTACTCAAGGGGAGGTCAATGTGACTGGTGTGATACCACTGACAACAACACCAACAAAATCTCATTTTGGAAATCTCAAAGGAACAAAGACCAGAGGGAAACTATGCCCAAACTGTCTCAACTGCACAGATCTGGATGTGGCCTTGGGCAGACCAATGTGTGTGGGGACCACACCTTCGGCAAAAGCTTCAATACTCCACGAAGTCAGACCTGTTACATCCGGGTGCTTTCCTATAATGCACGACAGAACAAAAATCAGACAGCTACCCAATCTTCTCAGAGGATATGAAAATATCAGATTATCAACCCAAAACGTTATCAACGCAGAAAAGGCACCAGGAGGACCCTACAGGCTTGGAACCTCAGGATCTTGCCCTAACGCTACCAGTAGAAGCGGATTTTTCGCAACAATGGCTTGGGCTGTCCCAAGGGACAACAACAAAACAGCAACAAATCCACTAACAGTAGAAGTACCATACATTTGTACAAAAGGAGAAGACCAAATTACTGTTTGGGGGTTCCATTCTGATAACAAAATCCAAATGAAAAACCTCTATGGAGACTCAAATCCTCAAAAGTTCACCTCATCTGCTAATGGAGTAACCACACATTATGTTTCTCAGATTGGCGGCTTCCCAGATCAAACAGAAGACGGAGGGCTACCACAAAGCGGCAGAATTGTTGTTGATTACATGGTGCAAAAACCTGGGAAAACAGGAACAATTGTCTATCAAAGAGGTGTTTTGTTGCCTCAAAAGGTGTGGTGCGCGAGTGGCAGGAGCAAAGTAATAAAAGGGTCCTTGCCTTTAATTGGTGAAGCAGATTGCCTTCACGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGAGAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTGAAAACACCTTTGAAGCTTGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGG',
},
{
'strain': 'B/Sichuan/379/99',
'isolate_id': 'EPI_ISL_21113',
'date': '1999-07-01', # (Month and day unknown)
'region': 'China',
'seq': 'GAGGCAATAATTGTACTACTCATGGTAGTAACATCCAATGCAGATCGAATCTGCACTGGGATAACATCGTCAAACTCACCTCATGTGGTCAAAACAGCTACTCAAGGGGAGGTCAATGTAACTGGTGCGATACCACTGACAACAACACCAACAAAATCTCATTTTGCAAATCTCAAAGGAACAAAGACCAGAGGGAAACTATGCCCAACCTGTCTCAACTGCACAGATCTGGATGTGGCCTTGGGCAGACCAATGTGTGTGGGGATCACACCTTCGGCAAAAGCTTCAATACTCCACGAAATCAAACCTGTTACATCCGGATGCTTTCCTATAATGCACGACAGAACAAAAATCAGACAGCTACCCAATCTTCTCAGAGGATATGAAAAAATCAGATTATCAACCCAAAACGTTATCAACGCAGAAAAGGCACCAGGAGGACCTTACAGACTTGGAACTTCAGGATCTTGCCCTAACGCTACCAGTAAAAGCGGATTTTTCGCAACAATGGCTTGGGCTGTCCCAAGGGACAACAACAAAACAGCAACGAATCCACTAACAGTAGAAGTACCACACATCTGTACAAAAGAAGAAGACCAAATTACTGTTTGGGGGTTCCATTCTGATGACAAAACCCAAATGAAAAACCTCTATGGAGACTCAAATCCTCAAAAGTTCACCTCATCTGCTAATGGAATAACCACACATTATGTTTCTCAGATTGGCGGCTTCCCGGACCAAACAGAGGACGGAGGGCTACCACAAAGCGGCAGAATTGTTGTTGATTACATGGTGCAAAAACCTGGGAAAACAGGAACAATTGTCTATCAAAGAGGGATTTTGTTGCCTCAAAAGGTGTGGTGCGCGAGTGGTAGGAGCAAAGTAATAAAAGGGTCCTTGCCTTTAATTGGTGAAGCAGATTGCCTTCATGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGAGAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTGAAAACACCTTTGAAGCTTGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGGGGTTTCT',
},
{
'strain': 'B/Shanghai/361/2002',
'isolate_id': 'EPI_ISL_2842',
'date': '2002-06-12',
'region': 'China',
'seq': 'AATGCAGATCGAATCTGCACTGGGATAACATCTTCAAACTCACCTCATGTGGTCAAAACAGCTACTCAAGGGGAGGTCAATGTGACTGGTGTGATACCACTGACAACAACTCCAATAAAATCTCATTTTGCAAATCTCAAAGGAACAAGGACTAGAGGGAAACTATGCCCAGATTGTCTCAACTGCACAGATCTGGATGTGGCCTTGGGCAGACCAATGTGTGTGGGGACCACACCTTCGGCAAAAGCTTCAATACTCCACGAAGTCAGACCTGTTACATCCGGGTGCTTTCCTATAATGCACGACAGAACAAAAATCAGACAACTACCCAATCTTCTCAGAGGATATGAAAATATCAGGTTATCAACCCAAAACGTTATCGATGCAGAAAAGGCCCTAGGAGGACCCTACAGACTTGGAACCTCAGGATCTTGCCCTAACGCCACCAGTAAAAGCGGATTTTTCGCAACAATGGCTTGGGCTGTCCCAAAGGACAACAACAAAAATGCAACGAACCCACTAACAGTAGAAGTACCATACATCTGTACAGAAGGGGAAGACCAAATTACTGTTTGGGGGTTCCATTCAGATGACAAAACCCAAATGAAAAACCTCTATGGAGACTCAAATCCTCAAAAGTTCACCTCATCTGCTAATGGAGTAACCACACATTATGTTTCTCAGATTGGCGGCTTCCCAGATCAAACAGAAGACGGAGGACTACCACAAAGCGGCAGAATTGTTGTTGATTACATGGTGCAAAAACCTGGGAAAACAGGAACAATTGTCTATCAAAGAGGTGTTTTGTTGCCTCAAAAGGTGTGGTGCGCGAGTGGCAGGAGCAAAGTAATAAAAGGGTCCTTGCCTTTAATTGGTGAAGCAGATTGCCTTCATGAAAAATACGGTGGGTTAAACAAAAGCAAGCCTTACTACACAGGAGAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTGAAAACACCTTTGAAGCTTGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGGGGTTTC',
},
{
'strain': 'B/Florida/4/2006',
'isolate_id': 'EPI_ISL_21307',
'date': '2006-11-01',
'region': 'NorthAmerica',
'seq': 'ATGAAGGCAATAATTGTACTACTCATGGTAGTAACATCCAATGCAGATCGAATCTGCACTGGAATAACATCTTCAAACTCACCTCATGTGGTCAAAACAGCCACTCAAGGGGAGGTCAATGTGACTGGTGTGATACCACTAACAACAACACCAACAAAATCTTATTTTGCAAATCTCAAAGGAACAAGGACCAGAGGGAAACTATGCCCAGACTGTCTCAACTGCACAGATCTGGATGTGGCTTTGGGCAGACCAATGTGTGTGGGGACCACACCTTCGGCGAAAGCTTCAATACTCCACGAAGTCAAACCTGTTACATCCGGGTGCTTTCCTATAATGCACGACAGAACAAAAATCAGGCAACTACCCAATCTTCTCAGAGGATATGAAAATATCAGGCTATCAACCCAAAACGTCATCGATGCGGAAAAGGCACCAGGAGGACCCTACAGACTTGGAACCTCAGGATCTTGCCCTAACGCTACCAGTAAGAGCGGATTTTTCGCAACAATGGCTTGGGCTGTCCCAAAGGACAACAACAAAAATGCAACGAACCCACTAACAGTAGAAGTACCATACATTTGTACAGAAGGGGAAGACCAAATCACTGTTTGGGGGTTCCATTCAGATGACAAAACCCAAATGAAGAACCTCTATGGAGACTCAAATCCTCAAAAGTTCACCTCATCTGCTAATGGAGTAACCACACACTATGTTTCTCAGATTGGCAGCTTCCCAGATCAAACAGAAGACGGAGGACTACCACAAAGCGGCAGGATTGTTGTTGATTACATGATGCAAAAACCTGGGAAAACAGGAACAATTGTCTACCAAAGAGGTGTTTTGTTGCCTCAAAAGGTGTGGTGCGCGAGTGGCAGGAGCAAAGTAATAAAAGGGTCCTTGCCTTTAATTGGTGAAGCAGATTGCCTTCATGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGAGAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTGAAAACACCTTTGAAGCTTGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGGGGTTTCTTCGGAGCTATTGCTGGTTTCCTAGAAGGAGGATGGGAAGGAATGATTGCAGGCTGGCACGGATACACATCTCACGGAGCACATGGAGTGGCAGTGGCGGCGGACCTTAAGAGTACGCAAGAAGCTATAAACAAGATAACAAAAAATCTCAATTCTTTGAGTGAGCTAGAAGTAAAGAATCTTCAAAGACTAAGTGGTGCCATGGATGAACTCCACAACGAAATACTCGAGCTGGATGAGAAAGTGGATGATCTCAGAGCTGACACTATAAGCTCGCAAATAGAACTTGCAGTCTTGCTTTCCAACGAAGGAATAATAAACAGTGAAGATGAGCATCTATTGGCACTTGAGAGAAAACTAAAGAAAATGCTGGGTCCCTCTGCTGTAGAGATAGGAAATGGATGCTTCGAAACCAAACACAAGTGCAACCAGACCTGCTTAGACAGGATAGCTGCTGGCACCTTTAATGCAGGAGAATTTTCTCTCCCCACTTTTGATTCACTGAACATTACTGCTGCATCTTTAAATGATGATGGATTGGATAACCATACTATACTGCTCTATTACTCAACTGCTGCTTCTAGTTTGGCTGTAACATTGATGCTAGCTATTTTTATTGTTTATATGGTCTCCAGAGACAACGTTTCATGCTCCATCTGTCTATAA'
},
{
'strain': 'B/Wisconsin/01/2010',
'isolate_id': 'EPI_ISL_76940',
'date': '2010-02-20',
'region': 'NorthAmerica',
'seq': 'ATGAAGGCAATAATTGTACTACTCATGGTAGTAACATCCAATGCAGATCGAATCTGCACTGGGATAACATCTTCAAACTCACCTCATGTGGTCAAAACAGCTACTCAAGGGGAGGTCAATGTGACTGGCGTGATACCACTGACAACAACACCAACAAAATCTTATTTTGCAAATCTCAAAGGAACAAGGACCAGAGGGAAACTATGCCCGGACTGTCTCAACTGTACAGATCTGGATGTGGCCTTGGGCAGGCCAATGTGTGTGGGGACCACACCTTCTGCTAAAGCTTCAATACTCCACGAGGTCAGACCTGTTACATCCGGGTGCTTTCCTATAATGCACGACAGAACAAAAATCAGGCAACTACCCAATCTTCTCAGAGGATATGAAAATATCAGGTTATCAACCCAAAACGTTATCGATGCAGAAAAAGCACCAGGAGGACCCTACAGACTTGGAACCTCAGGATCTTGCCCTAACGCTACCAGTAAAATCGGATTTTTTGCAACAATGGCTTGGGCTGTCCCAAAGGACAACTACAAAAATGCAACGAACCCACTAACAGTAGAAGTACCATACATTTGTACAGAAGGGGAAGACCAAATTACTGTTTGGGGGTTCCATTCAGATAACAAAACCCAAATGAAGAGCCTCTATGGAGACTCAAATCCTCAAAAGTTCACCTCATCTGCTAATGGAGTAACCACACATTATGTTTCTCAGATTGGCGACTTCCCAGATCAAACAGAAGACGGAGGACTACCACAAAGCGGCAGAATTGTTGTTGATTACATGATGCAAAAACCTGGGAAAACAGGAACAATTGTCTATCAAAGAGGTGTTTTGTTGCCTCAAAAGGTGTGGTGCGCGAGTGGCAGGAGCAAAGTAATAAAAGGGTCATTGCCTTTAATTGGTGAAGCAGATTGCCTTCATGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGAGAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTAAAAACACCTTTGAAGCTTGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTGAAGGAAAGGGGTTTCTTCGGAGCTATTGCTGGTTTCCTAGAAGGAGGATGGGAAGGAATGATTGCAGGTTGGCACGGATACACATCTCACGGAGCACATGGAGTGGCAGTGGCGGCAGACCTTAAGAGTACACAAGAAGCTATAAATAAGATAACAAAAAATCTCAATTCTTTGAGTGAGCTAGAAGTAAAGAACCTTCAAAGACTAAGTGGTGCCATGGATGAACTCCACAACGAAATACTCGAGCTGGATGAGAAAGTGGATGATCTCAGAGCTGACACTATAAGCTCACAAATAGAACTTGCAGTCTTGCTTTCCAACGAAGGAATAATAAACAGTGAAGACGAGCATCTATTGGCACTTGAGAGAAAACTAAAGAAAATGCTGGGTCCCTCTGCTGTAGACATAGGAAACGGATGCTTCGAAACCAAACACAAATGCAACCAGACCTGCTTAGACAGGATAGCTGCTGGCACCTTTAATGCAGGAGAATTTTCTCTCCCCACTTTTGATTCATTGAACATTACTGCTGCATCTTTAAATGATGATGGATTGGATAACCATACTATACTGCTCTATTACTCAACTGCTGCTTCTAGTTTGGCTGTAACATTAATGCTAGCTATTTTTATTGTTTATATGGTCTCCAGAGACAACGTTTCATGCTCCATCTGTCTATAA'
},
{
'strain': 'B/Massachusetts/02/2012',
'isolate_id': 'EPI_ISL_121434',
'date': '2012-03-13',
'region': 'NorthAmerica',
'seq': 'ATGAAGGCAATAATTGTACTACTAATGGTAGTAACATCCAATGCAGATCGAATCTGCACTGGGATAACATCTTCAAACTCACCTCATGTGGTCAAAACAGCTACTCAAGGGGAGGTCAATGTGACTGGTGTGATACCACTAACAACAACACCAACAAAATCTTATTTTGCAAATCTCAAAGGAACAAAGACCAGAGGGAAACTATGCCCAGACTGTCTCAACTGTACAGATCTGGATGTGGCCCTGGGCAGGCCAATGTGTGTGGGAACTACACCTTCTGCGAAAGCTTCAATACTTCACGAAGTCAGACCTGTTACATCCGGGTGCTTCCCTATAATGCACGACAGAACAAAAATCAGGCAACTAGCCAATCTTCTCAGAGGATATGAAAATATCAGGTTATCAACCCAAAACGTTATCGATGCAGAAAAGGCACCAGGAGGACCCTACAGACTTGGAACCTCAGGATCTTGCCCTAACGCTACCAGTAAAAGCGGATTTTTCGCAACAATGGCTTGGGCTGTCCCAAAGGACAACAACAAAAATGCAACGAACCCATTAACAGTAGAAGTACCATACATTTGTGCAGAAGGGGAAGACCAAATTACTGTTTGGGGGTTCCATTCAGATAACAAAACCCAAATGAAGAACCTCTATGGAGACTCAAATCCTCAAAAGTTCACCTCATCTGCTAATGGAGTAACCACACATTATGTTTCTCAGATTGGCGGCTTCCCAGATCAAACAGAAGACGGAGGACTACCACAAAGCGGCAGAATTGTCGTTGATTACATGATGCAAAAACCTGGGAAAACAGGAACAATTGTCTATCAAAGAGGTGTTTTGTTGCCTCAAAAGGTGTGGTGCGCGAGTGGCAGGAGCAAAGTAATAAAAGGGTCCTTGCCTTTAATTGGTGAAGCAGATTGCCTTCATGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGAGAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTGAAAACACCTTTGAAGCTTGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGGGGTTTCTTCGGAGCTATTGCTGGTTTCCTAGAAGGAGGATGGGAAGGAATGATTGCAGGTTGGCACGGATACACATCTCACGGAGCACATGGAGTGGCAGTTGCTGCAGACCTTAAGAGCACACAAGAAGCTATAAACAAGATAACAAAAAATCTCAACTCTTTGAGTGAGCTAGAAGTAAAGAATCTTCAAAGGCTAAGTGGTGCCATGGATGAACTCCACAACGAAATACTCGAGCTGGATGAGAAAGTGGATGACCTCAGAGCTGACACTATAAGTTCACAAATAGAACTTGCAGTCTTGCTTTCCAACGAAGGAATAATAAACAGTGAAGACGAGCATCTATTGGCACTTGAGAGAAAACTAAAGAAAATGCTGGGTCCCTCTGCTGTAGACATAGGAAATGGATGCTTCGAAACCAAACACAAATGCAACCAGACCTGCTTAGACAGGATAGCTGCTGGCACCTTTAATGCAGGAGAGTTTTCTCTCCCCACTTTTGATTCATTGAACATTACTGCTGCATCTTTAAATGATGATGGATTGGATAACCATACTATACTGCTCTATTACTCAACTGCTGCTTCTAGTTTGGCTGTAACATTGATGCTAGCTATTTTTATTGTTTATATGGTCTCCAGAGACAACGTTTCATGCTCCATCTGTCTATAA'
},
{
'strain': 'B/PHUKET/3073/2013',
'isolate_id': 'EPI_ISL_161843',
'date': '2013-11-21',
'region': 'SoutheastAsia',
'seq': 'ATGAAGGCAATAATTGTACTACTCATGGTAGTAACATCCAACGCAGATCGAATCTGCACTGGGATAACATCTTCAAACTCACCTCATGTGGTCAAAACAGCTACTCAAGGGGAGGTCAATGTGACTGGCGTGATACCACTGACAACAACACCAACAAAATCTTATTTTGCAAATCTCAAAGGAACAAGGACCAGAGGGAAACTATGCCCGGACTGTCTCAACTGTACAGATCTGGATGTGGCCTTGGGCAGGCCAATGTGTGTGGGGACCACACCTTCTGCTAAAGCTTCAATACTCCATGAGGTCAGACCTGTTACATCCGGGTGCTTTCCTATAATGCACGACAGAACAAAAATCAGGCAACTACCCAATCTTCTCAGAGGATATGAAAAGATCAGGTTATCAACCCAAAACGTTATCGATGCAGAAAAAGCACCAGGAGGACCCTACAGACTTGGAACCTCAGGATCTTGCCCTAACGCTACCAGTAAAATCGGATTTTTTGCAACAATGGCTTGGGCTGTCCCAAAGGACAACTACAAAAATGCAACGAACCCACTAACAGTGGAAGTACCATACATTTGTACAGAAGGGGAAGACCAAATTACTGTTTGGGGGTTCCATTCGGATAACAAAACCCAAATGAAGAGCCTCTATGGAGACTCAAATCCTCAAAAGTTCACCTCATCTGCTAATGGAGTAACCACGCATTATGTTTCTCAGATTGGCGACTTCCCAGATCAAACAGAAGACGGAGGACTACCACAAAGCGGCAGAATTGTTGTTGATTACATGATGCAAAAACCTGGGAAAACAGGAACAATTGTCTATCAAAGGGGTGTTTTGTTGCCTCAAAAGGTGTGGTGCGCGAGTGGCAGGAGCAAAGTAATAAAAGGGTCATTGCCTTTAATTGGTGAAGCAGATTGCCTTCATGAAGAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGAAAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTAAAAACACCTTTGAAGCTTGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTGAAGGAAAGGGGTTTCTTCGGAGCTATTGCTGGTTTCCTAGAAGGAGGATGGGAAGGAATGATTGCAGGTTGGCACGGATACACATCTCACGGAGCACATGGAGTGGCAGTGGCGGCAGACCTTAAGAGTACACAAGAAGCTATAAATAAGATAACAAAAAATCTCAATTCTTTGAGTGAACTAGAAGTAAAGAACCTTCAAAGACTAAGTGGTGCCATGGATGAACTCCACAACGAAATACTCGAGCTGGATGAAAAAGTGGATGATCTCAGAGCTGACACTATAAGCTCACAAATAGAACTTGCAGTCTTGCTTTCCAACGAAGGAATAATAAACAGTGAAGACGAGCATCTATTGGCACTTGAGAGAAAACTAAAGAAAATGCTGGGTCCCTCTGCTGTAGACATAGGAAACGGATGCTTCGAAACCAAACACAAATGCAACCAGACCTGCTTAGACAGGATAGCTGCTGGCACCTTTAATGCAGGAGAATTTTCTCTCCCCACTTTTGATTCATTGAACATTACTGCTGCATCTTTAAATGATGATGGATTGGATAACCATACTATACTGCTCTATTACTCAACTGCTGCTTCTAGTTTGGCTGTAACATTAATGCTAGCTATTTTTATTGTTTATATGGTCTCCAGAGACAACGTTTCATGCTCCATCTGTCTATAAAGAAGGTTAGGCCTTGTATTTTCCTTTATTGTAGTGCTTGTTTGCTTGTCATCATTACAAAGAAAC'
}
]
tmp_outgroup = SeqIO.read('source-data/Yam_outgroup.gb', 'genbank')
genome_annotation = tmp_outgroup.features
self.cds = {x.qualifiers['gene'][0]:x for x in genome_annotation
if 'gene' in x.qualifiers and x.type=='CDS' and
x.qualifiers['gene'][0] in ['SigPep', 'HA1', 'HA2']}
self.outgroup = {
'strain':'B/Singapore/11/94',
'isolate_id':'EPI_ISL_20980',
'date':'1994-05-10',
'region':'China',
'seq':str(tmp_outgroup.seq).upper()
}
def __init__(self, min_length=987, **kwargs):
'''
parameters
min_length -- minimal length for a sequence to be acceptable
'''
flu_filter.__init__(self, **kwargs)
self.min_length = min_length
self.vaccine_strains = [
{
'strain':
'B/Beijing/184/93',
'isolate_id':
'EPI_ISL_969',
'date':
'1993-07-01', #(Month and day unknown)
'region':
'china',
'country':
'china',
'seq':
'GATCGAATCTGTACTGGGATAACATCTTCAAACTCACCTCATGTGGTCAAAACAGCTACTCAAGGGGAGGTCAATGTGACTGGTGTGATACCACTGACAACAACACCAACAAAATCTCATTTTGGAAATCTCAAAGGAACAAAGACCAGAGGGAAACTATGCCCAAACTGTCTCAACTGCACAGATCTGGATGTGGCCTTGGGCAGACCAATGTGTGTGGGGACCACACCTTCGGCAAAAGCTTCAATACTCCACGAAGTCAGACCTGTTACATCCGGGTGCTTTCCTATAATGCACGACAGAACAAAAATCAGACAGCTACCCAATCTTCTCAGAGGATATGAAAATATCAGATTATCAACCCAAAACGTTATCAACGCAGAAAAGGCACCAGGAGGACCCTACAGGCTTGGAACCTCAGGATCTTGCCCTAACGCTACCAGTAGAAGCGGATTTTTCGCAACAATGGCTTGGGCTGTCCCAAGGGACAACAACAAAACAGCAACAAATCCACTAACAGTAGAAGTACCATACATTTGTACAAAAGGAGAAGACCAAATTACTGTTTGGGGGTTCCATTCTGATAACAAAATCCAAATGAAAAACCTCTATGGAGACTCAAATCCTCAAAAGTTCACCTCATCTGCTAATGGAGTAACCACACATTATGTTTCTCAGATTGGCGGCTTCCCAGATCAAACAGAAGACGGAGGGCTACCACAAAGCGGCAGAATTGTTGTTGATTACATGGTGCAAAAACCTGGGAAAACAGGAACAATTGTCTATCAAAGAGGTGTTTTGTTGCCTCAAAAGGTGTGGTGCGCGAGTGGCAGGAGCAAAGTAATAAAAGGGTCCTTGCCTTTAATTGGTGAAGCAGATTGCCTTCACGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGAGAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTGAAAACACCTTTGAAGCTTGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGG',
},
{
'strain':
'B/Sichuan/379/99',
'isolate_id':
'EPI_ISL_21113',
'date':
'1999-07-01', # (Month and day unknown)
'region':
'china',
'country':
'china',
'seq':
'GAGGCAATAATTGTACTACTCATGGTAGTAACATCCAATGCAGATCGAATCTGCACTGGGATAACATCGTCAAACTCACCTCATGTGGTCAAAACAGCTACTCAAGGGGAGGTCAATGTAACTGGTGCGATACCACTGACAACAACACCAACAAAATCTCATTTTGCAAATCTCAAAGGAACAAAGACCAGAGGGAAACTATGCCCAACCTGTCTCAACTGCACAGATCTGGATGTGGCCTTGGGCAGACCAATGTGTGTGGGGATCACACCTTCGGCAAAAGCTTCAATACTCCACGAAATCAAACCTGTTACATCCGGATGCTTTCCTATAATGCACGACAGAACAAAAATCAGACAGCTACCCAATCTTCTCAGAGGATATGAAAAAATCAGATTATCAACCCAAAACGTTATCAACGCAGAAAAGGCACCAGGAGGACCTTACAGACTTGGAACTTCAGGATCTTGCCCTAACGCTACCAGTAAAAGCGGATTTTTCGCAACAATGGCTTGGGCTGTCCCAAGGGACAACAACAAAACAGCAACGAATCCACTAACAGTAGAAGTACCACACATCTGTACAAAAGAAGAAGACCAAATTACTGTTTGGGGGTTCCATTCTGATGACAAAACCCAAATGAAAAACCTCTATGGAGACTCAAATCCTCAAAAGTTCACCTCATCTGCTAATGGAATAACCACACATTATGTTTCTCAGATTGGCGGCTTCCCGGACCAAACAGAGGACGGAGGGCTACCACAAAGCGGCAGAATTGTTGTTGATTACATGGTGCAAAAACCTGGGAAAACAGGAACAATTGTCTATCAAAGAGGGATTTTGTTGCCTCAAAAGGTGTGGTGCGCGAGTGGTAGGAGCAAAGTAATAAAAGGGTCCTTGCCTTTAATTGGTGAAGCAGATTGCCTTCATGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGAGAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTGAAAACACCTTTGAAGCTTGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGGGGTTTCT',
},
{
'strain':
'B/Shanghai/361/2002',
'isolate_id':
'EPI_ISL_2842',
'date':
'2002-06-12',
'region':
'china',
'country':
'china',
'seq':
'AATGCAGATCGAATCTGCACTGGGATAACATCTTCAAACTCACCTCATGTGGTCAAAACAGCTACTCAAGGGGAGGTCAATGTGACTGGTGTGATACCACTGACAACAACTCCAATAAAATCTCATTTTGCAAATCTCAAAGGAACAAGGACTAGAGGGAAACTATGCCCAGATTGTCTCAACTGCACAGATCTGGATGTGGCCTTGGGCAGACCAATGTGTGTGGGGACCACACCTTCGGCAAAAGCTTCAATACTCCACGAAGTCAGACCTGTTACATCCGGGTGCTTTCCTATAATGCACGACAGAACAAAAATCAGACAACTACCCAATCTTCTCAGAGGATATGAAAATATCAGGTTATCAACCCAAAACGTTATCGATGCAGAAAAGGCCCTAGGAGGACCCTACAGACTTGGAACCTCAGGATCTTGCCCTAACGCCACCAGTAAAAGCGGATTTTTCGCAACAATGGCTTGGGCTGTCCCAAAGGACAACAACAAAAATGCAACGAACCCACTAACAGTAGAAGTACCATACATCTGTACAGAAGGGGAAGACCAAATTACTGTTTGGGGGTTCCATTCAGATGACAAAACCCAAATGAAAAACCTCTATGGAGACTCAAATCCTCAAAAGTTCACCTCATCTGCTAATGGAGTAACCACACATTATGTTTCTCAGATTGGCGGCTTCCCAGATCAAACAGAAGACGGAGGACTACCACAAAGCGGCAGAATTGTTGTTGATTACATGGTGCAAAAACCTGGGAAAACAGGAACAATTGTCTATCAAAGAGGTGTTTTGTTGCCTCAAAAGGTGTGGTGCGCGAGTGGCAGGAGCAAAGTAATAAAAGGGTCCTTGCCTTTAATTGGTGAAGCAGATTGCCTTCATGAAAAATACGGTGGGTTAAACAAAAGCAAGCCTTACTACACAGGAGAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTGAAAACACCTTTGAAGCTTGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGGGGTTTC',
},
{
'strain':
'B/Florida/4/2006',
'isolate_id':
'EPI_ISL_21307',
'date':
'2006-11-01',
'region':
'north_america',
'country':
'usa',
'seq':
'ATGAAGGCAATAATTGTACTACTCATGGTAGTAACATCCAATGCAGATCGAATCTGCACTGGAATAACATCTTCAAACTCACCTCATGTGGTCAAAACAGCCACTCAAGGGGAGGTCAATGTGACTGGTGTGATACCACTAACAACAACACCAACAAAATCTTATTTTGCAAATCTCAAAGGAACAAGGACCAGAGGGAAACTATGCCCAGACTGTCTCAACTGCACAGATCTGGATGTGGCTTTGGGCAGACCAATGTGTGTGGGGACCACACCTTCGGCGAAAGCTTCAATACTCCACGAAGTCAAACCTGTTACATCCGGGTGCTTTCCTATAATGCACGACAGAACAAAAATCAGGCAACTACCCAATCTTCTCAGAGGATATGAAAATATCAGGCTATCAACCCAAAACGTCATCGATGCGGAAAAGGCACCAGGAGGACCCTACAGACTTGGAACCTCAGGATCTTGCCCTAACGCTACCAGTAAGAGCGGATTTTTCGCAACAATGGCTTGGGCTGTCCCAAAGGACAACAACAAAAATGCAACGAACCCACTAACAGTAGAAGTACCATACATTTGTACAGAAGGGGAAGACCAAATCACTGTTTGGGGGTTCCATTCAGATGACAAAACCCAAATGAAGAACCTCTATGGAGACTCAAATCCTCAAAAGTTCACCTCATCTGCTAATGGAGTAACCACACACTATGTTTCTCAGATTGGCAGCTTCCCAGATCAAACAGAAGACGGAGGACTACCACAAAGCGGCAGGATTGTTGTTGATTACATGATGCAAAAACCTGGGAAAACAGGAACAATTGTCTACCAAAGAGGTGTTTTGTTGCCTCAAAAGGTGTGGTGCGCGAGTGGCAGGAGCAAAGTAATAAAAGGGTCCTTGCCTTTAATTGGTGAAGCAGATTGCCTTCATGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGAGAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTGAAAACACCTTTGAAGCTTGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGGGGTTTCTTCGGAGCTATTGCTGGTTTCCTAGAAGGAGGATGGGAAGGAATGATTGCAGGCTGGCACGGATACACATCTCACGGAGCACATGGAGTGGCAGTGGCGGCGGACCTTAAGAGTACGCAAGAAGCTATAAACAAGATAACAAAAAATCTCAATTCTTTGAGTGAGCTAGAAGTAAAGAATCTTCAAAGACTAAGTGGTGCCATGGATGAACTCCACAACGAAATACTCGAGCTGGATGAGAAAGTGGATGATCTCAGAGCTGACACTATAAGCTCGCAAATAGAACTTGCAGTCTTGCTTTCCAACGAAGGAATAATAAACAGTGAAGATGAGCATCTATTGGCACTTGAGAGAAAACTAAAGAAAATGCTGGGTCCCTCTGCTGTAGAGATAGGAAATGGATGCTTCGAAACCAAACACAAGTGCAACCAGACCTGCTTAGACAGGATAGCTGCTGGCACCTTTAATGCAGGAGAATTTTCTCTCCCCACTTTTGATTCACTGAACATTACTGCTGCATCTTTAAATGATGATGGATTGGATAACCATACTATACTGCTCTATTACTCAACTGCTGCTTCTAGTTTGGCTGTAACATTGATGCTAGCTATTTTTATTGTTTATATGGTCTCCAGAGACAACGTTTCATGCTCCATCTGTCTATAA'
},
{
'strain':
'B/Wisconsin/01/2010',
'isolate_id':
'EPI_ISL_76940',
'date':
'2010-02-20',
'region':
'north_america',
'country':
'usa',
'seq':
'ATGAAGGCAATAATTGTACTACTCATGGTAGTAACATCCAATGCAGATCGAATCTGCACTGGGATAACATCTTCAAACTCACCTCATGTGGTCAAAACAGCTACTCAAGGGGAGGTCAATGTGACTGGCGTGATACCACTGACAACAACACCAACAAAATCTTATTTTGCAAATCTCAAAGGAACAAGGACCAGAGGGAAACTATGCCCGGACTGTCTCAACTGTACAGATCTGGATGTGGCCTTGGGCAGGCCAATGTGTGTGGGGACCACACCTTCTGCTAAAGCTTCAATACTCCACGAGGTCAGACCTGTTACATCCGGGTGCTTTCCTATAATGCACGACAGAACAAAAATCAGGCAACTACCCAATCTTCTCAGAGGATATGAAAATATCAGGTTATCAACCCAAAACGTTATCGATGCAGAAAAAGCACCAGGAGGACCCTACAGACTTGGAACCTCAGGATCTTGCCCTAACGCTACCAGTAAAATCGGATTTTTTGCAACAATGGCTTGGGCTGTCCCAAAGGACAACTACAAAAATGCAACGAACCCACTAACAGTAGAAGTACCATACATTTGTACAGAAGGGGAAGACCAAATTACTGTTTGGGGGTTCCATTCAGATAACAAAACCCAAATGAAGAGCCTCTATGGAGACTCAAATCCTCAAAAGTTCACCTCATCTGCTAATGGAGTAACCACACATTATGTTTCTCAGATTGGCGACTTCCCAGATCAAACAGAAGACGGAGGACTACCACAAAGCGGCAGAATTGTTGTTGATTACATGATGCAAAAACCTGGGAAAACAGGAACAATTGTCTATCAAAGAGGTGTTTTGTTGCCTCAAAAGGTGTGGTGCGCGAGTGGCAGGAGCAAAGTAATAAAAGGGTCATTGCCTTTAATTGGTGAAGCAGATTGCCTTCATGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGAGAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTAAAAACACCTTTGAAGCTTGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTGAAGGAAAGGGGTTTCTTCGGAGCTATTGCTGGTTTCCTAGAAGGAGGATGGGAAGGAATGATTGCAGGTTGGCACGGATACACATCTCACGGAGCACATGGAGTGGCAGTGGCGGCAGACCTTAAGAGTACACAAGAAGCTATAAATAAGATAACAAAAAATCTCAATTCTTTGAGTGAGCTAGAAGTAAAGAACCTTCAAAGACTAAGTGGTGCCATGGATGAACTCCACAACGAAATACTCGAGCTGGATGAGAAAGTGGATGATCTCAGAGCTGACACTATAAGCTCACAAATAGAACTTGCAGTCTTGCTTTCCAACGAAGGAATAATAAACAGTGAAGACGAGCATCTATTGGCACTTGAGAGAAAACTAAAGAAAATGCTGGGTCCCTCTGCTGTAGACATAGGAAACGGATGCTTCGAAACCAAACACAAATGCAACCAGACCTGCTTAGACAGGATAGCTGCTGGCACCTTTAATGCAGGAGAATTTTCTCTCCCCACTTTTGATTCATTGAACATTACTGCTGCATCTTTAAATGATGATGGATTGGATAACCATACTATACTGCTCTATTACTCAACTGCTGCTTCTAGTTTGGCTGTAACATTAATGCTAGCTATTTTTATTGTTTATATGGTCTCCAGAGACAACGTTTCATGCTCCATCTGTCTATAA'
},
{
'strain':
'B/Massachusetts/02/2012',
'isolate_id':
'EPI_ISL_121434',
'date':
'2012-03-13',
'region':
'north_america',
'country':
'usa',
'seq':
'ATGAAGGCAATAATTGTACTACTAATGGTAGTAACATCCAATGCAGATCGAATCTGCACTGGGATAACATCTTCAAACTCACCTCATGTGGTCAAAACAGCTACTCAAGGGGAGGTCAATGTGACTGGTGTGATACCACTAACAACAACACCAACAAAATCTTATTTTGCAAATCTCAAAGGAACAAAGACCAGAGGGAAACTATGCCCAGACTGTCTCAACTGTACAGATCTGGATGTGGCCCTGGGCAGGCCAATGTGTGTGGGAACTACACCTTCTGCGAAAGCTTCAATACTTCACGAAGTCAGACCTGTTACATCCGGGTGCTTCCCTATAATGCACGACAGAACAAAAATCAGGCAACTAGCCAATCTTCTCAGAGGATATGAAAATATCAGGTTATCAACCCAAAACGTTATCGATGCAGAAAAGGCACCAGGAGGACCCTACAGACTTGGAACCTCAGGATCTTGCCCTAACGCTACCAGTAAAAGCGGATTTTTCGCAACAATGGCTTGGGCTGTCCCAAAGGACAACAACAAAAATGCAACGAACCCATTAACAGTAGAAGTACCATACATTTGTGCAGAAGGGGAAGACCAAATTACTGTTTGGGGGTTCCATTCAGATAACAAAACCCAAATGAAGAACCTCTATGGAGACTCAAATCCTCAAAAGTTCACCTCATCTGCTAATGGAGTAACCACACATTATGTTTCTCAGATTGGCGGCTTCCCAGATCAAACAGAAGACGGAGGACTACCACAAAGCGGCAGAATTGTCGTTGATTACATGATGCAAAAACCTGGGAAAACAGGAACAATTGTCTATCAAAGAGGTGTTTTGTTGCCTCAAAAGGTGTGGTGCGCGAGTGGCAGGAGCAAAGTAATAAAAGGGTCCTTGCCTTTAATTGGTGAAGCAGATTGCCTTCATGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGAGAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTGAAAACACCTTTGAAGCTTGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGGGGTTTCTTCGGAGCTATTGCTGGTTTCCTAGAAGGAGGATGGGAAGGAATGATTGCAGGTTGGCACGGATACACATCTCACGGAGCACATGGAGTGGCAGTTGCTGCAGACCTTAAGAGCACACAAGAAGCTATAAACAAGATAACAAAAAATCTCAACTCTTTGAGTGAGCTAGAAGTAAAGAATCTTCAAAGGCTAAGTGGTGCCATGGATGAACTCCACAACGAAATACTCGAGCTGGATGAGAAAGTGGATGACCTCAGAGCTGACACTATAAGTTCACAAATAGAACTTGCAGTCTTGCTTTCCAACGAAGGAATAATAAACAGTGAAGACGAGCATCTATTGGCACTTGAGAGAAAACTAAAGAAAATGCTGGGTCCCTCTGCTGTAGACATAGGAAATGGATGCTTCGAAACCAAACACAAATGCAACCAGACCTGCTTAGACAGGATAGCTGCTGGCACCTTTAATGCAGGAGAGTTTTCTCTCCCCACTTTTGATTCATTGAACATTACTGCTGCATCTTTAAATGATGATGGATTGGATAACCATACTATACTGCTCTATTACTCAACTGCTGCTTCTAGTTTGGCTGTAACATTGATGCTAGCTATTTTTATTGTTTATATGGTCTCCAGAGACAACGTTTCATGCTCCATCTGTCTATAA'
},
{
'strain':
'B/PHUKET/3073/2013',
'isolate_id':
'EPI_ISL_161843',
'date':
'2013-11-21',
'region':
'southeast_asia',
'country':
'thailand',
'seq':
'ATGAAGGCAATAATTGTACTACTCATGGTAGTAACATCCAACGCAGATCGAATCTGCACTGGGATAACATCTTCAAACTCACCTCATGTGGTCAAAACAGCTACTCAAGGGGAGGTCAATGTGACTGGCGTGATACCACTGACAACAACACCAACAAAATCTTATTTTGCAAATCTCAAAGGAACAAGGACCAGAGGGAAACTATGCCCGGACTGTCTCAACTGTACAGATCTGGATGTGGCCTTGGGCAGGCCAATGTGTGTGGGGACCACACCTTCTGCTAAAGCTTCAATACTCCATGAGGTCAGACCTGTTACATCCGGGTGCTTTCCTATAATGCACGACAGAACAAAAATCAGGCAACTACCCAATCTTCTCAGAGGATATGAAAAGATCAGGTTATCAACCCAAAACGTTATCGATGCAGAAAAAGCACCAGGAGGACCCTACAGACTTGGAACCTCAGGATCTTGCCCTAACGCTACCAGTAAAATCGGATTTTTTGCAACAATGGCTTGGGCTGTCCCAAAGGACAACTACAAAAATGCAACGAACCCACTAACAGTGGAAGTACCATACATTTGTACAGAAGGGGAAGACCAAATTACTGTTTGGGGGTTCCATTCGGATAACAAAACCCAAATGAAGAGCCTCTATGGAGACTCAAATCCTCAAAAGTTCACCTCATCTGCTAATGGAGTAACCACGCATTATGTTTCTCAGATTGGCGACTTCCCAGATCAAACAGAAGACGGAGGACTACCACAAAGCGGCAGAATTGTTGTTGATTACATGATGCAAAAACCTGGGAAAACAGGAACAATTGTCTATCAAAGGGGTGTTTTGTTGCCTCAAAAGGTGTGGTGCGCGAGTGGCAGGAGCAAAGTAATAAAAGGGTCATTGCCTTTAATTGGTGAAGCAGATTGCCTTCATGAAGAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGAAAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTAAAAACACCTTTGAAGCTTGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTGAAGGAAAGGGGTTTCTTCGGAGCTATTGCTGGTTTCCTAGAAGGAGGATGGGAAGGAATGATTGCAGGTTGGCACGGATACACATCTCACGGAGCACATGGAGTGGCAGTGGCGGCAGACCTTAAGAGTACACAAGAAGCTATAAATAAGATAACAAAAAATCTCAATTCTTTGAGTGAACTAGAAGTAAAGAACCTTCAAAGACTAAGTGGTGCCATGGATGAACTCCACAACGAAATACTCGAGCTGGATGAAAAAGTGGATGATCTCAGAGCTGACACTATAAGCTCACAAATAGAACTTGCAGTCTTGCTTTCCAACGAAGGAATAATAAACAGTGAAGACGAGCATCTATTGGCACTTGAGAGAAAACTAAAGAAAATGCTGGGTCCCTCTGCTGTAGACATAGGAAACGGATGCTTCGAAACCAAACACAAATGCAACCAGACCTGCTTAGACAGGATAGCTGCTGGCACCTTTAATGCAGGAGAATTTTCTCTCCCCACTTTTGATTCATTGAACATTACTGCTGCATCTTTAAATGATGATGGATTGGATAACCATACTATACTGCTCTATTACTCAACTGCTGCTTCTAGTTTGGCTGTAACATTAATGCTAGCTATTTTTATTGTTTATATGGTCTCCAGAGACAACGTTTCATGCTCCATCTGTCTATAAAGAAGGTTAGGCCTTGTATTTTCCTTTATTGTAGTGCTTGTTTGCTTGTCATCATTACAAAGAAAC'
}
]
tmp_outgroup = SeqIO.read('source-data/Yam_outgroup.gb', 'genbank')
genome_annotation = tmp_outgroup.features
self.cds = {
x.qualifiers['gene'][0]: x
for x in genome_annotation
if 'gene' in x.qualifiers and x.type == 'CDS'
and x.qualifiers['gene'][0] in ['SigPep', 'HA1', 'HA2']
}
self.outgroup = {
'strain': 'B/Singapore/11/94',
'isolate_id': 'EPI_ISL_20980',
'date': '1994-05-10',
'region': 'China',
'seq': str(tmp_outgroup.seq).upper()
}
