def __init__(self, **kwargs):
upload.__init__(self, **kwargs)
self.removal_fields = [
'tested_by_fra', 'reported_by_fra', 'date',
'virus_collection_date', 'ref'
]
self.cleanup_fields = {'assay-type': 'assay_type'}
def __init__(self, **kwargs):
upload.__init__(self, **kwargs)
self.grouping_upload_fields = ['vtype', 'subtype', 'lineage']
# patterns from the subtype and lineage fields in the GISAID fasta file
self.patterns = {
('a / h1n1', 'pdm09'): ('a', 'h1n1', 'seasonal_h1n1pdm'),
('a / h1n2', ''): ('a', 'h1n2', None),
('a / h1n2', 'seasonal'): ('a', 'h1n2', 'seasonal_h1n2'),
('a / h2n2', ''): ('a', 'h2n2', None),
('a / h3n2', ''): ('a', 'h3n2', 'seasonal_h3n2'),
('a / h3n2', 'seasonal'): ('a', 'h3n2', 'seasonal_h3n2'),
('a / h3n3', ''): ('a', 'h3n3', None),
('a / h5n1', ''): ('a', 'h5n1', None),
('a / h5n2', ''): ('a', 'h5n2', None),
('a / h5n3', ''): ('a', 'h5n3', None),
('a / h5n4', ''): ('a', 'h5n4', None),
('a / h5n5', ''): ('a', 'h5n5', None),
('a / h5n6', ''): ('a', 'h5n6', None),
('a / h5n7', ''): ('a', 'h5n7', None),
('a / h5n8', ''): ('a', 'h5n8', None),
('a / h5n9', ''): ('a', 'h5n9', None),
('a / h5n6', ''): ('a', 'h5n6', None),
('a / h6n1', ''): ('a', 'h6n1', None),
('a / h7n1', ''): ('a', 'h7n1', None),
('a / h7n2', ''): ('a', 'h7n2', None),
('a / h7n3', ''): ('a', 'h7n3', None),
('a / h7n7', ''): ('a', 'h7n7', None),
('a / h7n9', ''): ('a', 'h7n9', None),
('a / h9n2', ''): ('a', 'h9n2', None),
('a / h10n7', ''): ('a', 'h10n7', None),
('a / h10n8', ''): ('a', 'h10n8', None),
('a / h11', ''): ('a', 'h11', None),
('b / h0n0', 'victoria'): ('b', None, 'seasonal_vic'),
('b / h0n0', 'yamagata'): ('b', None, 'seasonal_yam'),
('b', 'victoria'): ('b', None, 'seasonal_vic'),
('b', 'yamagata'): ('b', None, 'seasonal_yam'),
('h5n1', ''): ('a', 'h5n1', None),
('h7n9', ''): ('a', 'h7n9', None),
('h9n2', ''): ('a', 'h9n2', None)
}
self.outgroups = {
lineage: SeqIO.read('source-data/' + lineage + '_outgroup.gb',
'genbank')
for lineage in ['H3N2', 'H1N1pdm', 'Vic', 'Yam']
}
self.outgroup_patterns = {
'H3N2': ('a', 'h3n2', 'seasonal_h3n2'),
'H1N1': ('a', 'h1n1', 'seasonal_h1n1'),
'H1N1pdm': ('a', 'h1n1', 'seasonal_h1n1pdm'),
'Vic': ('b', None, 'seasonal_vic'),
'Yam': ('b', None, 'seasonal_yam')
}
self.strain_fix_fname = "source-data/flu_strain_name_fix.tsv"
self.location_fix_fname = "source-data/flu_location_fix.tsv"
self.virus_to_sequence_transfer_fields = ['submission_date']
self.fix = set()
def __init__(self, **kwargs):
upload.__init__(self, **kwargs)
self.removal_fields = [
'tested_by_fra', 'reported_by_fra', 'date',
'virus_collection_date', 'ref', 'virus_harvest_date', 'Boosted',
'RBC_species'
]
self.cleanup_fields = {
'assay-type': 'assay_type',
'lot #': 'lot_number'
}
def __init__(self, **kwargs):
upload.__init__(self, **kwargs)
self.grouping_upload_fields = ['vtype', 'subtype', 'lineage']
# patterns from the subtype and lineage fields in the GISAID fasta file
self.patterns = {('a / h1n1', 'pdm09'): ('a', 'h1n1', 'seasonal_h1n1pdm'),
('a / h1n2', ''): ('a', 'h1n2', None),
('a / h1n2', 'seasonal'): ('a', 'h1n2', 'seasonal_h1n2'),
('a / h2n2', ''): ('a', 'h2n2', None),
('a / h3n2', ''): ('a', 'h3n2', 'seasonal_h3n2'),
('a / h3n2', 'seasonal'): ('a', 'h3n2', 'seasonal_h3n2'),
('a / h3n3', ''): ('a', 'h3n3', None),
('a / h5n1', ''): ('a', 'h5n1', None),
('a / h5n6', ''): ('a', 'h5n6', None),
('a / h6n1', ''): ('a', 'h6n1', None),
('a / h7n1', ''): ('a', 'h7n1', None),
('a / h7n2', ''): ('a', 'h7n2', None),
('a / h7n3', ''): ('a', 'h7n3', None),
('a / h7n7', ''): ('a', 'h7n7', None),
('a / h7n9', ''): ('a', 'h7n9', None),
('a / h9n2', ''): ('a', 'h9n2', None),
('a / h10n7', ''): ('a', 'h10n7', None),
('a / h10n8', ''): ('a', 'h10n8', None),
('a / h11', ''): ('a', 'h11', None),
('b / h0n0', 'victoria'): ('b', None, 'seasonal_vic'),
('b / h0n0', 'yamagata'): ('b', None, 'seasonal_yam'),
('b', 'victoria'): ('b', None, 'seasonal_vic'),
('b', 'yamagata'): ('b', None, 'seasonal_yam')}
self.outgroups = {lineage: SeqIO.read('source-data/'+lineage+'_outgroup.gb', 'genbank') for lineage in ['H3N2', 'H1N1pdm', 'Vic', 'Yam']}
self.outgroup_patterns = {'H3N2': ('a', 'h3n2', 'seasonal_h3n2'),
'H1N1': ('a', 'h1n1', 'seasonal_h1n1'),
'H1N1pdm': ('a', 'h1n1', 'seasonal_h1n1pdm'),
'Vic': ('b', None, 'seasonal_vic'),
'Yam': ('b', None, 'seasonal_yam')}
self.strain_fix_fname = "source-data/flu_strain_name_fix.tsv"
self.virus_to_sequence_transfer_fields = ['submission_date']
self.fix = set()
def __init__(self, **kwargs):
upload.__init__(self, **kwargs)
def __init__(self, **kwargs):
upload.__init__(self, **kwargs)
self.strain_fix_fname = "source-data/dengue_strain_name_fix.tsv"
def __init__(self, **kwargs):
upload.__init__(self, **kwargs)
self.location_fields = ['location', 'division', 'country', 'region']
def __init__(self, **kwargs):
upload.__init__(self, **kwargs)
self.assay_type = kwargs['assay_type']
self.assay_date = None
def __init__(self, **kwargs):
upload.__init__(self, **kwargs)
self.strain_fix_fname = "source-data/yellow_fever_strain_name_fix.tsv"
def __init__(self, **kwargs):
upload.__init__(self, **kwargs)
self.strain_fix_fname = "source-data/measles_strain_name_fix.tsv"
self.location_fix_fname = "source-data/measles_location_fix.tsv"
self.date_fix_fname = "source-data/measles_date_fix.tsv"
def __init__(self, **kwargs):
upload.__init__(self, **kwargs)
def __init__(self, **kwargs):
upload.__init__(self, **kwargs)
self.strain_fix_fname = "source-data/mumps_strain_name_fix.tsv"
self.location_fix_fname = "source-data/zika_location_fix.tsv"
def __init__(self, **kwargs):
upload.__init__(self, **kwargs)
self.strain_fix_fname = "source-data/zika_strain_name_fix.tsv"
def __init__(self, **kwargs):
upload.__init__(self, **kwargs)
self.location_fix_fname = "source-data/ncov_location_fix.tsv"
def __init__(self, **kwargs):
upload.__init__(self, **kwargs)
self.location_fields = ['location', 'division', 'country']