def __init__(self, **kwargs): update.__init__(self, **kwargs) flu_upload.__init__(self, **kwargs) self.outgroups = {lineage: SeqIO.read('source-data/'+lineage+'_outgroup.gb', 'genbank') for lineage in ['H3N2', 'H1N1', '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')}
def __init__(self, **kwargs): update.__init__(self, **kwargs) mumps_upload.__init__(self, **kwargs)
def __init__(self, **kwargs): # upload.__init__(self, **kwargs) # update: sets virus, viruses_table, sequences_table, database, uploadable_databases; # initiates empty objects for strains, strain_fix_fname, virus_to_sequence_transfer_fields # parse: set gbdb, checks for accession-type data in kwargs. update.__init__(self, **kwargs) # update(upload(parse)) self.nonames=[]
def __init__(self, **kwargs): update.__init__(self, **kwargs) coronavirus_upload.__init__(self, **kwargs)
def __init__(self, **kwargs): update.__init__(self, **kwargs) ebola_upload.__init__(self, **kwargs)
def __init__(self, **kwargs): update.__init__(self, **kwargs) dengue_upload.__init__(self, **kwargs)
def __init__(self, **kwargs): update.__init__(self, **kwargs) zika_upload.__init__(self, **kwargs)