Example #1
0
 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')}
Example #2
0
 def __init__(self, **kwargs):
     update.__init__(self, **kwargs)
     mumps_upload.__init__(self, **kwargs)
Example #3
0
	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=[]
Example #4
0
 def __init__(self, **kwargs):
     update.__init__(self, **kwargs)
     coronavirus_upload.__init__(self, **kwargs)
Example #5
0
 def __init__(self, **kwargs):
     update.__init__(self, **kwargs)
     ebola_upload.__init__(self, **kwargs)
Example #6
0
	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=[]
Example #7
0
 def __init__(self, **kwargs):
     update.__init__(self, **kwargs)
     dengue_upload.__init__(self, **kwargs)
Example #8
0
 def __init__(self, **kwargs):
     update.__init__(self, **kwargs)
     zika_upload.__init__(self, **kwargs)