示例#1
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 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'}
示例#2
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 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()
示例#3
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 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'
     }
示例#4
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 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()
示例#5
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 def __init__(self, **kwargs):
     upload.__init__(self, **kwargs)
示例#6
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 def __init__(self, **kwargs):
     upload.__init__(self, **kwargs)
     self.strain_fix_fname = "source-data/dengue_strain_name_fix.tsv"
示例#7
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 def __init__(self, **kwargs):
     upload.__init__(self, **kwargs)
     self.location_fields = ['location', 'division', 'country', 'region']
示例#8
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 def __init__(self, **kwargs):
     upload.__init__(self, **kwargs)
     self.assay_type = kwargs['assay_type']
     self.assay_date = None
示例#9
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 def __init__(self, **kwargs):
     upload.__init__(self, **kwargs)
     self.strain_fix_fname = "source-data/yellow_fever_strain_name_fix.tsv"
示例#10
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 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"
示例#11
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 def __init__(self, **kwargs):
     upload.__init__(self, **kwargs)
示例#12
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 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"
示例#13
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 def __init__(self, **kwargs):
     upload.__init__(self, **kwargs)
     self.strain_fix_fname = "source-data/zika_strain_name_fix.tsv"
示例#14
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 def __init__(self, **kwargs):
     upload.__init__(self, **kwargs)
     self.location_fix_fname = "source-data/ncov_location_fix.tsv"
示例#15
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 def __init__(self, **kwargs):
     upload.__init__(self, **kwargs)
     self.location_fields = ['location', 'division', 'country']