# ],
'crotty-fna' : [
['RUj15_ALN-FNA_week3_groupD', 'RUj15_L-ILN-FNA_week3_groupD', 'RUj15_R-ILN-FNA_week3_groupD'],
['RUj15_ALN-FNA_week3_groupD', 'RUj15_L-ILN-FNA_week15_groupD', 'RUj15_R-ILN-FNA_week15_groupD'],
['ROp15_R-ILN-FNA_week3_groupC', 'ROp15_L-ILN-FNA_week3_groupC', 'ROp15_ALN-FNA_week3_groupC'],
['ROp15_R-ILN-FNA_week9_groupC', 'ROp15_L-ILN-FNA_week9_groupC', 'ROp15_ALN-FNA_week9_groupC'],
['ROp15_R-ILN-FNA_week15_groupC', 'ROp15_L-ILN-FNA_week15_groupC', 'ROp15_ALN-FNA_week15_groupC'],
['ROp15_R-ILN-FNA_week21_groupC', 'ROp15_L-ILN-FNA_week21_groupC', 'ROp15_ALN-FNA_week21_groupC'],
['RJk15_L-ILN-FNA_week3_groupB', 'RJk15_R-ILN-FNA_week3_groupB', 'RJk15_ALN-FNA_week3_groupB'],
['RJk15_L-ILN-FNA_week9_groupB', 'RJk15_R-ILN-FNA_week9_groupB'],
['RJk15_L-ILN-FNA_week15_groupB', 'RJk15_R-ILN-FNA_week15_groupB', 'RJk15_ALN-FNA_week15_groupB'],
['RJk15_L-ILN-FNA_week21_groupB', 'RJk15_R-ILN-FNA_week21_groupB', 'RJk15_ALN-FNA_week21_groupB'],
]
}
default_varvals['data'] = ':'.join([study + '/' + heads.full_dataset(heads.read_metadata(study), dset) for study in default_varvals['data'] for dset in default_varvals['data'][study]])
for study in all_data_groups:
for idp in range(len(all_data_groups[study])):
all_data_groups[study][idp] = [heads.full_dataset(heads.read_metadata(study), ds) for ds in all_data_groups[study][idp]]
# ----------------------------------------------------------------------------------------
parser = argparse.ArgumentParser()
parser.add_argument('action', choices=['mfreq', 'nsnp', 'multi-nsnp', 'prevalence', 'n-leaves', 'weibull', 'alcluster', 'gls-gen', 'data'])
parser.add_argument('--methods', default='partis') # not using <choices> 'cause it's harder since it's a list
parser.add_argument('--method-vs-method', action='store_true')
parser.add_argument('--sample-vs-sample', action='store_true')
parser.add_argument('--v-genes', default='IGHV4-39*01')
parser.add_argument('--locus', default='igh')
parser.add_argument('--all-regions', action='store_true') # it'd be nicer to just have an arg for which region we're running on, but i need a way to keep the directory structure for single-region plots the same as before I generalized to d and j
parser.add_argument('--varvals')
parser.add_argument('--n-event-list', default='1000:2000:4000:8000') # NOTE modified later for multi-nsnp also NOTE not used for gen-gset
parser.add_argument('--gls-gen-events', type=int, default=50000)
'RJk15_L-ILN-FNA_week3_groupB', 'RJk15_R-ILN-FNA_week3_groupB',
'RJk15_ALN-FNA_week3_groupB'
],
['RJk15_L-ILN-FNA_week9_groupB', 'RJk15_R-ILN-FNA_week9_groupB'],
[
'RJk15_L-ILN-FNA_week15_groupB', 'RJk15_R-ILN-FNA_week15_groupB',
'RJk15_ALN-FNA_week15_groupB'
],
[
'RJk15_L-ILN-FNA_week21_groupB', 'RJk15_R-ILN-FNA_week21_groupB',
'RJk15_ALN-FNA_week21_groupB'
],
]
}
default_varvals['data'] = ':'.join([
study + '/' + heads.full_dataset(heads.read_metadata(study), dset)
for study in default_varvals['data']
for dset in default_varvals['data'][study]
])
for study in all_data_groups:
for idp in range(len(all_data_groups[study])):
all_data_groups[study][idp] = [
heads.full_dataset(heads.read_metadata(study), ds)
for ds in all_data_groups[study][idp]
]
# ----------------------------------------------------------------------------------------
parser = argparse.ArgumentParser()
parser.add_argument('action',
choices=[
'mfreq', 'nsnp', 'multi-nsnp', 'prevalence',
'n-leaves', 'weibull', 'alcluster', 'gls-gen', 'data'