def fill_bxcan_vis_datadir(config):
sh._try_fill_config(config, 'bxcan_vis_datadir', default_params.BXCAN_VIS_DATADIR)
res = sh._try_to_format(
config['bxcan_vis_datadir'],
OrderedDict([('datadir', config['datadir'])])
)
return res
def fill_ld_clump_yaml(config):
sh._try_fill_config(config, 'ld_clump_yaml', default_params.LD_CLUMP_YAML)
config['ld_clump_yaml'] = sh._try_to_format(
config['ld_clump_yaml'],
OrderedDict([('datadir', config['datadir'])])
)
return config['ld_clump_yaml']
def fill_bxcan_report_data(config):
sh._try_fill_config(config, 'bxcan_idp_meta', default_params.BXCAN_IDP_META)
sh._try_fill_config(config, 'bxcan_color_code', default_params.BXCAN_COLOR_CODE)
meta = sh._try_to_format(
config['bxcan_idp_meta'],
OrderedDict([('datadir', config['datadir'])])
)
color = sh._try_to_format(
config['bxcan_color_code'],
OrderedDict([('datadir', config['datadir'])])
)
return meta, color
def fill_snp_bim(config):
sh._try_fill_config(config, 'idp_gwas_snp_pattern', default_params.IDP_GWAS_SNP_PATTERN)
sh._check_desired_wildcards(
config['idp_gwas_snp_pattern'], [ '{chr_num}' ]
)
arg = sh._try_to_format(
config['idp_gwas_snp_pattern'],
OrderedDict([
('datadir', config['datadir']),
('chr_num', '[chr_num]')
])
)
files = sh._try_format_for_list(
config['geno_cov_pattern'],
OrderedDict([('datadir', config['datadir'])]),
default_params.CHRS, 'chr_num'
)
return arg, files
def fill_mr_ld_panel(config):
sh._try_fill_config(config, 'gwas_pop', default_params.GWAS_POP)
sh._check_val_in_pool(config['gwas_pop'], default_params.GWAS_POPS)
sh._try_fill_config(config, 'mr_ld_panel_pattern', default_params.MR_LD_PANEL_PATTERN)
arg = sh._try_to_format(
config['mr_ld_panel_pattern'],
OrderedDict([
('datadir', config['datadir']),
('gwas_pop', config['gwas_pop'])
])
)
files = sh._try_format_for_list(
config['geno_cov_pattern'] + '.{suffix}',
OrderedDict([
('datadir', config['datadir']),
('gwas_pop', config['gwas_pop'])
]),
['bed', 'bim', 'fam'], 'suffix'
)
return arg, files
def fill_permz(config):
sh._try_fill_config(config, 'bxcan_ldblock_perm', default_params.BXCAN_LDBLOCK_PERM)
sh._try_fill_config(config, 'bxcan_ldblock_perm_seed', default_params.BXCAN_LDBLOCK_PERM_SEED)
sh._try_fill_config(config, 'bxcan_ldblock_perm_nrepeat', default_params.BXCAN_LDBLOCK_PERM_NREPEAT)
if config['model_type'] is 'elastic_net' and config['bxcan_ldblock_perm'] is not None:
print('WARNING: since model_type = elastic_net, we disable LD block based permutation calculation in BrainXcan. Shut down this check by setting bxcan_ldblock_perm_elastic_net=true')
config['bxcan_ldblock_perm'] = None
def fill_empz(config):
sh._try_fill_config(config, 'bxcan_empirical_z', default_params.BXCAN_EMPIRICAL_Z)
sh._try_fill_config(config, 'bxcan_empirical_z_seed', default_params.BXCAN_EMPIRICAL_Z_SEED)
sh._try_fill_config(config, 'bxcan_empirical_z_nrepeat', default_params.BXCAN_EMPIRICAL_Z_NREPEAT)
if config['model_type'] is 'elastic_net' and config['bxcan_empirical_z'] is True:
print('WARNING: since model_type = elastic_net, we disable empirical z-score calculation in BrainXcan')
config['bxcan_empirical_z'] = False
def fill_gwas_idp(config):
sh._try_fill_config(config, 'idp_gwas_pattern', default_params.IDP_GWAS_PATTERN)
sh._check_desired_wildcards(
config['idp_gwas_pattern'],
[ '{chr_num}', '{idp_code}', '{idp_modality}' ]
)
param = sh._try_to_format(
config['idp_gwas_pattern'],
OrderedDict([
('datadir', config['datadir']),
('idp_type', config['idp_type']),
('chr_num', '[chr_num]')
])
)
files = sh._try_format_for_list(
config['geno_cov_pattern'],
OrderedDict([
('datadir', config['datadir']),
('idp_type', config['idp_type'])
]),
default_params.CHRS, 'chr_num'
)
return param, files
def fill_patterns(config):
sh._try_fill_config(config, 'geno_cov_pattern', default_params.GENO_COV_PATTERN)
sh._try_fill_config(config, 'idp_weights_pattern', default_params.IDP_WEIGHTS_PATTERN)
sh._try_fill_config(config, 'idp_weights_cols', default_params.IDP_WEIGHTS_COLS)
sh._check_desired_wildcards(
config['geno_cov_pattern'], [ '{chr_num}' ]
)
sh._check_desired_wildcards(
config['idp_weights_pattern'], [ '{idp_modality}' ]
)
sh._check_list_all_in(
list(default_params.IDP_WEIGHTS_COLS.keys()),
config['idp_weights_cols']
)
config['idp_weights_pattern'] = sh._try_to_format(
config['idp_weights_pattern'],
OrderedDict([
('datadir', config['datadir']),
('idp_type', config['idp_type']),
('model_type', config['model_type'])
])
)
def fill_bxcan_region_vis(config):
sh._try_fill_config(config, 'bxcan_region_vis', default_params.BXCAN_REGION_VIS)
if config['bxcan_region_vis'] is True:
return '--region_vis'
else:
return ''
def fill_spearman_cutoff(config):
sh._try_fill_config(config, 'spearman_cutoff', default_params.SPEARMAN_CUTOFF)
return config['spearman_cutoff']
def fill_exe(config):
sh._try_fill_config(config, 'python_exe', default_params.PYTHON_EXE)
sh._try_fill_config(config, 'rscript_exe', default_params.RSCRIPT_EXE)
sh._try_fill_config(config, 'plink_exe', default_params.PLINK_EXE)
def fill_model_type(config):
sh._try_fill_config(
config, 'model_type',
default_params.MODEL_TYPE[0], default_params.MODEL_TYPE[1]
)
def fill_idp_type(config):
sh._try_fill_config(
config, 'idp_type',
default_params.IDP_TYPE[0], default_params.IDP_TYPE[1]
)