'hgnc_gene',
'user',
'whitelist',
'institute',
'event',
'case',
'gene_panel',
'hpo_term',
'disease_term',
'variant',
'acmg',
]
BUILDS = ['37', '38']
CYTOBANDS = parse_cytoband(cytobands_handle)
CHROMOSOMES = ('1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11', '12',
'13', '14', '15', '16', '17', '18', '19', '20', '21', '22', 'X',
'Y', 'MT')
# Maps chromosomes to integers
CHROMOSOME_INTEGERS = {chrom: i+1 for i,chrom in enumerate(CHROMOSOMES)}
PAR_COORDINATES = {
'37': {
'X': IntervalTree([Interval(60001, 2699521, 'par1'),
Interval(154931044, 155260561, 'par2')]),
'Y': IntervalTree([Interval(10001, 2649521, 'par1'),
Interval(59034050, 59363567, 'par2')])
'hgnc_gene',
'user',
'whitelist',
'institute',
'event',
'case',
'gene_panel',
'hpo_term',
'disease_term',
'variant',
'acmg',
]
BUILDS = ['37', '38']
CYTOBANDS = parse_cytoband(cytobands_handle)
CHROMOSOMES = ('1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11', '12',
'13', '14', '15', '16', '17', '18', '19', '20', '21', '22', 'X',
'Y', 'MT')
# Maps chromosomes to integers
CHROMOSOME_INTEGERS = {chrom: i + 1 for i, chrom in enumerate(CHROMOSOMES)}
PAR_COORDINATES = {
'37': {
'X':
IntervalTree([
Interval(60001, 2699521, 'par1'),
Interval(154931044, 155260561, 'par2')
]),
"hgnc_gene",
"user",
"institute",
"event",
"case",
"case_group",
"gene_panel",
"hpo_term",
"disease_term",
"variant",
"acmg",
]
BUILDS = ["37", "38", "GRCh38"]
CYTOBANDS_37 = parse_cytoband(cytobands_37_handle)
CYTOBANDS_38 = parse_cytoband(cytobands_38_handle)
AUTOSOMES = [str(nr) for nr in range(1, 23)]
CHROMOSOMES = AUTOSOMES + [
"X",
"Y",
"MT",
] # Chromosomes of build 37 would be default. I don't dare to change this yet since it's used all over the place. It needs major refactoring
CHROMOSOMES_38 = AUTOSOMES + ["X", "Y", "M"]
# Maps chromosomes to integers
CHROMOSOME_INTEGERS = {chrom: i + 1 for i, chrom in enumerate(CHROMOSOMES)}
PAR_COORDINATES = {