'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 = {