def get_my_mutations(quality_cutoff, coverage_cutoff): """Load mutations from working/""" # my_mutations = {} # with open('/home/perry/Projects/loh/working/murim.exome.aa_chg.vars') as f: # for line in f: # my_mutations[line.strip()] = True # return my_mutations bed_file = 'data/nimblegen/2.1M_Human_Exome_Annotation/2.1M_Human_Exome.bed' bed_chr2st2end, bed_chr2posLs = bed_tools.load_bed(bed_file, 'NimbleGen Tiled Regions') # NimbleGen Tiled Regions # Target Regions use_data_dir = '/home/perry/Projects/loh/data/all_non_ref_hg18/' all_somatic = {} all_inherited = {} cancer_qualities = mutations.get_consensus_qualities(use_data_dir + 'yusanT.ann') normal_qualities = mutations.get_consensus_qualities(use_data_dir + 'yusanN.ann') for exome in global_settings.exome_types: data_file = use_data_dir + exome inherited, somatic, murim = mutations.get_mutations(data_file, normal_qualities, cancer_qualities, quality_cutoff, False, coverage_cutoff) # only use the bed_tools NimbleGen # restriction for hg18 data for s in somatic['yusan']: chr, pos = s.split(':') if bed_tools.find_location_in_bed(chr, int(pos), bed_chr2posLs, bed_chr2st2end): all_somatic[s] = True for i in inherited['yusan']: chr, pos = s.split(':') if bed_tools.find_location_in_bed(chr, int(pos), bed_chr2posLs, bed_chr2st2end): all_inherited[i] = True return (set(all_somatic.keys()) & set(get_murim_covered(quality_cutoff)), set(all_inherited.keys()) & set(get_murim_covered(quality_cutoff)))