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)))
