def test_find_location_in_bed():
"""See if I'm using searching correctly w/ binary search"""
# this is in the file
chr = "chr5"
pos = 180603265
bed_file = "../data/nimblegen/2.1M_Human_Exome_Annotation/2.1M_Human_Exome.bed"
chr2st2end, chr2posLs = bed_tools.load_bed(bed_file, "NimbleGen Tiled Regions")
location = bed_tools.find_location_in_bed(chr, pos, chr2posLs, chr2st2end)
nose.tools.assert_equal(location, 180603263, "did not find location, found " + str(location))
# this is not in the file
# too large
chr = "chrY"
pos = 26180101
location = bed_tools.find_location_in_bed(chr, pos, chr2posLs, chr2st2end)
nose.tools.assert_true(not location, "found location in too big test, but should not have, found " + str(location))
# this is not in the file
# too small
chr = "chr12"
pos = 100
location = bed_tools.find_location_in_bed(chr, pos, chr2posLs, chr2st2end)
nose.tools.assert_true(
not location, "found location in too small test, but should not have, found " + str(location)
)
# this is not in the file
# between capture regions
chr = "chr6"
pos = 170731150
location = bed_tools.find_location_in_bed(chr, pos, chr2posLs, chr2st2end)
nose.tools.assert_true(not location, "found location in between test, but should not have, found " + str(location))
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)))
captureDataStrict = bed_tools.load_nb222_exome_capture_driver('tmp.bed', 0)
captureDataRelaxed = bed_tools.load_nb222_exome_capture_driver('tmp.bed', 100)
with open(fileToAnnotate) as f, open(outFile, 'w') as fout:
reader = csv.DictReader(f, delimiter='\t')
print('\t'.join(reader.fieldnames) + '\t'
+ '\t'.join(['CAPTURE_STRICT_' + title,
'CAPTURE_RELAXED_' + title,
]),
file=fout)
for row in reader:
chrom = row['chrom']
st,end = mkSnvBedFile.fixCoords(row)
st = int(st)
status = {}
for captureData, label in ( (captureDataStrict, 'STRICT'),
(captureDataRelaxed, 'RELAXED') ):
captureStatusSt = bed_tools.find_location_in_bed("chr" + chrom, st, captureData[1], captureData[0])
if captureStatusSt:
status[label] = 'CAP_%s_TRUE' % (label,)
else:
status[label] = 'CAP_%s_FALSE' % (label,)
print('\t'.join([row[x] for x in reader.fieldnames]
+ [status['STRICT'],
status['RELAXED'],
]),
file=fout)
os.system('rm tmp.bed')