def test_count_different_type_3():
"allow inconsis"
o = Namespace(verbos=False, allow_inconsist=True)
pair = {
('ref', 2, True): [('A', 60), ('T', 60), ('T', 60)],
('ref', 3, False): [('A', 60), ('T', 60), ('T', 60)]
}
mor, mnr, msr, oor, onr, osr, moa, mna, msa, ooa, ona, osa, inconsis = count_different_type(
o, pair, {}, 'T', 'A')
assert mor == 0
assert mnr == 0
assert msr == 0
assert oor == 1
assert onr == 1
assert osr == 0
assert moa == 1
assert mna == 1
assert msa == 0
assert ooa == 0
assert ona == 0
assert osa == 0
assert inconsis == 0
def anno(line):
line = line.rstrip().split('\t')
chr, pos, _, ref, alt = line[:5]
line[-3] += ':UDP' # format
line[-2] += ':' # gdna
line[-1] += ':' # cfdna
for i, sam in enumerate((o.cfdna, o.gdna)):
if sam != None:
reads = get_reads(o, sam, chr, pos)
unique_pairs, unique_single, *_ = aggregate_reads(
o, reads, None if o.fast else pad_softclip(sam))
mor, mnr, msr, oor, onr, osr, moa, mna, msa, ooa, ona, osa, _ = count_different_type(
o, unique_pairs, unique_single, alt, ref)
if o.simple:
line[-i - 1] += ','.join(
map(str, (moa, mna + msa, ooa, ona + osa)))
else:
line[-i - 1] += ','.join(
map(str, (mor, mnr, msr, oor, onr, osr, moa, mna,
msa, ooa, ona, osa)))
print(file=fout, sep='\t', *line)
def test_count_different_type_1():
"it should NOT count dna that more than 10% reads have different bases"
o = Namespace(verbos=False)
pair = {
('ref', 2, True): [('A', 60), ('T', 60), ('T', 60)],
('ref', 3, False): [('A', 60), ('T', 60), ('T', 60)]
}
mor, mnr, msr, oor, onr, osr, moa, mna, msa, ooa, ona, osa, inconsis = count_different_type(
o, pair, {}, 'T', 'A')
assert inconsis == 2
assert sum(
(mor, mnr, msr, oor, onr, osr, moa, mna, msa, ooa, ona, osa)) == 0
def test_count_different_type_2():
"basic non-trival test case"
o = Namespace(verbos=False)
pair = {
(2, 5, True): [('A', 60), ('A', 60)],
(3, 5, False): [('T', 60), ('T', 60), ('T', 60)],
(4, 5, False): [
('T', 60),
]
}
single = {
(2, 5, True): [('T', 60), ('A', 60)],
(3, 5, False): [('T', 60), ('T', 60), ('T', 60)],
(4, 5, False): [
('A', 60),
]
}
mor, mnr, msr, oor, onr, osr, moa, mna, msa, ooa, ona, osa, inconsis = count_different_type(
o, pair, single, 'T', 'A')
assert mor == 1
assert mnr == 0
assert msr == 0
assert oor == 0
assert onr == 0
assert osr == 1
assert moa == 0
assert mna == 1
assert msa == 1
assert ooa == 0
assert ona == 1
assert osa == 0
assert inconsis == 1
def output(poss, info, o, fout):
if o.verbos:
print("continus", poss)
if len(poss) > 2:
for i in poss:
print(info[i])
return
sep1 = info[poss[0]].split('\t')
sep2 = info[poss[1]].split('\t')
ref = sep1[3] + sep2[3]
alt = sep1[4] + sep2[4]
fetch = o.cfdna.fetch(sep1[0], poss[0], poss[1] + 1)
reads = []
for read in fetch:
reads.append(read)
new_reads = get_infor(o, reads, poss, ref)
mut_set, name_dict, unique_pairs, unique_single = snv_mut(
new_reads, o, ref, alt, None)
if len(mut_set) == 0:
if o.verbos:
print('continus fail ', poss)
for i in poss:
print(info[i])
return
sep1[-3] += ':UDP'
sep1[3] = ref
sep1[4] = alt
sep1[2] = int(sep1[1]) + 1
if o.verbos:
print("test\t", mut_set, sep1[0], poss[0], ref, sep1[3], sep1[4], alt,
len(name_dict), len(unique_pairs), len(unique_single))
mor, mnr, msr, oor, onr, osr, moa, mna, msa, ooa, ona, osa, _ = count_different_type(
o, unique_pairs, unique_single, alt, ref)
(nq10_a, nterminal_a, nmulti_a, noverlap_pe_a, noverlap_se_a, numi_a, nCN_1_a, nCN_2_a, nNonterminalMolecule_a, \
ave_mapqual_a, ave_insertSize_a) = extra_info(o, name_dict, ref, alt)
extra_1 = ','.join(
map(str, (nq10_a, nterminal_a, nmulti_a, noverlap_pe_a, noverlap_se_a,
numi_a, nCN_1_a, nCN_2_a, nNonterminalMolecule_a,
ave_mapqual_a, ave_insertSize_a)))
sep1[-1] += ':' + ','.join(
map(str, (mor, mnr, msr, oor, onr, osr, moa, mna, msa, ooa, ona, osa)))
fetch = o.gdna.fetch(sep1[0], poss[0], poss[1] + 1)
reads = []
for read in fetch:
reads.append(read)
new_reads = get_infor(o, reads, poss, ref)
mut_set, name_dict, unique_pairs, unique_single = snv_mut(
new_reads, o, ref, alt, None)
mor, mnr, msr, oor, onr, osr, moa, mna, msa, ooa, ona, osa, _ = count_different_type(
o, unique_pairs, unique_single, alt, ref)
(nq10_a, nterminal_a, nmulti_a, noverlap_pe_a, noverlap_se_a, numi_a, nCN_1_a, nCN_2_a, nNonterminalMolecule_a, \
ave_mapqual_a, ave_insertSize_a) = extra_info(o, name_dict, ref, alt)
extra_2 = ','.join(map(str, (nq10_a, nterminal_a, nmulti_a, noverlap_pe_a, noverlap_se_a, numi_a, nCN_1_a, nCN_2_a, \
nNonterminalMolecule_a, ave_mapqual_a, ave_insertSize_a)))
sep1[-2] += ':' + ','.join(
map(str, (mor, mnr, msr, oor, onr, osr, moa, mna, msa, ooa, ona, osa)))
sep1.append(extra_2)
sep1.append(extra_1)
print(file=fout, sep="\t", *sep1)
def output(chr, pos, alt, variation_info, o, fout, reads_pos, k, rep_ref):
tmp = ''.join((chr, str(pos), alt))
if k == 0:
variation_info[tmp][-3] += ':UDP'
line = deepcopy(variation_info[tmp])
ref = variation_info[tmp][3]
repeat = repeat_area(rep_ref, chr, pos + 1, o)
pos_set = [pos]
# to corporate with continous.py
new_reads = get_infor(o, reads_pos, pos_set, ref)
mut_set, name_dict, unique_pairs, unique_single = snv_mut(
new_reads, o, ref, alt, None if o.fast else pad_softclip(sam))
for each_mut in mut_set:
tmp = ''.join((chr, str(pos), each_mut))
if each_mut != alt:
# MNV(multiple nucleotide variation)
if k == 0:
# novel mutation in gdna
variation_info[tmp] = deepcopy(line)
variation_info[tmp][4] = each_mut
else:
if tmp not in variation_info:
# cfdna owing novel mutation while gnda not
# gdna owing novel muatation while cfdna not won't be output
variation_info[tmp] = deepcopy(line)
#This is copy from gdna-produced result
variation_info[tmp][4] = each_mut
try:
gdna_alt = variation_info[tmp][-3].split(
':')[-1].split(',')
for i in range(-6, 0):
gdna_alt[i] = '0'
variation_info[tmp][-3] = ':'.join(
(variation_info[tmp][-3].split(':')[:-1]
)) + ":" + ','.join(gdna_alt)
except:
raise Exception(gdna_alt, i, variation_info[tmp])
#extra_2 = repeat + ',' + ','.join(map(str, [0] * 9))
extra_2 = ','.join(map(str, [0] * 9))
variation_info[tmp][-1] = extra_2
mor, mnr, msr, oor, onr, osr, moa, mna, msa, ooa, ona, osa, _ = count_different_type(
o, unique_pairs, unique_single, each_mut, ref)
(nq10_a, nterminal_a, nmulti_a, noverlap_pe_a, noverlap_se_a, numi_a,
nCN_1_a, nCN_2_a, nNonterminalMolecule_a, ave_mapqual_a,
ave_insertSize_a) = extra_info(o, name_dict, ref, each_mut)
variation_info[tmp][-2] += ':' + ','.join(
map(str,
(mor, mnr, msr, oor, onr, osr, moa, mna, msa, ooa, ona, osa)))
extra_2 = ','.join(
map(str,
(nq10_a, nterminal_a, nmulti_a, noverlap_pe_a, noverlap_se_a,
numi_a, nCN_1_a, nCN_2_a, nNonterminalMolecule_a,
ave_mapqual_a, ave_insertSize_a)))
variation_info[tmp].append(extra_2)
if k == 1:
print(file=fout, sep='\t', *variation_info[tmp])
fout.flush()
del variation_info[tmp]
return variation_info