-
Notifications
You must be signed in to change notification settings - Fork 0
/
parse_bam.py
215 lines (191 loc) · 7.62 KB
/
parse_bam.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
import sys, re
import pysam as ps
import utils as ut
#### cigar operation:
BAM_CMATCH = 0 # M
BAM_CINS = 1 # I
BAM_CDEL = 2 # D
BAM_CREF_SKIP = 3 # N
BAM_CSOFT_CLIP = 4 # S
BAM_CHARD_CLIP = 5 # H
BAM_CPAD = 6 # P
BAM_CEQUAL = 7 # =
BAM_CDIFF = 8 # X
BAM_CBACK = 9 # B
# cigar stats:
# M BAM_CMATCH 0
# I BAM_CINS 1
# D BAM_CDEL 2
# N BAM_CREF_SKIP 3
# S BAM_CSOFT_CLIP 4
# H BAM_CHARD_CLIP 5
# P BAM_CPAD 6
# = BAM_CEQUAL 7
# X BAM_CDIFF 8
# B BAM_CBACK 9
# NM NM tag 10
def get_ref_op_length(cigar_stats=[]):
# get op length for MDNP=X
op_len = cigar_stats[0] + cigar_stats[2] + cigar_stats[3] + cigar_stats[6] + cigar_stats[7] + cigar_stats[8]
return op_len
def get_read_op_length(cigar_stats):
# get op length for MISH=X
op_len = cigar_stats[0] + cigar_stats[1] + cigar_stats[4] + cigar_stats[5] + cigar_stats[7] + cigar_stats[8]
return op_len
def get_aligned_read_length(cigar_stats):
# get op length for MI=X
op_len = cigar_stats[0] + cigar_stats[1] + cigar_stats[7] + cigar_stats[8]
return op_len
def minipulate_cigar(r=ps.AlignedSegment, old='', new=''):
r.cigarstring = re.sub(r'%s' % old, new, r.cigarstring)
def get_spec_MD(mdstr='', start=0, end=0): # '23AC20T', 10, 30 => ' 13AC5
mSub = re.sub(r'([ACGTNacgtn])', ' \\1 ', mdstr)
mSplit = re.split('[ ]+', mSub)
start_remain_len = start
end_remain_len = end - start
ret_md = []
mi = 0
# print mSplit, start_remain_len, end_remain_len
while start_remain_len > 0:
if mSplit[mi].isdigit():
if int(mSplit[mi]) > start_remain_len:
mSplit[mi] = str(int(mSplit[mi]) - start_remain_len)
start_remain_len = 0
break
else:
start_remain_len -= int(mSplit[mi])
else: # isalpha()
start_remain_len -= 1
mi += 1
while end_remain_len > 0:
if mSplit[mi].isdigit():
if int(mSplit[mi]) >= end_remain_len:
ret_md.append(str(end_remain_len))
end_remain_len = 0
break
else:
end_remain_len -= int(mSplit[mi])
ret_md.append(mSplit[mi])
else: # isalpha()
end_remain_len -= 1
ret_md.append(mSplit[mi])
mi += 1
# print ret_md
return ret_md
# MISMATCH: read_pos(first), ref_pos(first), len, read_base, ref_base
# INSERTION: ins_read_pos(first), ins_ref_pos(left), len, ins_base
# DELETION: del_read_pos(left), del_ref_pos(first), len, del_base
def get_error_from_MD(cigartuples=[], mdstr='', full_query_seq='', ref_start=0):
mis, ins, dele = [], [], []
last_error = ''
md_i, m_pos = 0, 0
mdSub = re.sub(r'([\\^][ACGTNacgtn]+)[0]*', ' \\1 ', mdstr)
mdSplit = mdSub.rsplit()
ref_pos, query_pos = ref_start, 0
for tuples in cigartuples:
if tuples[0] == BAM_CMATCH:
m = mdSplit[md_i]
if m.startswith('^'):
ut.format_time(sys.stderr, 'get_error_from_MD', 'Unexpected MD string: {}\n'.format(mdstr))
sys.exit(1)
mSub = re.sub(r'([ACGTNacgtn])', ' \\1 ', m)
m_len = sum(map(int, (re.sub(r'([ACGTNacgtn])', '1', mSub)).rsplit()))
# from m_pos to m_pos + tuples[1]
sub_ms = get_spec_MD(m, m_pos, m_pos + tuples[1])
for ms in sub_ms:
if ms.isalpha(): # MISMATCH
if last_error != 'MIS' or mis[-1][0] != query_pos - 1:
mis_error = [query_pos, ref_pos, 1, full_query_seq[query_pos], ms]
mis.append(mis_error)
else: # last_error == 'MIS' and mis[-1][1] == ap[0] - 1:
mis[-1][-3] += 1
mis[-1][-2] += full_query_seq[query_pos]
mis[-1][-1] += ms
query_pos += 1
ref_pos += 1
last_error = 'MIS'
elif ms.isdigit(): # MATCH
query_pos += int(ms)
ref_pos += int(ms)
if m_pos + tuples[1] == m_len:
md_i += 1
m_pos = 0
elif m_pos + tuples[1] < m_len:
m_pos += tuples[1]
else: #
ut.format_time(sys.stderr, 'get_error_from_MD', 'Unexpected MD string: {}\n'.format(mdstr))
sys.exit(1)
elif tuples[0] == BAM_CDEL:
m = mdSplit[md_i]
if not m.startswith('^'):
ut.format_time(sys.stderr, 'get_error_from_MD', 'Unexpected MD string: {}\n'.format(mdstr))
sys.exit(1)
del_error = [query_pos - 1, ref_pos, tuples[1], m[1:]]
dele.append(del_error)
ref_pos += tuples[1]
last_error = 'DEL'
md_i += 1
elif tuples[0] == BAM_CINS:
ins_error = [query_pos, ref_pos - 1, tuples[1], full_query_seq[query_pos:query_pos + tuples[1]]]
ins.append(ins_error)
query_pos += tuples[1]
last_error = 'INS'
elif tuples[0] == BAM_CSOFT_CLIP or tuples[0] == BAM_CHARD_CLIP:
query_pos += tuples[1]
elif tuples[0] == BAM_CREF_SKIP:
ref_pos += tuples[1]
else:
ut.format_time(sys.stderr, 'get_error_from_MD', 'Unexpected cigar: {}\n'.format(cigartuples))
sys.exit(1)
return mis, ins, dele
def get_error_from_Cigar(cigartuples=[], full_query_seq='', align_ref_seq='', ref_start=0):
mis, ins, dele = [], [], []
last_error = ''
ref_pos, query_pos = ref_start, 0
for tuples in cigartuples:
if tuples[0] == BAM_CMATCH:
for q, r in zip(full_query_seq[query_pos:query_pos + tuples[1]],
align_ref_seq[ref_pos - ref_start:ref_pos - ref_start + tuples[1]]):
if q != r: # MISMATCH
if last_error != 'MIS' or mis[-1][0] != query_pos - 1:
mis_error = [query_pos, ref_pos, 1, q, r]
mis.append(mis_error)
else: # last_error == 'MIS' and mis[-1][1] == ap[0] - 1:
mis[-1][-3] += 1
mis[-1][-2] += q
mis[-1][-1] += r
last_error = 'MIS'
ref_pos += 1
query_pos += 1
elif tuples[0] == BAM_CDEL:
del_error = [query_pos - 1, ref_pos, tuples[1],
align_ref_seq[ref_pos - ref_start:ref_pos - ref_start + tuples[1]]]
dele.append(del_error)
last_error = 'DEL'
ref_pos += tuples[1]
elif tuples[0] == BAM_CINS:
ins_error = [query_pos, ref_pos - 1, tuples[1], full_query_seq[query_pos:query_pos + tuples[1]]]
ins.append(ins_error)
last_error = 'INS'
query_pos += tuples[1]
elif tuples[0] == BAM_CHARD_CLIP or tuples[0] == BAM_CSOFT_CLIP:
query_pos += tuples[1]
elif tuples[0] == BAM_CREF_SKIP:
ref_pos += tuples[1]
else:
ut.format_time(sys.stderr, 'get_error_from_Cigar', 'Unexpected cigar: {}\n'.format(cigartuples))
sys.exit(1)
return mis, ins, dele
def get_exon_block(tid, is_rev, cigartuples=[], ref_start=0):
exon_block = []
start = ref_start
end = ref_start - 1
for tuples in cigartuples:
if tuples[0] == BAM_CMATCH or tuples[0] == BAM_CDEL:
end += tuples[1]
elif tuples[0] == BAM_CREF_SKIP:
exon_block.append((tid, is_rev, start, end))
start = end + tuples[1] + 1
end = start -1
exon_block.append((tid, is_rev, start, end))
return exon_block