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
|
"""
cigar is a simple library for dealing with cigar strings. the most useful
feature now is soft-masking from left or right. This allows one to adjust
a SAM record only by changing the cigar string to soft-mask a number of bases
such that the rest of the SAM record (pos, tlen, etc.) remain valid, but
downstream tools will not consider the soft-masked bases in further analysis.
>>> c = Cigar('100M')
>>> len(c)
100
>>> str(c)
'100M'
>>> list(c.items())
[(100, 'M')]
>>> c = Cigar('20H20M20S')
>>> len(c)
40
>>> str(c)
'20H20M20S'
>>> list(c.items())
[(20, 'H'), (20, 'M'), (20, 'S')]
>>> c.mask_left(29).cigar, c.cigar
('20H9S11M20S', '20H20M20S')
>>> c = Cigar('10M20S10M')
>>> c.mask_left(10).cigar
'30S10M'
>>> c.mask_left(9).cigar
'9S1M20S10M'
>>> Cigar('10S').mask_left(10).cigar
'10S'
>>> Cigar('10H').mask_left(10).cigar
'10H'
>>> Cigar('10H').mask_left(11).cigar
'10H'
>>> Cigar('10H').mask_left(9).cigar
'10H'
>>> Cigar('1M10H').mask_left(9).cigar
'1S10H'
>>> Cigar('5M10H').mask_left(9).cigar
'5S10H'
>>> c = Cigar('1S1H1S5H1S5M10H')
>>> c.mask_left(9).cigar == c.cigar
True
>>> c = Cigar('1S1H1S5H1S5M10H')
>>> c.mask_right(9).cigar == c.cigar
True
>>> c.mask_right(11).cigar
'1S1H1S5H1S4M1S10H'
"""
from __future__ import print_function
from itertools import groupby
from operator import itemgetter
__version__ = "0.1.3"
class Cigar(object):
read_consuming_ops = ("M", "I", "S", "=", "X")
ref_consuming_ops = ("M", "D", "N", "=", "X")
def __init__(self, cigar_string):
self.cigar = cigar_string
def items(self):
if self.cigar == "*":
yield (0, None)
raise StopIteration
cig_iter = groupby(self.cigar, lambda c: c.isdigit())
for g, n in cig_iter:
yield int("".join(n)), "".join(next(cig_iter)[1])
def __str__(self):
return self.cigar
def __repr__(self):
return "Cigar('%s')" % self
def __len__(self):
"""
sum of MIS=X ops shall equal the sequence length.
"""
return sum(l for l, op,in self.items() \
if op in Cigar.read_consuming_ops)
def reference_length(self):
return sum(l for l, op in self.items() \
if op in Cigar.ref_consuming_ops)
def mask_left(self, n_seq_bases, mask="S"):
"""
Return a new cigar with cigar string where the first `n_seq_bases` are
soft-masked unless they are already hard-masked.
"""
cigs = list(self.items())
new_cigs = []
c, cum_len = self.cigar, 0
for i, (l, op) in enumerate(cigs):
if op in Cigar.read_consuming_ops:
cum_len += l
if op == "H":
cum_len += l
new_cigs.append(cigs[i])
elif cum_len < n_seq_bases:
new_cigs.append(cigs[i])
else:
# the current cigar element is split by the masking.
right_extra = cum_len - n_seq_bases
new_cigs.append((l - right_extra, 'S'))
if right_extra != 0:
new_cigs.append((right_extra, cigs[i][1]))
if cum_len >= n_seq_bases: break
else:
pass
new_cigs[:i] = [(l, op if op in "HS" else "S") for l, op in
new_cigs[:i]]
new_cigs.extend(cigs[i + 1:])
return Cigar(Cigar.string_from_elements(new_cigs)).merge_like_ops()
@classmethod
def string_from_elements(self, elements):
return "".join("%i%s" % (l, op) for l, op in elements if l !=0)
def mask_right(self, n_seq_bases, mask="S"):
"""
Return a new cigar with cigar string where the last `n_seq_bases` are
soft-masked unless they are already hard-masked.
"""
return Cigar(Cigar(self._reverse_cigar()).mask_left(n_seq_bases, mask)._reverse_cigar())
def _reverse_cigar(self):
return Cigar.string_from_elements(list(self.items())[::-1])
def merge_like_ops(self):
"""
>>> Cigar("1S20M").merge_like_ops()
Cigar('1S20M')
>>> Cigar("1S1S20M").merge_like_ops()
Cigar('2S20M')
>>> Cigar("1S1S1S20M").merge_like_ops()
Cigar('3S20M')
>>> Cigar("1S1S1S20M1S1S").merge_like_ops()
Cigar('3S20M2S')
"""
cigs = []
for op, grps in groupby(self.items(), itemgetter(1)):
cigs.append((sum(g[0] for g in grps), op))
return Cigar(self.string_from_elements(cigs))
if __name__ == "__main__":
import doctest
doctest.testmod()
|
