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
216
217
218
219
220
221
222
223
224
225
226
227
228
|
import sys
import numpy as np
from .utils import Strand, log, breakpoint, new_strand, rev_cmpl
# ------------------------------------------------------------------------
# Node class: one visit along a path
class Node(object):
"""docstring for Node"""
def __init__(self, blk, num, strand):
self.blk = blk
self.num = num
self.strand = strand
def __str__(self):
return f"({self.blk}, {self.num}, {self.strand})"
def __repr__(self):
return str(self)
def __eq__(self, other):
return self.blk.id == other.blk.id and self.strand == other.strand
def __hash__(self):
return hash((self.blk.id, self.strand))
@classmethod
def from_dict(cls, d, blks):
N = Node()
N.blk = blks[d['id']]
N.num = d['num']
N.strand = Strand(d['strand'])
return N
def to_dict(self):
return {'id': self.blk.id, 'num': self.num, 'strand': int(self.strand)}
def length(self, name):
return self.blk.len_of(name, self.num)
# ------------------------------------------------------------------------
# Path class: (circular) list of blocks
class Path(object):
"""docstring for Path"""
def __init__(self, name, nodes, offset):
super(Path, self).__init__()
self.name = name
self.nodes = nodes if isinstance(nodes, list) else [nodes]
self.offset = offset
self.position = np.cumsum([0] + [n.length(name) for n in self.nodes])
def __str__(self):
return f"{self.name}: {[str(n) for n in self.nodes]}"
def __repr__(self):
return str(self)
@classmethod
def from_dict(cls, d):
P = Path()
P.name = d['name']
P.offset = d['offset']
P.nodes = [Node.from_dict(n) for n in d['nodes']]
return P
def to_dict(self):
return {'name': self.name, 'offset': self.offset, 'nodes': [n.to_dict() for n in self.nodes]}
def blocks(self):
return set([n.blk for n in self.nodes])
def sequence(self, verbose=False):
seq = ""
for n in self.nodes:
s = n.blk.extract(self.name, n.num, strip_gaps=True, verbose=verbose)
if n.strand == Strand.Plus:
seq += s
else:
seq += rev_cmpl(s)
if self.offset != 0:
seq = seq[self.offset:] + seq[:self.offset]
return seq
def rm_nil_blks(self):
good, popped = [], set()
for i, n in enumerate(self.nodes):
if n.blk.id in popped:
continue
if n.blk.is_empty(self.name, n.num):
if (self.name, n.num) not in n.blk.muts:
breakpoint("malformed mutation bookkeeping!")
n.blk.muts.pop((self.name, n.num))
else:
good.append(i)
if not n.blk.has(self.name):
popped.add(n.blk.id)
self.nodes = [self.nodes[i] for i in good]
self.position = np.cumsum([0] + [n.length(self.name) for n in self.nodes])
# TODO: debug cases w/ multiple runs
def merge(self, start, stop, new):
N = 0
while True:
ids = [n.blk.id for n in self.nodes]
try:
i, j = ids.index(start[0]), ids.index(stop[0])
if N > 0:
breakpoint("HIT")
if self.nodes[i].strand == start[1]:
beg, end, s = i, j, Strand.Plus
else:
beg, end, s = j, i, Strand.Minus
if beg < end:
self.nodes = self.nodes[:beg] + [Node(new, N, s)] + self.nodes[end+1:]
else:
self.offset += sum(n.blk.len_of(self.name, N) for n in self.nodes[beg:])
self.nodes = [Node(new, N, s)] + self.nodes[end+1:beg]
self.position = np.cumsum([0] + [n.length(self.name) for n in self.nodes])
N += 1
except:
return
def replace(self, blk, tag, new_blks, blk_map):
new = []
for n in self.nodes:
if n.blk.id == blk.id and n.num == tag[1]:
os = n.strand
mk = lambda b,ns,merged: Node(b, blk_map[b.id][blk.id][tag][1], new_strand(os, ns)) if merged else Node(b, n.num, new_strand(os, ns))
tmp = [mk(blk,ns,flag) for blk, ns, flag in new_blks]
if os == Strand.Minus:
tmp = tmp[::-1]
new.extend(tmp)
else:
new.append(n)
self.nodes = new
self.position = np.cumsum([0] + [n.length(self.name) for n in self.nodes])
def position_of(self, blk, num):
index = { n.num:i for i, n in enumerate(self.nodes) if n.blk == blk }
if not num in index:
return None
return (self.position[index[num]], self.position[index[num]+1])
def orientation_of(self, blk, num):
orientation = { n.num:n.strand for i, n in enumerate(self.nodes) if n.blk == blk }
if not num in orientation:
return None
return orientation[num]
# TODO: pull out common functionality into a helper function
# TODO: merge with other sequence function
def sequence_range(self, start=None, stop=None):
beg = start or 0
end = stop or self.position[-1]
l, r = "", ""
# if start == 159 and stop == 3659:
# breakpoint("test")
if beg < 0:
if len(self.nodes) > 1:
l = self.sequence_range(self.position[-1]+beg,self.position[-1])
beg = 0
if end > self.position[-1]:
if len(self.nodes) > 1:
r = self.sequence_range(0,end-self.position[-1])
end = self.position[-1]
if beg > end:
beg, end = end, beg
i = np.searchsorted(self.position, beg, side='right') - 1
j = np.searchsorted(self.position, end, side='left')
m = ""
if i < j:
if j >= len(self.position):
breakpoint("what?")
if i == j - 1:
m = self.nodes[i].blk.extract(self.name, self.nodes[i].num)[(beg-self.position[i]):(end-self.position[i])]
else:
m = self.nodes[i].blk.extract(self.name, self.nodes[i].num)[(beg-self.position[i]):]
for n in self.nodes[i+1:j-1]:
m += n.blk.extract(self.name, n.num)
n = self.nodes[j-1]
b = n.blk.extract(self.name, n.num)
m += b[0:(end-self.position[j-1])]
return l + m + r
def __getitem__(self, index):
if isinstance(index, slice):
beg = index.start or 0
end = index.stop or self.position[-1]
l, r = [], []
if beg < 0:
if len(self.nodes) > 1:
l = self[(self.position[-1]+beg):self.position[-1]]
beg = 0
if end > self.position[-1]:
if len(self.nodes) > 1:
r = self[0:(end-self.position[-1])]
end = self.position[-1]
if beg > end:
beg, end = end, beg
i = np.searchsorted(self.position, beg, side='right') - 1
j = np.searchsorted(self.position, end, side='left')
if i > j:
breakpoint(f"not sorted, {beg}-{end}")
return l + [n.blk for n in self.nodes[i:j]] + r
elif isinstance(index, int):
i = np.searchsorted(self.position, index, side='right') - 1
return self.nodes[i].blk
else:
raise ValueError(f"type '{type(index)}' not supported as index")
def __len__(self):
return self.position[-1]
|