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
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
|
#cython: language_level=3
'''
Created on 14 sept. 2009
@author: coissac
'''
from obitools3.libalign import AlignedSequence
from obitools3.libalign import Alignment
from copy import deepcopy
######
#
# Import standard memory management function to improve
# efficiency of the alignment code
#
#
cdef AlignMatrix* allocateMatrix(int hsize, int vsize,AlignMatrix *matrix=NULL):
vsize+=1
hsize+=1
if matrix is NULL:
matrix = <AlignMatrix*>malloc(sizeof(AlignMatrix))
matrix.vsize=0
matrix.hsize=0
matrix.msize=0
matrix.matrix=NULL
matrix.bestVJump=NULL
matrix.bestHJump=NULL
if hsize > matrix.hsize:
matrix.bestVJump = <int*>realloc(matrix.bestVJump,hsize * sizeof(int))
matrix.hsize=hsize
if vsize > matrix.vsize:
matrix.bestHJump = <int*>realloc(matrix.bestHJump,vsize * sizeof(int))
matrix.vsize=vsize
if (hsize * vsize) > matrix.msize:
matrix.msize = hsize * vsize
matrix.matrix = <AlignCell*>realloc(matrix.matrix, matrix.msize * sizeof(AlignCell))
return matrix
cdef void freeMatrix(AlignMatrix* matrix):
if matrix is not NULL:
if matrix.matrix is not NULL:
free(matrix.matrix)
if matrix.bestVJump is not NULL:
free(matrix.bestVJump)
if matrix.bestHJump is not NULL:
free(matrix.bestHJump)
free(matrix)
cdef void resetMatrix(AlignMatrix* matrix):
if matrix is not NULL:
if matrix.matrix is not NULL:
bzero(<void*>matrix.matrix, matrix.msize * sizeof(AlignCell))
if matrix.bestHJump is not NULL:
memset(<void*>matrix.bestHJump,255,matrix.vsize * sizeof(int))
if matrix.bestVJump is not NULL:
memset(<void*>matrix.bestVJump,255,matrix.hsize * sizeof(int))
cdef alignSequence* allocateSequence(object bioseq, alignSequence* seq=NULL) except *:
cdef bytes strseq
cdef int i
if seq is NULL:
seq = <alignSequence*>malloc(sizeof(alignSequence))
seq.length=0
seq.buffsize=0
seq.sequence=NULL
seq.quality=NULL
seq.hasQuality=False
seq.length=len(bioseq)
if seq.length > seq.buffsize:
#seq.sequence = <char*>realloc(seq.sequence,sizeof(char)*seq.length)
#seq.quality = <double*>realloc(seq.quality,sizeof(double)*seq.length)
seq.buffsize = seq.length
# TODO optimisable...
#strseq = bioseq.seq.lower()
#memcpy(seq.sequence,<char*>strseq,seq.length)
seq.sequence = bioseq.seq
return seq
cdef void freeSequence(alignSequence* seq):
if seq is not NULL:
#if seq.sequence is not NULL:
# free(<void*>seq.sequence)
#if seq.quality is not NULL:
# free(<void*>seq.quality)
free(seq)
cdef alignPath* allocatePath(long l1,long l2,alignPath* path=NULL):
cdef long length=l1+l2
if path is NULL:
path = <alignPath*>malloc(sizeof(alignPath))
path.length=0
path.buffsize=0
path.path=NULL
if length > path.buffsize:
path.buffsize=length
path.path=<long*>realloc(path.path,sizeof(long)*length)
path.length=0
path.vStart=0
path.hStart=0
return path
cdef void reversePath(alignPath* path):
cdef long i
cdef long j
j=path.length
for i in range(<long>(path.length/2)): # TODO not sure about the cast
j-=1
path.path[i],path.path[j]=path.path[j],path.path[i]
cdef void freePath(alignPath* path):
if path is not NULL:
if path.path is not NULL:
free(<void*>path.path)
free(<void*>path)
cdef int aascii = ord(b'a')
cdef int _basecode[26]
cdef int bitCount(int x):
cdef int i=0
while(x):
i+=1
x&=x-1
return i
cpdef bint iupacMatch(unsigned char a, unsigned char b):
cdef bint m
if a==42: # * ascii code
a=110 # n ascii code
if b==42: # * ascii code
b=110 # n ascii code
m = _basecode[a - aascii] & _basecode[b - aascii]
return m
cpdef unsigned char encodeBase(unsigned char lettre):
return _basecode[lettre - aascii]
cpdef double iupacPartialMatch(unsigned char a, unsigned char b):
cdef int codeA
cdef int codeB
cdef int good
cdef int all
cdef double partial
if a==42: # * ascii code
a=110 # n ascii code
if b==42: # * ascii code
b=110 # n ascii code
codeA = _basecode[a - aascii]
codeB = _basecode[b - aascii]
good = bitCount(codeA & codeB)
all = bitCount(codeA) * bitCount(codeB)
partial= <double>good / all
return partial
cdef class DynamicProgramming:
def __init__(self,opengap,extgap):
self.sequenceChanged=True
self.scoreChanged=True
self.matrix=NULL
self.hSeq=NULL
self.vSeq=NULL
self.path=NULL
self.horizontalSeq=None
self.verticalSeq=None
self._opengap=opengap
self._extgap=extgap
cdef int _vlen(self):
return self.vSeq.length
cdef int _hlen(self):
return self.hSeq.length
cdef int allocate(self) except -1:
assert self.horizontalSeq is not None,'Sequence A must be set'
assert self.verticalSeq is not None,'Sequence B must be set'
cdef long lenH=self._hlen()
cdef long lenV=self._vlen()
self.matrix=allocateMatrix(lenH,lenV,self.matrix)
return 0
cdef double doAlignment(self) except? 0:
pass
cdef bint _needToCompute(self):
return self.scoreChanged or self.sequenceChanged
cdef void backtrack(self):
pass
property seqA:
def __get__(self):
return self.horizontalSeq
def __set__(self, seq):
self.sequenceChanged = True
self.horizontalSeq = seq
self.hSeq = allocateSequence(self.horizontalSeq, self.hSeq)
property seqB:
def __get__(self):
return self.verticalSeq
def __set__(self, seq):
self.sequenceChanged = True
self.verticalSeq = seq
self.vSeq = allocateSequence(self.verticalSeq, self.vSeq)
property opengap:
def __get__(self):
return self._opengap
def __set__(self,opengap):
self._opengap=opengap
self.scoreChanged=True
property extgap:
def __get__(self):
return self._extgap
def __set__(self,extgap):
self._extgap=extgap
self.scoreChanged=True
property needToCompute:
def __get__(self):
return self.scoreChanged or self.sequenceChanged
property score:
def __get__(self):
return self.doAlignment()
cdef void reset(self):
self.scoreChanged=True
resetMatrix(self.matrix)
cdef inline int index(self, int x, int y):
return (self._hlen()+1) * y + x
cdef void clean(self):
freeMatrix(self.matrix)
freeSequence(self.hSeq)
freeSequence(self.vSeq)
freePath(self.path)
def __dealloc__(self):
self.clean()
def __call__(self):
cdef list hgaps=[]
cdef list vgaps=[]
cdef list b
cdef int hp=0
cdef int vp=0
cdef int lenh=0
cdef int lenv=0
cdef int h,v,p
cdef int i
cdef object ali
cdef double score
if self._needToCompute():
score = self.doAlignment()
self.backtrack()
for i in range(self.path.length-1,-1,-1):
p=self.path.path[i]
if p==0:
hp+=1
vp+=1
lenh+=1
lenv+=1
elif p>0:
hp+=p
lenh+=p
vgaps.append([vp,p])
vp=0
else:
vp-=p
lenv-=p
hgaps.append([hp,-p])
hp=0
if hp:
hgaps.append([hp,0])
if vp:
vgaps.append([vp,0])
if lenh < self._hlen():
hseq=self.horizontalSeq[self.path.hStart:self.path.hStart+lenh]
else:
hseq=self.horizontalSeq
hseq=AlignedSequence(hseq)
hseq.gaps=hgaps
if lenv < self._vlen():
vseq=self.verticalSeq[self.path.vStart:self.path.vStart+lenv]
else:
vseq=self.verticalSeq
vseq=AlignedSequence(vseq)
vseq.gaps=vgaps
ali=Alignment()
ali.append(hseq)
ali.append(vseq)
ali.score=score
self.alignment=ali
ali=self.alignment.clone()
ali.score=self.alignment.score
return ali
# initialize iupac carray
__basecode=[1,14,2,13,0,0,4,11,0,0,12,0,3,15,0,0,0,5,6,8,8,7,9,0,10,0]
for i in range(26):
_basecode[i]=__basecode[i]
|
