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
|
"""
Pyrex extension classes used by `seqmapping.py`.
"""
from cpython.buffer cimport (
PyBUF_SIMPLE,
PyBUF_WRITABLE,
PyBuffer_Release,
PyObject_GetBuffer,
)
from cpython.bytes cimport PyBytes_AsStringAndSize
from libc.stdlib cimport (
free,
malloc,
)
import random
import sys
from math import floor
from numpy import zeros
cdef class CharToIntArrayMapping:
"""Mapping for converting strings to int arrays"""
cdef int table[256]
cdef int out_size
cdef object reverse_table
def __cinit__( self ):
"""Init empty mapping (all characters map to -1)"""
cdef int i
for i from 0 <= i < 256: self.table[i] = -1
self.out_size = 0
def __init__( self ):
self.reverse_table = dict()
def set_mapping( self, c, int symbol ):
"""Modify mapping so 'chars' map to 'symbol'"""
char = ord( c )
self.table[ char ] = symbol
if self.out_size <= symbol:
self.out_size = symbol + 1
self.reverse_table[ symbol ] = chr( char )
def translate( self, string ):
"""Translate 'string' and return as int array"""
cdef Py_ssize_t s_len
cdef unsigned char * s_buf
cdef Py_buffer t_view
cdef int * t_buf
# Get direct access to string
PyBytes_AsStringAndSize( string, <char **> &s_buf, &s_len )
# Initialize empty array
rval = zeros( s_len, 'i' )
if PyObject_GetBuffer(rval, &t_view, PyBUF_WRITABLE) != 0:
raise ValueError("Unable to get buffer")
try:
t_buf = <int *>t_view.buf
# Translate
for i from 0 <= i < s_len:
t_buf[i] = self.table[s_buf[i]]
finally:
PyBuffer_Release(&t_view)
return rval
def translate_list( self, strings ):
"""Translate a list of strings into an int array"""
cdef Py_ssize_t i, s_len, text_len
cdef Py_buffer t_view
cdef int factor = 1
cdef unsigned char * s_buf
cdef int * t_buf
# No input, no output
if len( strings ) < 1: return None
# Length of result
text_len = len( strings[0] )
# Init result array
rval = zeros( text_len, 'i' )
if PyObject_GetBuffer(rval, &t_view, PyBUF_WRITABLE) != 0:
raise ValueError("Unable to get buffer")
try:
t_buf = <int *>t_view.buf
# Loop over seqs and accumulate result values
for string in strings:
PyBytes_AsStringAndSize(string, <char **> &s_buf, &s_len)
for i from 0 <= i < text_len:
if t_buf[i] >= 0:
if self.table[s_buf[i]] == -1:
t_buf[i] = -1
else:
t_buf[i] += self.table[s_buf[i]] * factor
factor *= self.out_size
finally:
PyBuffer_Release(&t_view)
return rval
def reverse_map( self, val, nseqs ):
factor = self.out_size ** (nseqs-1)
rval = []
while factor > 0:
rval.append( self.reverse_table[ int( floor( val / factor ) ) ] )
val = val - ( floor(val/factor) * factor )
factor = floor( factor / self.out_size )
rval.reverse()
return rval
def get_out_size( self ):
return self.out_size
cdef class IntToIntMapping:
cdef int* table
cdef int in_size
cdef int out_size
def __cinit__( self, int in_size ):
self.in_size = in_size
self.table = <int *> malloc( in_size * sizeof( int ) )
if self.table == NULL: raise "Malloc Failed"
for i from 0 <= i < in_size: self.table[i] = -1
self.out_size = 0
def __dealloc__( self ):
# sys.stderr.write( "freeing mapping_helper.IntToIntMapping\n" ); sys.stderr.flush()
free( self.table )
def set_mapping( self, int index, int symbol ):
assert ( -1 <= index < self.in_size ), "%d not between 0 and %s" % ( index, self.in_size )
self.table[index] = symbol
if self.out_size <= symbol:
self.out_size = symbol + 1
def translate( self, src ):
"""Translate `string` and return as int array"""
cdef Py_buffer s_view, t_view
cdef Py_ssize_t s_len
cdef int *s_buf
cdef int *t_buf
# Get direct access to string
if PyObject_GetBuffer(src, &s_view, PyBUF_SIMPLE) != 0:
raise ValueError("Unable to get buffer")
try:
s_len = s_view.len // sizeof(int)
s_buf = <int *>s_view.buf
assert s_len == len(src), "`src` argument must be a buffer of 32bit integers"
# Initialize empty array
rval = zeros(s_len, "i")
if PyObject_GetBuffer(rval, &t_view, PyBUF_WRITABLE) != 0:
raise ValueError("Unable to get buffer")
try:
t_buf = <int *>t_view.buf
# Translate
for i from 0 <= i < s_len:
if s_buf[i] == -1:
t_buf[i] = -1
elif s_buf[i] >= self.in_size:
t_buf[i] = -1
else:
t_buf[i] = self.table[s_buf[i]]
finally:
PyBuffer_Release(&t_view)
finally:
PyBuffer_Release(&s_view)
return rval
def __getitem__( self, int x ):
if x == -1: return -1
assert 0 <= x < self.in_size
return self.table[ x ]
def collapse( self, int a, int b ):
cdef int i
cdef IntToIntMapping copy
copy = IntToIntMapping( self.in_size )
copy.out_size = self.out_size - 1
if a > b: a, b = b, a
for i from 0 <= i < self.in_size:
if self.table[i] == b: copy.table[i] = a
elif self.table[i] == copy.out_size: copy.table[i] = b
else: copy.table[i] = self.table[i]
return copy
def expand( self, int x ):
"""Grow the alphabet by making 'a' a separate symbol. If it already mapped to a single symbol, do nothing"""
cdef int i, count, a, b
cdef IntToIntMapping copy
# Get the symbol x maps to
a = self.table[x]
# Symbols that map to -1 should not be touched
if a < 0: return self
# Count how many other input symbols map to a
count = 0
for i from 0 <= i < self.in_size:
if self.table[i] == a: count = count + 1
# Already a singleton
if count < 2: return self
# Otherwise, make a copy with the separated symbol
copy = IntToIntMapping( self.in_size )
copy.out_size = self.out_size + 1
for i from 0 <= i < self.in_size:
copy.table[i] = self.table[i]
copy.table[x] = self.out_size
return copy
def expand_out( self, int a ):
"""Grow the alphabet breaking 'a' into two symbols randomly"""
cdef int i, count, to_split, b
cdef IntToIntMapping copy
count = 0
for i from 0 <= i < self.in_size:
if self.table[i] == a: count = count + 1
if count < 2: return self
copy = IntToIntMapping( self.in_size )
copy.out_size = self.out_size + 1
b = self.out_size
to_split = random.randrange( count )
count = 0
for i from 0 <= i < self.in_size:
if self.table[i] == a:
if count == to_split: copy.table[i] = b
else: copy.table[i] = a
count = count + 1
else:
copy.table[i] = self.table[i]
return copy
def expand_random_split( self, int a ):
"""Grow the alphabet breaking 'a' into two symbols randomly"""
cdef int i, count, b
cdef IntToIntMapping copy
count = 0
for i from 0 <= i < self.in_size:
if self.table[i] == a: count = count + 1
if count < 2: return self
copy = IntToIntMapping( self.in_size )
copy.out_size = self.out_size + 1
b = self.out_size
to_split = random.sample( range( count ), count/2 )
count = 0
for i from 0 <= i < self.in_size:
if self.table[i] == a:
if count in to_split: copy.table[i] = b
else: copy.table[i] = a
count = count + 1
else:
copy.table[i] = self.table[i]
return copy
def get_in_size( self ):
return self.in_size
def get_out_size( self ):
return self.out_size
def get_table( self ):
rval = zeros( self.in_size, 'i' )
for i in range( self.in_size ):
rval[i] = self.table[i]
return rval
|
