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
|
"""
Extensions used by the `pwm` module.
"""
from cpython.version cimport PY_MAJOR_VERSION
cdef extern from "Python.h":
int PyBytes_AsStringAndSize(object obj, char **buffer, Py_ssize_t* length) except -1
cdef extern from "numpy/arrayobject.h":
ctypedef int intp
ctypedef extern class numpy.ndarray [object PyArrayObject]:
cdef char *data
cdef int nd
cdef intp *dimensions
cdef intp *strides
cdef int flags
# These might be other types in the actual header depending on platform
ctypedef int npy_int16
ctypedef float npy_float32
def score_string( ndarray matrix, ndarray char_to_index, object string, ndarray rval ):
"""
Score each position in string `string` using the scoring matrix `matrix`.
Characters in the string are mapped to columns in the matrix by `char_to_index`
and the score for each position is stored in `rval`.
matrix *must* be a 2d array of type float32
char_to_index *must* be a 1d array of type int16
rval *must* be a 1d array of type float32 and the same length as string
"""
cdef char *buffer
cdef Py_ssize_t len
cdef float score
cdef int i, j
cdef int matrix_width = matrix.dimensions[0]
cdef npy_int16 char_index
# Get input string as character pointer
if PY_MAJOR_VERSION >= 3:
bytes_string = string.encode()
else:
bytes_string = string
PyBytes_AsStringAndSize(bytes_string, &buffer, &len )
# Loop over each position in the string
cdef int stop = len - matrix.dimensions[0] + 1
for i from 0 <= i < stop:
score = 0.0
for j from 0 <= j < matrix_width:
char_index = ( <npy_int16 *> ( char_to_index.data + buffer[i+j] * char_to_index.strides[0] ) )[0]
if char_index < 0:
break
score += ( <npy_float32*> ( matrix.data + j * matrix.strides[0] + char_index * matrix.strides[1] ) )[0]
else:
( <npy_float32*> ( rval.data + i * rval.strides[0] ) )[0] = score
def score_string_with_gaps( ndarray matrix, ndarray char_to_index, object string, ndarray rval ):
"""
Score each position in string `string` using the scoring matrix `matrix`.
Characters in the string are mapped to columns in the matrix by `char_to_index`
and the score for each position is stored in `rval`.
matrix *must* be a 2d array of type float32
char_to_index *must* be a 1d array of type int16
rval *must* be a 1d array of type float32 and the same length as string
"""
cdef char *buffer
cdef Py_ssize_t len
cdef float score
cdef int i, j, string_pos
cdef int matrix_width = matrix.dimensions[0]
cdef npy_int16 char_index
# Get input string as character pointer
if PY_MAJOR_VERSION >= 3:
bytes_string = string.encode()
else:
bytes_string = string
PyBytes_AsStringAndSize(bytes_string, &buffer, &len )
# Loop over each position in the string
cdef int stop = len - matrix.dimensions[0] + 1
for i from 0 <= i < stop:
if buffer[i] == '-':
# Never start scoring at a gap
continue
score = 0.0
string_pos = i
for j from 0 <= j < matrix_width:
# Advance to the next non-gap character
while buffer[string_pos] == '-' and string_pos < len:
string_pos += 1
# Ran out of non-gap characters, no more scoring is possible
if string_pos == len:
return
# Find character for position and score
char_index = ( <npy_int16 *> ( char_to_index.data + buffer[string_pos] * char_to_index.strides[0] ) )[0]
if char_index < 0:
break
score += ( <npy_float32*> ( matrix.data + j * matrix.strides[0] + char_index * matrix.strides[1] ) )[0]
# Matched a character, move forward
string_pos += 1
else:
( <npy_float32*> ( rval.data + i * rval.strides[0] ) )[0] = score
|
