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"""
Pyrex/C extension for quickly finding potential CpG sites in pairs of
sequences.
"""
from cpython.version cimport PY_MAJOR_VERSION
cdef extern from "find_cpg.h":
int next_cpg( char * sp1, char * sp2, int start)
int next_cpg_restricted( char * sp1, char *sp2, int start)
int next_non_cpg( char * sp1, char * sp2, int start)
def find_cpg( sp1, sp2, start ):
cdef char* a
cdef char* b
cdef int pos
if PY_MAJOR_VERSION >= 3:
bytes_sp1, bytes_sp2 = sp1.encode(), sp2.encode()
else:
bytes_sp1, bytes_sp2 = sp1, sp2
a = bytes_sp1
b = bytes_sp2
pos = start
if pos > len(sp1): return -1
return next_cpg( a, b, pos )
def find_cpg_restricted( sp1, sp2, start ):
cdef char* a
cdef char* b
cdef int pos
if PY_MAJOR_VERSION >= 3:
bytes_sp1, bytes_sp2 = sp1.encode(), sp2.encode()
else:
bytes_sp1, bytes_sp2 = sp1, sp2
a = bytes_sp1
b = bytes_sp2
pos = start
if pos > len(sp1): return -1
return next_cpg_restricted( a, b, pos )
def find_non_cpg( sp1, sp2, start ):
cdef char* a
cdef char* b
cdef int pos
if PY_MAJOR_VERSION >= 3:
bytes_sp1, bytes_sp2 = sp1.encode(), sp2.encode()
else:
bytes_sp1, bytes_sp2 = sp1, sp2
a = bytes_sp1
b = bytes_sp2
pos = start
if pos > len(sp1): return -1
return next_non_cpg( a, b, pos )
def list_cpg( sp1, sp2 ):
cdef char * a
cdef char * b
cdef int start
if PY_MAJOR_VERSION >= 3:
bytes_sp1, bytes_sp2 = sp1.encode(), sp2.encode()
else:
bytes_sp1, bytes_sp2 = sp1, sp2
a = bytes_sp1
b = bytes_sp2
start = 0
cpglist = list()
while start > -1 and start < len(sp1):
start = next_cpg( a, b, start )
if start == -1: break
cpglist.append(start)
start = start + 1
return cpglist
def list_cpg_restricted( sp1, sp2 ):
cdef char * a
cdef char * b
cdef int start
if PY_MAJOR_VERSION >= 3:
bytes_sp1, bytes_sp2 = sp1.encode(), sp2.encode()
else:
bytes_sp1, bytes_sp2 = sp1, sp2
a = bytes_sp1
b = bytes_sp2
start = 0
cpglist = list()
while start > -1 and start < len(sp1):
start = next_cpg_restricted( a, b, start )
if start == -1: break
cpglist.append(start)
start = start + 1
return cpglist
def list_non_cpg( sp1, sp2 ):
cdef char * a
cdef char * b
cdef int start
if PY_MAJOR_VERSION >= 3:
bytes_sp1, bytes_sp2 = sp1.encode(), sp2.encode()
else:
bytes_sp1, bytes_sp2 = sp1, sp2
a = bytes_sp1
b = bytes_sp2
start = 0
cpglist = list()
while start > -1 and start < len(sp1):
start = next_non_cpg( a, b, start )
if start == -1: break
cpglist.append(start)
start = start + 1
return cpglist
def remove_gaps( sp, cpglist ):
for item in cpglist:
if sp[item] == '-':
cpglist.remove(item)
return cpglist
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