Cython API: added API to use apat (pattern search) C library
This commit is contained in:
Celine Mercier
61
python/obitools3/dms/capi/apat.pxd
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61
python/obitools3/dms/capi/apat.pxd
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#cython: language_level=3
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from obitools3.dms.capi.obiview cimport Obiview_p
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from obitools3.dms.capi.obidmscolumn cimport OBIDMS_column_p
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from obitools3.dms.capi.obitypes cimport index_t
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from libc.stdint cimport int32_t, uint32_t, uint8_t
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cdef extern from "libecoPCR/libapat/libstki.h" nogil:
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struct Stacki :
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int32_t size
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int32_t top
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int32_t cursor
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int32_t* val
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ctypedef Stacki* StackiPtr
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cdef extern from "libecoPCR/libapat/apat.h" nogil:
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extern int MAX_PATTERN
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struct Seq :
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char* name
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int32_t seqlen
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int32_t seqsiz
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int32_t datsiz
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int32_t circular
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uint8_t* data
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char* cseq
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StackiPtr* hitpos
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StackiPtr* hiterr
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ctypedef Seq* SeqPtr
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struct Pattern :
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int patlen
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int maxerr
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char* cpat
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int32_t* patcode
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uint32_t* smat
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uint32_t omask
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bint hasIndel
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bint ok
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ctypedef Pattern* PatternPtr
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int32_t ManberAll(Seq *pseq, Pattern *ppat, int patnum, int begin, int length)
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cdef extern from "libecoPCR/ecoPCR.h" nogil:
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SeqPtr ecoseq2apatseq(char* sequence, SeqPtr out, int32_t circular)
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int32_t delete_apatseq(SeqPtr pseq)
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PatternPtr buildPattern(const char *pat, int32_t error_max)
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PatternPtr complementPattern(PatternPtr pat)
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28
python/obitools3/libalign/apat_pattern.pxd
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python/obitools3/libalign/apat_pattern.pxd
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#cython: language_level=3
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from obitools3.dms.capi.apat cimport SeqPtr
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cdef class One_primer_search_result:
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cdef SeqPtr _pointer
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cdef int pattern_ref
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cdef int hit_count
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cdef inline SeqPtr pointer(self)
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@staticmethod
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cdef new(SeqPtr apat_seq_p, int pattern_ref, int hit_count)
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cpdef first_encountered(self)
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cdef class Primer_search:
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cdef SeqPtr apat_seq_p
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cdef list direct_primers
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cdef list revcomp_primers
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cpdef One_primer_search_result search_one_primer(self, bytes sequence,
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int primer_pair_index, int primer_index,
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bint reverse_comp=*,
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bint same_sequence=*,
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int pattern_ref=*,
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int begin=*)
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cpdef free(self)
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150
python/obitools3/libalign/apat_pattern.pyx
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python/obitools3/libalign/apat_pattern.pyx
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#cython: language_level=3
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from libc.stdint cimport uintptr_t
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from obitools3.dms.capi.apat cimport SeqPtr, \
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PatternPtr, \
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ecoseq2apatseq, \
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ManberAll, \
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delete_apatseq, \
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buildPattern, \
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complementPattern
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cdef class One_primer_search_result:
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cdef inline SeqPtr pointer(self) :
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return <SeqPtr>(self._pointer)
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@staticmethod
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cdef new(SeqPtr apat_seq_p, int pattern_ref, int hit_count) : # not __init__ method because need to pass pointer
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result = One_primer_search_result()
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result._pointer = apat_seq_p
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result.pattern_ref = pattern_ref
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result.hit_count = hit_count
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return result
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cpdef first_encountered(self):
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cdef int i
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cdef int first
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cdef int first_index
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cdef int hit_pos
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cdef int error_count
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cdef SeqPtr pointer
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pointer = self.pointer()
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first = -1
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for i in range(self.hit_count):
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hit_pos = pointer.hitpos[self.pattern_ref].val[i]
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if first == -1 or hit_pos < first:
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first = hit_pos
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first_index = i
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error_count = pointer.hiterr[self.pattern_ref].val[first_index]
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return error_count, first
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cdef class Primer_search:
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def __init__(self, list primers, int error_max) :
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cdef PatternPtr p1
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cdef PatternPtr p2
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cdef PatternPtr p3
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cdef PatternPtr p4
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cdef PatternPtr test
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cdef uintptr_t test_i
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cdef bytes test_b
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self.apat_seq_p = NULL
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self.direct_primers = []
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self.revcomp_primers = []
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for i in range(len(primers)):
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p1 = buildPattern(primers[i][0], error_max)
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p2 = buildPattern(primers[i][1], error_max)
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p3 = complementPattern(p1)
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p4 = complementPattern(p2)
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self.direct_primers.append((<uintptr_t>p1, <uintptr_t>p2))
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self.revcomp_primers.append((<uintptr_t>p3, <uintptr_t>p4))
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cpdef One_primer_search_result search_one_primer(self, bytes sequence,
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int primer_pair_index, int primer_index,
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bint reverse_comp=False,
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bint same_sequence=False,
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int pattern_ref=0,
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int begin=0) :
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'''
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begin = start of direct pattern if it was already searched + its length
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'''
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cdef One_primer_search_result result = None
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cdef PatternPtr primer_p
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cdef SeqPtr apat_seq_p
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cdef int hit_count
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if not same_sequence:
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self.apat_seq_p = <SeqPtr>(ecoseq2apatseq(sequence, self.apat_seq_p, 0))
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apat_seq_p = <SeqPtr>(self.apat_seq_p)
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if reverse_comp:
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primer_p = <PatternPtr>(<uintptr_t>(self.revcomp_primers[primer_pair_index][primer_index]))
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else:
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primer_p = <PatternPtr>(<uintptr_t>(self.direct_primers[primer_pair_index][primer_index]))
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begin = begin
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seqlen = (apat_seq_p.seqlen) - begin
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hit_count = ManberAll(apat_seq_p, primer_p, pattern_ref, begin, seqlen)
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if hit_count:
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result = One_primer_search_result.new(apat_seq_p, pattern_ref, hit_count)
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else:
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result = None
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return result
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cpdef free(self):
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delete_apatseq(self.apat_seq_p)
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# min_error_count = -1
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# best_hit = -1
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# for i in range(hit_count):
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# error_count = apat_seq_p.hiterr[pattern_ref].val[i]
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# hit_pos = apat_seq_p.hitpos[pattern_ref].val[i]
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# if min_error_count < 0 or error_count < min_error_count:
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# self.min_error_count = error_count
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# self.best_hit = i
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# def __call__(self, bytes sequence):
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# # TODO declare things
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# # Search ALL primers in the direct direction
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# p1 = search_one_primer(self, sequence, True, False, same_sequence=False)
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# p2 = search_one_primer(self, sequence, False, False, same_sequence=True)
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#
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# # Search each primer in both directions
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# # 1st direction
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# p1 = search_one_primer(self, sequence, True, False, same_sequence=False)
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# p2_revcomp = search_one_primer(self, sequence, False, True, same_sequence=True)
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# # 2nd direction
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# p2 = search_one_primer(self, sequence, False, False, same_sequence=True)
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# p1_revcomp = search_one_primer(self, sequence, True, True, same_sequence=True)
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# # Choose best hit (best score for direction and longest amplicon if multiple hits in one direction)
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# if p1.min_error_count + p2_revcomp.min_error_count < p2.min_error_count + p1_revcomp.min_error_count:
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# direct_hit = True
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# if p1.hit_count > 1:
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# pos1 = min((pos, idx) for (idx, pos) in enumerate(p1.hit_pos))[0]
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# if p2_revcomp.hit_count > 1:
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# pos2 = max((pos, idx) for (idx, pos) in enumerate(p2_revcomp.hit_pos))[0]
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# else:
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# direct_hit = False
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# if p2.hit_count > 1:
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# pos1 = min((pos, idx) for (idx, pos) in enumerate(p2.hit_pos))[0]
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# if p2_revcomp.hit_count > 1:
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# pos2 = max((pos, idx) for (idx, pos) in enumerate(p2_revcomp.hit_pos))[0]
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