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#cython: language_level=3
from cpython cimport array
from .solexapairend import iterOnAligment
from .shifted_ali cimport Ali_shifted
from obitools3.dms.capi.obiview cimport Obiview_p, QUALITY_COLUMN, NUC_SEQUENCE_COLUMN, \
REVERSE_SEQUENCE_COLUMN, REVERSE_QUALITY_COLUMN, \
obi_set_qual_int_with_elt_idx_and_col_p_in_view, \
obi_set_str_with_elt_idx_and_col_p_in_view
from obitools3.dms.capi.obidmscolumn cimport OBIDMS_column_p
from obitools3.dms.view.view cimport View
from obitools3.dms.column.column cimport Column
from math import log10
cdef class IterOnConsensus:
cdef object _ali
cdef int __seqASingle
cdef int __seqBSingle
cdef int __seqABMatch
cdef int __seqAMismatch
cdef int __seqBMismatch
cdef int __seqAInsertion
cdef int __seqBInsertion
cdef int __seqADeletion
cdef int __seqBDeletion
cdef object __ioa
cdef bint __firstSeqB
def __cinit__(self,ali):
self._ali=ali
self.__seqASingle=0
self.__seqBSingle=0
self.__seqABMatch=0
self.__seqAMismatch=0
self.__seqBMismatch=0
self.__seqAInsertion=0
self.__seqBInsertion=0
self.__seqADeletion=0
self.__seqBDeletion=0
self.__ioa = iterOnAligment(self._ali)
self.__firstSeqB=False
def get_seqASingle(self):
return self.__seqASingle
def get_seqBSingle(self):
return self.__seqBSingle
def get_seqABMatch(self):
return self.__seqABMatch
def get_seqAMismatch(self):
return self.__seqAMismatch
def get_seqBMismatch(self):
return self.__seqBMismatch
def get_seqAInsertion(self):
return self.__seqAInsertion
def get_seqBInsertion(self):
return self.__seqBInsertion
def get_seqADeletion(self):
return self.__seqADeletion
def get_seqBDeletion(self):
return self.__seqBDeletion
def __next__(self):
cdef bytes snuc0
cdef bytes snuc1
cdef char* nuc0
cdef char* nuc1
cdef char* dash=b"-"
cdef double score0
cdef double score1
cdef double h0
cdef double h1
while(1):
snuc0,score0,snuc1,score1 = self.__ioa.__next__()
nuc0=snuc0
nuc1=snuc1
if nuc0[0]==nuc1[0]:
if nuc1[0]!=dash[0]:
self.__firstSeqB=True
self.__seqABMatch+=1
self.__seqBSingle=0
return (nuc0,score0*score1)
else:
h0 = score0 * (1-score1/3)
h1 = score1 * (1-score0/3)
if h0 < h1:
if nuc0[0]!=dash[0]:
self.__seqBSingle=0
if nuc1[0]==dash[0]:
if self.__firstSeqB:
self.__seqAInsertion+=1
else:
self.__seqASingle+=1
else:
self.__firstSeqB=True
self.__seqAMismatch+=1
if score1==1.0: # Free end gap
return (nuc0,score0)
else:
return (nuc0,h0)
else:
self.__seqADeletion+=1
else:
if nuc1[0]!=dash[0]:
self.__firstSeqB=True
if nuc0[0]==dash[0]:
self.__seqBInsertion+=1
self.__seqBSingle+=1
else:
self.__seqBMismatch+=1
self.__seqBSingle=0
if score0==1.0: # Free end gap
return (nuc1,score1)
else:
return (nuc1,h1)
else:
self.__seqBSingle=0
self.__seqBDeletion+=1
def __iter__(self):
return self
seqASingle = property(get_seqASingle, None, None, "direct's docstring")
seqBSingle = property(get_seqBSingle, None, None, "reverse's docstring")
seqABMatch = property(get_seqABMatch, None, None, "idem's docstring")
seqAMismatch = property(get_seqAMismatch, None, None, "mismatchdirect's docstring")
seqBMismatch = property(get_seqBMismatch, None, None, "mismatchreverse's docstring")
seqAInsertion = property(get_seqAInsertion, None, None, "insertdirect's docstring")
seqBInsertion = property(get_seqBInsertion, None, None, "insertreverse's docstring")
seqADeletion = property(get_seqADeletion, None, None, "deletedirect's docstring")
seqBDeletion = property(get_seqBDeletion, None, None, "deletereverse's docstring")
def buildConsensus(ali, seq, ref_tags=None):
cdef list quality
cdef char aseq[1000]
cdef int i=0
cdef int j=0
cdef char* cnuc
cdef bytes nuc
cdef double score
cdef bytes sseq
cdef double p
cdef OBIDMS_column_p col_p
cdef Obiview_p view_p
cdef View view
cdef Column column
quality = []
if type(ali) == Ali_shifted:
view = seq.view
view_p = view.pointer()
column = view[QUALITY_COLUMN]
col_p = column.pointer()
# doesn't work because uint8_t* are forced into bytes by cython (nothing read/kept beyond 0 values)
#obi_set_qual_int_with_elt_idx_and_col_p_in_view(view_p, col_p, seq.index, 0, ali.consensus_qual, ali.consensus_len)
seq.set(ref_tags.id+b"_CONS", ali.consensus_seq, quality=ali.consensus_qual)
seq[b"seq_length"] = ali.consensus_len
seq[b"overlap_length"] = ali.overlap_len
seq[b'score_norm']=round(float(ali.score)/ali.overlap_len, 3)
seq[b'shift']=ali.shift
else:
if len(ali[0])>999: # TODO why?
raise AssertionError,"Too long alignment"
ic=IterOnConsensus(ali)
for nuc,score in ic:
cnuc=nuc
quality.append(score)
aseq[i]=cnuc[0]
i+=1
aseq[i]=0
sseq=aseq
# Reconvert quality from array of probabilities to array of raw quality values
i=0
for p in quality:
quality[i] = min(42, round(-10*log10(p)))
i+=1
seq.set(ali[0].wrapped.id+b"_CONS", sseq, quality=quality)
if hasattr(ali, "counter"):
seq[b'alignement_id']=ali.counter
seq[b'seq_a_single']=ic.seqASingle
seq[b'seq_b_single']=ic.seqBSingle
seq[b'seq_ab_match']=ic.seqABMatch
seq[b'seq_a_mismatch']=ic.seqAMismatch
seq[b'seq_b_mismatch']=ic.seqBMismatch
seq[b'seq_a_insertion']=ic.seqAInsertion
seq[b'seq_b_insertion']=ic.seqBInsertion-ic.seqBSingle
seq[b'seq_a_deletion']=ic.seqADeletion
seq[b'seq_b_deletion']=ic.seqBDeletion
seq[b'ali_length']=len(seq)-ic.seqASingle-ic.seqBSingle
if seq[b'ali_length']>0:
seq[b'score_norm']=float(ali.score)/seq[b'ali_length']
ref_tags = ali[0].wrapped
if hasattr(ali, "direction"):
seq[b'ali_direction']=ali.direction
seq[b'score']=ali.score
seq[b'mode']=b'alignment'
for tag in ref_tags:
if tag != REVERSE_SEQUENCE_COLUMN and tag != REVERSE_QUALITY_COLUMN and \
tag != NUC_SEQUENCE_COLUMN and tag != QUALITY_COLUMN:
seq[tag] = ref_tags[tag]
return seq
def buildJoinedSequence(ali, reverse, seq, forward=None):
if forward is not None:
forward = forward
else:
forward = ali[0].wrapped
s = forward.seq + reverse.seq
quality = forward.quality
quality.extend(reverse.quality)
seq.set(forward.id +b"_PairedEnd", s, definition=forward.definition, quality=quality)
seq[b"score"]=ali.score
if len(ali.direction) > 0:
seq[b"ali_direction"]=ali.direction
else:
seq[b"ali_direction"]=None
seq[b"mode"]=b"joined"
seq[b"pairedend_limit"]=len(forward)
seq[b"seq_length"] = ali.consensus_len
seq[b"overlap_length"] = ali.overlap_len
if ali.overlap_len > 0:
seq[b'score_norm']=round(float(ali.score)/ali.overlap_len, 3)
else:
seq[b"score_norm"]=0.0
for tag in forward:
if tag != REVERSE_SEQUENCE_COLUMN and tag != REVERSE_QUALITY_COLUMN and \
tag != NUC_SEQUENCE_COLUMN and tag != QUALITY_COLUMN:
seq[tag] = forward[tag]
return seq
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