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|
#cython: language_level=3
from obitools3.utils cimport bytes2str, str2bytes, tostr, tobytes
from obitools3.dms.view.view cimport View
from obitools3.dms.column.column cimport Column
from .capi.obitypes cimport index_t, OBI_QUAL
from .capi.obiview cimport NUC_SEQUENCE_COLUMN, \
ID_COLUMN, \
DEFINITION_COLUMN, \
QUALITY_COLUMN, \
COUNT_COLUMN
from .capi.obiutils cimport reverse_complement_sequence
from obitools3.format.fasta import FastaFormat
from obitools3.format.fastq import FastqFormat
from cpython cimport array
import array
from copy import deepcopy
import math
SEQUENCE_COLUMN = b"SEQ"
SPECIAL_COLUMNS = [NUC_SEQUENCE_COLUMN, SEQUENCE_COLUMN, ID_COLUMN, DEFINITION_COLUMN, QUALITY_COLUMN]
QUALITY_ASCII_BASE = 33
cdef class Seq(dict) :
def __init__(self, object id, object seq, object definition=None, object tags=None) :
cdef object k
cdef bytes k_b
self.id = id
self.seq = seq
self.definition = definition
self._index = -1
if tags is not None :
for k in tags:
k_b = tobytes(k)
if k_b not in SPECIAL_COLUMNS:
# TODO discuss convert value to bytes if str
if type(tags[k]) == str:
self[k_b] = str2bytes(tags[k])
else:
self[k_b] = tags[k]
@staticmethod
def new_from_stored(Seq_Stored seq_to_clone) :
cdef Seq new_seq
new_seq = Seq(seq_to_clone.id, seq_to_clone.seq, definition=seq_to_clone.definition, quality=seq_to_clone.quality, tags=seq_to_clone)
new_seq._index = seq_to_clone._index
return new_seq
def __contains__(self, object key):
return dict.__contains__(self, tobytes(key))
def __getitem__(self, object ref):
if type(ref) == int:
return self.get_symbol_at(ref)
elif type(ref) == slice:
return self.get_slice(ref)
else:
return super(Seq, self).__getitem__(tobytes(ref))
def __setitem__(self, object ref, object item):
super(Seq, self).__setitem__(tobytes(ref), item)
def __str__(self):
return self.get_str()
cpdef str get_str(self):
return tostr(self.seq)
def __len__(self):
return len(self.seq)
cpdef object clone(self):
cdef object seq_class
seq_class = type(self)
seq = seq_class(self.id, self.seq, definition=self.definition, quality=self.quality, tags=self)
return seq
cpdef object get_slice(self, slice slice_to_get):
cdef object new_seq
cdef list sliced_quality
cdef type seq_class
seq_class = type(self)
if QUALITY_COLUMN in self:
sliced_quality = self.quality[slice_to_get]
else:
sliced_quality = None
new_seq = seq_class(self.id+b"_SUB", self.seq[slice_to_get], definition=self.definition, quality=sliced_quality, tags=self) # TODO discuss suffix
return new_seq
cpdef get_symbol_at(self, int pos):
return self.seq[pos:pos+1]
# sequence id property getter and setter
@property
def id(self): # @ReservedAssignment
return self[ID_COLUMN]
@id.setter
def id(self, object new_id): # @ReservedAssignment @DuplicatedSignature
self[ID_COLUMN] = tobytes(new_id)
# sequence property getter and setter
@property
def seq(self):
return self[SEQUENCE_COLUMN]
@seq.setter
def seq(self, object new_seq): # @DuplicatedSignature
self[SEQUENCE_COLUMN] = tobytes(new_seq)
# sequence definition property getter and setter
@property
def definition(self):
return self[DEFINITION_COLUMN]
@definition.setter
def definition(self, object new_definition): # @DuplicatedSignature
if new_definition is not None:
new_definition = tobytes(new_definition)
self[DEFINITION_COLUMN] = new_definition
# sequence index (for reference in a view eventually) property getter and setter
@property
def index(self): # @ReservedAssignment
return self._index
@index.setter
def index(self, int idx): # @DuplicatedSignature
self._index = idx
cdef class Nuc_Seq(Seq) :
def __init__(self, object id, object seq, object definition=None, object quality=None, int offset=QUALITY_ASCII_BASE, object tags=None) :
cdef object k
cdef bytes k_b
cdef int q
cdef list q_proba_list
self.id = id
self.seq = seq
self.definition = definition
if quality is not None:
self.set_quality(quality, offset=offset)
self._is_revcomp = False
if tags is not None:
for k in tags:
k_b = tobytes(k)
if k_b not in SPECIAL_COLUMNS:
# TODO discuss convert value to bytes if str
if type(tags[k]) == str:
self[k_b] = str2bytes(tags[k])
else:
self[k_b] = tags[k]
@staticmethod
def new_from_stored(Nuc_Seq_Stored seq_to_clone) :
cdef Nuc_Seq new_seq
new_seq = Nuc_Seq(seq_to_clone.id, seq_to_clone.seq, definition=seq_to_clone.definition, quality=seq_to_clone.quality, tags=seq_to_clone)
new_seq._index = seq_to_clone.index
return new_seq
# is_revcomp property getter and setter (boolean indicating whether the sequence was created by reverse complementing another sequence)
@property
def is_revcomp(self):
return self._is_revcomp
@is_revcomp.setter
def is_revcomp(self, bint is_revcomp): # @DuplicatedSignature
self._is_revcomp = is_revcomp
# nuc sequence property getter and setter
@property
def seq(self):
return self[NUC_SEQUENCE_COLUMN]
@seq.setter
def seq(self, object new_seq): # @DuplicatedSignature
self[NUC_SEQUENCE_COLUMN] = tobytes(new_seq)
# sequence quality property getter and setter
@property
def quality(self):
if QUALITY_COLUMN in self:
return self[QUALITY_COLUMN]
else:
return None
cpdef set_quality(self, object new_quality, int offset=QUALITY_ASCII_BASE):
cdef list quality_int
if type(new_quality) == list:
quality_int = new_quality
elif type(new_quality) == str or type(new_quality) == bytes:
quality_int = []
for pos in range(len(new_quality)):
quality_int.append(ord(new_quality[pos:pos+1])-offset)
else:
raise Exception("Sequence quality in unrecognized format:", type(new_quality))
self[QUALITY_COLUMN] = quality_int
# sequence quality array property getter and setter
@property
def quality_array(self):
if self._quality_array is None:
if QUALITY_COLUMN in self:
self._quality_array = self.build_quality_array(self[QUALITY_COLUMN])
return self._quality_array
cpdef object build_quality_array(self, list quality):
cdef int q
cdef list q_proba_list
cdef object qual_array
q_proba_list = [(10.**(-q/10.)) for q in quality]
return array.array('d', q_proba_list)
# reverse complement property getter
@property
def reverse_complement(self):
cdef bytes rev_comp
cdef object seq_class
if self._reverse_complement is None:
rev_comp = self.build_reverse_complement()
if QUALITY_COLUMN in self:
reversed_quality = self.quality[::-1]
else:
reversed_quality = None
seq = Nuc_Seq(self.id+b"_CMP", rev_comp, definition=self.definition, quality=reversed_quality, tags=self)
seq.is_revcomp = True
self._reverse_complement = seq
return self._reverse_complement
cpdef bytes build_reverse_complement(self) :
cdef bytes rev_comp
rev_comp = deepcopy(self[NUC_SEQUENCE_COLUMN]).lower()
return <bytes>reverse_complement_sequence(rev_comp)
cdef class Seq_Stored(Line) :
def __getitem__(self, object ref):
if type(ref) == int:
return self.get_symbol_at(ref)
elif type(ref) == slice:
return self.get_slice(ref)
else:
return super(Seq_Stored, self).__getitem__(ref)
cpdef object get_slice(self, slice slice_to_get):
cdef object new_seq
cdef list sliced_quality
cdef type seq_class
seq_class = type(self)
if QUALITY_COLUMN in self:
sliced_quality = self.quality[slice_to_get]
else:
sliced_quality = None
new_seq = seq_class(self.id+b"_SUB", self.seq[slice_to_get], definition=self.definition, quality=sliced_quality, tags=self) # TODO discuss suffix
return new_seq
cpdef get_symbol_at(self, int pos):
return self.seq[pos:pos+1]
# sequence id property getter and setter
@property
def id(self): # @ReservedAssignment @DuplicatedSignature
return self._view.get_column(ID_COLUMN).get_line(self.index)
@id.setter
def id(self, object new_id): # @ReservedAssignment @DuplicatedSignature
self._view.get_column(ID_COLUMN).set_line(self._index, tobytes(new_id))
# sequence definition property getter and setter
@property
def definition(self):
return self._view.get_column(DEFINITION_COLUMN).get_line(self.index)
@definition.setter
def definition(self, object new_def): # @DuplicatedSignature
self._view.get_column(DEFINITION_COLUMN).set_line(self._index, tobytes(new_def))
cdef class Nuc_Seq_Stored(Seq_Stored) :
# def __init__(self, View view, index_t line_nb) :
# self = Seq_Stored.__init__(self, view, line_nb)
#self._reverse_complement = None # TODO unnecessary?
# def __setitem__(self, object column_name, object value):
# try:
# super(Seq, self).__setitem__(column_name, value)
# except CantGuessTypeException:
# column_name_b = tobytes(column_name)
# if column_name_b in SPECIAL_COLUMNS:
# self[column_name_b] = tags[column_name]
cpdef set(self, object id, object seq, object definition=None, object quality=None, int offset=QUALITY_ASCII_BASE, object tags=None):
cdef object k
cdef bytes k_b
cdef int q
cdef list q_proba_list
self[ID_COLUMN] = tobytes(id)
self[NUC_SEQUENCE_COLUMN] = tobytes(seq)
if definition is not None:
self.definition = tobytes(definition)
if quality is not None:
if type(quality) == list:
self.set_quality_int(quality)
elif type(quality) == str or type(quality) == bytes:
self.set_quality_char(quality, offset=offset)
else:
raise Exception("Sequence quality in unrecognized format")
if tags is not None:
for k in tags:
k_b = tobytes(k)
if k_b not in SPECIAL_COLUMNS:
if type(tags[k]) == str:
self[k_b] = str2bytes(tags[k])
else:
self[k_b] = tags[k]
# seq property getter and setter
@property
def seq(self):
if not self._view.read_only :
return self._view.get_column(NUC_SEQUENCE_COLUMN).get_line(self.index)
else:
if self._seq is None:
self._seq = self._view.get_column(NUC_SEQUENCE_COLUMN).get_line(self.index)
return self._seq
@seq.setter
def seq(self, object new_seq): # @DuplicatedSignature
self._view.get_column(NUC_SEQUENCE_COLUMN).set_line(self.index, tobytes(new_seq))
cpdef set_quality_int(self, list new_qual):
if QUALITY_COLUMN not in self:
Column.new_column(self._view, QUALITY_COLUMN, OBI_QUAL)
self._view.get_column(QUALITY_COLUMN).set_line(self.index, new_qual)
cpdef set_quality_char(self, object new_qual, int offset=QUALITY_ASCII_BASE):
if QUALITY_COLUMN not in self:
Column.new_column(self._view, QUALITY_COLUMN, OBI_QUAL)
self._view.get_column(QUALITY_COLUMN).set_str_line(self.index, tobytes(new_qual), offset=offset)
# quality property getter and setter
@property
def quality(self):
if QUALITY_COLUMN in self:
return self._view.get_column(QUALITY_COLUMN).get_line(self.index)
else:
return None
@quality.setter
def quality(self, object new_qual): # @DuplicatedSignature
if (new_qual is None) or (type(new_qual) == list) : # TODO check that quality column exists
self.set_quality_int(new_qual)
# WARNING: default offset used
elif (type(new_qual) == str) or (type(new_qual) == bytes) : # Quality is in str form
self.set_quality_char(new_qual)
else :
raise Exception("Sequence quality in unrecognized format")
# quality character string property getter
# WARNING: default offset used
@property
def quality_bytes(self):
if QUALITY_COLUMN in self:
return self._view.get_column(QUALITY_COLUMN).get_bytes_line(self._index)
else:
return None
# sequence quality array property getter and setter
@property
def quality_array(self):
if self._quality_array is None:
if QUALITY_COLUMN in self:
self._quality_array = self.build_quality_array(self._view.get_column(QUALITY_COLUMN).get_line(self.index))
return self._quality_array
cpdef object build_quality_array(self, list quality):
cdef int q
cdef list q_proba_list
cdef object qual_array
q_proba_list = [(10.**(-q/10.)) for q in quality]
return array.array('d', q_proba_list)
# reverse complement property getter
@property
def reverse_complement(self):
cdef bytes rev_comp
cdef list reversed_quality
if self._reverse_complement is None:
rev_comp = self.build_reverse_complement()
if QUALITY_COLUMN in self:
reversed_quality = self.quality[::-1]
else:
reversed_quality = None
seq = Nuc_Seq(self.id+b"_CMP", rev_comp, definition=self.definition, quality=reversed_quality, tags=self)
seq.is_revcomp = True
self._reverse_complement = seq
return self._reverse_complement
cpdef bytes build_reverse_complement(self) :
cdef bytes rev_comp
rev_comp = deepcopy(self[NUC_SEQUENCE_COLUMN]).lower()
return <bytes>reverse_complement_sequence(rev_comp)
def __str__(self):
return self.get_str()
cpdef str get_str(self):
return tostr(self._view.get_column(NUC_SEQUENCE_COLUMN).get_line(self.index))
def __len__(self):
return len(self._view.get_column(NUC_SEQUENCE_COLUMN).get_line(self.index))
def __repr__(self):
return bytes2str(self.repr_bytes())
cpdef repr_bytes(self):
if self.quality is None:
formatter = FastaFormat()
else:
formatter = FastqFormat()
return formatter(self)
|
