Cython API: Seq classes reworked
This commit is contained in:
Celine Mercier
@ -4,19 +4,21 @@ from .view.view cimport Line
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cdef class Seq(dict) :
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cdef dict _annotations
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cdef str _id
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cdef object _seq
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cdef str _definition
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cdef class Nuc_Seq(Seq) :
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cdef object _quality
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#cpdef object reverse_complement(self)
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cdef class Nuc_Seq_Stored(Line) :
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cpdef object get_str_quality(self)
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cdef class Seq_Stored(Line) :
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pass
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cdef class Nuc_Seq_Stored(Seq_Stored) :
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cpdef set_quality_int(self, list new_qual)
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cpdef set_quality_char(self, bytes new_qual, int offset=*)
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#cpdef object reverse_complement(self)
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@ -1,55 +1,68 @@
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#cython: language_level=3
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from obitools3.utils cimport bytes2str, str2bytes
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from obitools3.utils cimport bytes2str, str2bytes, tostr, tobytes
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from .capi.obiview cimport NUC_SEQUENCE_COLUMN, \
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ID_COLUMN, \
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DEFINITION_COLUMN, \
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QUALITY_COLUMN
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NUC_SEQUENCE_COLUMN_str = bytes2str(NUC_SEQUENCE_COLUMN)
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ID_COLUMN_str = bytes2str(ID_COLUMN)
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DEFINITION_COLUMN_str = bytes2str(DEFINITION_COLUMN)
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QUALITY_COLUMN_str = bytes2str(QUALITY_COLUMN)
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QUALITY_COLUMN, \
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COUNT_COLUMN
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cdef class Seq(dict) :
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def __init__(self, str id, object seq, object definition=None) :
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self.id = id
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self.seq = seq
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def __init__(self, object id, object seq, object definition=None, object quality=None, int offset=-1, object tags=None) :
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cdef object k
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cdef bytes k_b
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self[ID_COLUMN] = tobytes(id)
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self.seq = tobytes(seq)
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if definition is not None :
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self.definition = definition
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self.definition = tobytes(definition)
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self._annotations = {}
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if tags is not None :
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for k in tags:
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k_b = tobytes(k)
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self[k_b] = tags[k_b]
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def __contains__(self, object key):
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return dict.__contains__(self, tobytes(key))
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# sequence id property getter and setter
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@property
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def id(self): # @ReservedAssignment
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return self._id
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return self[ID_COLUMN]
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@id.setter
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def id(self, str new_id): # @ReservedAssignment @DuplicatedSignature
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self._id = new_id
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self[ID_COLUMN] = new_id
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def id(self, object new_id): # @ReservedAssignment @DuplicatedSignature
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self[ID_COLUMN] = tobytes(new_id)
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# sequence annotations property getter and setter
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@property
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def annotations(self): # @ReservedAssignment
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return self._annotations
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@annotations.setter
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def annotations(self, object annotations): # @ReservedAssignment @DuplicatedSignature
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self._annotations = annotations
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# sequence property getter and setter
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@property
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def seq(self):
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return self._seq
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return self[b"SEQ"]
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@seq.setter
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def seq(self, object new_seq): # @DuplicatedSignature
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self._seq = new_seq
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self["SEQ"] = new_seq # TODO discuss
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self[b"SEQ"] = tobytes(new_seq)
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# sequence definition property getter and setter
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@property
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def definition(self):
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return self._definition
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return self[DEFINITION_COLUMN]
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@definition.setter
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def definition(self, object new_definition): # @DuplicatedSignature
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self._definition = new_definition
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self[DEFINITION_COLUMN_str] = new_definition
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self[DEFINITION_COLUMN] = tobytes(new_definition)
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cdef class Nuc_Seq(Seq) :
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@ -62,65 +75,82 @@ cdef class Nuc_Seq(Seq) :
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@seq.setter
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def seq(self, object new_seq): # @DuplicatedSignature
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self._seq = new_seq
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self[NUC_SEQUENCE_COLUMN_str] = new_seq
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self[NUC_SEQUENCE_COLUMN] = tobytes(new_seq)
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# sequence quality property getter and setter
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@property
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def quality(self):
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return self._quality
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return self[QUALITY_COLUMN]
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@quality.setter
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def quality(self, object new_quality): # @DuplicatedSignature
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self._quality = new_quality
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self[QUALITY_COLUMN_str] = new_quality
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self[QUALITY_COLUMN] = tobytes(new_quality)
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# cpdef str reverse_complement(self) : TODO in C ?
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# pass
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cdef class Nuc_Seq_Stored(Line) :
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cdef class Seq_Stored(Line) :
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# sequence id property getter and setter
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@property
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def id(self): # @ReservedAssignment @DuplicatedSignature
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return self[ID_COLUMN_str]
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return self._view.get_column(ID_COLUMN).get_line(self.index)
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@id.setter
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def id(self, str new_id): # @ReservedAssignment @DuplicatedSignature
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self[ID_COLUMN_str] = new_id
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def id(self, object new_id): # @ReservedAssignment @DuplicatedSignature
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self._view.get_column(ID_COLUMN).set_line(self._index, tobytes(new_id))
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# sequence definition property getter and setter
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@property
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def definition(self):
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return self[DEFINITION_COLUMN_str]
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return self._view.get_column(DEFINITION_COLUMN).get_line(self.index)
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@definition.setter
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def definition(self, str new_def): # @DuplicatedSignature
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self[DEFINITION_COLUMN_str] = new_def
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def definition(self, object new_def): # @DuplicatedSignature
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self._view.get_column(DEFINITION_COLUMN).set_line(self._index, tobytes(new_def))
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cdef class Nuc_Seq_Stored(Seq_Stored) :
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cpdef set_quality_int(self, list new_qual):
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self._view.get_column(QUALITY_COLUMN).set_line(self.index, new_qual)
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cpdef set_quality_char(self, bytes new_qual, int offset=-1):
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self._view.get_column(QUALITY_COLUMN).set_str_line(self.index, new_qual, offset=offset)
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# nuc_seq property getter and setter
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@property
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def nuc_seq(self):
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return self[NUC_SEQUENCE_COLUMN_str]
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return self._view.get_column(NUC_SEQUENCE_COLUMN).get_line(self.index)
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@nuc_seq.setter
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def nuc_seq(self, object new_seq): # @DuplicatedSignature
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self[NUC_SEQUENCE_COLUMN_str] = new_seq
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self._view.get_column(NUC_SEQUENCE_COLUMN).set_line(self.index, tobytes(new_seq))
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# quality property getter and setter
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@property
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def quality(self):
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return self[QUALITY_COLUMN_str]
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return self._view.get_column(QUALITY_COLUMN).get_line(self.index)
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@quality.setter
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def quality(self, object new_qual): # @DuplicatedSignature
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if (type(new_qual) == list) or (new_qual is None) : # TODO check that quality column exists
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self[QUALITY_COLUMN_str] = new_qual
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else : # Quality is in str form
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self._view.get_column(QUALITY_COLUMN_str).set_str_line(self._index, new_qual)
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if (new_qual is None) or (type(new_qual) == list) : # TODO check that quality column exists
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self._view.get_column(QUALITY_COLUMN).set_line(self._index, new_qual)
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elif (type(new_qual) == str) or (type(new_qual) == bytes) : # Quality is in str form
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self._view.get_column(QUALITY_COLUMN).set_str_line(self._index, tobytes(new_qual))
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else :
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raise Exception("Sequence quality in unrecognized format")
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cpdef object get_str_quality(self) : # TODO not ideal. Make quality_int and quality_str properties
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return self._view.get_column(QUALITY_COLUMN_str).get_str_line(self._index)
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# quality character string property getter
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@property
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def quality_str(self):
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return self._view.get_column(QUALITY_COLUMN).get_str_line(self._index)
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def __str__(self):
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return bytes2str(self.nuc_seq)
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# cpdef str reverse_complement(self) : TODO in C ?
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# pass
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