From 62caf1346ebf4d897e6c26691b1ad3392603300f Mon Sep 17 00:00:00 2001 From: Eric Coissac Date: Mon, 26 Dec 2016 15:03:24 +0100 Subject: [PATCH] temporary remove some files --- python/obitools3/dms/_obidms.cfiles | 65 ---- python/obitools3/dms/_obidmscolumn.cfiles | 65 ---- .../obitools3/dms/_obidmscolumn_bool.cfiles | 65 ---- python/obitools3/dms/_obidmscolumn_bool.pxd | 57 ---- python/obitools3/dms/_obidmscolumn_bool.pyx | 294 ------------------ python/obitools3/dms/_obiseq.cfiles | 65 ---- python/obitools3/dms/_obiseq.pxd | 21 -- python/obitools3/dms/_obiseq.pyx | 188 ----------- python/obitools3/dms/_obitaxo.cfiles | 65 ---- python/obitools3/dms/_obitaxo.pxd | 20 -- python/obitools3/dms/_obitaxo.pyx | 129 -------- python/obitools3/dms/_obiview_nuc_seq.pxd | 25 -- python/obitools3/dms/_obiview_nuc_seq.pyx | 105 ------- .../obitools3/dms/_obiview_nuc_seq_qual.pxd | 25 -- .../obitools3/dms/_obiview_nuc_seq_qual.pyx | 90 ------ 15 files changed, 1279 deletions(-) delete mode 100644 python/obitools3/dms/_obidms.cfiles delete mode 100644 python/obitools3/dms/_obidmscolumn.cfiles delete mode 100644 python/obitools3/dms/_obidmscolumn_bool.cfiles delete mode 100644 python/obitools3/dms/_obidmscolumn_bool.pxd delete mode 100644 python/obitools3/dms/_obidmscolumn_bool.pyx delete mode 100644 python/obitools3/dms/_obiseq.cfiles delete mode 100644 python/obitools3/dms/_obiseq.pxd delete mode 100644 python/obitools3/dms/_obiseq.pyx delete mode 100644 python/obitools3/dms/_obitaxo.cfiles delete mode 100644 python/obitools3/dms/_obitaxo.pxd delete mode 100644 python/obitools3/dms/_obitaxo.pyx delete mode 100644 python/obitools3/dms/_obiview_nuc_seq.pxd delete mode 100644 python/obitools3/dms/_obiview_nuc_seq.pyx delete mode 100644 python/obitools3/dms/_obiview_nuc_seq_qual.pxd delete mode 100644 python/obitools3/dms/_obiview_nuc_seq_qual.pyx diff --git a/python/obitools3/dms/_obidms.cfiles b/python/obitools3/dms/_obidms.cfiles deleted file mode 100644 index 84e0436..0000000 --- a/python/obitools3/dms/_obidms.cfiles +++ /dev/null @@ -1,65 +0,0 @@ -../../../src/bloom.h -../../../src/bloom.c -../../../src/char_str_indexer.h -../../../src/char_str_indexer.c -../../../src/crc64.h -../../../src/crc64.c -../../../src/dna_seq_indexer.h -../../../src/dna_seq_indexer.c -../../../src/encode.h -../../../src/encode.c -../../../src/hashtable.h -../../../src/hashtable.c -../../../src/murmurhash2.h -../../../src/murmurhash2.c -../../../src/obi_align.h -../../../src/obi_align.c -../../../src/obiavl.h -../../../src/obiavl.c -../../../src/obiblob_indexer.h -../../../src/obiblob_indexer.c -../../../src/obiblob.h -../../../src/obiblob.c -../../../src/obidebug.h -../../../src/obidms_taxonomy.h -../../../src/obidms_taxonomy.c -../../../src/obidms.h -../../../src/obidms.c -../../../src/obidmscolumn_blob.c -../../../src/obidmscolumn_blob.h -../../../src/obidmscolumn_bool.c -../../../src/obidmscolumn_bool.h -../../../src/obidmscolumn_char.c -../../../src/obidmscolumn_char.h -../../../src/obidmscolumn_float.c -../../../src/obidmscolumn_float.h -../../../src/obidmscolumn_idx.h -../../../src/obidmscolumn_idx.c -../../../src/obidmscolumn_int.c -../../../src/obidmscolumn_int.h -../../../src/obidmscolumn_qual.h -../../../src/obidmscolumn_qual.c -../../../src/obidmscolumn_seq.c -../../../src/obidmscolumn_seq.h -../../../src/obidmscolumn_str.c -../../../src/obidmscolumn_str.h -../../../src/obidmscolumn.h -../../../src/obidmscolumn.c -../../../src/obidmscolumndir.h -../../../src/obidmscolumndir.c -../../../src/obierrno.h -../../../src/obierrno.c -../../../src/obilittlebigman.h -../../../src/obilittlebigman.c -../../../src/obitypes.h -../../../src/obitypes.c -../../../src/obiview.h -../../../src/obiview.c -../../../src/sse_banded_LCS_alignment.h -../../../src/sse_banded_LCS_alignment.c -../../../src/uint8_indexer.h -../../../src/uint8_indexer.c -../../../src/upperband.h -../../../src/upperband.c -../../../src/utils.h -../../../src/utils.c diff --git a/python/obitools3/dms/_obidmscolumn.cfiles b/python/obitools3/dms/_obidmscolumn.cfiles deleted file mode 100644 index 84e0436..0000000 --- a/python/obitools3/dms/_obidmscolumn.cfiles +++ /dev/null @@ -1,65 +0,0 @@ -../../../src/bloom.h -../../../src/bloom.c -../../../src/char_str_indexer.h -../../../src/char_str_indexer.c -../../../src/crc64.h -../../../src/crc64.c -../../../src/dna_seq_indexer.h -../../../src/dna_seq_indexer.c -../../../src/encode.h -../../../src/encode.c -../../../src/hashtable.h -../../../src/hashtable.c -../../../src/murmurhash2.h -../../../src/murmurhash2.c -../../../src/obi_align.h -../../../src/obi_align.c -../../../src/obiavl.h -../../../src/obiavl.c -../../../src/obiblob_indexer.h -../../../src/obiblob_indexer.c -../../../src/obiblob.h -../../../src/obiblob.c -../../../src/obidebug.h -../../../src/obidms_taxonomy.h -../../../src/obidms_taxonomy.c -../../../src/obidms.h -../../../src/obidms.c -../../../src/obidmscolumn_blob.c -../../../src/obidmscolumn_blob.h -../../../src/obidmscolumn_bool.c -../../../src/obidmscolumn_bool.h -../../../src/obidmscolumn_char.c -../../../src/obidmscolumn_char.h -../../../src/obidmscolumn_float.c -../../../src/obidmscolumn_float.h -../../../src/obidmscolumn_idx.h -../../../src/obidmscolumn_idx.c -../../../src/obidmscolumn_int.c -../../../src/obidmscolumn_int.h -../../../src/obidmscolumn_qual.h -../../../src/obidmscolumn_qual.c -../../../src/obidmscolumn_seq.c -../../../src/obidmscolumn_seq.h -../../../src/obidmscolumn_str.c -../../../src/obidmscolumn_str.h -../../../src/obidmscolumn.h -../../../src/obidmscolumn.c -../../../src/obidmscolumndir.h -../../../src/obidmscolumndir.c -../../../src/obierrno.h -../../../src/obierrno.c -../../../src/obilittlebigman.h -../../../src/obilittlebigman.c -../../../src/obitypes.h -../../../src/obitypes.c -../../../src/obiview.h -../../../src/obiview.c -../../../src/sse_banded_LCS_alignment.h -../../../src/sse_banded_LCS_alignment.c -../../../src/uint8_indexer.h -../../../src/uint8_indexer.c -../../../src/upperband.h -../../../src/upperband.c -../../../src/utils.h -../../../src/utils.c diff --git a/python/obitools3/dms/_obidmscolumn_bool.cfiles b/python/obitools3/dms/_obidmscolumn_bool.cfiles deleted file mode 100644 index 84e0436..0000000 --- a/python/obitools3/dms/_obidmscolumn_bool.cfiles +++ /dev/null @@ -1,65 +0,0 @@ -../../../src/bloom.h -../../../src/bloom.c -../../../src/char_str_indexer.h -../../../src/char_str_indexer.c -../../../src/crc64.h -../../../src/crc64.c -../../../src/dna_seq_indexer.h -../../../src/dna_seq_indexer.c -../../../src/encode.h -../../../src/encode.c -../../../src/hashtable.h -../../../src/hashtable.c -../../../src/murmurhash2.h -../../../src/murmurhash2.c -../../../src/obi_align.h -../../../src/obi_align.c -../../../src/obiavl.h -../../../src/obiavl.c -../../../src/obiblob_indexer.h -../../../src/obiblob_indexer.c -../../../src/obiblob.h -../../../src/obiblob.c -../../../src/obidebug.h -../../../src/obidms_taxonomy.h -../../../src/obidms_taxonomy.c -../../../src/obidms.h -../../../src/obidms.c -../../../src/obidmscolumn_blob.c -../../../src/obidmscolumn_blob.h -../../../src/obidmscolumn_bool.c -../../../src/obidmscolumn_bool.h -../../../src/obidmscolumn_char.c -../../../src/obidmscolumn_char.h -../../../src/obidmscolumn_float.c -../../../src/obidmscolumn_float.h -../../../src/obidmscolumn_idx.h -../../../src/obidmscolumn_idx.c -../../../src/obidmscolumn_int.c -../../../src/obidmscolumn_int.h -../../../src/obidmscolumn_qual.h -../../../src/obidmscolumn_qual.c -../../../src/obidmscolumn_seq.c -../../../src/obidmscolumn_seq.h -../../../src/obidmscolumn_str.c -../../../src/obidmscolumn_str.h -../../../src/obidmscolumn.h -../../../src/obidmscolumn.c -../../../src/obidmscolumndir.h -../../../src/obidmscolumndir.c -../../../src/obierrno.h -../../../src/obierrno.c -../../../src/obilittlebigman.h -../../../src/obilittlebigman.c -../../../src/obitypes.h -../../../src/obitypes.c -../../../src/obiview.h -../../../src/obiview.c -../../../src/sse_banded_LCS_alignment.h -../../../src/sse_banded_LCS_alignment.c -../../../src/uint8_indexer.h -../../../src/uint8_indexer.c -../../../src/upperband.h -../../../src/upperband.c -../../../src/utils.h -../../../src/utils.c diff --git a/python/obitools3/dms/_obidmscolumn_bool.pxd b/python/obitools3/dms/_obidmscolumn_bool.pxd deleted file mode 100644 index deaba52..0000000 --- a/python/obitools3/dms/_obidmscolumn_bool.pxd +++ /dev/null @@ -1,57 +0,0 @@ -#cython: language_level=3 - -from .capi.obiview cimport obi_get_bool_with_elt_name_and_col_p_in_view, \ - obi_get_bool_with_elt_idx_and_col_p_in_view, \ - obi_set_bool_with_elt_name_and_col_p_in_view, \ - obi_set_bool_with_elt_idx_and_col_p_in_view - -from cpython.bool cimport bool, PyBool_FromLong -from .capi.obitypes cimport index_t, \ - const_char_p, \ - OBIType_t, \ - obibool_t, \ - OBI_BOOL, \ - OBIBool_NA - -from .capi.obierrno cimport obi_errno - -from ._obidmscolumn cimport OBIDMS_column, \ - OBIDMS_column_line, \ - OBIDMS_column_p, \ - register_column_class - -from .capi.obidmscolumn cimport obi_column_get_obibool_with_elt_name, \ - obi_column_get_obibool_with_elt_idx, \ - obi_column_set_obibool_with_elt_name, \ - obi_column_set_obibool_with_elt_idx - - -from obitools3.utils cimport str2bytes, bytes2str - -cdef class OBIDMS_column_line_bool(OBIDMS_column_line) : - cdef update_pointer(self) - - @staticmethod - cdef bool obibool_t2bool(obibool_t value) - - @staticmethod - cdef bool2obibool_t(bool value) - - cpdef bool get_bool_item_by_name(self,bytes element_name) - cpdef bool get_bool_item_by_idx(self,index_t index) - cpdef set_bool_item_by_name(self,bytes element_name,bool value) - cpdef set_bool_item_by_idx(self,index_t index,bool value) - - -# cdef obibool_t [:] _data_view - -cdef class OBIDMS_column_bool(OBIDMS_column): - cdef OBIDMS_column _new(OBIView view, - bytes column_name, - index_t nb_elements_per_line=1, - object elements_names=None, - bytes comments=b""): - - cpdef object get_line(self, index_t line_nb) - cpdef set_line(self, index_t line_nb, object value) - diff --git a/python/obitools3/dms/_obidmscolumn_bool.pyx b/python/obitools3/dms/_obidmscolumn_bool.pyx deleted file mode 100644 index 20d3328..0000000 --- a/python/obitools3/dms/_obidmscolumn_bool.pyx +++ /dev/null @@ -1,294 +0,0 @@ -#cython: language_level=3 - - -cdef class OBIDMS_column_line_bool(OBIDMS_column_line) : - - cdef update_pointer(self): - """ - Checks if the obicolumn address changed since the last call and update - if need the `_column_p` and `_data_view` data structure fields. - """ - cdef OBIDMS_column_p column_p = self._column_pp[0] - - if column_p != self._column_p: - self._column_p = column_p -# self._data_view = ( (column_p.data)) + \ -# self._index * column_p.header.nb_elements_per_line - - @staticmethod - cdef bool obibool_t2bool(obibool_t value): - cdef bool result - - if value == OBIBool_NA : - result = None - else : - result = PyBool_FromLong(value) - - return result - - @staticmethod - cdef bool2obibool_t(bool value): - cdef obibool_t result - - if value is None: - result=OBIBool_NA - else: - result= value - - return result - - - def __init__(self, OBIDMS_column column, index_t line_nb) : - """ - Creates a new `OBIDMS_column_line_bool` - - @param column: an OBIDMS_column instance - @param line_nb: the line in the column - """ - - OBIDMS_column_line.__init__(self,column,line_nb) - self.update_pointer() - - - - cpdef bool get_bool_item_by_name(self,bytes element_name): - """ - Returns the value associated to the name `element_name` of the current line - - @param element_name: a `bytes` instance containing the name of the element - - @return: the `bool` value corresponding to the name - """ - cdef char* cname = element_name - cdef obibool_t value - global obi_errno - - self.update_pointer() - - value = obi_column_get_obibool_with_elt_name(self._column_p, - self._index, - cname) - - if obi_errno > 0 : - obi_errno = 0 - raise KeyError("Cannot access to key %s" % bytes2str(element_name)) - - return OBIDMS_column_line_bool.obibool_t2bool(value) - - cpdef bool get_bool_item_by_idx(self,index_t index): - """ - Returns the value associated to the name `element_name` of the current line - - @param index: a `int` instance containing the index of the element - - @return: the `bool` value corresponding to the name - """ - cdef obibool_t value # @DuplicatedSignature - global obi_errno - - - self.update_pointer() - - value = obi_column_get_obibool_with_elt_idx(self._column_p, - self._index, - index) - - if obi_errno > 0 : - obi_errno = 0 - raise IndexError("Cannot access to element %d" % index) - - return OBIDMS_column_line_bool.obibool_t2bool(value) - - - def __getitem__(self, object element_name) : - cdef bytes name - cdef int cindex - cdef obibool_t value - cdef type typearg = type(element_name) - cdef bool result - - - if typearg == int: - cindex=element_name - if cindex < 0: - cindex = self._len - cindex - result=self.get_bool_item_by_idx(cindex) - elif typearg == bytes: - result=self.get_bool_item_by_name(element_name) - elif typearg == str: - name = str2bytes(element_name) - result=self.get_bool_item_by_name(name) - - return result - - cpdef set_bool_item_by_name(self,bytes element_name,bool value): - """ - Sets the value associated to the name `element_name` of the current line - - @param element_name: a `bytes` instance containing the name of the element - @param value: a `bool` instance of the new value - - @return: the `bool` value corresponding to the name - """ - cdef char* cname = element_name - cdef obibool_t cvalue - - self.update_pointer() - cvalue = OBIDMS_column_line_bool.bool2obibool_t(value) - - if ( obi_column_set_obibool_with_elt_name(self._column_p, - self._index, - cname, - cvalue) < 0 ): - raise KeyError("Cannot access to key %s" % bytes2str(element_name)) - - cpdef set_bool_item_by_idx(self,index_t index,bool value): - """ - Sets the value associated to the name `element_name` of the current line - - @param index: a `int` instance containing the index of the element - @param value: a `bool` instance of the new value - - @return: the `bool` value corresponding to the name - """ - cdef obibool_t cvalue # @DuplicatedSignature - - self.update_pointer() - cvalue = OBIDMS_column_line_bool.bool2obibool_t(value) - - if ( obi_column_set_obibool_with_elt_idx(self._column_p, - self._index, - index, - cvalue) < 0 ): - raise IndexError("Cannot access to item index %d" % index) - - - - def __setitem__(self, object element_name, object value): - cdef bytes name - cdef int cindex - cdef type typearg = type(element_name) - cdef bool result - - - if typearg == int: - cindex=element_name - if cindex < 0: - cindex = self._len - cindex - self.set_bool_item_by_idx(cindex,value) - elif typearg == bytes: - self.set_bool_item_by_name(element_name,value) - elif typearg == str: - name = str2bytes(element_name) - self.set_bool_item_by_name(name,value) - - def __repr__(self) : - return str(self._column.get_line(self._index)) - - def __len__(self): - return self._len - - - -cdef class OBIDMS_column_bool(OBIDMS_column): - - @staticmethod - cdef OBIDMS_column _new(OBIView view, - bytes column_name, - index_t nb_elements_per_line=1, - object elements_names=None, - bytes comments=b""): - - cdef bytes elements_names_b - cdef char* elements_names_p - cdef OBIDMS_column new_column - - if elements_names is not None: - elements_names_b = b''.join([tobytes(x) for x in elements_names]) - elements_names_p = elements_names_b - else: - elements_names_p = NULL - - if (obi_view_add_column(view = view._pointer, - column_name = column_name, - version_number = -1, - alias = NULL, - data_type = OBI_BOOL, - nb_lines = len(view), - nb_elements_per_line = nb_elements_per_line, - elements_names = elements_names_p, - indexer_name = NULL, - associated_column_name = NULL, - associated_column_version = -1, - comments = comments, - create = True)<0): - raise RuntimeError("Cannot create column %s in view %s" % (bytes2str(column_name), - bytes2str(view.name))) - - view.__init_columns__() - new_column = self._columns[column_name] - - return new_column - - @staticmethod - def new(OBIView view, - object column_name, - index_t nb_elements_per_line=1, - object elements_names=None, - object comments=b""): - - return OBIDMS_column_bool._new(view, - tobytes(column_name), - nb_elements_per_line, - elements_names, - tobytes(comments)) - - cpdef add_to_view(self, - OBIView view, - object column_name=None, - object comments=b""): - - cdef OBIDMS_column_p column_p = self._column_pp[0] - cdef bytes alias - - if (column_name is None): - alias = self._alias - else: - alias = tobytes(column_name) - - obi_view_add_column(view = view._ponter, - column_name = column_p.header.name, - version_number = column_p.header.version, - alias = alias, - data_type = OBI_BOOL, - nb_lines = column_p.header.lines_used, - nb_elements_per_line = column_p.header.nb_elements_per_line, - elements_names = column_p.header.elements_names, - indexer_name = NULL, - associated_column_name = NULL, - associated_column_version = NULL, - comments = tobytes(comments), - create = False) - - cpdef object get_line(self, index_t line_nb): - cdef obibool_t value - cdef object result - global obi_errno - - value = obi_get_bool_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0) - if obi_errno > 0 : - raise IndexError(line_nb) - if value == OBIBool_NA : - result = None - else : - result = PyBool_FromLong(value) - return result - - cpdef set_line(self, index_t line_nb, object value): - if value is None : - value = OBIBool_NA - if obi_set_bool_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, value) < 0: - raise Exception("Problem setting a value in a column") - - -register_column_class(OBI_BOOL,OBIDMS_column_bool) \ No newline at end of file diff --git a/python/obitools3/dms/_obiseq.cfiles b/python/obitools3/dms/_obiseq.cfiles deleted file mode 100644 index 84e0436..0000000 --- a/python/obitools3/dms/_obiseq.cfiles +++ /dev/null @@ -1,65 +0,0 @@ -../../../src/bloom.h -../../../src/bloom.c -../../../src/char_str_indexer.h -../../../src/char_str_indexer.c -../../../src/crc64.h -../../../src/crc64.c -../../../src/dna_seq_indexer.h -../../../src/dna_seq_indexer.c -../../../src/encode.h -../../../src/encode.c -../../../src/hashtable.h -../../../src/hashtable.c -../../../src/murmurhash2.h -../../../src/murmurhash2.c -../../../src/obi_align.h -../../../src/obi_align.c -../../../src/obiavl.h -../../../src/obiavl.c -../../../src/obiblob_indexer.h -../../../src/obiblob_indexer.c -../../../src/obiblob.h -../../../src/obiblob.c -../../../src/obidebug.h -../../../src/obidms_taxonomy.h -../../../src/obidms_taxonomy.c -../../../src/obidms.h -../../../src/obidms.c -../../../src/obidmscolumn_blob.c -../../../src/obidmscolumn_blob.h -../../../src/obidmscolumn_bool.c -../../../src/obidmscolumn_bool.h -../../../src/obidmscolumn_char.c -../../../src/obidmscolumn_char.h -../../../src/obidmscolumn_float.c -../../../src/obidmscolumn_float.h -../../../src/obidmscolumn_idx.h -../../../src/obidmscolumn_idx.c -../../../src/obidmscolumn_int.c -../../../src/obidmscolumn_int.h -../../../src/obidmscolumn_qual.h -../../../src/obidmscolumn_qual.c -../../../src/obidmscolumn_seq.c -../../../src/obidmscolumn_seq.h -../../../src/obidmscolumn_str.c -../../../src/obidmscolumn_str.h -../../../src/obidmscolumn.h -../../../src/obidmscolumn.c -../../../src/obidmscolumndir.h -../../../src/obidmscolumndir.c -../../../src/obierrno.h -../../../src/obierrno.c -../../../src/obilittlebigman.h -../../../src/obilittlebigman.c -../../../src/obitypes.h -../../../src/obitypes.c -../../../src/obiview.h -../../../src/obiview.c -../../../src/sse_banded_LCS_alignment.h -../../../src/sse_banded_LCS_alignment.c -../../../src/uint8_indexer.h -../../../src/uint8_indexer.c -../../../src/upperband.h -../../../src/upperband.c -../../../src/utils.h -../../../src/utils.c diff --git a/python/obitools3/dms/_obiseq.pxd b/python/obitools3/dms/_obiseq.pxd deleted file mode 100644 index 62ecc5e..0000000 --- a/python/obitools3/dms/_obiseq.pxd +++ /dev/null @@ -1,21 +0,0 @@ -#cython: language_level=3 - -from ._obiview cimport OBIView_line - - -cdef class OBI_Seq(dict) : - cdef str _id - cdef object _seq - cdef str _definition - - -cdef class OBI_Nuc_Seq(OBI_Seq) : - cdef object _quality - cpdef object get_str_quality(self) - - #cpdef object reverse_complement(self) - -cdef class OBI_Nuc_Seq_Stored(OBIView_line) : - cpdef object get_str_quality(self) - - #cpdef object reverse_complement(self) diff --git a/python/obitools3/dms/_obiseq.pyx b/python/obitools3/dms/_obiseq.pyx deleted file mode 100644 index a0f1b94..0000000 --- a/python/obitools3/dms/_obiseq.pyx +++ /dev/null @@ -1,188 +0,0 @@ -#cython: language_level=3 - -from obitools3.utils cimport bytes2str, str2bytes - -from .capi.obiview cimport NUC_SEQUENCE_COLUMN, \ - ID_COLUMN, \ - DEFINITION_COLUMN, \ - QUALITY_COLUMN -from docutils.nodes import definition - - -cdef str __str__ID_COLUMN__ = bytes2str(ID_COLUMN) -cdef str __str__DEFINITION_COLUMN__ = bytes2str(DEFINITION_COLUMN) -cdef str __str__QUALITY_COLUMN__ = bytes2str(QUALITY_COLUMN) -cdef str __str__NUC_SEQUENCE_COLUMN__ = bytes2str(NUC_SEQUENCE_COLUMN) - - -cdef class OBI_Seq(dict) : - - def __init__(self, str id, - object seq, - str definition=None, - dict tags=None) : - - if tags is not None: - self.update(tags) - - self._id = id - self._seq = seq - - if definition is not None : - self._definition = definition - else: - self._definition = None - - - - def __getitem__(self,str key): - if key == __str__ID_COLUMN__: - return self._id - elif key == __str__DEFINITION_COLUMN__: - return self._definition - else: - return dict.__getitem__(self,key) - - def __setitem__(self,str key,object value): - if key == __str__ID_COLUMN__: - self._id=value - elif key == __str__DEFINITION_COLUMN__: - self._definition=value - else: - dict.__setitem__(self,key,value) - - # sequence id property getter and setter - @property - def id(self): # @ReservedAssignment - return self._id - @id.setter - def id(self, str new_id): # @ReservedAssignment @DuplicatedSignature - self._id = new_id - - # sequence property getter and setter - @property - def seq(self): - return self._seq - @seq.setter - def seq(self, object new_seq): # @DuplicatedSignature - self._seq = new_seq - # self["SEQ"] = new_seq # TODO discuss - - # sequence definition property getter and setter - @property - def definition(self): - return self._definition - @definition.setter - def definition(self, object new_definition): # @DuplicatedSignature - self._definition = new_definition - - -cdef class OBI_Nuc_Seq(OBI_Seq) : - - def __init__(self, str id, - object seq, - str quality=None, - str definition=None, - dict tags=None) : - OBI_Seq.__init__(self,id,seq,tags) - if quality is not None: - self._quality=quality - else: - self._quality=None - - - - def __getitem__(self,str key): - if key == __str__NUC_SEQUENCE_COLUMN__: - return self._seq - elif key == __str__QUALITY_COLUMN__: - return self._quality - else: - return OBI_Seq.__getitem__(self,key) - - def __setitem__(self,str key, object value): - if key == __str__NUC_SEQUENCE_COLUMN__: - self._seq = value - elif key == __str__QUALITY_COLUMN__: - self._quality=value - else: - OBI_Seq.__setitem__(self,key,value) - - - - cpdef object get_str_quality(self) : # TODO not ideal. Make quality_int and quality_str properties - return self._quality - - # nuc sequence property getter and setter - @property - def seq(self): - return self._seq - @seq.setter - def seq(self, object new_seq): # @DuplicatedSignature - self._seq = new_seq -# self[bytes2str(NUC_SEQUENCE_COLUMN)] = new_seq - - # sequence quality property getter and setter - @property - def quality(self): - return self._quality - @quality.setter - def quality(self, object new_quality): # @DuplicatedSignature - self._quality = new_quality -# self[bytes2str(QUALITY_COLUMN)] = new_quality - -# cpdef str reverse_complement(self) : TODO in C ? -# pass - - -cdef class OBI_Nuc_Seq_Stored(OBIView_line) : - - # TODO store the str version of column name macros? - - # sequence id property getter and setter - @property - def id(self): # @ReservedAssignment @DuplicatedSignature - return self[__str__ID_COLUMN__] - - @id.setter - def id(self, str new_id): # @ReservedAssignment @DuplicatedSignature - self[__str__ID_COLUMN__] = new_id - - # sequence definition property getter and setter - @property - def definition(self): - return self[__str__DEFINITION_COLUMN__] - - @definition.setter - def definition(self, str new_def): # @DuplicatedSignature - self[__str__DEFINITION_COLUMN__] = new_def - - # nuc_seq property getter and setter - @property - def nuc_seq(self): - return self[__str__NUC_SEQUENCE_COLUMN__] - - @nuc_seq.setter - def nuc_seq(self, object new_seq): # @DuplicatedSignature - self[__str__NUC_SEQUENCE_COLUMN__] = new_seq - - # quality property getter and setter - @property - def quality(self): - return self[__str__QUALITY_COLUMN__] - - @quality.setter - def quality(self, object new_qual): # @DuplicatedSignature - if (type(new_qual) == list) or (new_qual is None) : # TODO check that quality column exists - self[__str__QUALITY_COLUMN__] = new_qual - else : # Quality is in str form - (((self._view).columns)[__str__QUALITY_COLUMN__]).set_str_line(self._index, new_qual) - - cpdef object get_str_quality(self) : # TODO not ideal. Make quality_int and quality_str properties - return ((self._view).columns)[__str__QUALITY_COLUMN__].get_str_line(self._index) - -# cpdef str reverse_complement(self) : TODO in C ? -# pass - - # TODO static method to import OBI_Nuc_Seq to OBI_Nuc_Seq_Stored ? - diff --git a/python/obitools3/dms/_obitaxo.cfiles b/python/obitools3/dms/_obitaxo.cfiles deleted file mode 100644 index 84e0436..0000000 --- a/python/obitools3/dms/_obitaxo.cfiles +++ /dev/null @@ -1,65 +0,0 @@ -../../../src/bloom.h -../../../src/bloom.c -../../../src/char_str_indexer.h -../../../src/char_str_indexer.c -../../../src/crc64.h -../../../src/crc64.c -../../../src/dna_seq_indexer.h -../../../src/dna_seq_indexer.c -../../../src/encode.h -../../../src/encode.c -../../../src/hashtable.h -../../../src/hashtable.c -../../../src/murmurhash2.h -../../../src/murmurhash2.c -../../../src/obi_align.h -../../../src/obi_align.c -../../../src/obiavl.h -../../../src/obiavl.c -../../../src/obiblob_indexer.h -../../../src/obiblob_indexer.c -../../../src/obiblob.h -../../../src/obiblob.c -../../../src/obidebug.h -../../../src/obidms_taxonomy.h -../../../src/obidms_taxonomy.c -../../../src/obidms.h -../../../src/obidms.c -../../../src/obidmscolumn_blob.c -../../../src/obidmscolumn_blob.h -../../../src/obidmscolumn_bool.c -../../../src/obidmscolumn_bool.h -../../../src/obidmscolumn_char.c -../../../src/obidmscolumn_char.h -../../../src/obidmscolumn_float.c -../../../src/obidmscolumn_float.h -../../../src/obidmscolumn_idx.h -../../../src/obidmscolumn_idx.c -../../../src/obidmscolumn_int.c -../../../src/obidmscolumn_int.h -../../../src/obidmscolumn_qual.h -../../../src/obidmscolumn_qual.c -../../../src/obidmscolumn_seq.c -../../../src/obidmscolumn_seq.h -../../../src/obidmscolumn_str.c -../../../src/obidmscolumn_str.h -../../../src/obidmscolumn.h -../../../src/obidmscolumn.c -../../../src/obidmscolumndir.h -../../../src/obidmscolumndir.c -../../../src/obierrno.h -../../../src/obierrno.c -../../../src/obilittlebigman.h -../../../src/obilittlebigman.c -../../../src/obitypes.h -../../../src/obitypes.c -../../../src/obiview.h -../../../src/obiview.c -../../../src/sse_banded_LCS_alignment.h -../../../src/sse_banded_LCS_alignment.c -../../../src/uint8_indexer.h -../../../src/uint8_indexer.c -../../../src/upperband.h -../../../src/upperband.c -../../../src/utils.h -../../../src/utils.c diff --git a/python/obitools3/dms/_obitaxo.pxd b/python/obitools3/dms/_obitaxo.pxd deleted file mode 100644 index 51c6c0f..0000000 --- a/python/obitools3/dms/_obitaxo.pxd +++ /dev/null @@ -1,20 +0,0 @@ -#cython: language_level=3 - -from .capi.obitaxonomy cimport ecotx_t, OBIDMS_taxonomy_p -from ._obidms cimport OBIDMS - - -cdef class OBI_Taxonomy : - - cdef str _name - cdef OBIDMS_taxonomy_p _pointer - cdef OBIDMS _dms - - cpdef write(self, str prefix) - cpdef int add_taxon(self, str name, str rank_name, int parent_taxid, int min_taxid=*) - cpdef close(self) - - -cdef class OBI_Taxon : - - cdef ecotx_t* _pointer diff --git a/python/obitools3/dms/_obitaxo.pyx b/python/obitools3/dms/_obitaxo.pyx deleted file mode 100644 index b9d7e98..0000000 --- a/python/obitools3/dms/_obitaxo.pyx +++ /dev/null @@ -1,129 +0,0 @@ -#cython: language_level=3 - -from obitools3.utils cimport bytes2str, str2bytes - -from .capi.obitaxonomy cimport obi_read_taxonomy, \ - obi_read_taxdump, \ - obi_write_taxonomy, \ - obi_close_taxonomy, \ - obi_taxo_get_taxon_with_taxid, \ - obi_taxonomy_add_local_taxon, \ - ecotx_t - - -from ._obidms cimport OBIDMS - -from cpython.pycapsule cimport PyCapsule_New, PyCapsule_GetPointer -from logging import raiseExceptions - - -cdef class OBI_Taxonomy : - - # TODO function to import taxonomy? - - def __init__(self, OBIDMS dms, str name, bint taxdump=False) : - - self._dms = dms - self._name = name - if taxdump : - self._pointer = obi_read_taxdump(str2bytes(name)) - else : - self._pointer = obi_read_taxonomy(dms._pointer, str2bytes(name), True) # TODO discuss - # TODO if not found in DMS, try to import? - - - def __getitem__(self, object ref): - - cdef ecotx_t* taxon_p - cdef object taxon_capsule - - if type(ref) == int : - taxon_p = obi_taxo_get_taxon_with_taxid(self._pointer, ref) - if taxon_p == NULL : - raise Exception("Taxon not found") - taxon_capsule = PyCapsule_New(taxon_p, NULL, NULL) - return OBI_Taxon(taxon_capsule) - else : - raise Exception("Not implemented") - - - def __iter__(self): - - cdef ecotx_t* taxa - cdef ecotx_t* taxon_p - cdef object taxon_capsule - cdef int t - - taxa = self._pointer.taxa.taxon - - # Yield each taxid - for t in range(self._pointer.taxa.count): - taxon_p = (taxa+t) - taxon_capsule = PyCapsule_New(taxon_p, NULL, NULL) - yield OBI_Taxon(taxon_capsule) - - - cpdef write(self, str prefix) : - if obi_write_taxonomy(self._dms._pointer, self._pointer, str2bytes(prefix)) < 0 : - raise Exception("Error writing the taxonomy to binary files") - - - cpdef int add_taxon(self, str name, str rank_name, int parent_taxid, int min_taxid=10000000) : - cdef int taxid - taxid = obi_taxonomy_add_local_taxon(self._pointer, str2bytes(name), str2bytes(rank_name), parent_taxid, min_taxid) - if taxid < 0 : - raise Exception("Error adding a new taxon to the taxonomy") - else : - return taxid - - - cpdef close(self) : - if (obi_close_taxonomy(self._pointer) < 0) : - raise Exception("Error closing the taxonomy") - - - -cdef class OBI_Taxon : # TODO dict subclass? - - def __init__(self, object taxon_capsule) : - self._pointer = PyCapsule_GetPointer(taxon_capsule, NULL) - if self._pointer == NULL : - raise Exception("Error reading the taxonomy") - - # name property getter - @property - def name(self): - return bytes2str(self._pointer.name) - - # taxid property getter - @property - def taxid(self): - return self._pointer.taxid - - # rank property getter - @property - def rank(self): - return self._pointer.rank - - # farest property getter - @property - def farest(self): - return self._pointer.farest - - # parent property getter - @property - def parent(self): - cdef object parent_capsule - parent_capsule = PyCapsule_New(self._pointer.parent, NULL, NULL) - return OBI_Taxon(parent_capsule) - - def __repr__(self): - d = {} - d['taxid'] = self.taxid - d['name'] = self.name - d['parent'] = self.parent.taxid - d['farest'] = self.farest - return str(d) - - - diff --git a/python/obitools3/dms/_obiview_nuc_seq.pxd b/python/obitools3/dms/_obiview_nuc_seq.pxd deleted file mode 100644 index badb5c4..0000000 --- a/python/obitools3/dms/_obiview_nuc_seq.pxd +++ /dev/null @@ -1,25 +0,0 @@ -#cython: language_level=3 - -from ._obiview cimport OBIView -from ._obiseq cimport OBI_Nuc_Seq, OBI_Nuc_Seq_Stored - - -cdef class OBIView_NUC_SEQS_QUAL(OBIView_NUC_SEQS): - cpdef OBIView clone(self, - str view_name, - OBIView_line_selection line_selection=*, - str comments=*) - - @staticmethod - cpdef OBIView new(OBIDMS dms, - str view_name, - str comments=*) - - @staticmethod - cpdef OBIView open(OBIDMS dms, - str view_name) - -cdef class OBIView_NUC_SEQS_line_selection(OBIView_line_selection): - cpdef OBIView materialize(self, - str view_name, - str comments=*) diff --git a/python/obitools3/dms/_obiview_nuc_seq.pyx b/python/obitools3/dms/_obiview_nuc_seq.pyx deleted file mode 100644 index 6b58303..0000000 --- a/python/obitools3/dms/_obiview_nuc_seq.pyx +++ /dev/null @@ -1,105 +0,0 @@ -#cython: language_level=3 - -from .capi.obitypes cimport index_t - - -cdef class OBIView_NUC_SEQS(OBIView): - - cpdef OBIView clone(self, - str view_name, - str comments=""): - - cdef OBIView view = OBIView_NUC_SEQS(987654) - - view._pointer = obi_new_view_nuc_seqs(self._pointer.dms, - str2bytes(view_name), - self._pointer, - NULL, - str2bytes(comments), - False) - - if view._pointer == NULL : - raise RuntimeError("Error : Cannot clone view %s into view %s" - % (str(self.name), - view_name) - ) - - view.__init_columns__(self) - - return view - - @staticmethod - cpdef OBIView new(OBIDMS dms, - str view_name, - str comments=""): - - cdef OBIView view = OBIView_NUC_SEQS(987654) # @DuplicatedSignature - - view._pointer = obi_new_view_nuc_seqs(dms._pointer, - str2bytes(view_name), - NULL, - NULL, - str2bytes(comments), - False) - - if view._pointer == NULL : - raise RuntimeError("Error : Cannot create view %s" % view_name) - - view.__init_columns__(self) - - return view - - @staticmethod - cpdef OBIView open(OBIDMS dms, - str view_name): - - cdef OBIView view = OBIView_NUC_SEQS(987654) # @DuplicatedSignature - - view._pointer = obi_open_view(dms._pointer, - str2bytes(view_name)) - - if view._pointer == NULL : - raise RuntimeError("Error : Cannot open view %s" % view_name) - - view.__init_columns__(self) - - return view - - cpdef OBIView_line_selection new_selection(self,list lines=None): - return OBIView_NUC_SEQS_line_selection(self,lines) - - def __getitem__(self, object item) : - if type(item) == str : - return (self._columns)[item] - elif type(item) == int : - return OBI_Nuc_Seq_Stored(self, item) - - - def __setitem__(self, index_t line_idx, OBI_Nuc_Seq sequence_obj) : - for key in sequence_obj : - self[line_idx][key] = sequence_obj[key] - - -cdef class OBIView_NUC_SEQS_line_selection(OBIView_line_selection): - - cpdef OBIView materialize(self, - str view_name, - str comments=""): - - cdef OBIView view = OBIView_NUC_SEQS(987654) - - view._pointer = obi_new_view(self._view._pointer.dms, - str2bytes(view_name), - self._view._pointer, - self.__build_binary_list__(), - str2bytes(comments)) - - if view._pointer == NULL : - raise RuntimeError("Error : Cannot clone view %s into view %s" - % (str(self.name), - view_name) - ) - - view.__init_columns__(self) - - return view diff --git a/python/obitools3/dms/_obiview_nuc_seq_qual.pxd b/python/obitools3/dms/_obiview_nuc_seq_qual.pxd deleted file mode 100644 index 72259d9..0000000 --- a/python/obitools3/dms/_obiview_nuc_seq_qual.pxd +++ /dev/null @@ -1,25 +0,0 @@ -#cython: language_level=3 - -from ._obidms cimport OBIView -from ._obiseq cimport OBI_Nuc_Seq, OBI_Nuc_Seq_Stored - - -cdef class OBIView_NUC_SEQS_QUAL(OBIView_NUC_SEQS): - cpdef OBIView clone(self, - str view_name, - OBIView_line_selection line_selection=*, - str comments=*) - - @staticmethod - cpdef OBIView new(OBIDMS dms, - str view_name, - str comments=*) - - @staticmethod - cpdef OBIView open(OBIDMS dms, - str view_name) - -cdef class OBIView_NUC_SEQS_QUAL_line_selection(OBIView_NUC_SEQS_line_selection): - cpdef OBIView materialize(self, - str view_name, - str comments=*) diff --git a/python/obitools3/dms/_obiview_nuc_seq_qual.pyx b/python/obitools3/dms/_obiview_nuc_seq_qual.pyx deleted file mode 100644 index b6454ec..0000000 --- a/python/obitools3/dms/_obiview_nuc_seq_qual.pyx +++ /dev/null @@ -1,90 +0,0 @@ -#cython: language_level=3 - -from .capi.obitypes cimport index_t - - -cdef class OBIView_NUC_SEQS_QUAL(OBIView_NUC_SEQS): - - cpdef OBIView clone(self, - str view_name, - str comments=""): - - cdef OBIView view = OBIView_NUC_SEQS_QUAL(987654) - - view._pointer = obi_new_view_nuc_seqs(self._pointer.dms, - str2bytes(view_name), - self._pointer, - NULL, - str2bytes(comments), - True) - - if view._pointer == NULL : - raise RuntimeError("Error : Cannot clone view %s into view %s" - % (str(self.name), - view_name) - ) - - view.__init_columns__(self) - - return view - - @staticmethod - cpdef OBIView new(OBIDMS dms, - str view_name, - str comments=""): - - cdef OBIView view = OBIView_NUC_SEQS_QUAL(987654) # @DuplicatedSignature - - view._pointer = obi_new_view_nuc_seqs(dms._pointer, - str2bytes(view_name), - NULL, - NULL, - str2bytes(comments), - True) - - if view._pointer == NULL : - raise RuntimeError("Error : Cannot create view %s" % view_name) - - view.__init_columns__(self) - - return view - - @staticmethod - cpdef OBIView open(OBIDMS dms, - str view_name): - - cdef OBIView view = OBIView_NUC_SEQS_QUAL(987654) # @DuplicatedSignature - - view._pointer = obi_open_view(dms._pointer, - str2bytes(view_name)) - - if view._pointer == NULL : - raise RuntimeError("Error : Cannot open view %s" % view_name) - - view.__init_columns__(self) - - return view - -cdef class OBIView_NUC_SEQS_QUAL_line_selection(OBIView_NUC_SEQS_line_selection): - - cpdef OBIView materialize(self, - str view_name, - str comments=""): - - cdef OBIView view = OBIView_NUC_SEQS_QUAL(987654) - - view._pointer = obi_new_view(self._view._pointer.dms, - str2bytes(view_name), - self._view._pointer, - self.__build_binary_list__(), - str2bytes(comments)) - - if view._pointer == NULL : - raise RuntimeError("Error : Cannot clone view %s into view %s" - % (str(self.name), - view_name) - ) - - view.__init_columns__(self) - - return view