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New Cython API: compile but doesn't work

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This commit is contained in:
Celine Mercier
2017-02-17 15:14:06 +01:00
parent 071a3b61ab
commit f23315e26f
12 changed files with 241 additions and 346 deletions
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2
python/obitools3/commands/import.pyx
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@ -90,7 +90,7 @@ def addOptions(parser):
# TODO: Handling of NA values # TODO: Handling of NA values
def run(config): def run(config):
pb = ProgressBar(10000, config, seconde=5) # TODO should be number of records in file pb = ProgressBar(35000000, config, seconde=5) # TODO should be number of records in file
inputs = uopen(config['import']['filename']) inputs = uopen(config['import']['filename'])

26
python/obitools3/obidms/_obidms.pxd
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@ -2,9 +2,9 @@
from .capi.obidms cimport OBIDMS_p from .capi.obidms cimport OBIDMS_p
from .capi.obidmscolumn cimport OBIDMS_column_p from .capi.obidmscolumn cimport OBIDMS_column_p
from .capi.obiview cimport Obiview_p from .capi.obitypes cimport index_t
from .capi.obitypes cimport obiversion_t, OBIType_t, index_t
from ._obitaxo cimport OBI_Taxonomy from ._obitaxo cimport OBI_Taxonomy
from ._obiview cimport OBIView, OBIView_line_selection
cdef class OBIDMS_column: cdef class OBIDMS_column:
@ -30,31 +30,9 @@ cdef class OBIDMS_column_line:
cdef index_t _index cdef index_t _index
cdef class OBIView_line :
cdef index_t _index
cdef OBIView _view
cdef class OBIView_line_selection(list):
cdef OBIView _view
cdef str _view_name
cdef class OBIDMS: cdef class OBIDMS:
cdef OBIDMS_p _pointer cdef OBIDMS_p _pointer
cpdef close(self) cpdef close(self)
cpdef OBI_Taxonomy open_taxonomy(self, str taxo_name) cpdef OBI_Taxonomy open_taxonomy(self, str taxo_name)
cpdef OBIView new_view(self, str view_name, str view_type=*, bint quality_column=*, str comments=*)
cpdef OBIView clone_view(self, str view_name, object view_to_clone, str comments=*)
cpdef OBIView clone_view_with_line_selection(self, str view_name, OBIView_line_selection line_selection, str comments=*)
cpdef dict read_view_infos(self, str view_name)
# cpdef dict read_views(self) TODO

233
python/obitools3/obidms/_obidms.pyx
View File

@ -6,7 +6,6 @@ from .capi.obidms cimport obi_dms, \
obi_close_dms obi_close_dms
from .capi.obidmscolumn cimport obi_close_column, \ from .capi.obidmscolumn cimport obi_close_column, \
OBIDMS_column_p, \
OBIDMS_column_header_p, \ OBIDMS_column_header_p, \
obi_get_elements_names obi_get_elements_names
@ -21,15 +20,10 @@ from .capi.obitypes cimport const_char_p, \
OBI_QUAL, \ OBI_QUAL, \
OBI_STR, \ OBI_STR, \
OBI_SEQ, \ OBI_SEQ, \
name_data_type, \ name_data_type
only_ATGC # discuss
from ._obidms cimport OBIDMS, \ from .capi.obiview cimport Obiview_p, \
OBIDMS_column, \ obi_view_get_pointer_on_column_in_view
OBIView, \
OBIView_line
from ._obitaxo cimport OBI_Taxonomy
from ._obidmscolumn_int cimport OBIDMS_column_int, \ from ._obidmscolumn_int cimport OBIDMS_column_int, \
OBIDMS_column_multi_elts_int OBIDMS_column_multi_elts_int
@ -52,31 +46,7 @@ from ._obidmscolumn_str cimport OBIDMS_column_str, \
from ._obidmscolumn_seq cimport OBIDMS_column_seq, \ from ._obidmscolumn_seq cimport OBIDMS_column_seq, \
OBIDMS_column_multi_elts_seq OBIDMS_column_multi_elts_seq
from .capi.obiview cimport Obiview_p, \ from libc.stdlib cimport free
Obiview_infos_p, \
Alias_column_pair_p, \
obi_new_view_nuc_seqs, \
obi_new_view, \
obi_new_view_cloned_from_name, \
obi_new_view_nuc_seqs_cloned_from_name, \
obi_view_map_file, \
obi_view_unmap_file, \
obi_open_view, \
obi_view_delete_column, \
obi_view_add_column, \
obi_view_create_column_alias, \
obi_view_get_column, \
obi_view_get_pointer_on_column_in_view, \
obi_save_and_close_view, \
VIEW_TYPE_NUC_SEQS, \
NUC_SEQUENCE_COLUMN, \
ID_COLUMN, \
DEFINITION_COLUMN, \
QUALITY_COLUMN
from libc.stdlib cimport malloc, free
cdef class OBIDMS_column : cdef class OBIDMS_column :
@ -93,7 +63,7 @@ cdef class OBIDMS_column :
# Fill structure # Fill structure
self._alias = column_alias self._alias = column_alias
self._pointer = column_pp self._pointer = column_pp
self._view = view self._view = view
def __setitem__(self, index_t line_nb, object value): def __setitem__(self, index_t line_nb, object value):
self.set_line(line_nb, value) self.set_line(line_nb, value)
@ -269,88 +239,6 @@ cdef class OBIDMS_column_line :
###################################################################################################### ######################################################################################################
cdef class OBIView_line :
def __init__(self, OBIView view, index_t line_nb) :
self._index = line_nb
self._view = view
def __getitem__(self, str column_name) :
return ((self._view)._columns)[column_name][self._index]
def __setitem__(self, str column_name, object value):
# TODO detect multiple elements (dict type)? put somewhere else? but more risky (in get)
# TODO OBI_QUAL ?
cdef type value_type
cdef str value_obitype
cdef bytes value_b
if column_name not in self._view :
if value == None :
raise Exception("Trying to create a column from a None value (can't guess type)")
value_type = type(value)
if value_type == int :
value_obitype = 'OBI_INT'
elif value_type == float :
value_obitype = 'OBI_FLOAT'
elif value_type == bool :
value_obitype = 'OBI_BOOL'
elif value_type == str or value_type == bytes :
if value_type == str :
value_b = str2bytes(value)
else :
value_b = value
if only_ATGC(value_b) : # TODO detect IUPAC
value_obitype = 'OBI_SEQ'
elif len(value) == 1 :
value_obitype = 'OBI_CHAR'
elif (len(value) > 1) :
value_obitype = 'OBI_STR'
else :
raise Exception("Could not guess the type of a value to create a new column")
self._view.add_column(column_name, type=value_obitype)
(((self._view)._columns)[column_name]).set_line(self._index, value)
def __iter__(self):
for column_name in ((self._view)._columns) :
yield column_name
def __contains__(self, str column_name):
return (column_name in self._view._columns)
def __repr__(self):
cdef dict line
cdef str column_name
line = {}
for column_name in self._view._columns :
line[column_name] = self[column_name]
return str(line)
######################################################################################################
cdef class OBIView_line_selection(list):
def __init__(self, OBIView view) :
if view._pointer == NULL:
raise Exception("Error: trying to create a line selection with an invalidated view")
self._view = view
self._view_name = view.name
def append(self, index_t idx) :
if idx >= self._view.line_count :
raise Exception("Error: trying to select a line beyond the line count of a view")
# if idx in self : # TODO discuss. Discuss order too
# pass
# else :
super(OBIView_line_selection, self).append(idx)
######################################################################################################
cdef class OBIDMS : cdef class OBIDMS :
def __init__(self, str dms_name) : def __init__(self, str dms_name) :
@ -381,114 +269,3 @@ cdef class OBIDMS :
cpdef OBI_Taxonomy open_taxonomy(self, str taxo_name) : cpdef OBI_Taxonomy open_taxonomy(self, str taxo_name) :
return OBI_Taxonomy(self, taxo_name) return OBI_Taxonomy(self, taxo_name)
cpdef OBIView new_view(self, str view_name, str view_type="", bint quality_column=False, str comments="") :
cdef object view_class
# Get right subclass depending on view type
view_class = OBIView.get_view_subclass(view_type)
return view_class(self, view_name, new=True, comments=comments, quality_column=quality_column, view_type=view_type)
cpdef OBIView clone_view(self, str view_name, object view_to_clone, str comments="") :
cdef object view_class # @DuplicatedSignature
cdef str view_type
# Get right subclass depending on view type
if type(view_to_clone) == str :
view_type = self.read_view_infos(view_to_clone)["view_type"]
else :
view_type = view_to_clone.type
view_class = OBIView.get_view_subclass(view_type)
return view_class(self, view_name, new=True, view_to_clone=view_to_clone, comments=comments, view_type=view_type)
cpdef OBIView clone_view_with_line_selection(self, str view_name, OBIView_line_selection line_selection, str comments="") :
cdef object view_class # @DuplicatedSignature
# Get right subclass depending on view type
view_class = OBIView.get_view_subclass(line_selection._view.type)
return view_class(self, view_name, new=True, view_to_clone=line_selection._view, line_selection=line_selection, comments=comments)
cpdef dict read_view_infos(self, str view_name) :
cdef Obiview_infos_p view_infos_p
cdef dict view_infos_d
cdef Alias_column_pair_p column_refs
cdef int i, j
cdef str column_name
view_infos_p = obi_view_map_file(self._pointer, str2bytes(view_name), True)
view_infos_d = {}
view_infos_d["name"] = bytes2str(view_infos_p.name)
view_infos_d["comments"] = bytes2str(view_infos_p.comments)
view_infos_d["view_type"] = bytes2str(view_infos_p.view_type)
view_infos_d["column_count"] = <int> view_infos_p.column_count
view_infos_d["line_count"] = <int> view_infos_p.line_count
view_infos_d["created_from"] = bytes2str(view_infos_p.created_from)
view_infos_d["creation_date"] = bytes2str(obi_format_date(view_infos_p.creation_date))
if (view_infos_p.all_lines) :
view_infos_d["line_selection"] = None
else :
view_infos_d["line_selection"] = {}
view_infos_d["line_selection"]["column_name"] = bytes2str((view_infos_p.line_selection).column_name)
view_infos_d["line_selection"]["version"] = <int> (view_infos_p.line_selection).version
view_infos_d["column_references"] = {}
column_references = view_infos_p.column_references
for j in range(view_infos_d["column_count"]) :
column_name = bytes2str((column_references[j]).alias)
view_infos_d["column_references"][column_name] = {}
view_infos_d["column_references"][column_name]["original_name"] = bytes2str((column_references[j]).column_refs.column_name)
view_infos_d["column_references"][column_name]["version"] = (column_references[j]).column_refs.version
obi_view_unmap_file(self._pointer, view_infos_p)
return view_infos_d
# cpdef dict read_views(self) : # TODO function that prints the dic nicely and function that prints 1 view nicely. Add column type in col ref
#
# cdef Obiviews_infos_all_p all_views_p
# cdef Obiview_infos_p view_p
# cdef Column_reference_p column_refs
# cdef int nb_views
# cdef int i, j
# cdef str view_name
# cdef str column_name
# cdef dict views
# cdef bytes name_b
#
# views = {}
# all_views_p = obi_read_view_infos(self._pointer)
# if all_views_p == NULL :
# raise Exception("No views to read")
# nb_views = <int> (all_views_p.header).view_count
# for i in range(nb_views) :
# view_p = (<Obiview_infos_p> (all_views_p.view_infos)) + i
# view_name = bytes2str(view_p.name)
# views[view_name] = {}
# views[view_name]["comments"] = bytes2str(view_p.comments)
# views[view_name]["view_type"] = bytes2str(view_p.view_type)
# views[view_name]["column_count"] = <int> view_p.column_count
# views[view_name]["line_count"] = <int> view_p.line_count
# views[view_name]["view_number"] = <int> view_p.view_number
# views[view_name]["created_from"] = bytes2str(view_p.created_from)
# views[view_name]["creation_date"] = bytes2str(obi_format_date(view_p.creation_date))
# if (view_p.all_lines) :
# views[view_name]["line_selection"] = None
# else :
# views[view_name]["line_selection"] = {}
# views[view_name]["line_selection"]["column_name"] = bytes2str((view_p.line_selection).column_name)
# views[view_name]["line_selection"]["version"] = <int> (view_p.line_selection).version
# views[view_name]["column_references"] = {}
# column_refs = view_p.column_references
# for j in range(views[view_name]["column_count"]) :
# column_name = bytes2str((column_refs[j]).column_name)
# views[view_name]["column_references"][column_name] = {}
# views[view_name]["column_references"][column_name]["version"] = column_refs[j].version
#
# obi_close_view_infos(all_views_p);
#
# return views

1
python/obitools3/obidms/_obidmscolumn_bool.pyx
View File

@ -75,3 +75,4 @@ cdef class OBIDMS_column_multi_elts_bool(OBIDMS_column_multi_elts):
value = OBIBool_NA value = OBIBool_NA
if obi_set_bool_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name), <obibool_t> value) < 0: if obi_set_bool_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name), <obibool_t> value) < 0:
raise Exception("Problem setting a value in a column") raise Exception("Problem setting a value in a column")

2
python/obitools3/obidms/_obiseq.pxd
View File

@ -1,6 +1,6 @@
#cython: language_level=3 #cython: language_level=3
from ._obidms cimport OBIView_line from ._obiview cimport OBIView_line
cdef class OBI_Seq(dict) : cdef class OBI_Seq(dict) :

1
python/obitools3/obidms/_obiseq.pyx
View File

@ -6,7 +6,6 @@ from .capi.obiview cimport NUC_SEQUENCE_COLUMN, \
ID_COLUMN, \ ID_COLUMN, \
DEFINITION_COLUMN, \ DEFINITION_COLUMN, \
QUALITY_COLUMN QUALITY_COLUMN
from docutils.nodes import definition
cdef str __str__ID_COLUMN__ = bytes2str(ID_COLUMN) cdef str __str__ID_COLUMN__ = bytes2str(ID_COLUMN)

24
python/obitools3/obidms/_obiview.pxd
View File

@ -1,27 +1,33 @@
#cython: language_level=3 #cython: language_level=3
from ._obidms cimport OBIDMS
from .capi.obiview cimport Obiview_p
from .capi.obitypes cimport obiversion_t, index_t
cdef class OBIView: cdef class OBIView:
cdef Obiview_p _pointer cdef Obiview_p _pointer
cdef dict _columns cdef dict _columns
cdef __init_columns__(self): cdef __init_columns__(self)
cpdef OBIView clone(self, cpdef OBIView clone(self,
str view_name, str view_name,
OBIView_line_selection line_selection=*,
str comments=*) str comments=*)
@staticmethod @staticmethod
cpdef OBIView new(OBIDMS dms, cdef OBIView new(OBIDMS dms,
str view_name, str view_name,
str comments=*) str comments=*)
@staticmethod @staticmethod
cpdef OBIView open(OBIDMS dms, cdef OBIView open(OBIDMS dms,
str view_name) str view_name)
cpdef delete_column(self, str column_name) cpdef delete_column(self, str column_name)
cpdef add_column(self, cpdef add_column(self,
str column_name, str column_name,
obiversion_t version_number=*, obiversion_t version_number=*,
@ -36,18 +42,28 @@ cdef class OBIView:
str comments=*, str comments=*,
bint create=* bint create=*
) )
cpdef change_column_alias(self, str current_alias, str new_alias) cpdef change_column_alias(self, str current_alias, str new_alias)
cpdef update_column_pointers(self) cpdef update_column_pointers(self)
cpdef OBIView_line_selection new_selection(self, cpdef OBIView_line_selection new_selection(self,
list lines=*) list lines=*)
cdef class OBIView_line :
cdef index_t _index
cdef OBIView _view
cdef class OBIView_line_selection(list): cdef class OBIView_line_selection(list):
cdef OBIView _view cdef OBIView _view
cdef str _view_name cdef str _view_name
cdef index_t* __build_binary_list__(self) cdef index_t* __build_binary_list__(self)
cpdef OBIView materialize(self, cpdef OBIView materialize(self,
str view_name, str view_name,
str comments=*) str comments=*)

130
python/obitools3/obidms/_obiview.pyx
View File

@ -1,5 +1,33 @@
#cython: language_level=3 #cython: language_level=3
from obitools3.utils cimport bytes2str, str2bytes
from .capi.obitypes cimport OBI_INT, \
OBI_FLOAT, \
OBI_BOOL, \
OBI_CHAR, \
OBI_QUAL, \
OBI_STR, \
OBI_SEQ, \
only_ATGC
from .capi.obiview cimport Obiview_p, \
obi_new_view, \
obi_open_view, \
obi_view_delete_column, \
obi_view_add_column, \
obi_view_create_column_alias, \
obi_view_get_column, \
obi_view_get_pointer_on_column_in_view, \
obi_save_and_close_view
from .capi.obidmscolumn cimport OBIDMS_column_p
from ._obidms cimport OBIDMS, \
OBIDMS_column
from libc.stdlib cimport malloc
cdef class OBIView : cdef class OBIView :
@ -9,6 +37,7 @@ cdef class OBIView :
self._pointer = NULL self._pointer = NULL
self._columns = {} self._columns = {}
cdef __init_columns__(self): cdef __init_columns__(self):
cdef size_t i cdef size_t i
cdef str col_alias cdef str col_alias
@ -42,12 +71,13 @@ cdef class OBIView :
view_name) view_name)
) )
view.__init_columns__(self) view.__init_columns__()
return view return view
@staticmethod @staticmethod
cpdef OBIView new(OBIDMS dms, cdef OBIView new(OBIDMS dms,
str view_name, str view_name,
str comments=""): str comments=""):
@ -62,12 +92,13 @@ cdef class OBIView :
if view._pointer == NULL : if view._pointer == NULL :
raise RuntimeError("Error : Cannot create view %s" % view_name) raise RuntimeError("Error : Cannot create view %s" % view_name)
view.__init_columns__(self) view.__init_columns__()
return view return view
@staticmethod @staticmethod
cpdef OBIView open(OBIDMS dms, cdef OBIView open(OBIDMS dms,
str view_name): str view_name):
cdef OBIView view = OBIView(987654) # @DuplicatedSignature cdef OBIView view = OBIView(987654) # @DuplicatedSignature
@ -78,10 +109,11 @@ cdef class OBIView :
if view._pointer == NULL : if view._pointer == NULL :
raise RuntimeError("Error : Cannot open view %s" % view_name) raise RuntimeError("Error : Cannot open view %s" % view_name)
view.__init_columns__(self) view.__init_columns__()
return view return view
def __dealloc__(self): def __dealloc__(self):
if (obi_save_and_close_view(self._pointer) < 0) : if (obi_save_and_close_view(self._pointer) < 0) :
raise Exception("Problem closing a view") raise Exception("Problem closing a view")
@ -187,9 +219,11 @@ cdef class OBIView :
column = self._columns[column_n] column = self._columns[column_n]
column._pointer = <OBIDMS_column_p*> obi_view_get_pointer_on_column_in_view(self._pointer, str2bytes(column_n)) column._pointer = <OBIDMS_column_p*> obi_view_get_pointer_on_column_in_view(self._pointer, str2bytes(column_n))
cpdef OBIView_line_selection new_selection(self,list lines=None): cpdef OBIView_line_selection new_selection(self,list lines=None):
return OBIView_line_selection(self,lines) return OBIView_line_selection(self,lines)
def __iter__(self): def __iter__(self):
# Iteration on each line of all columns # Iteration on each line of all columns
@ -254,6 +288,70 @@ cdef class OBIView :
# TODO setter that concatenates new comments? # TODO setter that concatenates new comments?
cdef class OBIView_line :
def __init__(self, OBIView view, index_t line_nb) :
self._index = line_nb
self._view = view
def __getitem__(self, str column_name) :
return ((self._view)._columns)[column_name][self._index]
def __setitem__(self, str column_name, object value):
# TODO detect multiple elements (dict type)? put somewhere else? but more risky (in get)
# TODO OBI_QUAL ?
cdef type value_type
cdef str value_obitype
cdef bytes value_b
if column_name not in self._view :
if value == None :
raise Exception("Trying to create a column from a None value (can't guess type)")
value_type = type(value)
if value_type == int :
value_obitype = 'OBI_INT'
elif value_type == float :
value_obitype = 'OBI_FLOAT'
elif value_type == bool :
value_obitype = 'OBI_BOOL'
elif value_type == str or value_type == bytes :
if value_type == str :
value_b = str2bytes(value)
else :
value_b = value
if only_ATGC(value_b) : # TODO detect IUPAC
value_obitype = 'OBI_SEQ'
elif len(value) == 1 :
value_obitype = 'OBI_CHAR'
elif (len(value) > 1) :
value_obitype = 'OBI_STR'
else :
raise Exception("Could not guess the type of a value to create a new column")
self._view.add_column(column_name, type=value_obitype)
(((self._view)._columns)[column_name]).set_line(self._index, value)
def __iter__(self):
for column_name in ((self._view)._columns) :
yield column_name
def __contains__(self, str column_name):
return (column_name in self._view._columns)
def __repr__(self):
cdef dict line
cdef str column_name
line = {}
for column_name in self._view._columns :
line[column_name] = self[column_name]
return str(line)
cdef class OBIView_line_selection(list): cdef class OBIView_line_selection(list):
def __init__(self, OBIView view, lines=None) : def __init__(self, OBIView view, lines=None) :
@ -265,6 +363,7 @@ cdef class OBIView_line_selection(list):
if lines is not None: if lines is not None:
self.extend(lines) self.extend(lines)
def extend(self, iterable): def extend(self, iterable):
cdef index_t i cdef index_t i
cdef index_t max_i = self._view.line_count cdef index_t max_i = self._view.line_count
@ -278,27 +377,30 @@ cdef class OBIView_line_selection(list):
) )
list.append(self,i) list.append(self,i)
def append(self, index_t idx) : def append(self, index_t idx) :
if idx >= self._view.line_count : if idx >= self._view.line_count :
raise RuntimeError("Error: trying to select line %d beyond the line count %d of view %s" % raise RuntimeError("Error: trying to select line %d beyond the line count %d of view %s" %
(i, (idx,
max_i, self._view.line_count,
self._view_name) self._view_name)
) )
list.append(self,idx) list.append(self,idx)
cdef index_t* __build_binary_list__(self): cdef index_t* __build_binary_list__(self):
cdef index_t* line_selection_p = NULL cdef index_t* line_selection_p = NULL
cdef int i cdef int i
cdef size_t l_selection = len(self) cdef size_t len_selection = len(self)
line_selection_p = <index_t*> malloc((l_selection + 1) * sizeof(index_t)) # +1 for the -1 flagging the end of the array line_selection_p = <index_t*> malloc((len_selection + 1) * sizeof(index_t)) # +1 for the -1 flagging the end of the array
for i in range(l_selection) : for i in range(len_selection) :
line_selection_p[i] = line_selection[i] line_selection_p[i] = self[i]
line_selection_p[l_selection] = -1 # flagging the end of the array line_selection_p[len_selection] = -1 # flagging the end of the array
return line_selection_p return line_selection_p
cpdef OBIView materialize(self, cpdef OBIView materialize(self,
str view_name, str view_name,
str comments=""): str comments=""):
@ -312,12 +414,12 @@ cdef class OBIView_line_selection(list):
str2bytes(comments)) str2bytes(comments))
if view._pointer == NULL : if view._pointer == NULL :
raise RuntimeError("Error : Cannot clone view %s into view %s" raise RuntimeError("Error: Cannot clone view %s into view %s"
% (str(self.name), % (str(self.name),
view_name) view_name)
) )
view.__init_columns__(self) view.__init_columns__()
return view return view

26
python/obitools3/obidms/_obiview_nuc_seq.pxd
View File

@ -1,25 +1,29 @@
#cython: language_level=3 #cython: language_level=3
from ._obidms cimport OBIView from ._obidms cimport OBIDMS
from ._obiseq cimport OBI_Nuc_Seq, OBI_Nuc_Seq_Stored from ._obiview cimport OBIView, OBIView_line_selection
cdef class OBIView_NUC_SEQS_QUAL(OBIView_NUC_SEQS): cdef class OBIView_NUC_SEQS(OBIView):
cpdef OBIView clone(self, cpdef OBIView clone(self,
str view_name, str new_view_name,
OBIView_line_selection line_selection=*,
str comments=*) str comments=*)
@staticmethod cpdef OBIView_line_selection new_selection(self, list lines=*)
cpdef OBIView new(OBIDMS dms,
str view_name,
str comments=*)
@staticmethod @staticmethod
cpdef OBIView open(OBIDMS dms, cdef OBIView new(OBIDMS dms,
str view_name) str view_name,
str comments=*)
@staticmethod
cdef OBIView open(OBIDMS dms,
str view_name)
cdef class OBIView_NUC_SEQS_line_selection(OBIView_line_selection): cdef class OBIView_NUC_SEQS_line_selection(OBIView_line_selection):
cpdef OBIView materialize(self, cpdef OBIView materialize(self,
str view_name, str view_name,
str comments=*) str comments=*)

58
python/obitools3/obidms/_obiview_nuc_seq.pyx
View File

@ -2,17 +2,24 @@
from .capi.obitypes cimport index_t from .capi.obitypes cimport index_t
from ._obiseq cimport OBI_Nuc_Seq, OBI_Nuc_Seq_Stored
from .capi.obiview cimport obi_new_view_nuc_seqs, \
obi_open_view
from obitools3.utils cimport str2bytes
cdef class OBIView_NUC_SEQS(OBIView): cdef class OBIView_NUC_SEQS(OBIView):
cpdef OBIView clone(self, cpdef OBIView clone(self,
str view_name, str new_view_name,
str comments=""): str comments=""):
cdef OBIView view = OBIView_NUC_SEQS(987654) cdef OBIView view = OBIView_NUC_SEQS(987654)
view._pointer = obi_new_view_nuc_seqs(self._pointer.dms, view._pointer = obi_new_view_nuc_seqs(self._pointer.dms,
str2bytes(view_name), str2bytes(new_view_name),
self._pointer, self._pointer,
NULL, NULL,
str2bytes(comments), str2bytes(comments),
@ -20,18 +27,17 @@ cdef class OBIView_NUC_SEQS(OBIView):
if view._pointer == NULL : if view._pointer == NULL :
raise RuntimeError("Error : Cannot clone view %s into view %s" raise RuntimeError("Error : Cannot clone view %s into view %s"
% (str(self.name), % (str(self.name), new_view_name))
view_name)
)
view.__init_columns__(self) view.__init_columns__()
return view return view
@staticmethod @staticmethod
cpdef OBIView new(OBIDMS dms, cdef OBIView new(OBIDMS dms,
str view_name, str view_name,
str comments=""): str comments=""):
cdef OBIView view = OBIView_NUC_SEQS(987654) # @DuplicatedSignature cdef OBIView view = OBIView_NUC_SEQS(987654) # @DuplicatedSignature
@ -45,13 +51,14 @@ cdef class OBIView_NUC_SEQS(OBIView):
if view._pointer == NULL : if view._pointer == NULL :
raise RuntimeError("Error : Cannot create view %s" % view_name) raise RuntimeError("Error : Cannot create view %s" % view_name)
view.__init_columns__(self) view.__init_columns__()
return view return view
@staticmethod @staticmethod
cpdef OBIView open(OBIDMS dms, cdef OBIView open(OBIDMS dms,
str view_name): str view_name):
cdef OBIView view = OBIView_NUC_SEQS(987654) # @DuplicatedSignature cdef OBIView view = OBIView_NUC_SEQS(987654) # @DuplicatedSignature
@ -61,12 +68,14 @@ cdef class OBIView_NUC_SEQS(OBIView):
if view._pointer == NULL : if view._pointer == NULL :
raise RuntimeError("Error : Cannot open view %s" % view_name) raise RuntimeError("Error : Cannot open view %s" % view_name)
view.__init_columns__(self) view.__init_columns__()
return view return view
cpdef OBIView_line_selection new_selection(self,list lines=None):
return OBIView_NUC_SEQS_line_selection(self,lines) cpdef OBIView_line_selection new_selection(self, list lines=None):
return OBIView_NUC_SEQS_line_selection(self, lines)
def __getitem__(self, object item) : def __getitem__(self, object item) :
if type(item) == str : if type(item) == str :
@ -88,18 +97,17 @@ cdef class OBIView_NUC_SEQS_line_selection(OBIView_line_selection):
cdef OBIView view = OBIView_NUC_SEQS(987654) cdef OBIView view = OBIView_NUC_SEQS(987654)
view._pointer = obi_new_view(self._view._pointer.dms, view._pointer = obi_new_view_nuc_seqs(self._view._pointer.dms,
str2bytes(view_name), str2bytes(view_name),
self._view._pointer, self._view._pointer,
self.__build_binary_list__(), self.__build_binary_list__(),
str2bytes(comments)) str2bytes(comments),
False)
if view._pointer == NULL : if view._pointer == NULL :
raise RuntimeError("Error : Cannot clone view %s into view %s" raise RuntimeError("Error : Cannot clone view %s into view %s"
% (str(self.name), % (str(self.name), view_name))
view_name)
)
view.__init_columns__(self) view.__init_columns__()
return view return view

19
python/obitools3/obidms/_obiview_nuc_seq_qual.pxd
View File

@ -1,23 +1,26 @@
#cython: language_level=3 #cython: language_level=3
from ._obidms cimport OBIView from .capi.obitypes cimport index_t
from ._obiseq cimport OBI_Nuc_Seq, OBI_Nuc_Seq_Stored
from ._obidms cimport OBIDMS
from ._obiview cimport OBIView
from ._obiview_nuc_seq cimport OBIView_NUC_SEQS, OBIView_NUC_SEQS_line_selection
cdef class OBIView_NUC_SEQS_QUAL(OBIView_NUC_SEQS): cdef class OBIView_NUC_SEQS_QUAL(OBIView_NUC_SEQS):
cpdef OBIView clone(self, cpdef OBIView clone(self,
str view_name, str view_name,
OBIView_line_selection line_selection=*,
str comments=*) str comments=*)
@staticmethod @staticmethod
cpdef OBIView new(OBIDMS dms, cdef OBIView new(OBIDMS dms,
str view_name, str view_name,
str comments=*) str comments=*)
@staticmethod @staticmethod
cpdef OBIView open(OBIDMS dms, cdef OBIView open(OBIDMS dms,
str view_name) str view_name)
cdef class OBIView_NUC_SEQS_QUAL_line_selection(OBIView_NUC_SEQS_line_selection): cdef class OBIView_NUC_SEQS_QUAL_line_selection(OBIView_NUC_SEQS_line_selection):
cpdef OBIView materialize(self, cpdef OBIView materialize(self,

49
python/obitools3/obidms/_obiview_nuc_seq_qual.pyx
View File

@ -2,12 +2,17 @@
from .capi.obitypes cimport index_t from .capi.obitypes cimport index_t
from .capi.obiview cimport obi_new_view_nuc_seqs, \
obi_open_view
from obitools3.utils cimport bytes2str, str2bytes
cdef class OBIView_NUC_SEQS_QUAL(OBIView_NUC_SEQS): cdef class OBIView_NUC_SEQS_QUAL(OBIView_NUC_SEQS):
cpdef OBIView clone(self, cpdef OBIView clone(self,
str view_name, str view_name,
str comments=""): str comments=""):
cdef OBIView view = OBIView_NUC_SEQS_QUAL(987654) cdef OBIView view = OBIView_NUC_SEQS_QUAL(987654)
@ -20,18 +25,17 @@ cdef class OBIView_NUC_SEQS_QUAL(OBIView_NUC_SEQS):
if view._pointer == NULL : if view._pointer == NULL :
raise RuntimeError("Error : Cannot clone view %s into view %s" raise RuntimeError("Error : Cannot clone view %s into view %s"
% (str(self.name), % (str(self.name), view_name))
view_name)
)
view.__init_columns__(self) view.__init_columns__()
return view return view
@staticmethod @staticmethod
cpdef OBIView new(OBIDMS dms, cdef OBIView new(OBIDMS dms,
str view_name, str view_name,
str comments=""): str comments=""):
cdef OBIView view = OBIView_NUC_SEQS_QUAL(987654) # @DuplicatedSignature cdef OBIView view = OBIView_NUC_SEQS_QUAL(987654) # @DuplicatedSignature
@ -43,15 +47,16 @@ cdef class OBIView_NUC_SEQS_QUAL(OBIView_NUC_SEQS):
True) True)
if view._pointer == NULL : if view._pointer == NULL :
raise RuntimeError("Error : Cannot create view %s" % view_name) raise RuntimeError("Error: Cannot create view %s" % view_name)
view.__init_columns__(self) view.__init_columns__()
return view return view
@staticmethod @staticmethod
cpdef OBIView open(OBIDMS dms, cdef OBIView open(OBIDMS dms,
str view_name): str view_name):
cdef OBIView view = OBIView_NUC_SEQS_QUAL(987654) # @DuplicatedSignature cdef OBIView view = OBIView_NUC_SEQS_QUAL(987654) # @DuplicatedSignature
@ -59,12 +64,13 @@ cdef class OBIView_NUC_SEQS_QUAL(OBIView_NUC_SEQS):
str2bytes(view_name)) str2bytes(view_name))
if view._pointer == NULL : if view._pointer == NULL :
raise RuntimeError("Error : Cannot open view %s" % view_name) raise RuntimeError("Error: Cannot open view %s" % view_name)
view.__init_columns__(self) view.__init_columns__()
return view return view
cdef class OBIView_NUC_SEQS_QUAL_line_selection(OBIView_NUC_SEQS_line_selection): cdef class OBIView_NUC_SEQS_QUAL_line_selection(OBIView_NUC_SEQS_line_selection):
cpdef OBIView materialize(self, cpdef OBIView materialize(self,
@ -73,11 +79,12 @@ cdef class OBIView_NUC_SEQS_QUAL_line_selection(OBIView_NUC_SEQS_line_selection)
cdef OBIView view = OBIView_NUC_SEQS_QUAL(987654) cdef OBIView view = OBIView_NUC_SEQS_QUAL(987654)
view._pointer = obi_new_view(self._view._pointer.dms, view._pointer = obi_new_view_nuc_seqs(self._view._pointer.dms,
str2bytes(view_name), str2bytes(view_name),
self._view._pointer, self._view._pointer,
self.__build_binary_list__(), self.__build_binary_list__(),
str2bytes(comments)) str2bytes(comments),
True)
if view._pointer == NULL : if view._pointer == NULL :
raise RuntimeError("Error : Cannot clone view %s into view %s" raise RuntimeError("Error : Cannot clone view %s into view %s"
@ -85,6 +92,6 @@ cdef class OBIView_NUC_SEQS_QUAL_line_selection(OBIView_NUC_SEQS_line_selection)
view_name) view_name)
) )
view.__init_columns__(self) view.__init_columns__()
return view return view