Cython classes for nucleotide sequences (outside or in the context of a

view)

python/obitools3/obidms/_obidms.pyx

@@ -1,7 +1,5 @@
 #cython: language_level=3
 
-from pathlib import Path
-
 from obitools3.utils cimport bytes2str, str2bytes
 
 from .capi.obidms cimport obi_dms, \
@@ -23,9 +21,12 @@ from .capi.obitypes cimport const_char_p, \
                             name_data_type, \
                             only_ATGC    # discuss
                             
-from ._obidms cimport OBIDMS
+from ._obidms cimport OBIDMS, \
-from ._obidms cimport OBIDMS_column
+                      OBIDMS_column, \
-from ._obidms cimport OBIView_line
+                      OBIView, \
+                      OBIView_line
+
+from ._obiseq cimport OBI_Nuc_Seq, OBI_Nuc_Seq_Stored
 
 from ._obidmscolumn_int cimport OBIDMS_column_int, \
                                 OBIDMS_column_multi_elts_int
@@ -45,8 +46,6 @@ from ._obidmscolumn_str cimport OBIDMS_column_str, \
 from ._obidmscolumn_seq cimport OBIDMS_column_seq, \
                                 OBIDMS_column_multi_elts_seq
 
-from ._obidms cimport OBIView, OBIView_line
-
 from .capi.obiview cimport Obiview_p, \
                            Obiviews_infos_all_p, \
                            Obiview_infos_p, \
@@ -414,7 +413,7 @@ cdef class OBIView :
         # Declarations
         cdef index_t lines_used
         cdef index_t line_nb
-        cdef OBIView_line line
+        cdef OBIView_line line  # TODO for NUC SEQS View
         
         # Yield each line TODO line class
         lines_used = (self.pointer).line_count
@@ -563,6 +562,18 @@ cdef class OBIView_NUC_SEQS(OBIView):
         for column_n in self.columns :
             (self.columns[column_n]).update_pointer()
 
+            
+    def __getitem__(self, object item) :
+        if type(item) == str :
+            return (self.columns)[item]
+        elif type(item) == int :     # TODO 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]
+            
 
 #############################################
 
@@ -644,7 +655,7 @@ cdef class OBIDMS :
         
         view_infos = self.read_view_infos(view_name)
         
-        if view_infos["view_type"] == bytes2str(VIEW_TYPE_NUC_SEQS) :   # TODO not gonna work
+        if view_infos["view_type"] == bytes2str(VIEW_TYPE_NUC_SEQS) :
             view_class = OBIView_NUC_SEQS
         else :
             view_class = OBIView
@@ -657,7 +668,7 @@ cdef class OBIDMS :
         cdef object view_class
         
         if view_type is not None :
-            if view_type == bytes2str(VIEW_TYPE_NUC_SEQS) : # TODO not gonna work
+            if view_type == bytes2str(VIEW_TYPE_NUC_SEQS) :
                 view_class = OBIView_NUC_SEQS
         else :
             view_class = OBIView

python/obitools3/obidms/_obiseq.cfiles

@@ -0,0 +1,18 @@
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/obiview.h
+../../../src/obiview.c
+../../../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/private_at_functions.h
+../../../src/private_at_functions.c
+../../../src/obiavl.h
+../../../src/obiavl.c

python/obitools3/obidms/_obiseq.pxd

@@ -0,0 +1,34 @@
+#cython: language_level=3
+
+from ._obidms cimport OBIView_line
+
+
+cdef class OBI_Seq(dict) :
+    cdef str id
+    cdef str description
+    cdef str sequence
+
+    cpdef set_id(self, str id)
+    cpdef get_id(self)
+    cpdef set_description(self, str description)
+    cpdef get_description(self)
+    cpdef get_sequence(self)
+
+
+cdef class OBI_Nuc_Seq(OBI_Seq) :
+    #cpdef str reverse_complement(self)    
+    cpdef set_sequence(self, str sequence)
+
+
+cdef class OBI_Nuc_Seq_Stored(OBIView_line) :
+    cdef str id
+    cdef str description
+    cdef str sequence
+
+    cpdef set_id(self, str id)
+    cpdef get_id(self)
+    cpdef set_description(self, str description)
+    cpdef get_description(self)
+    cpdef set_sequence(self, str sequence)
+    cpdef get_sequence(self)
+   # cpdef str reverse_complement(self)

python/obitools3/obidms/_obiseq.pyx

@@ -0,0 +1,78 @@
+#cython: language_level=3
+
+from obitools3.utils cimport bytes2str, str2bytes
+
+from .capi.obiview cimport NUC_SEQUENCE_COLUMN, \
+                           ID_COLUMN, \
+                           DESCRIPTION_COLUMN
+
+cdef class OBI_Seq(dict) :
+
+    def __init__(self, str id, str seq, str description=None) :
+        self.set_id(id)
+        self.set_sequence(seq)
+        if description is not None :
+            self.set_description(description)
+        
+    cpdef set_id(self, str id) :
+        self.id = id
+        self[bytes2str(ID_COLUMN)] = id
+        
+    cpdef get_id(self) :
+        return self.id
+            
+    cpdef set_description(self, str description) :
+        self.description = description
+        self[bytes2str(DESCRIPTION_COLUMN)] = description
+        
+    cpdef get_description(self) :
+        return self.description
+        
+    cpdef get_sequence(self) :
+        return self.sequence
+
+    def __str__(self) :
+        return self.sequence    # or not
+
+
+cdef class OBI_Nuc_Seq(OBI_Seq) :
+    
+    cpdef set_sequence(self, str sequence) :
+        self.sequence = sequence
+        self[bytes2str(NUC_SEQUENCE_COLUMN)] = sequence
+
+#    cpdef str reverse_complement(self) :    TODO in C ?
+#        pass
+
+
+cdef class OBI_Nuc_Seq_Stored(OBIView_line) :
+
+    cpdef set_id(self, str id) :
+        self.id = id
+        self[bytes2str(ID_COLUMN)] = id
+        
+    cpdef get_id(self) :
+        return self.id
+            
+    cpdef set_description(self, str description) :
+        self.description = description
+        self[bytes2str(DESCRIPTION_COLUMN)] = description
+
+    cpdef get_description(self) :
+        return self.description
+
+    cpdef set_sequence(self, str sequence) :
+        self.sequence = sequence
+        self[bytes2str(NUC_SEQUENCE_COLUMN)] = sequence
+
+    cpdef get_sequence(self) :
+        return self.sequence
+    
+    def __str__(self) :
+        return self.sequence    # or not
+    
+#    cpdef str reverse_complement(self) :    TODO in C ?
+#        pass
+
+    # TODO static method to import?
+