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Fixed bugs with python view type when creating a new view, and a bug

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when trying to guess the obi type of a nucleotide sequence when its type
was bytes
This commit is contained in:
Celine Mercier
2016-11-08 11:23:54 +01:00
parent 8291693309
commit 36ac315125
1 changed files with 20 additions and 11 deletions
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21
python/obitools3/obidms/_obidms.pyx
View File

@ -289,7 +289,7 @@ cdef class OBIView :
line_selection_p[i] = line_selection[i] line_selection_p[i] = line_selection[i]
line_selection_p[len(line_selection)] = -1 # flagging the end of the array line_selection_p[len(line_selection)] = -1 # flagging the end of the array
self._pointer = self._open_or_create_view(dms, view_name, new=new, view_to_clone=view_to_clone, line_selection_p=line_selection_p, comments=comments, quality_column=quality_column, view_type=None) self._pointer = self._open_or_create_view(dms, view_name, new=new, view_to_clone=view_to_clone, line_selection_p=line_selection_p, comments=comments, quality_column=quality_column, view_type=view_type)
# Go through columns to build dictionaries of corresponding python instances # TODO make function? # Go through columns to build dictionaries of corresponding python instances # TODO make function?
self._columns = {} self._columns = {}
@ -314,7 +314,7 @@ cdef class OBIView :
view = obi_new_view(dms._pointer, str2bytes(view_name), (<OBIView> view_to_clone)._pointer, line_selection_p, str2bytes(comments)) view = obi_new_view(dms._pointer, str2bytes(view_name), (<OBIView> view_to_clone)._pointer, line_selection_p, str2bytes(comments))
else : else :
view = obi_new_view(dms._pointer, str2bytes(view_name), NULL, line_selection_p, str2bytes(comments)) view = obi_new_view(dms._pointer, str2bytes(view_name), NULL, line_selection_p, str2bytes(comments))
elif view_type == VIEW_TYPE_NUC_SEQS : elif view_type == bytes2str(VIEW_TYPE_NUC_SEQS) :
if view_to_clone is not None : if view_to_clone is not None :
if type(view_to_clone) == str : if type(view_to_clone) == str :
view = obi_new_view_nuc_seqs_cloned_from_name(dms._pointer, str2bytes(view_name), str2bytes(view_to_clone), line_selection_p, str2bytes(comments), quality_column) view = obi_new_view_nuc_seqs_cloned_from_name(dms._pointer, str2bytes(view_name), str2bytes(view_to_clone), line_selection_p, str2bytes(comments), quality_column)
@ -322,6 +322,8 @@ cdef class OBIView :
view = obi_new_view_nuc_seqs(dms._pointer, str2bytes(view_name), (<OBIView> view_to_clone)._pointer, line_selection_p, str2bytes(comments), quality_column) view = obi_new_view_nuc_seqs(dms._pointer, str2bytes(view_name), (<OBIView> view_to_clone)._pointer, line_selection_p, str2bytes(comments), quality_column)
else : else :
view = obi_new_view_nuc_seqs(dms._pointer, str2bytes(view_name), NULL, line_selection_p, str2bytes(comments), quality_column) view = obi_new_view_nuc_seqs(dms._pointer, str2bytes(view_name), NULL, line_selection_p, str2bytes(comments), quality_column)
else :
raise Exception("View type not recognized")
# Else, open the existing view # Else, open the existing view
else : else :
@ -595,6 +597,8 @@ cdef class OBIView_line :
# TODO OBI_QUAL ? # TODO OBI_QUAL ?
cdef type value_type cdef type value_type
cdef str value_obitype cdef str value_obitype
cdef bytes value_b
if column_name not in self._view : if column_name not in self._view :
if value == None : if value == None :
raise Exception("Trying to create a column from a None value (can't guess type)") raise Exception("Trying to create a column from a None value (can't guess type)")
@ -605,8 +609,12 @@ cdef class OBIView_line :
value_obitype = 'OBI_FLOAT' value_obitype = 'OBI_FLOAT'
elif value_type == bool : elif value_type == bool :
value_obitype = 'OBI_BOOL' value_obitype = 'OBI_BOOL'
elif value_type == str : elif value_type == str or value_type == bytes :
if only_ATGC(str2bytes(value)) : # TODO detect IUPAC? if value_type == str :
value_b = str2bytes(value)
else :
value_b = value
if only_ATGC(value_b) : # TODO detect IUPAC?
value_obitype = 'OBI_SEQ' value_obitype = 'OBI_SEQ'
elif len(value) == 1 : elif len(value) == 1 :
value_obitype = 'OBI_CHAR' value_obitype = 'OBI_CHAR'
@ -714,9 +722,10 @@ cdef class OBIDMS :
else : else :
view_class = OBIView view_class = OBIView
# Check the type of the view to clone if there is one # TODO make generic for future other view types # Check the type of the view to clone if there is one # TODO make generic for future other view types
if view_to_clone is not None and \ if (view_to_clone is not None and \
((type(view_to_clone) == str and self.read_view_infos(view_to_clone)["view_type"] == bytes2str(VIEW_TYPE_NUC_SEQS)) or \ ((type(view_to_clone) == str and self.read_view_infos(view_to_clone)["view_type"] == bytes2str(VIEW_TYPE_NUC_SEQS)) or \
isinstance(view_to_clone, OBIView_NUC_SEQS)) : isinstance(view_to_clone, OBIView_NUC_SEQS))) or \
(line_selection is not None and isinstance(line_selection._view, OBIView_NUC_SEQS)) :
view_type = bytes2str(VIEW_TYPE_NUC_SEQS) view_type = bytes2str(VIEW_TYPE_NUC_SEQS)
view_class = OBIView_NUC_SEQS view_class = OBIView_NUC_SEQS