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Added OBIView_line_selection class to make new line selections

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associated with the view to clone, and improved and renamed method
closing a view
This commit is contained in:
Celine Mercier
2016-09-30 17:48:53 +02:00
parent d88811ed7d
commit 9cd57deca9
10 changed files with 90 additions and 33 deletions
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4
python/obi.py
View File

@ -21,7 +21,9 @@ default_config = { 'software' : "The OBITools",
'log' : False,
'loglevel' : 'INFO',
'progress' : True,
'defaultdms' : None
'defaultdms' : None,
'inputview' : None,
'outputview' : None
}
root_config_name='obi'

9
python/obitools3/commands/align.pyx
View File

@ -108,18 +108,15 @@ def run(config):
# Call cython alignment function
iview.align(oview)
print(oview.__repr__())
repr(oview)
iview.save_and_close()
oview.save_and_close()
iview.close()
oview.close()
d.close()
print("Done.")

2
python/obitools3/commands/export.pyx
View File

@ -85,7 +85,7 @@ def run(config):
print(toprint)
i+=1
iview.save_and_close()
iview.close()
d.close()
print("Done.")

6
python/obitools3/commands/grep.pyx
View File

@ -75,10 +75,10 @@ def run(config):
# Create output view with the line selection
oview = d.new_view(config['obi']['outputview'], view_to_clone=iview, line_selection=selection, comments="obi grep: "+config['grep']['predicate']+"\n")
print(oview.__repr__())
repr(oview)
iview.save_and_close()
oview.save_and_close()
iview.close()
oview.close()
d.close()
print("Done.")

8
python/obitools3/commands/import.pyx
View File

@ -4,9 +4,9 @@ from obitools3.parsers.fasta import fastaIterator
from obitools3.parsers.fastq import fastqIterator
from obitools3.obidms._obidms import OBIDMS
import time
__title__="Counts sequences in a sequence set"
@ -90,7 +90,7 @@ def addOptions(parser):
# TODO: Handling of NA values
def run(config):
#pb = ProgressBar(35000000, config, seconde=5)
pb = ProgressBar(35000000, config, seconde=5)
inputs = uopen(config['import']['filename'])
@ -113,7 +113,7 @@ def run(config):
i = 0
for seq in iseq:
#pb(i)
pb(i)
view[i].set_id(seq['id'])
view[i].set_definition(seq['definition'])
view[i].set_sequence(seq['sequence'])
@ -125,7 +125,7 @@ def run(config):
print(view.__repr__())
view.save_and_close()
view.close()
d.close()
print("Done.")

11
python/obitools3/commands/test.pyx
View File

@ -1,5 +1,6 @@
from obitools3.apps.progress cimport ProgressBar # TODO I absolutely don't understand why it doesn't work without that line
from obitools3.obidms._obidms import OBIDMS # TODO cimport doesn't work
from obitools3.obidms._obidms import OBIView_line_selection
from obitools3.utils cimport str2bytes
import shutil
@ -120,7 +121,7 @@ def test_add_col(config, infos):
# else :
# alias = ''
# infos['view'].add_column(random_column_refs['name'], version_number=random_column_refs['version'], alias=alias, create=False)
# random_view.save_and_close()
# random_view.close()
#else :
create_random_column(config, infos)
print_test(config, ">>> Add column test OK")
@ -215,7 +216,7 @@ def random_new_view(config, infos, first=False):
quality_col = False # TODO
if not first:
infos['view_names'].append(infos['view'].name)
infos['view'].save_and_close()
infos['view'].close()
v_to_clone = infos['dms'].open_view(random.choice(infos["view_names"]))
v_type = None
print_test(config, "View to clone: ")
@ -223,7 +224,7 @@ def random_new_view(config, infos, first=False):
create_line_selection = random_bool(config)
if create_line_selection and v_to_clone.line_count > 0:
print_test(config, "New view with new line selection.")
line_selection = []
line_selection = OBIView_line_selection(v_to_clone)
for i in range(random.randint(1, v_to_clone.line_count)) :
line_selection.append(random.randint(0, v_to_clone.line_count-1))
#print_test(config, "New line selection: "+str(line_selection))
@ -241,7 +242,7 @@ def random_new_view(config, infos, first=False):
assert v_to_clone.line_count == infos['view'].line_count, "New view and cloned view don't have the same line count"
else :
assert len(line_selection) == infos['view'].line_count, "New view with new line selection does not have the right line count"
v_to_clone.save_and_close()
v_to_clone.close()
if first :
fill_view(config, infos)
@ -370,7 +371,7 @@ def run(config):
#print(infos)
infos['view'].save_and_close()
infos['view'].close()
infos['dms'].close()
shutil.rmtree(config['obi']['defaultdms']+'.obidms', ignore_errors=True)

2
python/obitools3/format/fasta.pyx
View File

@ -1,6 +1,4 @@
cimport cython
from libc.stdlib cimport malloc, free, realloc
from libc.string cimport strncpy
cdef class FastaFormat:

10
python/obitools3/obidms/_obidms.pxd
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@ -52,7 +52,7 @@ cdef class OBIView:
)
cpdef change_column_alias(self, str current_alias, str new_alias)
cpdef update_column_pointers(self)
cpdef save_and_close(self)
cpdef close(self)
cdef class OBIView_NUC_SEQS(OBIView):
@ -73,6 +73,12 @@ cdef class OBIView_line :
cdef OBIView _view
cdef class OBIView_line_selection(list):
cdef OBIView _view
cdef str _view_name
cdef class OBIDMS:
cdef OBIDMS_p _pointer
@ -80,7 +86,7 @@ cdef class OBIDMS:
cpdef close(self)
cpdef OBI_Taxonomy open_taxonomy(self, str taxo_name)
cpdef OBIView open_view(self, str view_name)
cpdef OBIView new_view(self, str view_name, object view_to_clone=*, list line_selection=*, str view_type=*, str comments=*, bint quality_column=*)
cpdef OBIView new_view(self, str view_name, object view_to_clone=*, OBIView_line_selection line_selection=*, str view_type=*, str comments=*, bint quality_column=*)
cpdef dict read_view_infos(self, str view_name)
# cpdef dict read_views(self) TODO

55
python/obitools3/obidms/_obidms.pyx
View File

@ -273,7 +273,7 @@ cdef class OBIDMS_column_line :
cdef class OBIView :
def __init__(self, OBIDMS dms, str view_name, bint new=False, object view_to_clone=None, list line_selection=None, str comments="", bint quality_column=False):
def __init__(self, OBIDMS dms, str view_name, bint new=False, object view_to_clone=None, OBIView_line_selection line_selection=None, str comments="", bint quality_column=False):
# TODO quality_column is only here because it's needed for OBIView_NUC_SEQS views, not clean?
cdef Obiview_p view = NULL
@ -420,9 +420,11 @@ cdef class OBIView :
column._pointer = <OBIDMS_column_p*> obi_view_get_pointer_on_column_in_view(self._pointer, str2bytes(column_n))
cpdef save_and_close(self) :
cpdef close(self) :
if (obi_save_and_close_view(self._pointer) < 0) :
raise Exception("Problem closing a view")
self._pointer = NULL
self._columns = {}
def __iter__(self):
@ -483,11 +485,13 @@ cdef class OBIView :
return bytes2str(self._pointer.infos.comments)
# TODO setter that concatenates new comments?
#############################################
######################################################################################################
cdef class OBIView_NUC_SEQS(OBIView):
def __init__(self, OBIDMS dms, str view_name, bint new=False, object view_to_clone=None, list line_selection=None, str comments="", bint quality_column=False):
def __init__(self, OBIDMS dms, str view_name, bint new=False, object view_to_clone=None, OBIView_line_selection line_selection=None, str comments="", bint quality_column=False):
cdef Obiview_p view = NULL
cdef index_t* line_selection_p
@ -497,10 +501,20 @@ cdef class OBIView_NUC_SEQS(OBIView):
cdef object subclass
if line_selection is not None :
line_selection_p = <index_t*> malloc((len(line_selection) + 1) * sizeof(index_t))
# Check that the line selection is associated with the view to clone
if view_to_clone is None :
raise Exception("Error creating a view: there is a new line selection but no associated view to clone")
if type(view_to_clone) == str :
if line_selection._view_name != view_to_clone :
raise Exception("Error creating a view: the new line selection isn't associated with the view to clone")
elif line_selection._view != view_to_clone :
raise Exception("Error creating a view: the new line selection isn't associated with the view to clone")
# Build the C array corresponding to the line selection
line_selection_p = <index_t*> malloc((len(line_selection) + 1) * sizeof(index_t)) # +1 for the -1 flagging the end of the array
for i in range(len(line_selection)) :
line_selection_p[i] = line_selection[i]
line_selection_p[len(line_selection)] = -1
line_selection_p[len(line_selection)] = -1 # flagging the end of the array
else :
line_selection_p = NULL
@ -602,7 +616,8 @@ cdef class OBIView_NUC_SEQS(OBIView):
raise Exception("Error aligning sequences")
#############################################
######################################################################################################
cdef class OBIView_line :
@ -656,7 +671,29 @@ cdef class OBIView_line :
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 :
@ -704,7 +741,7 @@ cdef class OBIDMS :
return view_class(self, view_name)
cpdef OBIView new_view(self, str view_name, object view_to_clone=None, list line_selection=None, str view_type=None, str comments="", bint quality_column=False) :
cpdef OBIView new_view(self, str view_name, object view_to_clone=None, OBIView_line_selection line_selection=None, str view_type=None, str comments="", bint quality_column=False) :
cdef object view_class

16
src/obiview.c
View File

@ -1132,6 +1132,22 @@ Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_cl
int i;
index_t line_nb;
// Check that the DMS is a valid pointer
if (dms == NULL)
{
obi_set_errno(OBIVIEW_ERROR);
obidebug(1, "\nError creating a view: DMS pointer is NULL");
return NULL;
}
// Check that the view name pointer is valid
if (view_name == NULL)
{
obi_set_errno(OBIVIEW_ERROR);
obidebug(1, "\nError creating a view: view name is NULL");
return NULL;
}
// Check uniqueness of name
if (view_exists(dms, view_name))
{