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Changed the cython API to create new views so as to have different

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functions for the different cases
This commit is contained in:
Celine Mercier
2016-12-07 14:17:57 +01:00
parent 936be64c34
commit fa4e4ffaff
4 changed files with 64 additions and 51 deletions
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2
python/obitools3/commands/grep.pyx
View File

@ -77,7 +77,7 @@ def run(config):
selection.append(i)
# Create output view with the line selection
oview = d.new_view(config['obi']['outputview'], line_selection=selection, comments="obi grep: "+str(config['grep']['predicates'])+"\n")
oview = d.clone_view_with_line_selection(config['obi']['outputview'], selection, comments="obi grep: "+str(config['grep']['predicates'])+"\n")
#print("\n")
#print(repr(oview))

19
python/obitools3/commands/test.pyx
View File

@ -8,7 +8,7 @@ import string
import random
VIEW_TYPES = [None, "NUC_SEQS_VIEW"]
VIEW_TYPES = ["", "NUC_SEQS_VIEW"]
COL_TYPES = ["OBI_BOOL", "OBI_CHAR", "OBI_FLOAT", "OBI_INT", "OBI_SEQ", "OBI_STR"]
NUC_SEQUENCE_COLUMN = "NUC_SEQ"
ID_COLUMN = "ID"
@ -212,13 +212,12 @@ def fill_view(config, infos):
def random_new_view(config, infos, first=False):
v_to_clone = None
line_selection = None
clone = False
quality_col = False # TODO
if not first:
infos['view_names'].append(infos['view'].name)
infos['view'].close()
v_to_clone = infos['dms'].open_view(random.choice(infos["view_names"]))
v_type = None
v_type = ""
print_test(config, "View to clone: ")
print_test(config, repr(v_to_clone))
create_line_selection = random_bool(config)
@ -230,12 +229,14 @@ def random_new_view(config, infos, first=False):
#print_test(config, "New line selection: "+str(line_selection))
else :
v_type = random_view_type()
infos['view'] = infos['dms'].new_view(random_unique_name(infos),
view_to_clone=v_to_clone,
line_selection=line_selection,
view_type=v_type,
comments=random_str_with_max_len(config['test']['commentsmaxlen']),
quality_column=quality_col)
if line_selection is not None :
infos['view'] = infos['dms'].clone_view_with_line_selection(random_unique_name(infos), line_selection, comments=random_str_with_max_len(config['test']['commentsmaxlen']))
elif v_to_clone is not None :
infos['view'] = infos['dms'].clone_view(random_unique_name(infos), v_to_clone, comments=random_str_with_max_len(config['test']['commentsmaxlen']))
else :
infos['view'] = infos['dms'].new_view(random_unique_name(infos), view_type=v_type, comments=random_str_with_max_len(config['test']['commentsmaxlen']), quality_column=quality_col)
print_test(config, repr(infos['view']))
if v_to_clone is not None :
if line_selection is None: