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obi import: fixed the import of old obitools files with premerged

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informations, and other minor improvements
This commit is contained in:
Celine Mercier
2020-05-07 17:03:04 +02:00
parent 69cb434a6c
commit 773b36ec37
1 changed files with 13 additions and 7 deletions
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20
python/obitools3/commands/import.pyx
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@ -25,7 +25,8 @@ from obitools3.dms.capi.obiview cimport VIEW_TYPE_NUC_SEQS, \
DEFINITION_COLUMN, \ DEFINITION_COLUMN, \
QUALITY_COLUMN, \ QUALITY_COLUMN, \
COUNT_COLUMN, \ COUNT_COLUMN, \
TAXID_COLUMN TAXID_COLUMN, \
MERGED_PREFIX
from obitools3.dms.capi.obidms cimport obi_import_view from obitools3.dms.capi.obidms cimport obi_import_view
@ -163,7 +164,7 @@ def run(config):
taxo.write(taxo_name) taxo.write(taxo_name)
taxo.close() taxo.close()
o_dms.record_command_line(" ".join(sys.argv[1:])) o_dms.record_command_line(" ".join(sys.argv[1:]))
o_dms.close() o_dms.close(force=True)
logger("info", "Done.") logger("info", "Done.")
return return
@ -217,11 +218,14 @@ def run(config):
logger("info", "Read %d entries", i) logger("info", "Read %d entries", i)
for tag in entry : for tag in entry :
newtag = tag
if tag[:7] == b"merged_":
newtag = MERGED_PREFIX+tag[7:]
if type(entry[tag]) == dict : if type(entry[tag]) == dict :
if tag in dict_dict: if tag in dict_dict:
dict_dict[tag][0].update(entry[tag].keys()) dict_dict[newtag][0].update(entry[tag].keys())
else: else:
dict_dict[tag] = [set(entry[tag].keys()), get_obitype(entry[tag])] dict_dict[newtag] = [set(entry[tag].keys()), get_obitype(entry[tag])]
i+=1 i+=1
if pb is not None: if pb is not None:
@ -288,6 +292,8 @@ def run(config):
tag = TAXID_COLUMN tag = TAXID_COLUMN
if tag == b"count": if tag == b"count":
tag = COUNT_COLUMN tag = COUNT_COLUMN
if tag[:7] == b"merged_":
tag = MERGED_PREFIX+tag[7:]
if tag not in dcols : if tag not in dcols :
@ -328,8 +334,8 @@ def run(config):
try: try:
# Check that it's not the case where the first entry contained a dict of length 1 and now there is a new key # Check that it's not the case where the first entry contained a dict of length 1 and now there is a new key
if type(value) == dict and \ if type(value) == dict and \
dcols[tag][0].nb_elements_per_line == 1 and len(value.keys()) == 1 \ dcols[tag][0].nb_elements_per_line == 1 \
and dcols[tag][0].elements_names[0] != list(value.keys())[0] : and set(dcols[tag][0].elements_names) != set(value.keys()) :
raise IndexError # trigger column rewrite raise IndexError # trigger column rewrite
# Fill value # Fill value
@ -402,7 +408,7 @@ def run(config):
except AttributeError: except AttributeError:
pass pass
try: try:
output[0].close() output[0].close(force=True)
except AttributeError: except AttributeError:
pass pass