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import: now automatically renames scientific_name tag to

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`SCIENTIFIC_NAME`, and suggests using `--input-na-string` when a
sequence import fails
This commit is contained in:
Celine Mercier
2023-02-13 10:40:38 +13:00
parent 755ce179ad
commit eeb93afa7d
1 changed files with 5 additions and 3 deletions
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8
python/obitools3/commands/import.pyx
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@ -400,12 +400,14 @@ def run(config):
for tag in entry : for tag in entry :
if tag != ID_COLUMN and tag != DEFINITION_COLUMN and tag != NUC_SEQUENCE_COLUMN and tag != QUALITY_COLUMN : # TODO dirty if tag != ID_COLUMN and tag != DEFINITION_COLUMN and tag != NUC_SEQUENCE_COLUMN and tag != QUALITY_COLUMN : # TODO dirty
value = entry[tag] value = entry[tag]
if tag == b"taxid": if tag == b"taxid":
tag = TAXID_COLUMN tag = TAXID_COLUMN
if tag == b"count": if tag == b"count":
tag = COUNT_COLUMN tag = COUNT_COLUMN
if tag == b"scientific_name":
tag = SCIENTIFIC_NAME_COLUMN
if tag[:7] == b"merged_": if tag[:7] == b"merged_":
tag = MERGED_PREFIX+tag[7:] tag = MERGED_PREFIX+tag[7:]
@ -418,7 +420,7 @@ def run(config):
pass pass
if tag not in dcols : if tag not in dcols :
value_type = type(value) value_type = type(value)
nb_elts = 1 nb_elts = 1
value_obitype = OBI_VOID value_obitype = OBI_VOID
@ -516,7 +518,7 @@ def run(config):
dcols[tag][0][i] = value dcols[tag][0][i] = value
except Exception as e: except Exception as e:
print("\nCould not import sequence:", repr(entry), "(error raised:", e, ")") print("\nCould not import sequence:\n", repr(entry), "\nError raised:", e, "\n/!\ Check if '--input-na-string' option needs to be set")
if 'skiperror' in config['obi'] and not config['obi']['skiperror']: if 'skiperror' in config['obi'] and not config['obi']['skiperror']:
raise e raise e
else: else: