createGermlines.py error
Issue #192
resolved
Can you help me find the source of this error?
START> CreateGermlines
FILE> scoper_out_20220705_21:32:10.tsv
GERM_TYPES> dmask
SEQ_FIELD> sequence_alignment
V_FIELD> v_call
D_FIELD> d_call
J_FIELD> j_call
CLONED> False
Traceback (most recent call last):
File "/usr/local/bin/CreateGermlines.py", line 354, in <module>
createGermlines(**args_dict)
File "/usr/local/bin/CreateGermlines.py", line 148, in createGermlines
for key, records in receptor_iter:
File "/usr/local/bin/CreateGermlines.py", line 133, in <genexpr>
receptor_iter = ((x.sequence_id, [x]) for x in db_iter)
File "/usr/local/lib/python3.9/site-packages/changeo/IO.py", line 75, in __next__
record = next(self.reader)
File "/usr/local/lib/python3.9/site-packages/airr/io.py", line 99, in __next__
raise ValueError('row has extra data')
ValueError: row has extra data
Thank you
Comments (2)
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reporter -
reporter - changed status to resolved
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Fixed it. The column names shifted to the right when saving the output from R.
row.names = FALSE
will be ingrained into my head forever.