matched alpha beta
hejing3283 opened this issue · 3 comments
Input file format example (transposed )
command :
DTCRU.Get_Data(directory=input_dir, Load_Prev_Data=False, aggregate_by_aa=True,
aa_column_alpha=1,
aa_column_beta=2,
count_column=22,
v_alpha_column=7,
j_alpha_column=13,
v_beta_column=8,
j_beta_column=14,
d_beta_column=11,
hla=infile_hla,
sep=",",
n_jobs=NJOBS)
Error msg start --------------------
Loading Data...
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/ubuntu/anaconda3/envs/dl/lib/python3.6/multiprocessing/pool.py", line 119, in worker
result = (True, func(*args, **kwds))
File "/home/ubuntu/anaconda3/envs/dl/lib/python3.6/multiprocessing/pool.py", line 47, in starmapstar
return list(itertools.starmap(args[0], args[1]))
File "/home/ubuntu/anaconda3/envs/dl/lib/python3.6/site-packages/DeepTCR/functions/data_processing.py", line 117, in Get_DF_Data
df = df.iloc[:,cols_to_keep]
File "/home/ubuntu/anaconda3/envs/dl/lib/python3.6/site-packages/pandas/core/indexing.py", line 1472, in getitem
return self._getitem_tuple(key)
File "/home/ubuntu/anaconda3/envs/dl/lib/python3.6/site-packages/pandas/core/indexing.py", line 2013, in _getitem_tuple
self._has_valid_tuple(tup)
File "/home/ubuntu/anaconda3/envs/dl/lib/python3.6/site-packages/pandas/core/indexing.py", line 222, in _has_valid_tuple
self._validate_key(k, i)
File "/home/ubuntu/anaconda3/envs/dl/lib/python3.6/site-packages/pandas/core/indexing.py", line 1968, in _validate_key
raise IndexError("positional indexers are out-of-bounds")
IndexError: positional indexers are out-of-bounds
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/ubuntu/deepLearning/run_deepTCR_1_main_unsup.py", line 66, in
n_jobs=NJOBS)
File "/home/ubuntu/anaconda3/envs/dl/lib/python3.6/site-packages/DeepTCR/DeepTCR.py", line 274, in Get_Data
DF = p.starmap(Get_DF_Data, args)
File "/home/ubuntu/anaconda3/envs/dl/lib/python3.6/multiprocessing/pool.py", line 274, in starmap
return self._map_async(func, iterable, starmapstar, chunksize).get()
File "/home/ubuntu/anaconda3/envs/dl/lib/python3.6/multiprocessing/pool.py", line 644, in get
raise self._value
IndexError: positional indexers are out-of-bounds
Process finished with exit code 1
Error msg end --------------------
is there still a problem loading alpha/beta data?