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sidhomj / DeepTCR

Deep Learning Methods for Parsing T-Cell Receptor Sequencing (TCRSeq) Data
https://sidhomj.github.io/DeepTCR/
MIT License
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matched alpha beta #11

Closed hejing3283 closed 4 years ago

hejing3283 commented 5 years ago

Input file format example (transposed ) image

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 --------------------

sidhomj commented 4 years ago

is there still a problem loading alpha/beta data?

hejing3283 commented 4 years ago

Not at all. Thanks!!

On Tue, Oct 22, 2019 at 2:07 PM John-William Sidhom < notifications@github.com> wrote:

Closed #11 https://github.com/sidhomj/DeepTCR/issues/11.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/sidhomj/DeepTCR/issues/11?email_source=notifications&email_token=AAUAIIIZJBCX6CTHMWCVEW3QP46N5A5CNFSM4HM67NU2YY3PNVWWK3TUL52HS4DFWZEXG43VMVCXMZLOORHG65DJMZUWGYLUNFXW5KTDN5WW2ZLOORPWSZGOUL47INA#event-2734289972, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAUAIILZDYK7NJIMPKSB77LQP46N5ANCNFSM4HM67NUQ .

-- Cheers! Jing