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hkimlab / DeepPrime

Source codes and examples for DeepPrime
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ends = seq[0] + seq[-1] -- IndexError: string index out of range #4

Closed j-fife closed 1 year ago

j-fife commented 1 year ago

I was able to run the example after altering the files described in this issue by julianeweller. I've now created a file with 20 sequences and I receive the following error pasted below. It should be noted that all the sequences in question were able to run through the genet package, but I would like to be able to use the model in the error (PE2max_epegRNA_Opti_HEK293T).

`

Start: my_test - PE2max_epegRNA_Opti_HEK293T

Input subset range: 0 20 MATPLOTLIB - Rank Plot - pegRNA1.2924 MATPLOTLIB - Rank Plot - pegRNA1.2999 MATPLOTLIB - Rank Plot - pegRNA1.2974 MATPLOTLIB - Rank Plot - pegRNA1.2899 MATPLOTLIB - Rank Plot - pegRNA1.2949 MATPLOTLIB - Rank Plot - pegRNA2.3799 MATPLOTLIB - Rank Plot - pegRNA2.3749 MATPLOTLIB - Rank Plot - pegRNA2.3849 MATPLOTLIB - Rank Plot - pegRNA2.3637 MATPLOTLIB - Rank Plot - pegRNA2.3687 MATPLOTLIB - Rank Plot - pegRNA3.2924 MATPLOTLIB - Rank Plot - pegRNA3.2999 MATPLOTLIB - Rank Plot - pegRNA3.2974 MATPLOTLIB - Rank Plot - pegRNA3.2899 MATPLOTLIB - Rank Plot - pegRNA3.2949 MATPLOTLIB - Rank Plot - pegRNA4.2924 MATPLOTLIB - Rank Plot - pegRNA4.2999 MATPLOTLIB - Rank Plot - pegRNA4.2974 MATPLOTLIB - Rank Plot - pegRNA4.2899 MATPLOTLIB - Rank Plot - pegRNA4.2949 multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "[MY_PATH]/miniconda3/envs/genet/lib/python3.8/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, *kwds)) File "[MY_PATH]/miniconda3/envs/genet/lib/python3.8/multiprocessing/pool.py", line 48, in mapstar return list(map(args)) File "main_src.py", line 368, in mp_processor deep_prime(analysistag, id, wtseq, editedseq, edit, dict_params, outdir) File "main_src.py", line 403, in deep_prime cFeat.determine_secondary_structure() File "[MY_PATH]/deepprime_repo/DeepPrime_src_wExamples/DeepPrime/src/biofeat.py", line 437, in determine_secondary_structure self.determine_Tm(sPAMKey, sSeqKey) File "[MY_PATH]/jf9645/deepprime_repo/DeepPrime_src_wExamples/DeepPrime/src/biofeat.py", line 452, in determine_Tm fTm1 = mt.Tm_NN(seq=Seq(sForTm1), nn_table=mt.R_DNA_NN1) File "[MY_PATH]/miniconda3/envs/genet/lib/python3.8/site-packages/Bio/SeqUtils/MeltingTemp.py", line 1021, in Tm_NN ends = seq[0] + seq[-1] IndexError: string index out of range """

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "main_src.py", line 739, in locals()function_name File "main_src.py", line 134, in main_run p.map_async(mp_processor, parameters).get() File "[MY_PATH]/miniconda3/envs/genet/lib/python3.8/multiprocessing/pool.py", line 771, in get raise self._value IndexError: string index out of range

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Goosang-Yu commented 1 year ago

Thank you for using DeepPrime. I appreciate your support. I will work to resolve any issues in the source code as soon as possible.

In the meantime, I would recommend using the GenET package, which offers a much more user-friendly experience.

Have a great day!

Best regards, Goosang

Goosang-Yu commented 1 year ago

We have now updated the source code and ReadMe. Could you please check if it is functioning properly?

While the command-line version of DeepPrime has improved in terms of convenience, we still recommend using GenET.

I hope it works well in your environment.

Goosang

j-fife commented 1 year ago

The new fixes work great! Thanks for the help.