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rraadd88 / beditor

A Computational Workflow for Designing Libraries of sgRNAs for CRISPR-Mediated Base Editing, and much more
GNU General Public License v3.0
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error when run the test dataset #4

Closed chengwsh closed 5 years ago

chengwsh commented 5 years ago

Hi, The beditor is really helpful! Would you please take a look on one error which occured when I run the test dataset?

Traceback (most recent call last): File "/home/chengwsh/miniconda3/envs/beditor/lib/python3.6/multiprocessing/pool.py", line 119, in worker result = (True, func(*args, *kwds)) File "/home/chengwsh/miniconda3/envs/beditor/lib/python3.6/multiprocessing/pool.py", line 44, in mapstar return list(map(args)) File "/home/chengwsh/miniconda3/envs/beditor/lib/python3.6/site-packages/beditor/pipeline.py", line 98, in pipeline_chunks dseq2dmutagenesis(cfg) File "/home/chengwsh/miniconda3/envs/beditor/lib/python3.6/site-packages/beditor/lib/get_mutations.py", line 484, in dseq2dmutagenesis host=cfg['host']) File "/home/chengwsh/miniconda3/envs/beditor/lib/python3.6/site-packages/beditor/lib/get_mutations.py", line 317, in get_possible_mutagenesis dmutagenesis['nucleotide mutation: count']=[len(s) for s in dmutagenesis['nucleotide mutation']] File "/home/chengwsh/miniconda3/envs/beditor/lib/python3.6/site-packages/beditor/lib/get_mutations.py", line 317, in dmutagenesis['nucleotide mutation: count']=[len(s) for s in dmutagenesis['nucleotide mutation']] TypeError: object of type 'float' has no len() """

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

Traceback (most recent call last): File "/home/chengwsh/miniconda3/envs/beditor/bin/beditor", line 11, in sys.exit(main()) File "/home/chengwsh/miniconda3/envs/beditor/lib/python3.6/site-packages/beditor/pipeline.py", line 491, in main test=args.test,force=args.force) File "/home/chengwsh/miniconda3/envs/beditor/lib/python3.6/site-packages/beditor/pipeline.py", line 425, in pipeline pool.map(pipeline_chunks, chunkcfgps) File "/home/chengwsh/miniconda3/envs/beditor/lib/python3.6/multiprocessing/pool.py", line 266, in map return self._map_async(func, iterable, mapstar, chunksize).get() File "/home/chengwsh/miniconda3/envs/beditor/lib/python3.6/multiprocessing/pool.py", line 644, in get raise self._value TypeError: object of type 'float' has no len() bash command error: 1 source activate beditor;cd dataset_homo_sapiens;beditor --cfg mutation_format_nucleotide_mutation_mutations_for.yml

Thank you very much!

rraadd88 commented 5 years ago

Hi @chengwsh , Sorry to hear that. I just checked the commands you used. There were no errors in my case. Just to be sure, are you using my version of pyensembl (installed from https://github.com/rraadd88/pyensembl) or the main pyensembl from openvax?

Could you send me the versions of beditor and pyensembl you are using? I will be happy to help you. Thanks.

chengwsh commented 5 years ago

Thank you for replying me! The beditor version I used is v1.1.3. And the pyensembl is using your version of pyensembl (installed from https://github.com/rraadd88/pyensembl) Thank you very much!

rraadd88 commented 5 years ago

I am not sure what's the issue in your case. I would suggest recreating the test datasets again. Also, you could send me the full traceback messages for python make_datasets.py and python test_datasets.py.

rraadd88 commented 5 years ago

Hi @chengwsh , In the recent version (v1.1.4), in order to simplify usage of the program, I have implemented a minimal gui for beditor. You might want to give a try. May be that would help.

chengwsh commented 5 years ago

Hi Rohan Dandage, Thank you very much. I have used the new version bedior. When I use the test dataset, it can export results, but when I use my own input file, it still has error [cid:image003.png@01D4CF68.143F53F0]

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发件人: Rohan Dandage notifications@github.com 发送时间: Thursday, February 28, 2019 1:27:27 AM 收件人: rraadd88/beditor 抄送: chengwsh; Mention 主题: Re: [rraadd88/beditor] error when run the test dataset (#4)

Hi @chengwshhttps://github.com/chengwsh , In the recent version (v1.1.4), in order to simplify usage of the program, I have implemented a minimal gui for beditor. You might want to give a try. May be that would help.

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rraadd88 commented 5 years ago

HI @chengwsh , we could discuss the issue with your input file over email.

(Closing the issue.)