“LSTM_extract.py” problem

[zzf77]

Hi, I tried to run this command in step 3: python3 LSTM_extract.py --fast5 ${fast5_fn} --corr_grp ${RawGenomeCorrected_000} --bam ${bam_fn} --sites ${candidate_predict_pos.txt} --label ${any meaningful string} --windows 2 2

I used the command: python3 LSTM_extract.py --fast5 con-output/workspace/0/ --corr_grp ./con-output/RawGenomeCorrected_001 --bam ./con-basecalls.bam --sites ./candidate_predict_pos.txt --label LSTM-control --windows 2 2

But I received the following message: Warning: The BRI module could not be loadedUsage: LSTM_extract.py [-h] {get_pos,predict} ... LSTM_extract.py: Error: argument command: invalid choice: 'con-output/workspace' (choose from 'get_pos', 'predict')

How could I resolve it? Thanks! ZFZHANG

[weir12]

Hi: Sorry for my late reply. Please add predict as a subcommand after LSTM_extract.py. For example： python3 LSTM_extract.py predict --fast5 con-output/workspace/0/ --corr_grp ./con-output/RawGenomeCorrected_001 --bam ./con-basecalls.bam --sites ./candidate_predict_pos.txt --label LSTM-control --windows 2 2

Weir

[zzf77]

thank you！---- Replied Message ----FromLiang @.>Date04/07/2022 19:45 @.> @.**@.>SubjectRe: [weir12/DENA] “LSTM_extract.py” problem (Issue #10)

Hi:

Sorry for my late reply.

Please add predict as a subcommand after LSTM_extract.py.

For example：

python3 LSTM_extract.py predict --fast5 con-output/workspace/0/ --corr_grp ./con-output/RawGenomeCorrected_001 --bam ./con-basecalls.bam --sites ./candidate_predict_pos.txt --label LSTM-control --windows 2 2

Weir

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