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broadinstitute / adapt

A package for designing activity-informed nucleic acid diagnostics for viruses.
MIT License
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running using fasta file #72

Open najibveto opened 8 months ago

najibveto commented 8 months ago

hello, i am trying to run the following command: design.py [complete-targets] fasta [INHV_N.fasta] -o [out-tsv] however i got the following error:

usage: design.py [-h] {sliding-window,complete-targets} ...
design.py: error: argument search_cmd: invalid choice: '[-h]' (choose from 'sliding-window', 'complete-targets')

i would like to know what is the correct command for doing it. thank you for your help.

haydenm commented 8 months ago

The command that you run should not contain the square brackets, [ and ]; these indicate what you should fill in. For instance, in your example, the command you run could be:

design.py complete-targets fasta INHV_N.fasta -o out

Sorry for the confusion about this in the README.

The examples section in the README has additional examples without the square brackets.

najibveto commented 8 months ago

The command that you run should not contain the square brackets, [ and ]; these indicate what you should fill in. For instance, in your example, the command you run could be:

design.py complete-targets fasta INHV_N.fasta -o out

Sorry for the confusion about this in the README.

The examples section in the README has additional examples without the square brackets.

thank a lot for yoru reply. just one question if possible, i run the command and i got the following message:

Traceback (most recent call last):
  File "/home/najib/miniconda3/envs/adapt/bin/design.py", line 1728, in <module>
    run(argv_to_args(sys.argv))
  File "/home/najib/miniconda3/envs/adapt/bin/design.py", line 970, in run
    design_for_id(args)
  File "/home/najib/miniconda3/envs/adapt/bin/design.py", line 756, in design_for_id
    raise Exception(("Either --predict-activity-model-path or "
Exception: Either --predict-activity-model-path or --predict-cas13a-activity-model must be specified if --obj is 'maximize-activity'. Alternatively, if you cannot use our pre-trained Cas13a model nor another model, you can set --use-simple-binary-activity-prediction

i run it again and i got the results. i am curious should i opt for pre-trained Cas13a and can give better accuracy?. thank you for your help.

haydenm commented 8 months ago

I suggest using the model, by specifying --predict-cas13a-activity-model, if and only if the designs are to be used for RNA detection with LwaCas13a. Otherwise, you could specify --use-simple-binary-activity-prediction to instead use a simple mismatch and PFS-based model for the crRNAs.

najibveto commented 8 months ago

I suggest using the model, by specifying --predict-cas13a-activity-model, if and only if the designs are to be used for RNA detection with LwaCas13a. Otherwise, you could specify --use-simple-binary-activity-prediction to instead use a simple mismatch and PFS-based model for the crRNAs.

thank you a lot for your help.