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run_structure_prediction.py accepts comma separated list of input folds and optionally dedicated output_directories for each fold #357
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…ds and optionally dedicated output_directories for each fold
I guess in the case of padding, you may also need to update the
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object_to_model, flags_dict, postprocess_flags, output_dir = pre_modelling_setup(interactors, FLAGS) | ||
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if len(FLAGS.input) != len(FLAGS.output_directory): | ||
FLAGS.output_directory *= len(FLAGS.input) |
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this covers the case when we have 1 output dir and many inputs, right?
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Exactly!
@dingquanyu from your PR at KosinskiLab/AlphaPulldownSnakemake#13 it seemed like you wanted run_multimer_jobs.py to use a single output directory and create subdirectories for each fold according to use_ap_style. We could extend run_multimer_jobs.py to allow multiple output_paths, but since run_multimer_jobs.py uses the file-based fold specification, where the user might not know the number of folds beforehand, I think having a single output directory makes the most sense |
I see. This means in the snakemake pipeline, you will bypass run_multimer_jobs.py and launch run_structure_prediction.py directly with a cluster of jobs ? |
Exactly. I added a checkpoint that performs the clustering and then extended the current rule using run_structure_prediction.py to run on each cluster separately. This way we don't need additional rules. I just pushed these changes for reference bfa71c7ac5d013a0c1aea3b78fc347381a3ca06c |
I see. Thanks for the commit. Now it makes sense to me. |
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