Job execution using pyprophet brutus driver - PyProphet/pyprophet-cli GitHub Wiki

If the three modules have been properly configured, PyProphet jobs can be submitted using the following command:

pyprophet-cli run_on_brutus \
--data-folder="/tmp/openswath_results/" \
--data-filename-pattern="openswath_output_*.tsv" --sample-factor=0.1 --job-count=10 \
--extra-args-prepare --extra-group-column=ProteinName \
--extra-args-score --lambda=0.8

The example works as following:

• --data-folder: /tmp/openswath_results/ contains 10 files, openswath_output_0.tsv - openswath_output_9.tsv.
• --data-filename-pattern: This regular expression is used to grab the correct files.
• --sample-factor: This value can be anything from 0 - 1. We recommend to use 1/(#runs), here 1/10=0.1.
• --job-count: Specifies the number of parallel jobs to submit.
• --extra-args-prepare --extra-group-column=ProteinName: Also compute protein-level q-values
• --extra-args-score --lambda=0.8: Set lambda to 0.8 for q-value estimation.

There are further parameters that can be set, please refer to:

pyprophet-cli --help