TP_predict/Additional_analyses/Analyse_cutoff_thresholdsb0ed141ed508master
TP_predict/Additional_analyses/Analyse_cutoff_thresholds
b0ed141ed508master
Analyse_cutoff_thresholds
Analyse_cutoff_thresholds
README.md
README.md
Analyze cutoff thresholds
Purpose
This script evaluates the effect of choosing different cutoff thresholds in the TP predictions. The evaluated parameters are generation and max TPs.
Input
The script uses 5 input files, one for each tested TP prediction model.
- Output from find_best_TPs.py
- Output from EAWAG-PPS batch prediction: resuts_EAWAG-PPS.tsv
- List of experimentally confirmed TPs (SMILES): confirmed_TPs.txt
Output
The script outputs the number of true positive predictions for a range of thresholds, for each parameter searately:
- Cutoff_thresholds_Generation threshold.txt
- Cutoff_thresholds_Maximum TP threshold.txt
The results are plotted as PDF:
- Plot_cutoff_analysis.pdf
Run script in Spyder
- open the script: compare_methods_pps.py
- change the pathway of the input files according to the filepath on your harddrive
- click somewhere in the left window and press F5 or click "Run File", if Run settings windows appears, click run
- wait for the script to finish running (you can see the progress in the bottom right window, "Script finished successfully" marks end of script)
Author: Jasmin Hafner, 2022
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