Program that integrates results from Luciphor (PTM localization scoring algorithm) into DTASelect output files.
Input:
- luciphor output file (-luc path)
- dtaselect output file (-dta path)
- localLFR threshold [optional] (-lflr double)
- globalLFR threshold [optional] (-gflr double)
- remove or not PSMs that don't pass the thresholds (-rem)
Output:
- It overrides the sequences of the PSMs on the DTASelect file that pass the thresholds (if available) on the luciphor output.
- It also adds 6 new columns ('original_sequence', 'luciphor_pep1Score', 'luciphor_pep2Score', 'luciphor_deltaScore', 'globalFLR', 'localFLR') for ONLY the PSMs that pass the luciphor score thresholds.
- If the PTM localization proposed by Luciphor is the same as the original one, the column original_sequence will remain empty.
- The original DTASelect file is backed up to a new file adding “_original” to the end of its name.