Scout Extensions

Extensions to use the cross-linking tool Scout with other software.

Requirements

Python 3.7+ and the following packages are required:

• Install pandas: pip install pandas
• Install xlsxwriter: pip install xlsxwriter

Scout to IMP-X-FDR converter

The main purpose of this script is to convert Scout output files to MS Annika format - which are usable with the IMP-X-FDR tool. This way Scout can be benchmarked on synthetic peptide libraries.

DESCRIPTION:
A script to convert Scout *.csv result files to MS Annika format as
Microsoft Excel worksheets for usage with IMP-X-FDR (v1.1.0).

USAGE:
scoutToIMPXFDR.py f [f ...]
                    [-o OUTPUT]
                    [-xl CROSSLINKER]
                    [-xlmod CROSSLINKER_MODIFICATION]
                    [-h]
                    [--version]

positional arguments:
  f                     Scout result file to process, if second filename
                        is given it will be used as the output name!

optional arguments:
  -h, --help            show this help message and exit.
  -o OUTPUT, --output OUTPUT
                        Name of the output file.
  -xl CROSSLINKER, --crosslinker CROSSLINKER
                        Name of the Crosslinker e.g. DSSO.
  -xlmod CROSSLINKER_MODIFICATION, --crosslinker-modification CROSSLINKER_MODIFICATION
                        Residue that the Crosslinker binds to e.g. K for DSSO.
  --version             show program's version number and exit.

Example Usage:

python scoutToIMPXFDR.py my_scout_results.csv -o my_scout_results_converted -xl DSSO -xlmod K

License

MIT License

Contact

micha.birklbauer@fh-hagenberg.at