Command line interface

Run MS²Rescore

MS²Rescore: Sensitive PSM rescoring with predicted features.

usage: ms2rescore [-h] [-v] [-p [FILE ...]] [-t STR] [-s FILE/DIR] [-c FILE]
                  [-o FILE] [-l STR] [-n INT] [-f FILE] [--write-report]
                  [--profile]

Named Arguments

-v, --version

show program’s version number and exit

-p, --psm-file

path to PSM file (PIN, mzIdentML, MaxQuant msms, X!Tandem XML…)

-t, --psm-file-type

PSM file type (default: ‘infer’)

-s, --spectrum-path

path to MGF/mzML spectrum file or directory with spectrum files (default: derived from identification file)

-c, --config-file

path to MS²Rescore configuration file (see README.md)

-o, --output-path

Path and stem for output file names (default: derive from identification file)

-l, --log-level

logging level (default: info)

-n, --processes

number of parallel processes available to MS²Rescore

-f, --fasta-file

path to FASTA file

--write-report

boolean to enable profiling with cProfile

Default: False

--profile

boolean to enable profiling with cProfile

Default: False

Other commands

Generate HTML report

Generate a report from MS²Rescore result file(s):

ms2rescore-report [OPTIONS] OUTPUT_PREFIX

or

python -m ms2rescore.report [OPTIONS] OUTPUT_PREFIX

Start graphical user interface

Start the graphical user interface. For more info, see Graphical user interface.

ms2rescore-gui

or

python -m ms2rescore.gui