ms2rescore.py arguments list

[prvst]

Description of feature

Please consider adding the following cli arguments to the quantms-utils :: ms2rescore.py script:

-log_level
-psm_id_pattern
-spectrum_id_pattern

Thanks

[ypriverol]

What will be the values for the patterns? and spectrum ID? Can you elaborate @prvst

[prvst]

Here's the description from the schema:

                "log_level": {
                    "description": "Logging level",
                    "type": "string",
                    "enum": ["debug", "info", "warning", "error", "critical"]
                },
                "spectrum_id_pattern": {
                    "description": "Regex pattern to extract index or scan number from spectrum file. Requires at least one capturing group.",
                    "oneOf": [{ "type": "string" }, { "type": "null" }],
                    "default": "(.*)",
                    "format": "regex"
                },
                "psm_id_pattern": {
                    "description": "Regex pattern to extract index or scan number from PSM file. Requires at least one capturing group.",
                    "oneOf": [{ "type": "string" }, { "type": "null" }],
                    "default": "(.*)",
                    "format": "regex"
                },
                

[ypriverol]

@prvst Can you give us one example about how to use this parameters?

[prvst]

This is an example from an actual parameter file - all three arguments are passed as strings

        "log_level": "debug",
        "psm_id_pattern": "scan=(\\d+)",
        "spectrum_id_pattern": "scan=(\\d+)",

[ypriverol]

Done in quantms-utils 0.0.11 #419