compomics / ms2pip

MS²PIP: Fast and accurate peptide spectrum prediction for multiple fragmentation methods, instruments, and labeling techniques.
https://ms2pip.readthedocs.io
Apache License 2.0
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Enable passthrough of DeepLC options in fasta2speclib #138

Closed RalfG closed 2 years ago

RalfG commented 3 years ago

To enable DeepLC calibration and other DeepLC options in fasta2speclib, the fasta2speclib config (from json file) should be passed to the ms2pip.retention_time module:

Replace this line: https://github.com/compomics/ms2pip_c/blob/2e0c2af34d9d81317a5313b837d9d4111a96981f/fasta2speclib/fasta2speclib.py#L342

With

        rt_predictor = RetentionTime(config=params)

This makes it possible to add a deeplc entry to the fasta2speclib config file:

{
    ...
    "elude_model_file":null,
    "rt_predictions_file":null,
    "add_retention_time":true,
    "deeplc": {
        "calibration_file": "/path/to/deeplc/peptide/file.csv"
    }
}

Other options under “deeplc" could be any option from the DeepLC API.

RalfG commented 2 years ago

Was already fixed in #135.