proteobench.io.params.quantms module#

Quantms is a nextflow pipeline that execution depends on the settings in an SDRF file. It is executed using a parameters file in JSON format.

However, the version of packages are dumped to a versions yaml file. And some parameters are taken from the SDRF file.

proteobench.io.params.quantms.extract_params(file1: IO, file2: IO, file3: IO = None, json_file='/home/docs/checkouts/readthedocs.org/user_builds/proteobench/envs/v0.15.1/lib/python3.11/site-packages/proteobench/io/params/json/Quant/quant_lfq_DDA_ion.json') → ProteoBenchParameters[source]#

Extract parameters from the parsed SDRF and version file. We use both the parsed SDRF file and the yaml file of versions to extract the parameters. The function needs to be able to handle any order of files as the streamlit interfaces does allow the user to select any order.

This might be changed in a newer quantms version with one central parameters file.

Parameters:

  • file1 (IO) – File object of the first file.

  • file2 (IO) – File object of the second file.

  • file3 (IO) – File object of the third file, by default None.

Returns:

The extracted parameters as a ProteoBenchParameters object.

Return type:

ProteoBenchParameters

proteobench.io.params.quantms.load_files(file1: IO, file2: IO, file3: IO = None) → Tuple[dict, DataFrame | None, dict][source]#

Load file independent of order they are provided in.

SDRF file is optional.

Parameters:

  • file1 (IO) – File object of the first file.

  • file2 (IO) – File object of the second file.

  • file3 (IO, optional) – File object of the third file, by default None.

Returns:

Tuple with the versions, parsed SDRF and pipeline parameters.

Return type:

tuple[dict, pd.DataFrame | None, dict]

proteobench.io.params.quantms.load_parsed_sdrf(file: str | Path | IO) → DataFrame[source]#

Load the parsed SDRF file.

Parameters:

file (Union[str, pathlib.Path, IO]) – File path or file object of the parsed SDRF file.

Returns:

Parsed SDRF file as a pandas DataFrame.

Return type:

pd.DataFrame

proteobench.io.params.quantms.load_versions(file: IO) → dict[source]#

Load the versions of the tools used in the quantms pipeline.

Parameters:

file (IO) – File object of the quantms pipeline versions file.

Returns:

Dictionary with the versions of the tools used in the quantms pipeline.

Return type:

dict