proteobench.io.params.msangel module#

MSAngel creates modular pipelines that allows several search engines to identify peptides, which are then quantified with Proline. The parameters are provided in a .json file. MSAngel allows for multiple search engines to be used in the same pipeline. So it requires a list of search engines and their respective parameters, which are then concatenated.

Relevant information in file: -

proteobench.io.params.msangel.extract_params(fname: str | Path, json_file='/home/docs/checkouts/readthedocs.org/user_builds/proteobench/envs/v0.15.5/lib/python3.11/site-packages/proteobench/io/params/json/Quant/quant_lfq_DDA_ion.json') → ProteoBenchParameters[source]#

Parse MSAangel quantification tool JSON parameter file and extract relevant parameters.

Parameters:

fname (str or pathlib.Path) – The path to the MSAngel JSON parameter file.

Returns:

The extracted parameters as a ProteoBenchParameters object.

Return type:

ProteoBenchParameters

proteobench.io.params.msangel.extract_params_mascot_specific(search_params: list, input_params: ProteoBenchParameters) → ProteoBenchParameters[source]#

Extract search parameters from the JSON data of a workflow running Mascot. Adds them to the partially completed input_params ProteoBenchParameters object.

Parameters:

  • search_params (list) – The list of search parameters extracted from the JSON file.

  • input_params (ProteoBenchParameters) – The partially completed input_params object.

Returns:

The input_params object with the extracted parameters added.

Return type:

ProteoBenchParameters

proteobench.io.params.msangel.extract_params_xtandem_specific(search_params: list, input_params: ProteoBenchParameters) → ProteoBenchParameters[source]#

Extract search parameters from the JSON data of a workflow running X!Tandem. Adds them to the partially completed input_params ProteoBenchParameters object.

Parameters:

  • search_params (list) – The list of search parameters extracted from the JSON file.

  • input_params (ProteoBenchParameters) – The partially completed input_params object.

Returns:

The input_params object with the extracted parameters added.

Return type:

ProteoBenchParameters

proteobench.io.params.msangel.extract_search_engine(search_params: list) → dict[source]#

Extract search engine name from the JSON data. It only works for workflows using a single search engine.

Parameters:

search_params (list) – The list of search parameters extracted from the JSON file.

Returns:

The search engine name.

Return type:

dict