From ff4e090fab09456df4216324ef51ec66d8949896 Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Sat, 11 Nov 2023 13:42:13 +0100 Subject: [PATCH] added sage to supported search engines --- docs/config.rst | 2 +- oktoberfest/preprocessing/preprocessing.py | 4 +++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/docs/config.rst b/docs/config.rst index b51955b8..59f44c9b 100644 --- a/docs/config.rst +++ b/docs/config.rst @@ -42,7 +42,7 @@ Required for CE calibration and rescoring +----------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------+ | search_results | Path to directory or file containing the search results | +----------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------+ - | search_results_type | Format description for search results; can be "Maxquant", "Msfragger", "Mascot" or "`Internal <./internal_format.html>`_"; default = "Maxquant" | + | search_results_type | Format description for search results; can be "Maxquant", "Msfragger", "Mascot", "Sage" or "`Internal <./internal_format.html>`_"; default = "Maxquant" | +----------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------+ | spectra | Path to directory or file containing mass spectrometry results | +----------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------+ diff --git a/oktoberfest/preprocessing/preprocessing.py b/oktoberfest/preprocessing/preprocessing.py index 782a737d..0adb515c 100644 --- a/oktoberfest/preprocessing/preprocessing.py +++ b/oktoberfest/preprocessing/preprocessing.py @@ -10,7 +10,7 @@ from spectrum_fundamentals.mod_string import internal_without_mods, maxquant_to_internal from spectrum_io.file import csv from spectrum_io.raw import ThermoRaw -from spectrum_io.search_result import Mascot, MaxQuant, MSFragger +from spectrum_io.search_result import Mascot, MaxQuant, MSFragger, Sage from spectrum_io.spectral_library import digest as digest_io from ..data.spectra import FragmentType, Spectra @@ -227,6 +227,8 @@ def convert_search( search_result = MSFragger elif search_engine == "mascot": search_result = Mascot + elif search_engine == "sage": + search_result = Sage else: raise ValueError(f"Unknown search engine provided: {search_engine}")