Merge pull request #153 from wilhelm-lab/feature/sage

added sage to supported search engines
wilhelm-lab · Nov 11, 2023 · 4436cef · 4436cef
2 parents 9aa8e31 + 3736e9c
commit 4436cef
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Showing 5 changed files with 90 additions and 223 deletions.
diff --git 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
@@ -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}")