change name of library file to "predicted_library"

wilhelm-lab · Jul 18, 2024 · 3af36b1 · 3af36b1
1 parent 922be6c
commit 3af36b1
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Showing 2 changed files with 6 additions and 5 deletions.
diff --git a/docs/outputs.rst b/docs/outputs.rst
@@ -37,9 +37,9 @@ Files in the results directory
     +=======================================+==============================================================================================================================================================================================+
     | <spectra_file>_ce.txt                 | Contains the best collision energy according to the collision energy calibration where <spectra_file> is replaced with the name of the spectra file for which the calibration was performed  |
     +---------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-    | myPrositLib.<csv|msp>                 | Contains the spectral library in either csv or msp format depending on what format was chosen                                                                                                |
+    | predicted_library.<csv|msp|dlib>      | Contains the spectral library in either spectronaut, msp, or dlib format depending on what format was chosen in the configuration file                                                       |
     +---------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-    | prosit_input.csv	                    | Contains the peptide list including metadata needed for spectral library generation when providing a fasta file for in-silico digestion                                                      |
+    | peptides_internal.csv	                | Contains the peptide list including metadata needed for spectral library generation when providing a fasta file for in-silico digestion or a peptides list                                   |
     +---------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 
 

diff --git a/oktoberfest/runner.py b/oktoberfest/runner.py
@@ -289,12 +289,13 @@ def _speclib_from_digestion(config: Config) -> Spectra:
 
 
 def _get_writer_and_output(results_path: Path, output_format: str) -> Tuple[Type[SpectralLibrary], Path]:
+    libfile_prefix = "predicted_library"
     if output_format == "msp":
-        return MSP, results_path / "myPrositLib.msp"
+        return MSP, results_path / f"{libfile_prefix}.msp"
     elif output_format == "spectronaut":
-        return Spectronaut, results_path / "myPrositLib.csv"
+        return Spectronaut, results_path / f"{libfile_prefix}.csv"
     elif output_format == "dlib":
-        return DLib, results_path / "myPrositLib.dlib"
+        return DLib, results_path / f"{libfile_prefix}.dlib"
     else:
         raise ValueError(f"{output_format} is not supported as spectral library type")