From 3af36b12dd5bf300212ad1a41c83ff0d3e65cbd9 Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Thu, 18 Jul 2024 13:06:49 +0200 Subject: [PATCH] change name of library file to "predicted_library" --- docs/outputs.rst | 4 ++-- oktoberfest/runner.py | 7 ++++--- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/docs/outputs.rst b/docs/outputs.rst index 2b6cb6bc..740459bb 100644 --- a/docs/outputs.rst +++ b/docs/outputs.rst @@ -37,9 +37,9 @@ Files in the results directory +=======================================+==============================================================================================================================================================================================+ | _ce.txt | Contains the best collision energy according to the collision energy calibration where is replaced with the name of the spectra file for which the calibration was performed | +---------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ - | myPrositLib. | Contains the spectral library in either csv or msp format depending on what format was chosen | + | predicted_library. | 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 index d9abdaa2..7b12c649 100644 --- 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")