From a19dcd9b9536710ca26dd3623a48b3d6ef6fa8cf Mon Sep 17 00:00:00 2001 From: CCranney <11773171+CCranney@users.noreply.github.com> Date: Tue, 8 Aug 2023 08:21:55 -0700 Subject: [PATCH] minor bug fixes in full code execution --- csodiaq/csodiaq.py | 8 +++----- csodiaq/peptide_quantification.py | 9 ++++++++- 2 files changed, 11 insertions(+), 6 deletions(-) diff --git a/csodiaq/csodiaq.py b/csodiaq/csodiaq.py index ac84f7a..7caefcd 100755 --- a/csodiaq/csodiaq.py +++ b/csodiaq/csodiaq.py @@ -36,13 +36,11 @@ def main(): outFileHeader = create_outfile_header(args['outDirectory'], queryFile, args['correction']) for dfType, df in outputDict.items(): - if dfType != "fullOutput": - dfType += "FDR" df.to_csv(f'{outFileHeader}_{dfType}.csv', index=False) if args["proteinTargets"]: - targetedReanalysisDict = create_mass_spec_input_dataframes_for_targeted_reanalysis_of_identified_peptides(outputDict["proteinFDR"], isIncludeHeavy=args['heavyMz'], maximumPeptidesPerProtein=args['proteinTargets']) + targetedReanalysisDict = create_mass_spec_input_dataframes_for_targeted_reanalysis_of_identified_peptides(outputDict["proteinFDR"], isIncludeHeavyIsotopes=args['heavyMz'], maximumPeptidesPerProtein=args['proteinTargets']) else: - targetedReanalysisDict = create_mass_spec_input_dataframes_for_targeted_reanalysis_of_identified_peptides(outputDict["peptideFDR"], isIncludeHeavy=args['heavyMz'], maximumPeptidesPerProtein=args['proteinTargets']) + targetedReanalysisDict = create_mass_spec_input_dataframes_for_targeted_reanalysis_of_identified_peptides(outputDict["peptideFDR"], isIncludeHeavyIsotopes=args['heavyMz'], maximumPeptidesPerProtein=args['proteinTargets']) for dfType, df in targetedReanalysisDict.items(): if "CV" in dfType: df.to_csv(f'{outFileHeader}_mostIntenseTargs_{dfType}.txt', index=False, sep='\t') @@ -96,7 +94,7 @@ def main(): # Post-processing # Check whether we should do anything if args['commonpeptide']: - print(f'Performing protein quantification and identifying common peptpides...', flush=True) + print(f'Performing protein quantification and identifying common peptides...', flush=True) peptide_quantification.get_all_peptide_quantities(file_list=args['files'], library_file=args['library'], csodiaq_output_dir=args['outDirectory'], diff --git a/csodiaq/peptide_quantification.py b/csodiaq/peptide_quantification.py index 0967da0..850149c 100644 --- a/csodiaq/peptide_quantification.py +++ b/csodiaq/peptide_quantification.py @@ -137,7 +137,14 @@ def get_peptide_quantities(file_list: list, if common_dataframe.shape[0] == 0: return # Load library - library_dataframe = pd.read_csv(library_file, sep='\t') + if library_file.endswith('.csv'): + sep = ',' + elif library_file.endswith('.tsv'): + sep = '\t' + else: + raise ValueError('library must be either .csv or .tsv') + + library_dataframe = pd.read_csv(library_file, sep=sep) # Get experimental spectra exp_data = []