From 837fde4f7c2a313b4df3a2fb10fd74b2eb374b85 Mon Sep 17 00:00:00 2001 From: Sven <6873303+gieses@users.noreply.github.com> Date: Sun, 15 Oct 2023 21:29:59 +0200 Subject: [PATCH] let's pass the qc plots for now --- xirt/__main__.py | 25 ++++++++++++++----------- 1 file changed, 14 insertions(+), 11 deletions(-) diff --git a/xirt/__main__.py b/xirt/__main__.py index 76f5979..f63b33d 100644 --- a/xirt/__main__.py +++ b/xirt/__main__.py @@ -289,7 +289,7 @@ def xirt_runner(peptides_file, out_dir, xirt_loc, setup_loc, nrows=None, perform yrefit = training_data.get_classes(training_data.train_idx, frac_cols=frac_cols, cont_cols=cont_cols) xirtnetwork.build_model(siamese=xirt_params["siamese"]["use"], - alphabet=len(training_data.le.classes_)+1) + alphabet=len(training_data.le.classes_) + 1) xirtnetwork.compile() if learning_params["train"]["pretrained_weights"].lower() != "none": @@ -317,7 +317,7 @@ def xirt_runner(peptides_file, out_dir, xirt_loc, setup_loc, nrows=None, perform else: logger.info("Loading model weights.") xirtnetwork.build_model(siamese=xirt_params["siamese"]["use"], - alphabet=len(training_data.le.classes_)+1) + alphabet=len(training_data.le.classes_) + 1) xirtnetwork.compile() xirtnetwork.model.load_weights(learning_params["train"]["pretrained_weights"]) logger.info("Reassigning prediction index for prediction mode.") @@ -362,17 +362,20 @@ def xirt_runner(peptides_file, out_dir, xirt_loc, setup_loc, nrows=None, perform # only training procedure includes qc if perform_qc and (learning_params["train"]["mode"] != "predict"): logger.info("Generating qc plots.") - qc.plot_epoch_cv(callback_path=xirtnetwork.callback_p["callback_path"], - tasks=xirtnetwork.tasks, xirt_params=xirt_params, outpath=outpath) + try: + qc.plot_epoch_cv(callback_path=xirtnetwork.callback_p["callback_path"], + tasks=xirtnetwork.tasks, xirt_params=xirt_params, outpath=outpath) - qc.plot_summary_strip(model_summary_df, tasks=xirtnetwork.tasks, xirt_params=xirt_params, - outpath=outpath) + qc.plot_summary_strip(model_summary_df, tasks=xirtnetwork.tasks, xirt_params=xirt_params, + outpath=outpath) - qc.plot_cv_predictions(training_data.prediction_df, training_data.psms, - xirt_params=xirt_params, outpath=outpath) + qc.plot_cv_predictions(training_data.prediction_df, training_data.psms, + xirt_params=xirt_params, outpath=outpath) - qc.plot_error_characteristics(training_data.prediction_df, training_data.psms, - xirtnetwork.tasks, xirt_params, outpath, max_fdr=0.01) + qc.plot_error_characteristics(training_data.prediction_df, training_data.psms, + xirtnetwork.tasks, xirt_params, outpath, max_fdr=0.01) + except Exception as e: + logger.warning("QC plots failed. Error: {}".format(e)) logger.info("Writing output tables.") # store setup in summary @@ -421,7 +424,7 @@ def main(): # pragma: no cover # check if parameter for option writing is supplied if "-s" in sys.argv[1:]: - outfile = sys.argv[1:][sys.argv[1:].index("-s")+1] + outfile = sys.argv[1:][sys.argv[1:].index("-s") + 1] # write config files if outfile != "": print(f"Writing default config (learning) to file {outfile}.")