Ville Koskinen

Numerical differences in output between Windows and Linux

1

There are often numerical differences in output between the Windows and Linux versions. This is the command line I used: percolator.exe -i 10 -D 14 -v 2 -U -B F003877.decoy.pop...

The ms2_tolerance parameter to MS2PIPFeatureGenerator only supports Da. It would be nice if it supported relative units like ppm as well.

Uncaught exception in DeepLCFeatureGenerator if not enough peptides for calibration set

2

I'm getting an uncaught exception when trying to use ms2rescore.feature_generators.ms2pip.DeepLCFeatureGenerator. The error happens when there are not enough peptides in psm_list for the calibration set. Here's how I create the...

Add user control for whether models are downloaded automatically

2

Currently, when MS2PIPFeatureGenerator calls ms2pip.correlate(), the latter may download xgboost_models_files from the Internet if they are not present in the model_dir directory. Can we please have a control to disable...

DeepLCFeatureGenerator multiprocessing issue when number of processes is more than 1

2

When I run DeepLCFeatureGenerator with processes=8, it takes a long time, much longer than processes=1. Python correctly starts 8 python.exe multiprocesses, but often the execution just hangs (I've waited more...

MS2PIPFeatureGenerator and DeepLCFeatureGenerator, provide a progress callback

1

Currently (ms2rescore 3.0.3), MS2PIPFeatureGenerator has some code to provide a progress bar when running in a terminal. It's done using rich.progress.track. DeepLCFeatureGenerator seems to not use it. When a script...

I've compiled Perl 5.38 with VS2019, then zlib, libpng, jpeglib and libgd with VS2019. I'd like to use the standard procedure for building GD, but it's failing at a few...

I'm getting `IndexError: Out of bounds on buffer access (axis 0)` from ms2pip/core.py when called from MS2PIPFeatureGenerator in MS2Rescore. I'm not sure if the root cause is in MS2PIPFeatureGenerator or...

Take Unimod modification compositions from psims.controlled_vocabulary.unimod

2

Currently, DeepLC hardcodes Unimod modification compositions in unimod_to_formula.csv. As new modifications are added, this file will grow out of date. It would be better to take modification compositions from a...

Tons of warnings when using iTRAQ4plex or iTRAQ8plex

3

If you use a modification like iTRAQ4plex or iTRAQ8plex, whose composition includes 13C or 15N, you get tons of warnings like: ``` 2024-07-16 15:36:18,842 WARNING Could not add the following...