mokapot

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Issue with decoy prefix when trying to get protein level confidence.

2

Hi! I am having an issue with getting protein level confidence. I have an MS Amanda output file that I am reading using the `psm_utils` package, and then converting that...

louisebuur

Can't get protein level confidence. "IndexError: index -3 is out of bounds for axis 0 with size 1"

3

I'm trying to run mokapot on this file (TestAX.pin): https://drive.google.com/file/d/1T4447c9Y24hx3qHla_cW55HEg4A_XEuW/view?usp=sharing Which works great to give peptide confidence: ```python psms = mokapot.read_pin("TestAX.pin") results, models = mokapot.brew(psms) print(results) ``` ``` A mokapot.confidence.LinearConfidence...

roushrsh

[Breaking enhancement] Swap out Pandas for Polars

1

This is a huge, in-progress PR swapping out the Pandas backend for Polars. The goal is to improve the speed and scalability of mokapot. In addition to this huge change,...

wfondrie

Add workflow for building Windows installer

5

This PR partially addresses #101: - `pyinstaller.spec` instructs PyInstaller to freeze mokapot with all its dependencies (including Python) in an executable. - `innosetup.iss` instructs InnoSetup to bundle everything in a...

RalfG

File schema via pydantic

3

The PsmSchema definition is currently implemented via dataclasses. It's great to have the ability to validate a dataframe with a schema! Pydantic is a library for defining schemas and validation...

gessulat

[Question] executable(e.g. pyinstaller)

7

Hi, thanks for the great tool and for making it open source. Do you know if it is easily possible/has some experience to create executables for different platforms for mokapot?...

timosachsenberg

Mokapot is a workflow that broadly consists of the following steps - data preprocessing: optionally subsetting the input data and then doing a 3-fold split to tho generate training data...

gessulat

Multi-threaded writing of output files

2

For very large datasets, single-threaded IO operations are currently a speed bottleneck. Pyarrow datasets natively support: - partitioning a dataframe - [multi-threaded read](https://arrow.apache.org/cookbook/py/io.html#reading-partitioned-data) - [multi-threaded](https://github.com/apache/arrow/blob/main/python/pyarrow/dataset.py#L873C1-L875C62) [write](https://arrow.apache.org/cookbook/py/io.html#writing-partitioned-datasets) - [specifying number of...

gessulat

@sambenfredj 's pull requests introduces streaming at several places of the workflow but those intermediary file formats are not specified and documented yet. In addition, switching to a binary format...

gessulat

Decoy Prefix results in many unmapped peptides

1

Hi Will, Thanks for your time in advance: I am trying to use Mokapot on sage results of timsTOF DDA data - nothing special. The issue I encounter is the...

jonathan-krieger-bruker