Omics reader

[lucas-diedrich]

This PR addresses Issue #11

Implementation of readers and documentation for proteomics data. Implementation in dvpio.read.omics submodule.

Not ready to merge yet, pending tests for read_precursor_table factory.

Pending

• Test data for read_precursor_table

Functionality

Implemented functions are

• parse_df Generic, custom function that enables users to parse any pandas dataframe (e.g. a protein.group table) to an anndata object.
• read_precursor_table A function that enables users to parse most PSM reports, parse them to a filtered protein group table, and convert them to anndata. This function wraps the alphabase.anndata.AnnDataFactory class (see development branch on alphabase, and PR291)

Tutorials

Tutorial on real-world single-cell DVP data by Rosenberger et al, 2023

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 97.77778% with 1 line in your changes missing coverage. Please review.

Project coverage is 93.22%. Comparing base (d9c46f5) to head (6eb7fa1).
Report is 25 commits behind head on main.

Files with missing lines	Patch %	Lines
src/dvpio/read/omics/report_reader.py	96.87%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #58      +/-   ##
==========================================
+ Coverage   92.14%   93.22%   +1.07%     
==========================================
  Files          11       14       +3     
  Lines         191      236      +45     
==========================================
+ Hits          176      220      +44     
- Misses         15       16       +1     

Files with missing lines	Coverage Δ
src/dvpio/_utils.py	100.00% <100.00%> (ø)
src/dvpio/read/omics/__init__.py	100.00% <100.00%> (ø)
src/dvpio/read/omics/report_reader.py	96.87% <96.87%> (ø)