Single protein

[JanniRoebbecke]

Description

• The goal of this pr is to enable mapping between the the protein df and the peptide/evidence df by aligning the 'Protein ID' column
• The 'Protein ID' column now contains a single protein id for each entry in both the protein df as well as peptide/evidence df
• For the protein df the first valid Protein of the 'Majority Protein' column is selected
• For the peptide/evidence df the leading razor Protein is selected
• These changes make it possible to map at least one peptide of the peptide df for every protein in the protein df
• Should a future step need the complete Protein Groups they can easily be added as an additional column 'Protein Group'

Changes

• The importing Methods where changed to select the new columns
• clean Protein Groups was changed to retain the initial order of the Protein Group and then select the first of the Group
• Tests where changed to accommodate the new behavior

Testing

• Import a protein df and compare the read with the resulting dataframe
• Execute the 'Filter Peptides of Protein' method. It should select at least one peptide for every protein you select

PR checklist

Development

• [ ] If necessary, I have updated the documentation (README, docstrings, etc.)
• [ ] If necessary, I have created / updated tests.

Mergeability

• [ ] main-branch has been merged into local branch to resolve conflicts
• [ ] The tests and linter have passed AFTER local merge
• [ ] The code has been formatted with black

Code review

• [ ] I have self-reviewed my code.
• [ ] At least one other developer reviewed and approved the changes

[github-actions[bot]]

Coverage report

Click to see where and how coverage changed

File	Statements	Missing	Coverage	Coverage (new stmts)	Lines missing
protzilla
run.py
run_helper.py
runner.py
protzilla/data_analysis
differential_expression_anova.py
differential_expression_linear_model.py
differential_expression_t_test.py
protein_graphs.py
protzilla/data_integration
di_plots.py
enrichment_analysis_gsea.py
protzilla/data_preprocessing
filter_proteins.py
outlier_detection.py
peptide_filter.py
transformation.py
protzilla/importing
ms_data_import.py					28, 122, 244, 249, 255, 266-276
peptide_import.py
protzilla/methods
data_analysis.py					631-641
data_preprocessing.py
importing.py					142
protzilla/utilities
utilities.py
ui/main
settings.py
ui/runs
fields.py
views.py
views_helper.py
ui/runs/forms
data_analysis.py					926-934, 962
importing.py
Project Total

The report is truncated to 25 files out of 74. To see the full report, please visit the workflow summary page.

This report was generated by python-coverage-comment-action