Filter peptides step

[JanniRoebbecke]

Description

• implements the 'Filter Peptides of Protein' Step
• the step takes a Protein of interest and selects all Peptides of this Protein in the Peptide file
• two methods where implemented
  1. Letting the user select a protein of interest from a list of proteins, which could either be the a list of all Proteins in the Protein dataframe or the list of significant proteins from a previous data Differential Expression Test
  2. Automatically selecting the most significant Protein from a previous Differential Expression Test

Changes

• the file 'filter_peptides_of_protein.py' was added containing the core functionality of filtering
• a step and form class where added to support accessing this method from the GUI
• in order to enable sending messages in the 'insert_dataframes' method, the clearing of messages was moved in the 'calculate' method

Testing

• add the step 'Peptide Import' / 'Evidence Import' to the standard workflow
• import a peptide/evidence-file
• step through the preprocessing and inspect the resulting dataframes additionally
• inspect the new tests and test the code with them

PR checklist

Development

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

Mergeability

• [x] 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

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

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Coverage report

Click to see where and how coverage changed

File	Statements	Missing	Coverage	Coverage (new stmts)	Lines missing
protzilla
steps.py
protzilla/data_analysis
ptm_analysis.py
protzilla/data_preprocessing
filter_proteins.py
outlier_detection.py
peptide_filter.py
transformation.py
protzilla/importing
peptide_import.py
protzilla/methods
data_analysis.py					623, 626-649
data_preprocessing.py
importing.py					142
ui/runs/forms
data_analysis.py					889, 916-962
Project Total

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