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Peptides #533

Closed
wants to merge 46 commits into from
Closed

Peptides #533

wants to merge 46 commits into from

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JanniRoebbecke
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Description

  • revert changes to the intensity name
  • intensity name in the imported data frame is now under the name from the source data frame

Changes

  • switch out name

Testing

  • Import a peptide data frame and inspect data frame by opening the file or using the table view

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

janni.roebbecke and others added 30 commits March 23, 2024 15:29
evidence import
fa28ee3
tests
2f0c566
filter proteins
49be94b
filter sampels
2bdae08
@antonneubauer @henninggaertner
Select Peptides by group or sample for coverage visualisation (#410)
104c49b 
* untested working, needs cleanup

* linter

* remove dupliacte method (merge screw-up)

* add doc strings, fix first few tests (miss. args)

* metadata df now optional param + adjusted asserts, fixed test

* formatting

* conditional metadata input for protein graphs

* import logging levels, formatting

* add grouping tests for peptides, add error handling

* spelling, formatting

* remove unused import, format

* fix error msgs in tests

* fix line length

* Convert has_metadata to property

* Use logger instead of print statement

* An attempt at consistent text-casing

* formatting

---------

Co-authored-by: henninggaertner <[email protected]>
tests for filter_proteins with peptide file
9b983dd
tests for filter_proteins with peptide file, better mock dataframe
ba0d58e
output types
f07ff7e
added testing that only filtered Proteins are removed from peptides_df
12c1d5c
tests for filter_samples with peptide file
66cd83b
extract test that peptide filtering matches protein filtering into Me…
f18c8c4 
…thod
Merge branch '456-addapt-outlier-detection-for-peptides' into 454-add…
16f71ea 
…apt-filtering-for-peptides
refactor: shortened tests by integrating extracted method and mock data
2aedccd
exclude peptides
a297922
tests
7d115ff
minor fixes in test
4e738e6
minor fixes in test
d77da64
fix test that peptide filtering matches protein filtering Method
6f7d8f7
fix test that peptide filtering matches protein filtering Method
6f12a76
fix test that peptide filtering matches protein filtering Method
f635008
fix test that peptide filtering matches protein filtering Method
cd8fa06
match mock protein dataframe to mock peptide dataframe
f62b4f6
extract test that peptide filtering matches protein filtering into Me…
1c73f76 
…thod
implementation
83fd7a5
tests
1766d36
tests improve error logging
6584acd
tests git testing
f578555
peptide import added missing column
3bf6a7d
Merge remote-tracking branch 'refs/remotes/origin/452-import-evidence…
25f15e8 
…-file' into peptides

# Conflicts:
#	protzilla/importing/peptide_import.py
#	tests/protzilla/data_preprocessing/test_peptide_preprocessing.py
#	tests/protzilla/importing/test_peptide_import.py
merge peptide filtering
2beca7a
janni.roebbecke added 15 commits May 28, 2024 10:34
Merge remote-tracking branch 'refs/remotes/origin/456-addapt-outlier-…
0cee245 
…detection-for-peptides' into peptides

# Conflicts:
#	protzilla/data_preprocessing/outlier_detection.py
#	tests/protzilla/data_preprocessing/test_outlier_detection.py
merge peptide filtering and outlier_detection
084a10d
Merge remote-tracking branch 'refs/remotes/origin/455-addapt-transfor…
dc790be 
…mation-for-peptides' into peptides

# Conflicts:
#	protzilla/data_preprocessing/transformation.py
#	tests/protzilla/data_preprocessing/test_peptide_preprocessing.py
#	tests/protzilla/data_preprocessing/test_transformation.py
merge peptide transformation
0e1886a
implement passing of peptide data between preprocessing steps
4733972
complete implement passing of peptide data between preprocessing steps
fd8b555
implement overhead for new step evidence import
e722b27
Fix EvidenceImport class (now the right method is called)
590396a
implement suggested changes: remove default values and correct gramma…
c90e845 
…r mistake
make preprocessing work without peptide_df
8a2f243
clean up
2a22e61
add cleaning of protein groups to evidence import
4e7d4a8
clean Protein IDs for peptide_import and name intensity column Intensity
c13c6b5
implement requested changes: make peptide_df input optional for all p…
8a49a7b 
…reprocessing steps, remove peptide_df input in preprocessing steps, where it is not used
Fixed Intensity name
2b05a0b
@JanniRoebbecke JanniRoebbecke self-assigned this Sep 13, 2024
Merge branch 'refs/heads/dev' into peptides
219ccaf 
# Conflicts:
#	protzilla/constants/location_mapping.py
#	protzilla/constants/workflow_meta.json
#	protzilla/importing/peptide_import.py
#	protzilla/methods/importing.py
#	tests/protzilla/data_preprocessing/test_filter_proteins.py
#	tests/protzilla/data_preprocessing/test_filter_samples.py
#	tests/protzilla/data_preprocessing/test_outlier_detection.py
#	tests/protzilla/data_preprocessing/test_transformation.py
#	tests/protzilla/importing/test_peptide_import.py
#	tests/ui/test_views.py
#	ui/runs/forms/importing.py
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Coverage report

Click to see where and how coverage changed

FileStatementsMissingCoverageCoverage
(new stmts)		Lines missing
  protzilla
  run.py
  run_helper.py
  runner.py
  protzilla/data_analysis
  differential_expression_helper.py 125, 143
  differential_expression_kruskal_wallis.py 227
  differential_expression_linear_model.py
  differential_expression_mann_whitney.py 266
  differential_expression_t_test.py
  protein_graphs.py
  ptm_analysis.py 74, 119-120, 138-140
  protzilla/data_integration
  di_plots.py
  protzilla/data_preprocessing
  outlier_detection.py
  transformation.py
  protzilla/importing
  ms_data_import.py 122, 276
  protzilla/methods
  data_analysis.py 21, 174, 250, 283, 308, 351, 916, 935
  data_preprocessing.py
  importing.py 144
  protzilla/utilities
  transform_dfs.py
  utilities.py
  ui/main
  settings.py
  ui/runs
  fields.py
  views.py
  views_helper.py
  ui/runs/forms
  data_analysis.py 318-322, 379, 409, 445, 468, 1183, 1224-1228, 1252
  importing.py
Project Total  

The report is truncated to 25 files out of 56. To see the full report, please visit the workflow summary page.

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

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@lucatreide lucatreide Awaiting requested review from lucatreide

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@JanniRoebbecke @antonneubauer