Matrix processing - #60
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Existing rows are replaced in place (preserves row order); new kinases are appended. Preserves CRLF line endings and TRUE/FALSE boolean format. Uses na_filter=False to keep legacy 'nan' string cells intact.
Removed (folded into the new API):
- save_matrices_to_database
- save_kinase_matrices
- save_kinase_to_database
Added:
- save_matrices(processed_results, kin_type, output_dir=None,
update_database=False, confirm=True, kinome_info=None) — unified
batch save with both targets
- kinases_from_densitometry_dir(...) — process every *_densitometry.txt
in a folder, returns dict of {name: kl.Kinase}
- kinase_from_densitometry mirrors the same flags so a one-call
shortcut works
- kin.save(output_dir, update_database, confirm, kinome_info) bound
method — single entry point for both save targets
When update_database=True (atomic, with confirmation prompt):
1. Write raw/norm/log2 matrices to the package database
2. Persist source densitometry to package/densitometry/ so the kinase
can be re-processed in the future from the package alone
3. Rebuild combined *_all_matrices.tsv files (now enumerated from raw/
instead of densitometry/, so brand-new kinases get picked up)
4. Update kinome_information.tsv via interactive prompts or a provided
kinome_info arg (file path / DataFrame / dict). Existing rows ask
for y/n confirmation before being overwritten.
5. Re-score phosphoproteomes
6. Print remaining-manual-steps banner (CHANGELOG, README, version, tests)
If only output_dir is set, files are written there and the package is
left completely untouched (no prompt, no reminder).
Default behavior (no flags) is purely ephemeral — kinase_from_densitometry
returns a kl.Kinase ready for plot_data, score, percentile, etc., with
no side effects on the package.
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Adding options to process matrices from densitometries with and without updating the database.