protein-expression-workbook-intake

Protein Expression Workbook Intake

Start here for protein_expression.xlsx. The workbook is edited in place, so the Task sheet surface has to be read once and recorded before anything is written to it. Every later stage works from the recorded surface rather than re-guessing row numbers.

This stage writes no Task-sheet cell and no formula.

Inputs

• protein_expression.xlsx

Outputs

• protein_expression_baseline.xlsx — byte copy of the untouched workbook
• pex_workflow/workbook_layout_checkpoint.json
• pex_workflow/side_file_intake.json

What to freeze

Read the Task sheet and record the handles the rest of the workflow needs:

• task_target_rows — the 10 protein IDs in A11:A20 with their gene symbols, the statistics column each one owns in row 24-27 (B for row 11, C for row 12, … K for row 20), and the fold-change row each one owns in 32-41
• task_sample_columns — the 10 sample names in C10:L10 with the group label above each one in row 9
• task_expression_block, task_statistics_block, task_fold_change_block
• task_fold_change_headers — read C31 and D31 rather than assuming an order; the header row is the authority for which column takes Fold Change and which takes Log2 FC

Then read the Data sheet and record where the lookup ranges actually start: the protein IDs live in column A from row 2, the sample headers in row 1, and the expression values begin at the first column whose header matches a Task sample name (the leading columns are Protein_ID, Gene_Symbol and Description).

Do not serialize the full 200 × 50 value grid here. That extraction belongs to the next stage.

The pre-edit reference copy

Because the deliverable and the source are the same file, copy the untouched workbook to protein_expression_baseline.xlsx before any write happens. Its only job is to hold the pre-edit Data-sheet values until they have been extracted into a structured basis.

Record it in pex_workflow/side_file_intake.json with:

• retention_class: retention_review_required — it is a working reference, not a permanent archive, and the next stage owns the review
• review_owner: protein-expression-matrix-basis

protein_expression.xlsx itself is listed under primary_deliverable with retention_class: protected. It is never a cleanup target at any point in this workflow.

Run

python3 skills/protein-expression-workbook-intake/scripts/observe_workbook_surface.py

Verification

• pex_workflow/workbook_layout_checkpoint.json resolves 10 target proteins and 10 samples, and the group labels split into Control and Treated.
• pex_workflow/side_file_intake.json classifies protein_expression_baseline.xlsx as retention_review_required and protein_expression.xlsx as protected.
• The Task sheet is unchanged.

Stop condition

Stop once the checkpoint and the intake record exist. Do not write lookup formulas, statistics or fold changes here. Next: protein-expression-matrix-basis.

Count-Study Continuation

After this stage's local outputs are complete, read the protein-expression-matrix-basis skill before continuing. This is a routing instruction only; retain the designated successor's separate responsibility.