[WIP] # Complete Agent Directive: Implement Excel Cleavage Mapping Pipeline ## Mission Statement You are tasked with implementing a complete Excel-based cleavage mapping pipeline for bioinformatics protein sequence analysis. This is a **formula-only automat...

[Copilot]

Thanks for asking me to work on this. I will get started on it and keep this PR's description up to date as I form a plan and make progress.

Original description:

Complete Agent Directive: Implement Excel Cleavage Mapping Pipeline

Mission Statement

You are tasked with implementing a complete Excel-based cleavage mapping pipeline for bioinformatics protein sequence analysis. This is a formula-only automation solution (no VBA) that processes CSV data through structured Excel templates with dynamic output tables.

Project Context

• Repository: mnechromancer/cleavage_mapper
• Current State: Documentation and planning phase - Excel templates need to be built from specifications
• Target Users: Bioinformatics researchers who need Excel-based protein sequence analysis
• Core Philosophy: Pure Excel formulas, template-based workflow, no external scripts

Primary Deliverable

Create excel/CleavagePipeline_Template.xlsx with the following structure:

Required Worksheets

1. Raw_100, Raw_200, Raw_500 - Data input sheets for different mgd concentrations
2. Calc_100, Calc_200, Calc_500 - Formula processing sheets with automated calculations
3. Dashboard (optional) - Summary view with key metrics

Raw Sheets Structure (Columns A-I)

Column A: # (Row numbers from source data)
Column B: Sequence (Protein sequences with cleavage indicators: "(E)AEDLQVGQVELGGGPGAGSLQ(P)")
Columns C-I: Function data (Han_StemCells_[concentration]mgdl_Glucose_AspN_Fxn2 through Fxn8)

Calc Sheets Structure (Columns A-S)

Core Processing (A-I):

• A: Sequence → =Raw_100!B2
• B: LeftResidue → =IF(ISERROR(FIND("(",A2)),"",MID(A2,FIND("(",A2)+1,FIND(")",A2)-FIND("(",A2)-1))
• C: RightResidue → =IF(LEN(A2)-LEN(SUBSTITUTE(A2,"(",""))<2,"",MID(A2,FIND("(",SUBSTITUTE(A2,"(","♦",LEN(A2)-LEN(SUBSTITUTE(A2,"(",""))-1))+1,FIND(")",A2,FIND("(",SUBSTITUTE(A2,"(","♦",LEN(A2)-LEN(SUBSTITUTE(A2,"(",""))-1)))-FIND("(",SUBSTITUTE(A2,"(","♦",LEN(A2)-LEN(SUBSTITUTE(A2,"(",""))-1))-1))
• D: CorePeptide → =IF(OR(ISERROR(FIND(")",A2)),LEN(A2)-LEN(SUBSTITUTE(A2,"(",""))<2),"",MID(A2,FIND(")",A2)+1,FIND("(",SUBSTITUTE(A2,"(","♦",LEN(A2)-LEN(SUBSTITUTE(A2,"(",""))-1))-FIND(")",A2)-1))
• E: Left_Sum → =SUM(Raw_100!C2:I2)
• F: Right_Sum → =0 (placeholder for future Right function columns)
• G: Total_Sum → =E2+F2
• H: Left_Percentage → =IF(G2=0,0,E2/G2*100)
• I: Right_Percentage → =IF(G2=0,0,F2/G2*100)

Dynamic Output Tables (K-S):

• K-N: Left-Anchored Cleavage Table → =FILTER(B2:E100,(B2:B100<>"")*(E2:E100>0))
• P-S: Right-Anchored Cleavage Table → =FILTER(C2:E100,(C2:C100<>"")*(E2:E100>0))

Critical Implementation Requirements

Formula Standards

1. Error Handling: All formulas must include IF(ISERROR()) checks
2. Dynamic Arrays: Use FILTER, SORTBY, HSTACK for output tables (Office 365/Excel 2021+)
3. Sheet References: Adjust Raw_100! references for Raw_200 and Raw_500 variants
4. Copy-Pasteable: Formulas must work when copied down rows automatically

Data Format Specifications

Input Sequence Format: (LEFT_RESIDUE)CORE_PEPTIDE(RIGHT_RESIDUE)

• Example: (E)AEDLQVGQVELGGGPGAGSLQ(P)
• LeftResidue: E
• CorePeptide: AEDLQVGQVELGGGPGAGSLQ
• RightResidue: P

Testing Requirements

Create sample data that demonstrates:

• Multiple protein sequences with different residue patterns
• Function values that generate meaningful Left_Sum calculations
• Sequences that test edge cases (missing parentheses, single residues)

Secondary Deliverables

Documentation Files

1. docs/FORMULAS.md - Complete technical formula reference with explanations
2. docs/WORKFLOW.md - Step-by-step user guide for non-technical researchers
3. data/sample_[100|200|500]mgd.csv - Test data files for validation

Sample Data Requirements

Each CSV should contain:

• 3-5 rows of realistic protein sequence data
• Function values (Fxn2-Fxn8) that create testable sum calculations
• Mix of different LeftResidue/RightResidue combinations
• Headers matching Raw sheet column structure

Technical Constraints

• Excel Version: Modern Excel with dynamic array support required
• No VBA: Pure formula-based solution only
• No External Dependencies: Standard Excel functions only
• Performance: Formulas should recalculate efficiently with 100+ rows of data

Success Criteria

1. Template Functionality: Users can paste CSV data into Raw sheets and see automatic calculations in Calc sheets
2. Dynamic Tables: Left/Right-anchored views update automatically when new data is added
3. Formula Accuracy: Residue extraction and sum calculations match expected bioinformatics analysis patterns
4. Documentation Quality: Technical and user documentation enables independent usage
5. Sample Data Validation: Provided test files demonstrate complete workflow

File Organization Priority

1. excel/CleavagePipeline_Template.xlsx (primary deliverable)
2. data/sample_*.csv files (testing)
3. docs/FORMULAS.md (technical reference)
4. docs/WORKFLOW.md (user guide)

Execute this implementation systematically, ensuring each component works independently and integrates seamlessly into the complete pipeline workflow.

---

💡 You can make Copilot smarter by setting up custom instructions, customizing its development environment and configuring Model Context Protocol (MCP) servers. Learn more Copilot coding agent tips in the docs.