fix: Add support for Drosophila melanogaster

[DanielM812]

I noticed two errors that occured while working with RNA-Seq data from Drosophila melanogaster and tried to fix them:

1. Gene names for the fruit fly can sometimes have a colon in them, when belonging to a gene family (e.g. His4:CG33869 and His4:CG31611). This leads to an error when selecting the correct name and value in postprocess_go_enrichment.py as they are also separated by a colon. The separation then results in three parts (His4, CG33869, 0.73842) instead of two parts.
2. For Drosophila melanogaster the "ensembl_transcript_id_version" attribute from the Ensembl mart does not exist. This attribute is part of the 3-prime attributes which (I assume?) are not needed for standard RNA-Seq analysis.

Summary by CodeRabbit

• Bug Fixes
  • Improved transcript processing to dynamically detect and use available identifier attributes, enhancing output stability.
  • Enhanced gene value extraction to accurately handle varied input formats, ensuring more reliable results.

[coderabbitai]

Walkthrough

The changes update two scripts by refining how attributes and parsed values are handled. In the R script, the attribute "ensembl_transcript_id_version" is now conditionally included via a helper function and renamed robustly using a flexible approach. In the Python script, the extract_study_items function has been modified to extract gene information from different positions in a split string. No public or exported entities were affected.

Changes

File(s)	Change Summary
workflow/.../get-transcript-info.R	Uses use_if_available to conditionally include "ensembl_transcript_id_version" for three_prime_attributes and applies any_of for robust column renaming.
workflow/.../postprocess_go_enrichment.py	Adjusts indexing in extract_study_items to retrieve the gene name from parts[-2] and its value from parts[-1] after splitting the input string.

Sequence Diagram(s)

sequenceDiagram
    participant RScript as get-transcript-info.R
    participant AttrFunc as use_if_available
    participant Data as available_attributes
    RScript->>AttrFunc: Check for "ensembl_transcript_id_version"
    alt Attribute Exists
        AttrFunc-->>RScript: Return attribute value
    else Attribute Missing
        AttrFunc-->>RScript: Return NULL/skip
    end
    RScript->>RScript: Rename column with any_of in other_annotations

Loading

sequenceDiagram
    participant Func as extract_study_items
    participant Input as raw_input_string
    participant Split as parts_list
    Func->>Input: Receive input string
    Func->>Split: Split string by delimiter
    Note over Func: Use parts[-2] for gene, parts[-1] for value
    Func->>Func: Process and assign gene data

Loading

Poem

Hop, hop, through lines of code I race,
Checking attributes at a steady pace.
With functions guiding every twist,
Parsing genes through each new list.
A joyful bound from bug to grace!
🐇✨

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📜 Recent review details

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Review profile: CHILL
Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between d0e6e78 and 075315f.

📒 Files selected for processing (2)

• workflow/scripts/get-transcript-info.R (2 hunks)
• workflow/scripts/postprocess_go_enrichment.py (1 hunks)

🔇 Additional comments (3)

workflow/scripts/postprocess_go_enrichment.py (1)

19-20:

❓ Verification inconclusive

Verify the gene name extraction works for all Drosophila melanogaster gene formats

The change from fixed indexing to negative indexing addresses the issue with gene names containing colons (like "His4:CG33869"). However, this approach assumes a specific format where the gene identifier is always the second-to-last part after splitting on colons.

For gene names with multiple colons, this approach might not capture the complete gene name. Consider a more robust solution if you need to handle diverse gene name formats in the future.

---

🏁 Script executed:

#!/bin/bash
# Check for different gene:value patterns in the input data
echo "Checking for various gene:value patterns in GO enrichment data..."
grep -o "[^,]*:[^,]*" $(find workflow -name "*go_enrichment*" -type f | head -1) | sort | uniq -c | sort -nr | head -10

Length of output: 672

---

Action required: Verify gene name extraction comprehensively

The revised extraction using negative indices (i.e. gene = parts[-2]) now correctly handles gene names with a single colon (e.g., "His4:CG33869"). However, this solution still assumes that the gene identifier is always the second-to-last segment when splitting on colons. If a gene name contains multiple colons, the current logic might not capture the intended full identifier.

• Please validate the extraction logic against actual GO enrichment input data containing diverse Drosophila gene formats.
• If you encounter gene names with more than one colon, consider refining the parsing mechanism (or adding unit tests) to ensure the full gene identifier is reliably retrieved.

workflow/scripts/get-transcript-info.R (2)

93-93: Good defensive programming approach

Using the use_if_available function to conditionally include the "ensembl_transcript_id_version" attribute is an excellent approach. This makes the code more robust by ensuring it works correctly even when this attribute is not available for certain species like Drosophila melanogaster.

---

175-175: Proper handling of conditional column renaming

Using any_of() in the rename function ensures that the operation won't fail if the "ensembl_transcript_id_version" column doesn't exist. This is a good defensive programming practice that improves the robustness of the code.

✨ Finishing Touches

• 📝 Generate Docstrings

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[dlaehnemann]

Thanks for these generalizations. Good catches, and sorry for the inconvenience.