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📝 WalkthroughWalkthroughThe PR updates project metadata with additional keywords and revised URLs, modifies unified design format parsing to make Label and LabelType optional columns, and implements flexible label normalization via case-insensitive substring matching for SILAC and MTRAQ formats. The f_table construction now conditionally includes Label only when present and multi-valued. ChangesProject Metadata Update
Unified Design Format Parsing
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Actionable comments posted: 1
🤖 Prompt for all review comments with AI agents
Verify each finding against the current code and only fix it if needed.
Inline comments:
In `@quantmsutils/diann/diann2msstats.py`:
- Around line 185-199: The replacement is case-sensitive because
df["Label"].replace(...) uses original casing while detection uses labels_lower;
update the logic for both silac_dict and mtraq_dict to perform lookups against
labels_lower (which is already lowercased) using lowercase keys and then write
back mapped values while preserving non-matches (e.g., use
labels_lower.map(lowercased_dict).fillna(df["Label"]) or equivalent) so that
variables labels_lower, silac_dict/mtraq_dict, and df["Label"] are used for
case-insensitive replacement and original values are kept when there is no
match.
🪄 Autofix (Beta)
Fix all unresolved CodeRabbit comments on this PR:
- Push a commit to this branch (recommended)
- Create a new PR with the fixes
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Run ID: da498a12-8aac-46b4-ab96-cc891245f736
📒 Files selected for processing (3)
pyproject.tomlquantmsutils/diann/diann2msstats.pytests/test_commands.py
| if labels_lower.str.contains("silac").any(): | ||
| silac_dict = { | ||
| "SILAC light": "L", | ||
| "SILAC medium": "M", | ||
| "SILAC heavy": "H", | ||
| } | ||
| df["Label"] = df["Label"].replace(silac_dict) | ||
|
|
||
| if labels_lower.str.contains("mtraq").any(): | ||
| mtraq_dict = { | ||
| "MTRAQ0": "0", | ||
| "MTRAQ4": "4", | ||
| "MTRAQ8": "8", | ||
| } | ||
| df["Label"] = df["Label"].replace(mtraq_dict) |
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#!/bin/bash
# Search for Label column values in test design files to confirm expected casing
rg -n --type tsv "mTRAQ\|MTRAQ\|SILAC\|silac" --glob "*.tsv"
# Also check any usage in Python source that constructs or references these label strings
rg -n "mTRAQ\|MTRAQ\|SILAC light\|silac" --type pyRepository: bigbio/quantms-utils
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echo "=== PXD026600_diann_design.tsv ==="
head -5 ./tests/test_data/diann2msstats/PXD026600_diann_design.tsv | cat -v
echo -e "\n=== PXD026600.sdrf_openms_design.tsv ==="
head -5 ./tests/test_data/diann2msstats/PXD026600.sdrf_openms_design.tsv | cat -v
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Case-sensitive replacement will silently no-op for mTRAQ labels once multiplex support is enabled.
The multiplexing code (lines 185-199) currently appears unreachable: dianncfg.py (line 106) marks multiplex support as a TODO and explicitly rejects multiplexed experiments (mTRAQ, TMT, iTRAQ, Dimethyl modifications) with an error message. However, the bug is real and will manifest once this feature is implemented.
When enabled, labels_lower holds the lowercased values (for detection), but both df["Label"].replace(silac_dict) and df["Label"].replace(mtraq_dict) match against the original casing of df["Label"].
- SILAC: keys
"SILAC light"/"SILAC medium"/"SILAC heavy"match the SDRF convention exactly — works only when the upstream file uses that exact casing. - mTRAQ: keys
"MTRAQ0"/"MTRAQ4"/"MTRAQ8"are all-caps, but the standard notation used throughout the codebase (e.g.,dianncfg.py) is"mTRAQ"(lowercasem). Once multiplex support is added and design files contain"mTRAQ0", the replacement will silently no-op — detection triggers, replacement fails to match,df["Label"]retains"mTRAQ0", and the downstream merge against DIA-NN'sChannelvalues ("0"/"4"/"8") produces all-NaN rows that are dropped, yielding an empty MSstats output.
Fix: run the replacement on labels_lower (already lowercase) using lowercase dict keys to ensure case-insensitive matching.
🐛 Proposed fix
labels_lower = df["Label"].astype(str).str.lower()
if labels_lower.str.contains("silac").any():
silac_dict = {
- "SILAC light": "L",
- "SILAC medium": "M",
- "SILAC heavy": "H",
+ "silac light": "L",
+ "silac medium": "M",
+ "silac heavy": "H",
}
- df["Label"] = df["Label"].replace(silac_dict)
+ df["Label"] = labels_lower.map(silac_dict).fillna(df["Label"])
if labels_lower.str.contains("mtraq").any():
mtraq_dict = {
- "MTRAQ0": "0",
- "MTRAQ4": "4",
- "MTRAQ8": "8",
+ "mtraq0": "0",
+ "mtraq4": "4",
+ "mtraq8": "8",
}
- df["Label"] = df["Label"].replace(mtraq_dict)
+ df["Label"] = labels_lower.map(mtraq_dict).fillna(df["Label"])Using labels_lower.map(dict).fillna(df["Label"]) performs case-insensitive lookup while preserving the original value for labels that do not match any key.
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.
In `@quantmsutils/diann/diann2msstats.py` around lines 185 - 199, The replacement
is case-sensitive because df["Label"].replace(...) uses original casing while
detection uses labels_lower; update the logic for both silac_dict and mtraq_dict
to perform lookups against labels_lower (which is already lowercased) using
lowercase keys and then write back mapped values while preserving non-matches
(e.g., use labels_lower.map(lowercased_dict).fillna(df["Label"]) or equivalent)
so that variables labels_lower, silac_dict/mtraq_dict, and df["Label"] are used
for case-insensitive replacement and original values are kept when there is no
match.
2 participants
Summary by CodeRabbit
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Documentation & Project Metadata
Bug Fixes