major changes in mztab for large datasets #43
Conversation
make diann2mztab optional for large-scale datasets
WalkthroughThe pull request introduces two main changes: updating the module version number and adding a new command-line option to control mzTab conversion in the Changes
Sequence DiagramsequenceDiagram
participant User
participant diann2mztab Function
User->>diann2mztab Function: Call with enable_diann2mztab flag
alt Flag is True
diann2mztab Function->>mzTab: Convert to mzTab
else Flag is False
diann2mztab Function->>Other Formats: Convert to MSstats/Triqler
end
Poem
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Actionable comments posted: 1
🔭 Outside diff range comments (1)
quantmsutils/diann/diann2mztab.py (1)
Line range hint
1392-1394: Optimize protein coverage calculation for large datasetsThe protein coverage calculation could be optimized by using vectorized operations and reducing memory usage.
- for acc in acc_to_ids: - matches = fasta_df[fasta_df["id"].str.contains(acc)]["id"] + # Vectorize the operation using pandas str.extract + pattern = "|".join(map(re.escape, acc_to_ids.keys())) + matches = fasta_df["id"].str.extract(f"({pattern})", expand=False) + acc_to_fasta_ids = dict(zip(matches.dropna(), fasta_df.loc[matches.dropna().index, "id"]))Also applies to: 1401-1403
🧹 Nitpick comments (3)
quantmsutils/diann/diann2mztab.py (3)
48-48: Improve the click option descriptionThe click option could benefit from a more descriptive help message to explain its purpose and default value.
-@click.option("--enable_diann2mztab", "-e", is_flag=True) +@click.option("--enable_diann2mztab", "-e", is_flag=True, help="Enable conversion to mzTab format. Disabled by default to improve performance for large datasets.")
Line range hint
1024-1025: Consider extracting file finding logic into a separate functionThe file finding logic in
__find_infocould be moved to a utility function as it might be useful in other contexts.+def find_file_by_pattern(directory: Path, pattern: str) -> Path: + """Find a file matching the given pattern in the directory. + + Args: + directory: Directory to search in + pattern: File pattern to match + + Returns: + Path to the matched file + + Raises: + ValueError: If no file or multiple files are found + """ + files = list(Path(directory).rglob(pattern)) + if not files: + raise ValueError(f"Could not find file matching pattern {pattern} in {directory}") + if len(files) > 1: + raise ValueError(f"Found multiple files matching pattern {pattern} in {directory}: {files}") + return files[0] + def __find_info(directory, n): - files = list(Path(directory).rglob(f"{n}_ms_info.parquet")) - if not files: - raise ValueError(f"Could not find {n} info file in {directory}") - if len(files) > 1: - raise ValueError(f"Found multiple {n} info files in {directory}: {files}") - return files[0] + return find_file_by_pattern(directory, f"{n}_ms_info.parquet")Also applies to: 1031-1032
Line range hint
1024-1032: Add input validation for directory parameterThe
__find_infofunction should validate the input directory parameter.def __find_info(directory, n): + if not isinstance(directory, (str, Path)): + raise TypeError(f"directory must be a string or Path, got {type(directory)}") + directory = Path(directory) + if not directory.exists(): + raise ValueError(f"Directory {directory} does not exist") files = list(Path(directory).rglob(f"{n}_ms_info.parquet")) if not files: raise ValueError(f"Could not find {n} info file in {directory}") if len(files) > 1: raise ValueError(f"Found multiple {n} info files in {directory}: {files}") return files[0]
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📒 Files selected for processing (2)
quantmsutils/__init__.py(1 hunks)quantmsutils/diann/diann2mztab.py(3 hunks)
✅ Files skipped from review due to trivial changes (1)
- quantmsutils/init.py
🔇 Additional comments (1)
quantmsutils/diann/diann2mztab.py (1)
182-192: LGTM! Well-structured conditional block
The mzTab conversion is properly encapsulated within the conditional block, allowing users to skip this conversion for better performance with large datasets.
| diann_directory.convert_to_mztab( | ||
| report=report, | ||
| f_table=f_table, | ||
| charge=charge, | ||
| missed_cleavages=missed_cleavages, | ||
| dia_params=dia_params, | ||
| out=mztab_out, |
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🛠️ Refactor suggestion
Improve error handling in convert_to_mztab
The function should handle potential errors during file operations and data processing.
diann_directory.convert_to_mztab(
report=report,
f_table=f_table,
charge=charge,
missed_cleavages=missed_cleavages,
dia_params=dia_params,
out=mztab_out,
+ try:
+ diann_directory.convert_to_mztab(
+ report=report,
+ f_table=f_table,
+ charge=charge,
+ missed_cleavages=missed_cleavages,
+ dia_params=dia_params,
+ out=mztab_out,
+ )
+ except Exception as e:
+ logger.error(f"Failed to convert to mzTab format: {str(e)}")
+ raiseCommittable suggestion skipped: line range outside the PR's diff.
Summary by CodeRabbit
New Features
--enable_diann2mztabfor more flexible mzTab conversion control.Documentation
diann2mztabfunction to include the new parameter.