readme

Author: pgarrett-scripps

README.md

@@ -18,6 +18,7 @@ Extract MS2 format files (compatible with MS-GF+, Comet, etc.):
 ```bash
 ms2-extractor /path/to/sample.d
 ms2-extractor /path/to/sample.d --output custom_output.ms2 --min-intensity 100 --min-charge 2
+ms2-extractor /path/to/directory_with_multiple_d_folders --output /path/to/output_directory
 ```
 
 ### MGF Extraction  
@@ -26,16 +27,34 @@ Extract MGF format files (compatible with Mascot, MaxQuant, etc.):
 ```bash
 mgf-extractor /path/to/sample.d
 mgf-extractor /path/to/sample.d --casanovo  # Optimized for Casanovo de novo sequencing
+mgf-extractor /path/to/directory_with_multiple_d_folders --output /path/to/output_directory
 ```
 
+## Output Options
+
+Both extractors support flexible output options:
+
+1. **No output specified**: Files are created within each .D folder with auto-generated names
+2. **Specific file path**: Use `-o filename.ms2` or `-o filename.mgf` for single .D folder processing
+3. **Output directory**: Use `-o /path/to/output_dir` for batch processing multiple .D folders
+4. **Overwrite protection**: Use `--overwrite` to replace existing output files
+
+### Batch Processing
+
+When processing multiple .D folders, the extractors will:
+- Automatically find all .D folders in the specified directory
+- Create output files with names matching the .D folder names
+- Skip existing files unless `--overwrite` is specified
+- Create the output directory if it doesn't exist
+
 ## Command Line Arguments
 
 ### MS2 Extractor Arguments
 
 | Argument | Type | Default | Description |
 |----------|------|---------|-------------|
-| `analysis_dir` | str | - | Path to the .D analysis directory |
-| `-o, --output` | str | `<analysis_dir_name>.ms2` | Output MS2 file path |
+| `analysis_dir` | str | - | Path to the .D analysis directory or directory containing .D folders |
+| `-o, --output` | str | `<analysis_dir_name>.ms2` | Output MS2 file path or directory |
 | `--remove-precursor` | flag | False | Remove precursor peaks from MS/MS spectra |
 | `--precursor-peak-width` | float | 2.0 | Width around precursor m/z to remove (Da) |
 | `--batch-size` | int | 100 | Batch size for processing spectra |
@@ -49,14 +68,15 @@ mgf-extractor /path/to/sample.d --casanovo  # Optimized for Casanovo de novo seq
 | `--max-rt` | float | None | Maximum retention time filter (seconds) |
 | `--min-ccs` | float | None | Minimum CCS filter |
 | `--max-ccs` | float | None | Maximum CCS filter |
+| `--overwrite` | flag | False | Overwrite existing output files |
 | `-v, --verbose` | flag | False | Enable verbose logging |
 
 ### MGF Extractor Arguments
 
 | Argument | Type | Default | Description |
 |----------|------|---------|-------------|
-| `analysis_dir` | str | - | Path to the .D analysis directory |
-| `-o, --output` | str | `<analysis_dir_name>.mgf` | Output MGF file path |
+| `analysis_dir` | str | - | Path to the .D analysis directory or directory containing .D folders |
+| `-o, --output` | str | `<analysis_dir_name>.mgf` | Output MGF file path or directory |
 | `--remove-precursor` | flag | False | Remove precursor peaks from MS/MS spectra |
 | `--precursor-peak-width` | float | 2.0 | Width around precursor m/z to remove (Da) |
 | `--batch-size` | int | 100 | Batch size for processing spectra |
@@ -70,5 +90,25 @@ mgf-extractor /path/to/sample.d --casanovo  # Optimized for Casanovo de novo seq
 | `--max-rt` | float | None | Maximum retention time filter (seconds) |
 | `--min-ccs` | float | None | Minimum CCS filter |
 | `--max-ccs` | float | None | Maximum CCS filter |
+| `--overwrite` | flag | False | Overwrite existing output files |
 | `-v, --verbose` | flag | False | Enable verbose logging |
 | `--casanovo` | flag | False | Preset for Casanovo: enables precursor removal, top-150 peaks, min intensity 0.01, m/z 50-2500 |
+
+## Features
+
+- **Multiple format support**: Export to MS2 and MGF formats
+- **Flexible output options**: Single files, batch processing, custom directories
+- **Flexible filtering**: Filter by charge state, m/z range, retention time, CCS, and intensity
+- **Batch processing**: Process multiple .D folders at once
+- **Precursor removal**: Option to remove precursor peaks from spectra
+- **Peak selection**: Keep only the most intense peaks per spectrum
+- **DDA and PRM support**: Works with both Data-Dependent Acquisition and Parallel Reaction Monitoring data
+- **Overwrite protection**: Prevents accidental file overwrites unless explicitly requested
+
+## Requirements
+
+- Python ≥ 3.8
+- tdfpy ≥ 0.1.7
+- serenipy ≥ 0.2.6
+- tqdm
+- pandas

src/tdfextractor/ms2_extractor.py

@@ -472,7 +472,7 @@ def main():
 
     parser.add_argument(
         "--overwrite",
-        action="store_true",
+        action="store_true", 
         help="Overwrite existing output file if it exists",
     )