update

Author: pgarrett-scripps

.github/workflows/pylint.yml

@@ -7,6 +7,10 @@ All notable changes to this project will be documented in this file.
 - mgf file
 - cli
 - more args
+- readme
+- updated ms2 args
+- rm linting action
+- formatted with black
 
 ## [0.1.3]
 ### Added

CHANGLOG.md

@@ -1,3 +1,74 @@
 # tdfextractor
 
-a python package to extract ms files from Bruker's raw files
+A Python package to extract MS/MS spectra from Bruker TimsTOF .D folders and convert them to standard formats (MS2 and MGF).
+
+## Installation
+
+```bash
+pip install tdfextractor
+```
+
+## Usage
+
+tdfextractor provides two command-line tools for extracting spectra:
+
+### MS2 Extraction
+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
+```
+
+### MGF Extraction  
+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
+```
+
+## 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 |
+| `--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 |
+| `--top-n-spectra` | int | None | Keep only top N most intense peaks per spectrum |
+| `--min-intensity` | float | 0.0 | Minimum intensity threshold for peaks |
+| `--min-charge` | int | None | Minimum charge state filter |
+| `--max-charge` | int | None | Maximum charge state filter |
+| `--min-mz` | float | None | Minimum m/z filter |
+| `--max-mz` | float | None | Maximum m/z filter |
+| `--min-rt` | float | None | Minimum retention time filter (seconds) |
+| `--max-rt` | float | None | Maximum retention time filter (seconds) |
+| `--min-ccs` | float | None | Minimum CCS filter |
+| `--max-ccs` | float | None | Maximum CCS filter |
+| `-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 |
+| `--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 |
+| `--top-n-spectra` | int | None | Keep only top N most intense peaks per spectrum |
+| `--min-intensity` | float | 0.0 | Minimum intensity threshold for peaks |
+| `--min-charge` | int | None | Minimum charge state filter |
+| `--max-charge` | int | None | Maximum charge state filter |
+| `--min-mz` | float | None | Minimum m/z filter |
+| `--max-mz` | float | None | Maximum m/z filter |
+| `--min-rt` | float | None | Minimum retention time filter (seconds) |
+| `--max-rt` | float | None | Maximum retention time filter (seconds) |
+| `--min-ccs` | float | None | Minimum CCS filter |
+| `--max-ccs` | float | None | Maximum CCS filter |
+| `-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 |

README.md

@@ -25,17 +25,11 @@ license = {file = "LICENSE"}
 
 [project.scripts]
 mgf-extractor = "tdfextractor.mgf_exctractor:main"
+ms2-extractor = "tdfextractor.ms2_extractor:main"
 
 
 [tool.setuptools]
 package-dir = {"" = "src"}
 
 [tool.setuptools.dynamic]
-version = {attr = "tdfextractor.__version__"}
-
-
-[tool.pylint]
-max-line-length = 120
-fail-under = 9.0
-good-names = ["mz" ,"td", "ms", "tdf", "tdfpy", "tdfextra", "i"]
-disable = ["too-many-arguments", "too-many-locals", "too-many-statements"]
+version = {attr = "tdfextractor.__version__"}