updated testcases and added testfile

.gitignore

@@ -1,6 +1,4 @@
-tests/test_data
-tests/test_data/*
-modification_cache/*
+mumble/package_data/modifications_cache.pkl
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

README.md

@@ -28,9 +28,87 @@ pip install mumble
 ```
 
 
-### Basic Usage
+## Usage
 
-Here's a quick example of how to use the PSM Modification Handler for single PSMs:
+### Command-Line Interface (CLI) Usage
+
+Mumble provides a command-line interface to modify PSMs based on mass shifts, as well as several parameters for customization. You can use the `mumble` command to interact with the tool.
+
+#### Basic Command Syntax
+
+To run the CLI, use the following command:
+
+```bash
+mumble [OPTIONS] INPUT_FILE
+```
+
+Where `INPUT_FILE` is the path to the input file containing the PSM data.
+
+#### Parameters:
+
+Here are the available options you can pass when running the command:
+
+- **`--psm-list`**: (required) Path to the input file containing the PSM data. Must be provided if not already set via arguments.
+- **`--modification-file`**: Path to a restriction list of modifications to use from Unimod. Defaults to `default_ptm_list.tsv` included with the package.
+- **`--psm-file-type`**: Type of the input file to read with PSM_utils (e.g., `mzid`, `tsv`). Default is "infer".
+- **`--aa-combinations`**: Number of amino acid combinations to add as modification. Requires a `fasta_file`. Default is `0`.
+- **`--fasta-file`**: Path to a fasta file (for use with `aa_combinations`).
+- **`--mass-error`**: Mass error for the mass shift, default is `0.02`.
+- **`--output-file`**: Path to the output file to write modified PSMs.
+- **`--filetype-write`**: Type of the output file to write with PSM_utils (e.g., `tsv`, `csv`). Default is `tsv`.
+- **`--include-decoy-psm`**: Flag to parse modifications for decoys in the modified PSM list.
+- **`--include-original-psm`**: Flag to keep the original PSMs in the modified PSM list.
+- **`--combination-length`**: Maximum number of modifications per combination. All lower numbers will be included as well. Default is `1`.
+- **`--exclude-mutations`**: If set, modifications with the classification 'AA substitution' will be excluded.
+- **`--config-file`**: Path to a config file for additional configuration parameters (e.g., custom modification sets, advanced settings).
+- **`--log-level`**: Set the logging level. Options: `DEBUG`, `INFO`, `WARNING`, `ERROR`, `CRITICAL`. Default is `INFO`.
+- **`--clear-cache`**: Remove the modification cache file and exit early.
+- **`--all-unimod-modifications`**: Use all available modifications from Unimod instead of a subset.
+
+#### Examples:
+
+1. **Modify a single PSM**:
+```bash
+mumble --psm-list "path/to/psm_file.mzid" --mass-error 0.02 --output-file "modified_psms.tsv"
+```
+
+2. **Modify a list of PSMs with custom configurations**:
+```bash
+mumble --psm-list "path/to/psm_file.mzid" --fasta-file "path/to/proteins.fasta" --aa-combinations 5 --config-file "path/to/config_file.toml"
+```
+
+3. **Clear the cache and exit**:
+```bash
+mumble --clear-cache
+```
+
+4. **Using a custom modification file**:
+```bash
+mumble --psm-list "path/to/psm_file.mzid" --modification-file "path/to/custom_ptm_list.tsv"
+```
+
+#### Config file usage
+
+You can also use a configuration file to specify options that will be loaded automatically when running the command. This allows you to store commonly used parameters without needing to pass them every time.
+
+Example configuration file (`config_file.json`):
+
+```json
+{"mass_error" : 0.05
+"aa_combinations" : 2
+"psm_file_type" : "mzid"
+"output_file" : "output.tsv"
+}
+```
+
+You can then specify the path to this file using the `--config-file` option:
+
+```bash
+mumble --config-file "path/to/config_file.toml"
+```
+
+### Python API 
+Here's a quick example of how to use the PSM Modification Handler through the python API for single PSMs:
 
 ```python
 >>> from mumble import PSMHandler
@@ -59,7 +137,7 @@ Here's a quick example of how to use the PSM Modification Handler for single PSM
 #     )
 # ]
 ```
-Here's a quick example of how to use the PSM Modification Handler for PSM lists:
+Here's a quick example of how to use the PSM Modification Handler through the python API for PSM lists:
 ```python
 >>> # Or load a PSM list (from a file or PSMList object)
 >>> psm_list = psm_handler.parse_psm_list("path/to/psm_file.mzid", psm_file_type="mzid")
@@ -71,6 +149,7 @@ Here's a quick example of how to use the PSM Modification Handler for PSM lists:
 >>> psm_handler.write_modified_psm_list(modified_psm_list, output_file="modified_psms.tsv", psm_file_type="tsv")
 ```
 For more information on PSM objects and PSM lists visit [psm_utils](https://github.com/compomics/psm_utils)
+
 ## Testing
 
 The project includes unit tests using `pytest` to ensure code reliability.

mumble/__init__.py

@@ -1,4 +1,4 @@
 __version__ = "0.2.0"
-__all__ = ["PSMHandler"]
+__all__ = ["PSMHandler", "remove_modification_cache"]
 
-from mumble.mumble import PSMHandler
+from mumble.mumble import PSMHandler, remove_modification_cache

mumble/__main__.py

@@ -1,10 +1,10 @@
 import click
 import logging
-
+import sys
+import importlib
 from rich.logging import RichHandler
 
-from mumble import PSMHandler
-
+from mumble import PSMHandler, remove_modification_cache
 
 # setup logging
 logging.basicConfig(
@@ -20,9 +20,11 @@
         "type": click.Path(exists=True),
         "help": "Path to the input file.",
     },
-    "unimod_modification_file": {
+    "modification_file": {
         "type": click.Path(exists=True),
         "help": "Restriction list of modifications to use from Unimod.",
+        "default": str(importlib.resources.files("mumble.package_data") / "default_ptm_list.tsv"),
+        "show_default": True,
     },
     "psm_file_type": {
         "type": click.STRING,
@@ -57,13 +59,13 @@
         "default": "tsv",
         "show_default": True,
     },
-    "generate_modified_decoys": {
+    "include_decoy_psm": {
         "is_flag": True,
         "help": "Parse modifications for decoys in modified PSMlist",
         "default": False,
         "show_default": True,
     },
-    "keep_original": {
+    "include_original_psm": {
         "is_flag": True,
         "help": "Keep the original PSMs in the modified PSMlist",
         "default": False,
@@ -86,15 +88,43 @@
         "help": "Path to a config file",
         "default": None,
     },
+    "log_level": {
+        "type": click.Choice(["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"]),
+        "default": "INFO",
+        "help": "Set the logging level",
+        "show_default": True,
+    },
+    "all_unimod_modifications": {
+        "is_flag": True,
+        "default": False,
+        "help": "Instead of using a subset of modifications from Unimod, use all available modifications.",
+        "show_default": True,
+    },
 }
 
 
 @click.command("cli", context_settings={"show_default": True})
-@click.argument("input_file", type=click.Path(exists=True), default=None)
-def main(**kwargs):
+@click.argument("input_file", type=click.Path(exists=True), default=None, required=False)
+@click.option(
+    "--clear-cache/--no-clear-cache",
+    is_flag=True,
+    default=False,
+    help="Remove the modification cache file and exit early.",
+)
+def main(clear_cache, **kwargs):
     """
     Finding the perfect match for your mass shift.
     """
+    # if the user just wants to clear the cache, do it and quit
+    if clear_cache:
+        remove_modification_cache()
+        logging.info("Exiting Mumble. You will find your match another time.")
+        sys.exit(0)
+
+    # Set the logging level based on the CLI option
+    log_level = kwargs.get("log_level", "INFO").upper()
+    logging.getLogger().setLevel(log_level)
+
     ctx = click.get_current_context()
 
     # Extract CLI-provided parameters