Merge pull request #129 from compomics/feature/document-config-extens…

…ions

Document supported and allowed extensions for config file

README.md

@@ -114,7 +114,7 @@ MS²PIP predictions can be compared to spectra in an
 ### Command line interface
 ```
 usage: ms2pip [-h] -c CONFIG_FILE [-s MGF_FILE] [-w FEATURE_VECTOR_OUTPUT]
-              [-r] [-x] [-t] [-n NUM_CPU]
+              [-r] [-x] [-m] [-t] [-n NUM_CPU] [--sqldb-uri SQLDB_URI]
               <PEPREC file>
 
 positional arguments:
@@ -131,9 +131,14 @@ optional arguments:
   -r, --retention-time  add retention time predictions (requires DeepLC python
                         package)
   -x, --correlations    calculate correlations (if MGF is given)
+  -m, --match-spectra   match peptides to spectra based on predicted spectra
+                        (if MGF is given)
   -t, --tableau         create Tableau Reader file
   -n NUM_CPU, --num-cpu NUM_CPU
                         number of CPUs to use (default: all available)
+  --sqldb-uri SQLDB_URI
+                        use sql database of observed spectra instead of MGF
+                        files
 ```
 
 ### Input files

ms2pip/__main__.py

@@ -39,7 +39,7 @@ def argument_parser():
         action="store",
         required=True,
         dest="config_file",
-        help="config file",
+        help="Configuration file: text-based (extensions `.txt`, `.config`, or `.ms2pip`) or TOML (extension `.toml`).",
     )
     parser.add_argument(
         "-s", "--spectrum-file",

ms2pip/config_parser.py

@@ -105,10 +105,14 @@ def load(self, filepath=None, config_format=None):
 
         if config_format == "toml":
             self._load_toml()
-        elif config_format in ("txt", "config"):
+        elif config_format in ("txt", "config", "ms2pip"):
             self._load_ms2pip_txt()
         else:
-            raise UnsupportedConfigFormatError(config_format)
+            raise UnsupportedConfigFormatError(
+                "Configuration file should have extension `txt`, `config`, or "
+                "`ms2pip` (text-based format) or `toml` (TOML-based format), not "
+                f"`{config_format}`",
+            )
 
     def write(self, filepath=None, config_format="toml"):
         """