Fix/argument handling 20240807 (#7)

* version: -> 0.9.7

* fix: changed argument order in handle_args so that placement of positional arguments does not cause `argument not found` errors (s. #6)
* fix: changed default db format from bed to hmmer
* doc: removed misleading references to db format from readme
* doc: corrected argument types of `annotation_db`, `bwa_index` to positional

README.md

@@ -59,21 +59,18 @@ cayman \
   <input_options> \
   </path/to/db> \
   </path/to/bwa_index> \
-  --db_format hmmer \
   [--out_prefix <prefix>] \
   [--min_identity <float>] \
   [--min_seqlen <int>] \
   [--cpus_for_alignment <int>]
 ```
 
-`cayman`'s default input format is bed4. `--db_format hmmer` is required when using the csv-formatted hmmer annotations from [Zenodo](https://zenodo.org/records/10473258).
-
 ### Mandatory parameters
 
 * `<input_options>`
 
   1. Read files need to be in fastq format (best with `fastq` or `fq` file ending) and can be gzip compressed.
-  
+
   2. The `<input_options>` parameters depend on the library layout of your samples:
       * Paired-end data can be specified with `--reads1 </path/to/reads1> --reads2 </path/to/reads2>`. Each read will be counted as `0.5`.
       * Single-end data can be specified with `--singles </path/to/reads>`. Each read will be counted as `1`.

cayman/__init__.py

@@ -1,3 +1,3 @@
 """ module docstring """
-__version__ = "0.9.6"
+__version__ = "0.9.7"
 __toolname__ = "cayman"

cayman/handle_args.py

@@ -34,6 +34,7 @@ def handle_args(args):
         formatter_class=argparse.RawTextHelpFormatter,
         parents=(log_ap,),
     )
+
     ap.add_argument(
         "annotation_db",
         type=str,
@@ -44,10 +45,20 @@ def handle_args(args):
         ),
     )
 
+    ap.add_argument(
+        "bwa_index",
+        type=str,
+        help=textwrap.dedent(
+            """\
+            Path to the bwa reference index.
+            """
+        ),
+    )
+
     ap.add_argument(
         "--db_format",
         type=str,
-        default="bed",
+        default="hmmer",
         choices=("bed", "hmmer"),
         help="Format of the annotation database.",
     )
@@ -67,15 +78,6 @@ def handle_args(args):
     #     help="Separator-character for the annotation database file Default: '\\t'."
     # )
 
-    ap.add_argument(
-        "bwa_index",
-        type=str,
-        help=textwrap.dedent(
-            """\
-            Path to the bwa reference index.
-            """
-        ),
-    )
 
     ap.add_argument(
         "-1",