Merge pull request #129 from epifluidlab/patch-missing-arg

Patch missing arg

CHANGELOG.md

@@ -7,6 +7,12 @@ The format is based on
 and this project adheres to
 [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.10.1] - 2024-12-18
+
+### Fixed
+- Added missing `-n` arg to `end-motifs`.
+- Fixed incorrect `ValueError` regarding the `negative_strand` arg.
+
 ## [0.10.0] - 2024-12-18
 
 ### Changed

src/finaletoolkit/cli/main_cli.py

@@ -670,6 +670,13 @@ def main_cli_parser():
         dest="both_strands",
         help="Set flag to only consider one strand for end-motifs."
     )
+    cli_motifs.add_argument(
+        '-n',
+        '--negative-strand',
+        action="store_true",
+        help="Set flag in conjunction with -B to only consider 5' end motifs "
+        "on the negative strand."
+    )
     cli_motifs.add_argument(
         '-o',
         '--output-file',

src/finaletoolkit/frag/_end_motifs.py

@@ -571,9 +571,9 @@ def region_end_motifs(
     if verbose:
         start_time = time()
 
-    if not both_strands and negative_strand:
+    if both_strands and negative_strand:
         raise ValueError(
-            'Cannot have both both_strands=False and negative_strand=True.')
+            'Cannot have both both_strands and negative_strand.')
 
     # iterable of fragments
     frag_ends = frag_generator(

src/finaletoolkit/version.py

@@ -2,4 +2,4 @@
 Single-source module for the package version number.
 """
 
-__version__ = "0.10.0"
+__version__ = "0.10.1"