Merge pull request #130 from efriman/master

Added ignore_group_order argument

.readthedocs.yml

@@ -1,8 +1,29 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+    # You can also specify other tool versions:
+    # nodejs: "19"
+    # rust: "1.64"
+    # golang: "1.19"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
-   configuration: docs/conf.py
+   configuration: docs/source/conf.py
+
+# If using Sphinx, optionally build your docs in additional formats such as PDF
+# formats:
+#    - pdf
 
+# Optionally declare the Python requirements required to build your docs
 python:
-   setup_py_install: false
    install:
    - requirements: docs/requirements.txt

coolpuppy/CLI.py

@@ -185,6 +185,16 @@ def parse_args_coolpuppy():
                 '1' and '2', i.e. if features have a column 'group', specify 'group1 group2'.,
                 e.g. --groupby chrom1 chrom2""",
     )
+    parser.add_argument(
+        "--ignore_group_order",
+        nargs="*",
+        required=False,
+        help="""When using groupby, reorder so that e.g. group1-group2 and group2-group1 will be 
+                combined into one and flipped to the correct orientation. If using multiple paired
+                groupings (e.g. group1-group2 and category1-category2), need to specify which
+                grouping should be prioritised, e.g. "group" or "group1 group2". For flip_negative_strand,
+                +- and -+ strands will be combined""",
+    )
     parser.add_argument(
         "--flip_negative_strand",
         "--flip-negative-strand",
@@ -366,6 +376,19 @@ def _excepthook(exc_type, value, tb):
     else:
         args.by_distance = False
         distance_edges = False
+
+    if args.ignore_group_order is not None:
+        if len(args.ignore_group_order) > 0:
+            try:
+                args.ignore_group_order = [str(item) for item in args.ignore_group_order]
+            except:
+                raise ValueError(
+                    "ignore_group_order must be one or two strings separated with spaces."
+                )
+        else:
+            args.ignore_group_order = True
+    else:
+        args.ignore_group_order = False
 
     logger = logging.getLogger("coolpuppy")
     logger.setLevel(getattr(logging, args.logLevel))
@@ -528,6 +551,7 @@ def _excepthook(exc_type, value, tb):
         by_strand=args.by_strand,
         by_distance=distance_edges,
         groupby=[] if args.groupby is None else args.groupby,
+        ignore_group_order=args.ignore_group_order,
         flip_negative_strand=args.flip_negative_strand,
         local=args.local,
         coverage_norm=args.coverage_norm,