v1.0.1 Release

CITATION.cff

@@ -2,7 +2,7 @@ cff-version: 1.2.0
 message: "If you use ModDotPlot in your research, please cite the article below."
 type: software
 title: "ModDotPlot"
-version: "1.0.0"
+version: "1.0.1"
 authors:
   - family-names: "Sweeten"
     given-names: "Alexander P."

README.md

@@ -84,7 +84,7 @@ Finally, confirm that the installation completed correctly and that your version
  | |  | | (_) | (_| | | |__| | (_) | |_  | |    | | (_) | |_ 
  |_|  |_|\___/ \__,_| |_____/ \___/ \__| |_|    |_|\___/ \__|
 
- v1.0.0
+ v1.0.1
 
 usage: moddotplot [-h] [--quiet] [{static,interactive}] ...
 

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "ModDotPlot"
-version = "1.0.0"
+version = "1.0.1"
 requires-python = ">=3.10,<3.15"
 dependencies = [
   "pandas",

src/moddotplot/annotations.py

@@ -17,11 +17,30 @@
 ]
 
 
+def _ucsc_directive_rows(filepath):
+    """Return zero-based rows containing UCSC ``track`` or ``browser`` lines."""
+
+    rows = []
+    with open(filepath, "r", encoding="utf-8") as bed_file:
+        for line_number, line in enumerate(bed_file):
+            fields = line.lstrip().split(maxsplit=1)
+            if fields and fields[0] in {"track", "browser"}:
+                rows.append(line_number)
+    return rows
+
+
 def read_annotation_bed(filepath):
     """Read the BED3-BED9 subset used by ModDotPlot annotations."""
 
     try:
-        dataframe = pd.read_csv(filepath, sep="\t", comment="#", header=None, dtype=str)
+        dataframe = pd.read_csv(
+            filepath,
+            sep="\t",
+            comment="#",
+            header=None,
+            dtype=str,
+            skiprows=_ucsc_directive_rows(filepath),
+        )
     except pd.errors.EmptyDataError:
         return pd.DataFrame(columns=BED_COLUMNS[:3])
 

src/moddotplot/const.py

@@ -1,4 +1,4 @@
-VERSION = "1.0.0"
+VERSION = "1.0.1"
 DIRECTION_COLORS = {"Forward": "#2166AC", "Reverse": "#D01C8B"}
 COLS = [
     "#query_name",

src/moddotplot/moddotplot.py

@@ -650,7 +650,7 @@ def _apply_static_config(args, config):
     else:
         args.fasta = config.get("fasta")
         args.load = config.get("load")
-    args.bed = config.get("bed")
+    args.bed = config.get("bed", args.bed)
 
     # Distance matrix commands
     args.kmer = config.get("kmer", args.kmer)

tests/test_annotation_track.py

@@ -51,6 +51,24 @@ def test_read_annotation_bed_accepts_bed3_through_bed9(
     assert dataframe.loc[0, "end"] == 20
 
 
+def test_read_annotation_bed_ignores_ucsc_directives(tmp_path):
+    bed_path = tmp_path / "annotations.bed"
+    bed_path.write_text(
+        'track name="annotations" visibility=2 itemRgb="On"\n'
+        "browser position chr1:1-100\n"
+        "# comment\n"
+        "chr1\t10\t20\tfeature\t0\t+\t10\t20\t12,34,56\n"
+    )
+
+    dataframe = read_annotation_bed(bed_path)
+
+    assert len(dataframe) == 1
+    assert dataframe.loc[0, "chrom"] == "chr1"
+    assert dataframe.loc[0, "start"] == 10
+    assert dataframe.loc[0, "end"] == 20
+    assert dataframe.loc[0, "itemRgb"] == "12,34,56"
+
+
 @pytest.mark.parametrize(
     "record",
     [

tests/test_cli_runtime.py

@@ -490,6 +490,42 @@ def test_static_config_accepts_sequence_selection():
     assert args.sequence == ["chr1", "chr2"]
 
 
+def test_static_config_preserves_cli_bed_when_config_omits_bed():
+    args = cli.get_parser().parse_args(
+        [
+            "static",
+            "--config",
+            "plot.json",
+            "--fasta",
+            "sequence.fa",
+            "--bed",
+            "provided.bed",
+        ]
+    )
+
+    cli._apply_static_config(args, {"identity": 90})
+
+    assert args.bed == "provided.bed"
+
+
+def test_static_config_bed_overrides_cli_bed():
+    args = cli.get_parser().parse_args(
+        [
+            "static",
+            "--config",
+            "plot.json",
+            "--fasta",
+            "sequence.fa",
+            "--bed",
+            "provided.bed",
+        ]
+    )
+
+    cli._apply_static_config(args, {"bed": "configured.bed"})
+
+    assert args.bed == "configured.bed"
+
+
 def test_static_config_preserves_explicit_input_and_output_paths():
     args = cli.parse_args(
         [