Merge pull request #118 from SamBryce-Smith/to-gtf-gff3-phase-frame-fix

fix (to_gtf, to_gff3): stop 'phase' (gtf) and 'frame' (to_gff3) being erroneously added to attributes field

Author: marco-mariotti

CHANGELOG.txt

@@ -1,3 +1,6 @@
+# 1.1.8 (30.12.25)
+- to_gtf and to_gff3: fix bug where 'phase' (gtf) and 'frame' (gff3) are erroneously added to attributes field
+
 # 1.1.7 (16.12.25)
 - window_ranges: fix sort order issue in  when using by (#98 and #105)
 - window_ranges: added argument add_window_id, updated documentation

README.md

@@ -22,6 +22,9 @@ available at https://pyranges1.readthedocs.io/
 ## Recent Changelog
 
 ```
+# 1.1.8 (30.12.25)
+- to_gtf and to_gff3: fix bug where 'phase' (gtf) and 'frame' (gff3) are erroneously added to attributes field
+
 # v1.1.7 (16.12.25)
 - window_ranges: fix sort order issue in  when using by (#98 and #105)
 - window_ranges: added argument add_window_id, updated documentation

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pyranges1"
-version = "1.1.7"
+version = "1.1.8"
 description = "GenomicRanges for Python."
 requires-python = ">=3.12.0"
 readme = "README.md"

pyranges/core/out.py

@@ -240,12 +240,12 @@ def _pyranges_to_gtf_like(
     if out_format == "gtf":
         all_columns = _ordered_gtf_columns[:-1]
         # first: gff column to pyranges column
-        rename_columns = GFF3_COLUMNS_TO_PYRANGES.copy()
+        rename_columns = GTF_COLUMNS_TO_PYRANGES.copy()
         attribute_formatter = gtf_formatter
     elif out_format == "gff3":
         all_columns = _ordered_gff3_columns[:-1]
         # first: gff column to pyranges column
-        rename_columns = GTF_COLUMNS_TO_PYRANGES.copy()
+        rename_columns = GFF3_COLUMNS_TO_PYRANGES.copy()
         attribute_formatter = gff3_formatter
     else:
         msg = f"Invalid output format: {out_format}. Must be one of 'gtf' or 'gff3'."