Allow the BED reader to split on tabs and spaces

fulcrumgenomics · Mar 26, 2024 · ca6c6fa · ca6c6fa
1 parent 674567c
commit ca6c6fa
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Showing 2 changed files with 9 additions and 3 deletions.
diff --git a/pybedlite/bed_source.py b/pybedlite/bed_source.py
@@ -125,7 +125,7 @@ def parse_rgb(x: str) -> Tuple[int, int, int]:
  continue
  if line.strip() == "":
  continue
- fields = line.strip().split("\t")
+ fields = line.strip().split()
  assert len(fields) >= 3, (
  "BED records must conform to specifications, which requires at least 3 input "
  + f"fields. On line {i} in {self._path} had only {len(fields)} fields"

diff --git a/pybedlite/tests/test_pybedlite.py b/pybedlite/tests/test_pybedlite.py
@@ -14,9 +14,15 @@
 # Test header, with a line with whitespace below it.
 
 # More header
+
+# BED record with tabs as a separator
 1 100 150 test_record1 100 + 100 100 0,0,0 1 50 0
-1 200 300 test_record2 100 - 210 290 0,0,0 1 100 0
-2 200 300 test_record3 . . . . . . . .
+
+# BED record with spaces as a separator
+1 200 300 test_record2 100 - 210 290 0,0,0 1 100 0
+
+# BED record with a mix of spaces and tabs as a separator
+2 200 300 test_record3 . . . . . . . .
 """