From 18bc1c25d3e03db556d802e1df732c2f316c1747 Mon Sep 17 00:00:00 2001
From: Matt Stone <matt@fulcrumgenomics.com>
Date: Fri, 8 Mar 2024 12:55:27 -0500
Subject: [PATCH] feat: add bedrecord/interval converters

---
 pybedlite/bed_record.py           | 46 +++++++++++++++++++++++++++++++
 pybedlite/tests/test_pybedlite.py | 32 +++++++++++++++++++++
 2 files changed, 78 insertions(+)

diff --git a/pybedlite/bed_record.py b/pybedlite/bed_record.py
index 0ba692f..e4596ea 100644
--- a/pybedlite/bed_record.py
+++ b/pybedlite/bed_record.py
@@ -11,12 +11,16 @@
     - :class:`~pybedtools.bed_record.BedRecord` -- Lightweight class for storing information
         pertaining to a BED record.
 """
+
 import attr
 import enum
 from typing import Optional
 from typing import Tuple
 from typing import List
 from typing import ClassVar
+from typing import Type
+
+from pybedlite.overlap_detector import Interval
 
 
 """Maximum BED fields that can be present in a well formed BED file written to specification"""
@@ -188,3 +192,45 @@ def as_bed_line(self, number_of_output_fields: Optional[int] = None) -> str:
         )
         fields = self.bed_fields[:number_of_output_fields]
         return "\t".join(fields)
+
+    def to_interval(self) -> Interval:
+        """
+        Convert a `BedRecord` to an `Interval` instance.
+
+        Note that when the `BedRecord` does not have a specified strand, the `Interval`'s negative
+        attribute is set to False. This mimics the behavior of `OverlapDetector.from_bed()` when
+        reading a record that does not have a specified strand.
+
+        Returns:
+            An `Interval` corresponding to the same region specified in the record.
+        """
+        return Interval(
+            refname=self.chrom,
+            start=self.start,
+            end=self.end,
+            negative=self.strand is BedStrand.Negative,
+            name=self.name,
+        )
+
+    @classmethod
+    def from_interval(cls: Type["BedRecord"], interval: Interval) -> "BedRecord":
+        """
+        Construct a `BedRecord` instance from an `Interval` instance.
+
+        **Note that `Interval` cannot represent a `BedRecord` with a missing strand.**
+        Converting a record with no strand to `Interval` and then back to `BedRecord` will result in
+        a record with **positive strand**.
+
+        Args:
+            interval: The `Interval` instance to convert.
+
+        Returns:
+            A `BedRecord` corresponding to the same region specified in the interval.
+        """
+        return cls(
+            chrom=interval.refname,
+            start=interval.start,
+            end=interval.end,
+            strand=BedStrand.Negative if interval.negative else BedStrand.Positive,
+            name=interval.name,
+        )
diff --git a/pybedlite/tests/test_pybedlite.py b/pybedlite/tests/test_pybedlite.py
index e9d46f1..c15e26b 100644
--- a/pybedlite/tests/test_pybedlite.py
+++ b/pybedlite/tests/test_pybedlite.py
@@ -252,3 +252,35 @@ def test_preopened_bed_writing(
                 record_number=i,
                 num_fields=bed_field_number,
             )
+
+
+@pytest.mark.parametrize("record", bed_records())
+def test_conversion_to_interval(record: BedRecord) -> None:
+    """
+    Test that we can convert a BedRecord to an Interval.
+    """
+    interval = record.to_interval()
+
+    assert interval.refname == record.chrom
+    assert interval.start == record.start
+    assert interval.end == record.end
+    assert interval.negative is (record.strand is BedStrand.Negative)
+    assert interval.name == record.name
+
+
+@pytest.mark.parametrize("record", bed_records())
+def test_construction_from_interval(record: BedRecord) -> None:
+    """
+    Test that we can convert a BedRecord to an Interval and back.
+    """
+    new_record = BedRecord.from_interval(record.to_interval())
+
+    assert new_record == record.chrom
+    assert new_record.start == record.start
+    assert new_record.end == record.end
+    assert new_record.name == record.name
+
+    if record.strand is None:
+        assert new_record.strand is BedStrand.Positive
+    else:
+        assert new_record.strand is record.strand