chore: suit review from @nh13

fgpyo/fastx/__init__.py

@@ -1,6 +1,6 @@
 """
-Examples of Zipping FASTX Files
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Zipping FASTX Files
+~~~~~~~~~~~~~~~~~~~
 
 Zipping a set of FASTA/FASTQ files into a single stream of data is a common task in bioinformatics
 and can be achieved with the :class:`~fgpyo.fastx.FastxZipped` context manager. The context manager
@@ -59,23 +59,25 @@ def __enter__(self) -> "FastxZipped":
         self._fastx = tuple(FastxFile(str(path), persist=self._persist) for path in self._paths)
         return self
 
-    def _next_record_safe(self, fastx: FastxFile) -> Optional[FastxRecord]:
-        """Return the next record from a FASTX file or :py:obj:`None` if there are none left."""
-        try:
-            return next(fastx)
-        except StopIteration:
-            return None
+    @staticmethod
+    def _name_minus_ordinal(name: str) -> str:
+        """Return the name of the FASTX record minus its ordinal suffix (e.g. "/1" or "/2")."""
+        return name[:len(name) - 2] if len(name) >= 2 and name[-2] == "/" else name
 
     def __next__(self) -> Tuple[FastxRecord, ...]:
         """Return the next set of FASTX records from the zipped FASTX files."""
-        records = tuple(self._next_record_safe(handle) for handle in self._fastx)
+        records = tuple(next(handle, None) for handle in self._fastx)
         if all(record is None for record in records):
             raise StopIteration
         elif any(record is None for record in records):
-            raise ValueError("One or more of the FASTX files is truncated!")
+            sequence_name: str = [record.name for record in records if record is not None][0]
+            raise ValueError(
+                f"One or more of the FASTX files is truncated for sequence {sequence_name}:\n\t"
+                + "\n\t".join(str(self._paths[i]) for i, record in enumerate(records) if record is None)
+            )
         else:
             records = cast(Tuple[FastxRecord, ...], records)
-            record_names = {record.name for record in records}
+            record_names: set[str] = {self._name_minus_ordinal(record.name) for record in records}
             if len(record_names) != 1:
                 raise ValueError(f"FASTX record names do not all match: {record_names}")
             return records

fgpyo/fastx/tests/test_fastx_zipped.py

@@ -106,7 +106,7 @@ def tests_fastx_zipped_raises_exception_on_truncated_fastx(tmp_path: Path) -> No
         assert record1.sequence == "AAAA"
         assert record2.name == "seq1"
         assert record2.sequence == "CCCC"
-        with pytest.raises(ValueError, match=r"One or more of the FASTX files is truncated!"):
+        with pytest.raises(ValueError, match=r"One or more of the FASTX files is truncated.*"):
             next(handle)
 
     assert all(fastx.closed for fastx in context_manager._fastx)
@@ -118,7 +118,7 @@ def tests_fastx_zipped_raises_exception_on_truncated_fastx(tmp_path: Path) -> No
         assert record1.sequence == "CCCC"
         assert record2.name == "seq1"
         assert record2.sequence == "AAAA"
-        with pytest.raises(ValueError, match=r"One or more of the FASTX files is truncated!"):
+        with pytest.raises(ValueError, match=r"One or more of the FASTX files is truncated.*"):
             next(handle)
 
     assert all(fastx.closed for fastx in context_manager._fastx)
@@ -164,3 +164,34 @@ def tests_fastx_zipped_raises_exception_on_mismatched_sequence_names(tmp_path: P
             next(handle)
 
     assert all(fastx.closed for fastx in context_manager._fastx)
+
+
+def tests_fastx_zipped_handles_sequence_names_with_suffixes(tmp_path: Path) -> None:
+    """Test that :class:`FastxZipped` does not use sequence name suffixes in equality tests."""
+    input = tmp_path / "input"
+    input.mkdir()
+    fasta1 = input / "input1.fasta"
+    fasta2 = input / "input2.fasta"
+    fasta1.write_text(">seq1/1\nAAAA\n")
+    fasta2.write_text(">seq1/2\nCCCC\n")
+
+    context_manager = FastxZipped(fasta1, fasta2)
+    with context_manager as handle:
+        (record1, record2) = next(handle)
+        assert record1.name == "seq1/1"
+        assert record1.sequence == "AAAA"
+        assert record2.name == "seq1/2"
+        assert record2.sequence == "CCCC"
+
+    assert all(fastx.closed for fastx in context_manager._fastx)
+
+def tests_fastx_zipped__name_minus_ordinal_works_with_r1_and_r2_ordinals() -> None:
+    assert FastxZipped._name_minus_ordinal("seq1") == "seq1"
+    assert FastxZipped._name_minus_ordinal("seq1/1") == "seq1"
+    assert FastxZipped._name_minus_ordinal("seq1/2") == "seq1"
+    assert FastxZipped._name_minus_ordinal("1") == "1"
+    assert FastxZipped._name_minus_ordinal("1/1") == "1"
+    assert FastxZipped._name_minus_ordinal("1/2") == "1"
+    assert FastxZipped._name_minus_ordinal("") == ""
+    assert FastxZipped._name_minus_ordinal("/1") == ""
+    assert FastxZipped._name_minus_ordinal("/2") == ""