Switch to the compressed granges list (#71)

Author: jkanche

CHANGELOG.md

@@ -1,8 +1,9 @@
 # Changelog
 
-## Version 0.8.0
+## Version 0.8.0 - 0.8.1
 
 - Implement parsers for compressed list objects.
+- Switch `GenomicRangesList` to the `CompressedGenomicRangesList` implementation.
 
 ## Version 0.7.0 - 0.7.3
 

setup.cfg

@@ -66,11 +66,12 @@ optional =
     hdf5array
     scipy
     biocframe
-    genomicranges>=0.4.9
-    summarizedexperiment>=0.4.1
-    singlecellexperiment>=0.4.1
-    multiassayexperiment
-    compressed_lists>=0.3.0
+    genomicranges>=0.8.4
+    summarizedexperiment>=0.6.5
+    singlecellexperiment>=0.6.2
+    multiassayexperiment>=0.6.0
+    compressed_lists>=0.4.4
+    biocutils>=0.3.4
 
 # Add here test requirements (semicolon/line-separated)
 testing =

src/rds2py/read_granges.py

@@ -76,21 +76,22 @@ def read_genomic_ranges(robject: dict, **kwargs):
 
 
 def read_granges_list(robject: dict, **kwargs):
-    """Convert an R `GenomicRangesList` object to a Python :py:class:`~genomicranges.GenomicRangesList`.
+    """Convert an R `CompressedGenomicRangesList` object to a Python :py:class:`~genomicranges.grangeslist.CompressedGenomicRangesList`.
 
     Args:
         robject:
-            Dictionary containing parsed GenomicRangesList data.
+            Dictionary containing parsed CompressedGenomicRangesList data.
 
         **kwargs:
             Additional arguments.
 
     Returns:
-        A Python `GenomicRangesList` object containing containing multiple
+        A Python `CompressedGenomicRangesList` object containing containing multiple
         `GenomicRanges` objects.
     """
 
-    from genomicranges import GenomicRangesList
+    from compressed_lists import Partitioning
+    from genomicranges import CompressedGenomicRangesList
 
     _cls = get_class(robject)
 
@@ -106,11 +107,16 @@ def read_granges_list(robject: dict, **kwargs):
 
     _partitionends = _dispatcher(robject["attributes"]["partitioning"]["attributes"]["end"], **kwargs)
 
-    _grelist = []
+    _part_obj = Partitioning(ends=_partitionends, names=_groups)
 
-    current = 0
-    for _pend in _partitionends:
-        _grelist.append(_gre[current:_pend])
-        current = _pend
+    element_metadata = None
+    if "elementMetadata" in robject["attributes"]:
+        element_metadata = _dispatcher(robject["attributes"]["elementMetadata"], **kwargs)
 
-    return GenomicRangesList(ranges=_grelist, names=_groups)
+    metadata = None
+    if "metadata" in robject["attributes"]:
+        metadata = _dispatcher(robject["attributes"]["metadata"], **kwargs)
+
+    return CompressedGenomicRangesList(
+        unlist_data=_gre, partitioning=_part_obj, element_metadata=element_metadata, metadata=metadata
+    )

tests/test_granges.py

@@ -1,6 +1,6 @@
 from rds2py import read_rds
 
-from genomicranges import GenomicRanges, GenomicRangesList
+from genomicranges import GenomicRanges, CompressedGenomicRangesList
 import numpy as np
 
 __author__ = "jkanche"
@@ -32,5 +32,5 @@ def test_granges():
 def test_granges_list():
     gr = read_rds("tests/data/grangeslist.rds")
 
-    assert isinstance(gr, GenomicRangesList)
+    assert isinstance(gr, CompressedGenomicRangesList)
     assert len(gr) == 5