From 30d240c76fbe3d4dccecd09232d4597bdd849ee1 Mon Sep 17 00:00:00 2001
From: Jayaram Kancherla <jayaram.kancherla@gmail.com>
Date: Mon, 20 May 2024 15:08:28 -0700
Subject: [PATCH] Use `alt_read_object` and `alt_save_object` functions (#3)

Incase the user had custom readers and writers.
---
 src/dolomite_ranges/read_genomic_ranges.py      |  8 +++-----
 src/dolomite_ranges/read_genomic_ranges_list.py | 10 +++-------
 src/dolomite_ranges/save_genomic_ranges.py      |  6 ++++--
 src/dolomite_ranges/save_genomic_ranges_list.py |  8 +++++---
 4 files changed, 15 insertions(+), 17 deletions(-)

diff --git a/src/dolomite_ranges/read_genomic_ranges.py b/src/dolomite_ranges/read_genomic_ranges.py
index c1dc20d..c8587c7 100644
--- a/src/dolomite_ranges/read_genomic_ranges.py
+++ b/src/dolomite_ranges/read_genomic_ranges.py
@@ -7,8 +7,6 @@
 from genomicranges import GenomicRanges
 from iranges import IRanges
 
-from .read_sequence_information import read_sequence_information
-
 read_object_registry["genomic_ranges"] = "dolomite_ranges.read_genomic_ranges"
 
 
@@ -34,7 +32,7 @@ def read_genomic_ranges(path: str, metadata: Optional[dict], **kwargs) -> Genomi
         A :py:class:`~genomicranges.GenomicRanges.GenomicRanges` object.
     """
     _seqinfo_path = os.path.join(path, "sequence_information")
-    seqinfo = read_sequence_information(path=_seqinfo_path, metadata=None)
+    seqinfo = dl.alt_read_object(path=_seqinfo_path, **kwargs)
 
     with h5py.File(os.path.join(path, "ranges.h5"), "r") as handle:
         ghandle = handle["genomic_ranges"]
@@ -64,12 +62,12 @@ def read_genomic_ranges(path: str, metadata: Optional[dict], **kwargs) -> Genomi
 
     _range_annotation_path = os.path.join(path, "range_annotations")
     if os.path.exists(_range_annotation_path):
-        _mcols = dl.read_object(_range_annotation_path)
+        _mcols = dl.alt_read_object(_range_annotation_path, **kwargs)
         gr = gr.set_mcols(_mcols)
 
     _meta_path = os.path.join(path, "other_annotations")
     if os.path.exists(_meta_path):
-        _meta = dl.read_object(_meta_path)
+        _meta = dl.alt_read_object(_meta_path, **kwargs)
         gr = gr.set_metadata(_meta.as_dict())
 
     return gr
diff --git a/src/dolomite_ranges/read_genomic_ranges_list.py b/src/dolomite_ranges/read_genomic_ranges_list.py
index c547098..017b264 100644
--- a/src/dolomite_ranges/read_genomic_ranges_list.py
+++ b/src/dolomite_ranges/read_genomic_ranges_list.py
@@ -6,8 +6,6 @@
 from dolomite_base.read_object import read_object_registry
 from genomicranges import GenomicRangesList
 
-from .read_genomic_ranges import read_genomic_ranges
-
 read_object_registry["genomic_ranges_list"] = "dolomite_ranges.read_genomic_ranges_list"
 
 
@@ -48,9 +46,7 @@ def read_genomic_ranges_list(
                 ghandle["names"], expected_type=str, report_1darray=True
             )
 
-    _all_granges = read_genomic_ranges(
-        path=os.path.join(path, "concatenated"), metadata=None
-    )
+    _all_granges = dl.alt_read_object(path=os.path.join(path, "concatenated"), **kwargs)
 
     counter = 0
     _split_granges = []
@@ -66,12 +62,12 @@ def read_genomic_ranges_list(
 
     _elem_annotation_path = os.path.join(path, "element_annotations")
     if os.path.exists(_elem_annotation_path):
-        _mcols = dl.read_object(_elem_annotation_path)
+        _mcols = dl.alt_read_object(_elem_annotation_path, **kwargs)
         grl = grl.set_mcols(_mcols)
 
     _meta_path = os.path.join(path, "other_annotations")
     if os.path.exists(_meta_path):
-        _meta = dl.read_object(_meta_path)
+        _meta = dl.alt_read_object(_meta_path, **kwargs)
         grl = grl.set_metadata(_meta.as_dict())
 
     return grl
diff --git a/src/dolomite_ranges/save_genomic_ranges.py b/src/dolomite_ranges/save_genomic_ranges.py
index 8a0a5b0..17ed725 100644
--- a/src/dolomite_ranges/save_genomic_ranges.py
+++ b/src/dolomite_ranges/save_genomic_ranges.py
@@ -71,7 +71,7 @@ def save_genomic_ranges(
 
     _range_annotation = x.get_mcols()
     if _range_annotation is not None and _range_annotation.shape[1] > 0:
-        dl.save_object(
+        dl.alt_save_object(
             _range_annotation,
             path=os.path.join(path, "range_annotations"),
             **data_frame_args
@@ -79,6 +79,8 @@ def save_genomic_ranges(
 
     _meta = x.get_metadata()
     if _meta is not None and len(_meta) > 0:
-        dl.save_object(_meta, path=os.path.join(path, "other_annotations"))
+        dl.alt_save_object(
+            _meta, path=os.path.join(path, "other_annotations"), **kwargs
+        )
 
     return
diff --git a/src/dolomite_ranges/save_genomic_ranges_list.py b/src/dolomite_ranges/save_genomic_ranges_list.py
index 3a13d88..720ed67 100644
--- a/src/dolomite_ranges/save_genomic_ranges_list.py
+++ b/src/dolomite_ranges/save_genomic_ranges_list.py
@@ -57,11 +57,11 @@ def save_genomic_ranges_list(
     if isinstance(_all_ranges, list) and len(_all_ranges) > 1:
         _all_ranges = combine_sequences(*x.get_ranges())
 
-    dl.save_object(_all_ranges, path=os.path.join(path, "concatenated"))
+    dl.alt_save_object(_all_ranges, path=os.path.join(path, "concatenated"), **kwargs)
 
     _elem_annotation = x.get_mcols()
     if _elem_annotation is not None and _elem_annotation.shape[1] > 0:
-        dl.save_object(
+        dl.alt_save_object(
             _elem_annotation,
             path=os.path.join(path, "element_annotations"),
             **data_frame_args
@@ -69,6 +69,8 @@ def save_genomic_ranges_list(
 
     _meta = x.get_metadata()
     if _meta is not None and len(_meta) > 0:
-        dl.save_object(_meta, path=os.path.join(path, "other_annotations"))
+        dl.alt_save_object(
+            _meta, path=os.path.join(path, "other_annotations"), **kwargs
+        )
 
     return