parse strands for granges

BiocPy · Jul 14, 2024 · 5377d5f · 5377d5f
1 parent 6a2923a
commit 5377d5f
Showing 1 changed file with 14 additions and 17 deletions.
diff --git a/src/rds2py/granges.py b/src/rds2py/granges.py
@@ -36,33 +36,29 @@ def as_granges(robj):
 
     _seqnames = _as_list(robj["attributes"]["seqnames"])
 
-    _strand_obj = robj["attributes"]["strand"]["attributes"]["values"]
-    _strands = _strand_obj["data"]
+    _strands = robj["attributes"]["strand"]
+    _fstrand = None
     if "attributes" in _strands:
-        if "levels" in _strands["attributes"]:
-            _levels_data = _strands["attributes"]["levels"]["data"]
-            _strands = [_levels_data[x] for x in _strands]
+        _lengths = _strands["attributes"]["lengths"]["data"]
+        _factors = _strands["attributes"]["values"]["data"]
+        _levels = _strands["attributes"]["values"]["attributes"]["levels"]["data"]
+        _strds = [_levels[x - 1] for x in _factors]
+        _fstrand = []
+        for i, x in enumerate(_lengths):
+            _fstrand.extend([_strds[i]] * x)
 
     _seqinfo_seqnames = robj["attributes"]["seqinfo"]["attributes"]["seqnames"]["data"]
-    _seqinfo_seqlengths = robj["attributes"]["seqinfo"]["attributes"]["seqlengths"][
-        "data"
-    ]
-    _seqinfo_is_circular = robj["attributes"]["seqinfo"]["attributes"]["is_circular"][
-        "data"
-    ]
+    _seqinfo_seqlengths = robj["attributes"]["seqinfo"]["attributes"]["seqlengths"]["data"]
+    _seqinfo_is_circular = robj["attributes"]["seqinfo"]["attributes"]["is_circular"]["data"]
     _seqinfo_genome = robj["attributes"]["seqinfo"]["attributes"]["genome"]["data"]
     _seqinfo = SeqInfo(
         seqnames=_seqinfo_seqnames,
         seqlengths=[None if x == -2147483648 else int(x) for x in _seqinfo_seqlengths],
-        is_circular=[
-            None if x == -2147483648 else bool(x) for x in _seqinfo_is_circular
-        ],
+        is_circular=[None if x == -2147483648 else bool(x) for x in _seqinfo_is_circular],
         genome=_seqinfo_genome,
     )
 
-    _mcols = BiocFrame.from_pandas(
-        as_pandas_from_dframe(robj["attributes"]["elementMetadata"])
-    )
+    _mcols = BiocFrame.from_pandas(as_pandas_from_dframe(robj["attributes"]["elementMetadata"]))
 
     _gr_names = None
     if "NAMES" in robj["attributes"]:
@@ -71,6 +67,7 @@ def as_granges(robj):
     return GenomicRanges(
         seqnames=_seqnames,
         ranges=_ranges,
+        strand=_fstrand,
         names=_gr_names,
         mcols=_mcols,
         seqinfo=_seqinfo,