add GRegionTree

chaochungkuo · Mar 7, 2024 · 2ecb284 · 2ecb284
1 parent f2e3f3d
commit 2ecb284
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Showing 7 changed files with 942 additions and 2 deletions.
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -5,4 +5,5 @@ pysam==0.22.0
 tqdm
 pyBigWig==0.3.22
 pandas
-scipy
+scipy
+intervaltree
diff --git a/genomkit/__init__.py b/genomkit/__init__.py
@@ -1,5 +1,6 @@
 from .regions.gregion import GRegion
 from .regions.gregions import GRegions
+from .regions.gregions_intervaltree import GRegionsTree
 from .regions.gregions_set import GRegionsSet
 from .sequences.gsequence import GSequence
 from .sequences.gsequences import GSequences

diff --git a/genomkit/regions/gregions.py b/genomkit/regions/gregions.py
@@ -1064,3 +1064,8 @@ def filter_by_score(self, larger_than=0, smaller_than=0, inplace=False):
             self.elements = res.elements
         else:
             return res
+
+    # def rename_by_GRegions(self, name_source, strandness: bool = True,
+    #                        inplace: bool = True):
+    #     assert isinstance(name_source, GRegions)
+
-Original file line number
+Diff line change
@@ Expand Up / @@ -5,4 +5,5 @@ pysam==0.22.0 @@
     tqdm
     pyBigWig==0.3.22
     pandas
-    scipy
+    scipy
+    intervaltree