geney 1.4.35__py2.py3-none-any.whl → 1.4.37__py2.py3-none-any.whl
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- geney/utils/spliceai_pytorch_utils.py +1 -1
- geney/utils/spliceai_utils.py +1 -1
- {geney-1.4.35.dist-info → geney-1.4.37.dist-info}/METADATA +2 -1
- {geney-1.4.35.dist-info → geney-1.4.37.dist-info}/RECORD +6 -6
- {geney-1.4.35.dist-info → geney-1.4.37.dist-info}/WHEEL +0 -0
- {geney-1.4.35.dist-info → geney-1.4.37.dist-info}/top_level.txt +0 -0
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@@ -72,7 +72,7 @@ def sai_predict_probs(seq: str, model) -> list:
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probs = torch.softmax(y, dim=1) # shape: [1, 3, L]
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acceptor_probs = probs[0, :, 1] # [L]
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donor_probs = probs[0, :, 2] # [L]
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return acceptor_probs.tolist() + [0], donor_probs.tolist() + [0]
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return np.array(acceptor_probs.tolist() + [0]), np.array(donor_probs.tolist() + [0])
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def run_spliceai_seq(seq, indices, threshold=0):
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geney/utils/spliceai_utils.py
CHANGED
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@@ -26,7 +26,7 @@ if sys.platform == 'darwin':
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model_filenames = [f"models/spliceai{i}.h5" for i in range(1, 6)]
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model_paths = [resources.files('spliceai').joinpath(f) for f in model_filenames]
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else:
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model_paths = [f"/tamir2/nicolaslynn/
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model_paths = [f"/tamir2/nicolaslynn/tools/SpliceAI/spliceai/models/spliceai{i}.h5"
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for i in range(1, 6)]
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# Load models onto correct device
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@@ -1,6 +1,6 @@
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Metadata-Version: 2.1
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Name: geney
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Version: 1.4.
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Version: 1.4.37
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Summary: A Python package for gene expression modeling.
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Home-page: https://github.com/nicolaslynn/geney
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Author: Nicolas Lynn
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@@ -31,4 +31,5 @@ Requires-Dist: pyfastx
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Requires-Dist: tensorflow
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Requires-Dist: keras
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Requires-Dist: redis
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Requires-Dist: seaborn
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@@ -43,11 +43,11 @@ geney/utils/TranscriptLibrary.py,sha256=W1hv4Y8wRlmwTs3iFdn4_IqS-2suVDzZe4fwti2K
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geney/utils/__init__.py,sha256=-nJ-DMx1JzP-ZCe_QuQCeM0ZYIT_16jxoXDhUaO_4Oc,714
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geney/utils/mutation_utils.py,sha256=r-pHr56gEa5kh_DPX8MjFY3ZfYaOtyo4CUfJ5ZHlXPw,3243
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geney/utils/pangolin_utils.py,sha256=JQSPbWxdzqGFYfWQktkfLMaMSGR28eGQhNzO7MLMe5M,6162
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-
geney/utils/spliceai_pytorch_utils.py,sha256=
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geney/utils/spliceai_utils.py,sha256=
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geney/utils/spliceai_pytorch_utils.py,sha256=u827JR1H7mfOEpT44xoye5pq6QTo7zsknbEKRoOlBhQ,2877
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geney/utils/spliceai_utils.py,sha256=8CBMCo13vRaj-E3h0eZkjiRmRpYI9po4_42O43vKaME,2691
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geney/utils/splicing_utils.py,sha256=JpUmuuzlzVZUI_zzaIwa03Xv-NGXzR6jlOmDAbNTYzc,20966
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geney/utils/utils.py,sha256=GXqlatNhix1akt3fburNzIwhiW9ZdCQSt2vmU80neyA,2370
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geney-1.4.
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geney-1.4.
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geney-1.4.
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geney-1.4.
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geney-1.4.37.dist-info/METADATA,sha256=NAgbzKDbjq_rlVY5-J5Sb1uPmI0bNSKTrO8tSwxQ1g0,1013
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geney-1.4.37.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
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geney-1.4.37.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
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geney-1.4.37.dist-info/RECORD,,
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File without changes
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File without changes
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