geney 1.4.31__py2.py3-none-any.whl → 1.4.32__py2.py3-none-any.whl

geney/utils/SeqMats.py

@@ -215,6 +215,8 @@ class SeqMat:
         #     else:
         #         raise ValueError(f"Unsupported mutation {pos}:{ref}:{alt}.")
         # Bucket mutations
+
+
         subs, ins, dels = [], [], []
         for p, r, a in mutations:
             # left-normalize
@@ -286,18 +288,30 @@ class SeqMat:
         self.notes['total_mutations'] = self.notes.get('total_mutations', 0) + applied_mutations
         return self
 
-    def complement(self) -> SeqMat:
-        comp = {b'A': b'T', b'T': b'A', b'C': b'G', b'G': b'C', b'-': b'-'}
-        nts = np.array([comp[x] for x in self.seq_array['nt']], dtype='S1')
-        new = self.clone()
-        new.seq_array['nt'] = nts
-        return new
+    # def complement(self) -> SeqMat:
+    #     comp = {b'A': b'T', b'T': b'A', b'C': b'G', b'G': b'C', b'-': b'-'}
+    #     nts = np.array([comp[x] for x in self.seq_array['nt']], dtype='S1')
+    #     new = self.clone()
+    #     new.seq_array['nt'] = nts
+    #     return new
+    #
+    # def reverse_complement(self) -> SeqMat:
+    #     new = self.complement().clone()
+    #     new.seq_array = new.seq_array[::-1].copy()
+    #     new.rev = not self.rev
+    #     return new
+    def complement(self) -> "SeqMat":
+        comp_dict = {b"A": b"T", b"T": b"A", b"C": b"G", b"G": b"C", b"-": b"-", b"N": b"N"}
+        comp_seq = np.array([comp_dict[nt] for nt in self.seq_array["nt"]], dtype="S1")
+        new_instance = self.clone()
+        new_instance.seq_array["nt"] = comp_seq
+        return new_instance
 
-    def reverse_complement(self) -> SeqMat:
-        new = self.complement().clone()
-        new.seq_array = new.seq_array[::-1].copy()
-        new.rev = not self.rev
-        return new
+    def reverse_complement(self) -> "SeqMat":
+        rev_comp_seq = self.complement().seq_array[::-1]
+        self.seq_array = rev_comp_seq.copy()
+        self.rev = not self.rev
+        return self
 
     def __getitem__(self, key: Union[int, slice]) -> np.ndarray:
         coords = self.seq_array['index']
@@ -424,7 +438,7 @@ class SeqMat:
 
         # Run the splicing prediction engine (function assumed to be defined externally)
         from .splicing_utils import run_splicing_engine
-        donor_probs, acceptor_probs = run_splicing_engine(seq, engine)
+        donor_probs, acceptor_probs = run_splicing_engine(seq=seq, splicing_engine=engine)
         # Trim off the fixed flanks before returning results.
         seq = seq[5000:-5000]
         indices = indices[5000:-5000]

geney/utils/splicing_utils.py

@@ -27,7 +27,7 @@ def run_splicing_engine(seq: Optional[str] = None, engine: str = 'spliceai') ->
             from geney.utils.spliceai_utils import sai_predict_probs, sai_models
             acceptor_probs, donor_probs = sai_predict_probs(seq, models=sai_models)
 
-        case 'spliceai_pytorch':
+        case 'spliceai-pytorch':
             from geney.utils.spliceai_pytorch_utils import sai_predict_probs, model
             acceptor_probs, donor_probs = sai_predict_probs(seq, model=model)
 

{geney-1.4.31.dist-info → geney-1.4.32.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.4.31
+Version: 1.4.32
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.4.31.dist-info → geney-1.4.32.dist-info}/RECORD

@@ -37,7 +37,7 @@ geney/translation_initiation/tis_utils.py,sha256=AF3siFjuQH-Rs44EV-80zHdbxRMvN4w
 geney/translation_initiation/resources/kozak_pssm.json,sha256=pcd0Olziutq-6H3mFWDCD9cujQ_AlZO-iiOvBl82hqE,1165
 geney/translation_initiation/resources/tis_regressor_model.joblib,sha256=IXb4DUDhJ5rBDKcqMk9zE3ECTZZcdj7Jixz3KpoZ7OA,2592025
 geney/utils/Fasta_segment.py,sha256=weB5NJ65P0XiyAJCiCHx4T9sHC1pWLpuQeOy0B85gyg,11364
-geney/utils/SeqMats.py,sha256=PaUp6PMKYDYZ8RTodmKAmCa9ywHnkqSEqTjPoATr82k,17616
+geney/utils/SeqMats.py,sha256=-eoSKJFZR5OelhjXVkTIJbqYgp2xoWvgo8KWfKIBkRk,18197
 geney/utils/SeqMatsOld.py,sha256=syRU5DAuTh3xUfGW_qP9wlcBO5pHsG_y5PlrfXTIxUY,18502
 geney/utils/TranscriptLibrary.py,sha256=W1hv4Y8wRlmwTs3iFdn4_IqS-2suVDzZe4fwti2KbR4,2076
 geney/utils/__init__.py,sha256=-nJ-DMx1JzP-ZCe_QuQCeM0ZYIT_16jxoXDhUaO_4Oc,714
@@ -45,9 +45,9 @@ geney/utils/mutation_utils.py,sha256=r-pHr56gEa5kh_DPX8MjFY3ZfYaOtyo4CUfJ5ZHlXPw
 geney/utils/pangolin_utils.py,sha256=JQSPbWxdzqGFYfWQktkfLMaMSGR28eGQhNzO7MLMe5M,6162
 geney/utils/spliceai_pytorch_utils.py,sha256=wwBoT2utKZjjaWAUo11mSoympVK1vkNxAxcJvXAh8SM,2792
 geney/utils/spliceai_utils.py,sha256=VtrIbjyQxk_3lw86eWjftRYyal9OzxArJ0GV5u_ymTg,2721
-geney/utils/splicing_utils.py,sha256=joAXSaNdXztKcxR-ZqQ2ypcrnyAc5OQvb-84ODVD0Hs,20965
+geney/utils/splicing_utils.py,sha256=Z0Z645fJhFnszpIueeMNaa-NMRLFFyJoRBR_yFbzrN0,20965
 geney/utils/utils.py,sha256=GXqlatNhix1akt3fburNzIwhiW9ZdCQSt2vmU80neyA,2370
-geney-1.4.31.dist-info/METADATA,sha256=bMLtt_0GC1DLyBTF0evhQenP8OctQiNSLbe_0awmpqQ,990
-geney-1.4.31.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
-geney-1.4.31.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.4.31.dist-info/RECORD,,
+geney-1.4.32.dist-info/METADATA,sha256=SLfl8T6fgOlpb2Plf1iJxcaD-IXjclU4ZFcD3SWZTbM,990
+geney-1.4.32.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
+geney-1.4.32.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.4.32.dist-info/RECORD,,