geney 1.3.19__py2.py3-none-any.whl → 1.3.21__py2.py3-none-any.whl

geney/SeqMats.py

@@ -213,6 +213,7 @@ class SeqMat:
 
 
     def _rel_index(self, pos):
+        pos = int(pos)
         if pos in self.indices:
             return np.where(self.seqmat[self.ROW_INDS, :] == pos)[0][0]
         else:
@@ -293,6 +294,11 @@ class SeqMat:
         return self.seqmat[self.ROW_INDS, self.seqmat[self.ROW_SEQ, :] != 5] + (
                     self.seqmat[self.ROW_SUPERINDS, self.seqmat[self.ROW_SEQ, :] != 5] / 10)
 
+    @property
+    def raw_indices(self):
+        return self.seqmat[self.ROW_INDS, :] + (self.seqmat[self.ROW_SUPERINDS, :] / 10)
+
+
     def mutate(self, mut, inplace=False):
         """
         Apply mutations to the sequence matrix.

geney/splicing_utils.py

@@ -363,22 +363,19 @@ def find_transcript_missplicing_seqs(ref_seq, var_seq, donors, acceptors, thresh
     missplicing = {'missed_acceptors': dap, 'missed_donors': ddp, 'discovered_acceptors': iap,
                    'discovered_donors': idp}
     missplicing = {outk: {float(k): v for k, v in outv.items()} for outk, outv in missplicing.items()}
-    temp = {outk: {int(k) if k.is_integer() else k: v for k, v in outv.items()} for outk, outv in
+    missplicing = {outk: {int(k) if k.is_integer() else k: v for k, v in outv.items()} for outk, outv in
             missplicing.items()}
-    return Missplicing(temp, threshold=threshold)
+    return Missplicing(missplicing, threshold=threshold)
 
 
 def process_pairwise_epistasis(mids, engine='pangolin', fprint=False, db=None):
     results = []
     for mid in mids:
         m1, m2 = mid.split('|')
-        # missplicing1 = find_transcript_missplicing(m1, threshold=0.25, engine=engine)
-        # missplicing2 = find_transcript_missplicing(m2, threshold=0.25, engine=engine)
-        # missplicing_both = find_transcript_missplicing(mid, threshold=0.25, engine=engine)
 
-        missplicing1 = Missplicing(find_transcript_missplicing(m1, engine=engine, db=db), threshold=0.25)
-        missplicing2 = Missplicing(find_transcript_missplicing(m2, engine=engine, db=db), threshold=0.25)
-        missplicing_both = Missplicing(find_transcript_missplicing(mid, engine=engine, db=db), threshold=0.25)
+        missplicing1 = find_transcript_missplicing(m1, engine=engine, db=db)
+        missplicing2 = find_transcript_missplicing(m2, engine=engine, db=db)
+        missplicing_both = find_transcript_missplicing(mid, engine=engine, db=db)
 
         if fprint:
             print(missplicing1)

{geney-1.3.19.dist-info → geney-1.3.21.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.3.19
+Version: 1.3.21
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.3.19.dist-info → geney-1.3.21.dist-info}/RECORD

@@ -1,6 +1,6 @@
 geney/Fasta_segment.py,sha256=99HxNGNh_MfdVW6hhtlb1vOn7eSmT7oFoEfHDFMxG8w,11275
 geney/Gene.py,sha256=JGWtfA6-d1W3I9YRASwaF8vaZ6CCuY0KEawQNdloIqY,6259
-geney/SeqMats.py,sha256=jkXmXAs0OpnFeyCfiJcKKpHHSi9JpKgiOIwsu63e1CQ,18557
+geney/SeqMats.py,sha256=-Wx9fCSTZL98UoTKZGj6fKDnT4zsJHFuvuHabSoXTU0,18712
 geney/Transcript.py,sha256=eRZXVVxDVBbv0l385bnAOBFRBSzBwppXcbBq8KXkwlo,14443
 geney/__init__.py,sha256=eBdDl42N6UhcYeZDjOnv199Z88fI5_8Y6xW8447OKXM,755
 geney/_mutation_utils.py,sha256=dHssUsnii_mf-wuRoMmF13UlD7k3ml_VwQMItTYnXpU,1132
@@ -16,7 +16,7 @@ geney/pangolin_utils.py,sha256=i5j5vEMCWOTIa1mRP2377BAhlUFZjHBzTQBips4lA_4,2934
 geney/power_utils.py,sha256=MehZFUdkJ2EFUot709yPEDxSkXmH5XevMebX2HD768A,7330
 geney/seqmat_utils.py,sha256=wzb3PX5it5bpIFQvcxyzlxfhoJTbHHbsjg0rzh05iVs,19753
 geney/spliceai_utils.py,sha256=PFIhTK8Ihrj-cv5tgRN0UFPYEmC4uxtqXSP9bBLnZRM,3077
-geney/splicing_utils.py,sha256=fnbke3LcCq98Rk1DYdCtMFxyYscVlFq9MugBPfysdGo,35880
+geney/splicing_utils.py,sha256=FLBmVglyALQbu3SEBq9VaKtRjqWabudvTz0jvPtJEuA,35538
 geney/survival_utils.py,sha256=KnAzEviMuXh6SnVXId9PgsFLSbgkduTvYoIthxN7FPA,6886
 geney/tcga_utils.py,sha256=D_BNHm-D_K408dlcJm3hzH2c6QNFjQsKvUcOPiQRk7g,17612
 geney/tis_utils.py,sha256=2makfGfVlDFVIbxzXE85AY9jmAjcNmxyIAxjvkRA5LY,7396
@@ -25,7 +25,7 @@ geney/translation_initiation/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NM
 geney/translation_initiation/tis_utils.py,sha256=AF3siFjuQH-Rs44EV-80zHdbxRMvN4woLFSHroWIETc,4448
 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-1.3.19.dist-info/METADATA,sha256=EeklEkrP-VGX0xmIhc-AHyGDnGYial941niSF_FT4pg,971
-geney-1.3.19.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
-geney-1.3.19.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.3.19.dist-info/RECORD,,
+geney-1.3.21.dist-info/METADATA,sha256=I-cnugoCjWnQJSG7GVvr_xD8D3mPgIdLADpAvBsSJfk,971
+geney-1.3.21.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
+geney-1.3.21.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.3.21.dist-info/RECORD,,