geney 1.2.49__py2.py3-none-any.whl → 1.2.51__py2.py3-none-any.whl

geney/seqmat_utils.py

@@ -197,7 +197,7 @@ class SeqMat:
                     return SeqMat().set_seqmat(temp.subseq_prefix(index))  # Not include the stop codon
 
             # If no stop codon is found, return the full sequence
-            return SeqMat().set_seqmat(temp.seq)
+            return temp
 
         else:
             return SeqMat('ATG')

geney/survival_utils.py

@@ -97,11 +97,11 @@ class SurvivalAnalysis:
         p_value = self.log_rank(df[df[feature] == 1], df[df[feature] == 0])
 
         if plot:
-            ax.text(0.82, 0.6, rf'Survival $p{{v}}$: {p_value:.3e}', transform=ax.transAxes, fontsize=10,
-                    horizontalalignment='center')
+            ax.text(0.6, 0.6, rf'Survival $p{{v}}$: {p_value:.3e}', transform=ax.transAxes, fontsize=10,
+                    horizontalalignment='left')
             if tmb_p_value:
-                ax.text(0.82, 0.53, rf'TMB $p{{v}}$: {tmb_p_value:.3e}', transform=ax.transAxes, fontsize=10,
-                        horizontalalignment='center')
+                ax.text(0.6, 0.53, rf'TMB $p{{v}}$: {tmb_p_value:.3e}', transform=ax.transAxes, fontsize=10,
+                        horizontalalignment='left')
             # Grid and spines
             ax.grid(True, which="major", linestyle="--", linewidth=0.5, color="grey", alpha=0.7)
             ax.spines['top'].set_visible(False)
@@ -109,7 +109,7 @@ class SurvivalAnalysis:
             ax.tick_params(axis="both", which="major", labelsize=10)
             if title:
                 ax.set_title(title, fontsize=12)
-            legend = ax.legend(fontsize=9, loc='upper right', frameon=True)
+            legend = ax.legend(fontsize=9, loc='best', frameon=True)
             legend.get_frame().set_facecolor('white')  # Set the background color to white
             legend.get_frame().set_edgecolor('black')  # Set the edge color to black
             plt.xlabel('Time (years)')

{geney-1.2.49.dist-info → geney-1.2.51.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.2.49
+Version: 1.2.51
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.2.49.dist-info → geney-1.2.51.dist-info}/RECORD

@@ -9,10 +9,10 @@ geney/mutation_utils.py,sha256=C_kv2MB_L8LlhX3W2ooXjJ3uDoJ8zX1WeDtZKoBZJkI,1547
 geney/oncosplice.py,sha256=nP8SEXvaZbU-K_pzIOKJ6BNAl3QJgidRiptm7xBzACM,23440
 geney/pangolin_utils.py,sha256=lLmnjJdJjqwWS85-1jlPLIjD2z14sWjzU87hS-8xxpQ,2873
 geney/power_utils.py,sha256=MehZFUdkJ2EFUot709yPEDxSkXmH5XevMebX2HD768A,7330
-geney/seqmat_utils.py,sha256=YV5DFLbfjXLIswPGvqK1-eEfwn9TUby0b2kewdGAKws,18372
+geney/seqmat_utils.py,sha256=2cRXT_Ox4IdzCM8x3H2HexxFZzjo5WHs0HZiUQv8fBM,18347
 geney/spliceai_utils.py,sha256=gIGPC8u3J15A7EQrk2Elho5PbF9MmUUNopGGH-eEV8s,1873
 geney/splicing_utils.py,sha256=lGBNknnAdKhcJ3MqPQ5c9oz_NKcL2lcFAr78StjKa6o,16151
-geney/survival_utils.py,sha256=5DkV4HuXdFIfbVshRhdCFa59QD6DWAwLjjt98oBfGZ8,6893
+geney/survival_utils.py,sha256=FKcXGL7FNp9yuVyNaUudVgn-JBuZfrhvS1c1NZE-tZ4,6880
 geney/tcga_utils.py,sha256=D_BNHm-D_K408dlcJm3hzH2c6QNFjQsKvUcOPiQRk7g,17612
 geney/tis_utils.py,sha256=vA2ci4gNfwwQZlCjPpO5ehvL2NRVeM7lHI_VyfT-_10,8049
 geney/utils.py,sha256=EsKvBM-Nz2a3_4ZAhF4Dxd4PwT7_6YYKpxEN4LLgg10,2174
@@ -20,7 +20,7 @@ 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-1.2.49.dist-info/METADATA,sha256=lKeYqaJwqQigXx3rmxyumCqWx7Y2j2H7gq5OsCeUFuM,948
-geney-1.2.49.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
-geney-1.2.49.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.2.49.dist-info/RECORD,,
+geney-1.2.51.dist-info/METADATA,sha256=E_TbmjJ5ylFzUqgTAEFmL9ARawLGuFH9wzZ0fUMltOQ,948
+geney-1.2.51.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
+geney-1.2.51.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.2.51.dist-info/RECORD,,