geney 1.2.44__py2.py3-none-any.whl → 1.2.46__py2.py3-none-any.whl

geney/oncosplice.py

@@ -402,7 +402,7 @@ def oncosplice(mut_id, splicing_threshold=0.5, protein_coding=True, primary_tran
                         sorted(cons_vector).index(next(x for x in sorted(cons_vector) if x >= affected_cons_scores)) / len(
                     cons_vector))
 
-            report = {} #OncospliceAnnotator(reference_transcript, transcript, mutation)
+            report = OncospliceAnnotator(reference_transcript, transcript, mutation)
             report['mut_id'] = mut_id
             report['oncosplice_score'] = affected_cons_scores
             report['percentile'] = percentile

geney/survival_utils.py

@@ -88,21 +88,29 @@ class SurvivalAnalysis:
             auc_vals.append(auc)
             if plot:
                 if count == 0:
-                    ax = kmf.plot_survival_function()
+                    ax = kmf.plot_survival_function(ci_show=True, color="#2430e0", lw=2)
                 else:
-                    kmf.plot_survival_function(ax=ax)
+                    kmf.plot_survival_function(ax=ax, ci_show=True, color="#e60215", lw=2)
                 count += 1
+
         p_value = self.log_rank(df[df[feature] == 1], df[df[feature] == 0])
 
         if plot:
-            ax.text(0.5, 0.85, f'p-value: {p_value:.4f}', transform=ax.transAxes, fontsize=12,
+            ax.text(0.5, 0.85, rf'$Survival p{{v}}$: {p_value:.4f}', transform=ax.transAxes, fontsize=9,
                     horizontalalignment='center')
-            plt.title('Kaplan-Meier Survival Curves')
-            plt.xlabel('Time')
+            # Grid and spines
+            ax.grid(True, which="major", linestyle="--", linewidth=0.5, color="grey", alpha=0.7)
+            ax.spines['top'].set_visible(False)
+            ax.spines['right'].set_visible(False)
+            ax.tick_params(axis="both", which="major", labelsize=12)
+            ax.legend(fontsize=12, frameon=False, loc='upper right')
+            plt.xlabel('Time (years)')
             plt.ylabel('Survival Probability')
             if time_cap:
                 plt.xlim([0, cap_time])
-            plt.show()
+            plt.tight_layout()
+
+            # plt.show()
 
         results['p_value'] = p_value
         results['auc_target'] = auc_vals[-1]

geney/tcga_utils.py

@@ -170,8 +170,8 @@ class TCGAGene:
         return self.df[self.df.case_id == case_id]
 
     def get_patients_affected(self, mut_id, read_ratio=0, exclude_filters=None):
-        # returns all patients affected by ALL the mutatins in mut_id
-        pass
+        return self.data[self.data.mut_id == mut_id].case_id.unique().tolist()
+
 
     def get_patients_unaffected(self, mut_id, must_contain_all=False, read_ratio=0, exclude_filters=None):
         # returns all patients not affected by ALL the mutation in mut id (patients containg individual mutations only allowed) unless must_contain_all= True

{geney-1.2.44.dist-info → geney-1.2.46.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.2.44
+Version: 1.2.46
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.2.44.dist-info → geney-1.2.46.dist-info}/RECORD

@@ -6,21 +6,21 @@ geney/graphic_utils.py,sha256=oMsBpB9YeEn96gGpKh4MmtagJffWZbk-xPrIwHvkFhA,11016
 geney/gtex_utils.py,sha256=asL2lHyU5KsbWpV096vkf1Ka7hSo_RRfZqw7p5nERmE,1919
 geney/immune_utils.py,sha256=ZRni5ttrhpYBnmNr0d0ZatIbNPYs4nmQuoUO00SpsS4,5271
 geney/mutation_utils.py,sha256=C_kv2MB_L8LlhX3W2ooXjJ3uDoJ8zX1WeDtZKoBZJkI,1547
-geney/oncosplice.py,sha256=Tmhkswohr6lcagpci26yms_XyXU14V6MqsRcV1XvQaI,23444
+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/spliceai_utils.py,sha256=gIGPC8u3J15A7EQrk2Elho5PbF9MmUUNopGGH-eEV8s,1873
 geney/splicing_utils.py,sha256=lGBNknnAdKhcJ3MqPQ5c9oz_NKcL2lcFAr78StjKa6o,16151
-geney/survival_utils.py,sha256=2CAkC2LsspicHIdrqsiPnjgvpr5KHDUfLFFqnRbPJqs,5762
-geney/tcga_utils.py,sha256=wM52QZ1M_54CrXZ_uj05R14ycZh23gTZUI8b0ZMtPd0,17615
+geney/survival_utils.py,sha256=usBLTwGnFzYOcl70p3lwM4SEfy1KG-UVyx-dDmXTQWY,6196
+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
 geney/translation_initiation/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 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-1.2.44.dist-info/METADATA,sha256=tVK1pP7jxfft_dc8kghB1pvLShd_C9tsYAL2vGcueAs,948
-geney-1.2.44.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
-geney-1.2.44.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.2.44.dist-info/RECORD,,
+geney-1.2.46.dist-info/METADATA,sha256=-MelhppfvYVO4W_1hwKuToXWF-SEubjyQLuGJ_DuxeQ,948
+geney-1.2.46.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
+geney-1.2.46.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.2.46.dist-info/RECORD,,