updated

build/lib/emergenet/__init__.py

@@ -0,0 +1,19 @@
+"""
+Emergenet: Fast Scalable Emergence Risk Assessment of Influenza A Strains Circulating In Non-human Hosts
+
+Emergenet is a general tool to infer digital twins of the wild viral evolutionary dynamics. The current implementation targets  Influenza A strains circulating in non-human hosts to ranl-order strains according to their risk of emergence.
+
+The underlying theory is based on uncovering an intrinsic distancebetween viral strains that scales with the probability of spontaneous jump  in the wild.
+
+                                                                                
+---                                                                                                                                            
+## Installation: 
+```                                                                         
+   pip install emergenet                                                        
+```                                                                         
+                                                                                
+## Notes:        
+
+Depends on the `quasinet` package
+
+"""

build/lib/emergenet/emergenet.py

@@ -1,3 +1,6 @@
+"""
+Emergenet: Fast Scalable Emergence Risk Assessment of Influenza A Strains Circulating In Non-human Hosts
+"""
 import re, os, json, joblib
 import numpy as np
 import pandas as pd
@@ -167,7 +170,7 @@ def _compute_risks(self, segment:str, seq_df:pd.DataFrame, enet:Qnet) -> pd.Data
         elif segment == 'NA':
             TRUNC = NA_TRUNC
             target_seq = np.array(list(self.na_seq[:TRUNC]))
-        qdist = qdistance_matrix(np.array([target_seq]), seq_arr, enet, enet)
+        qdist = qdistance_matrix(seq_arr, np.array([target_seq]), enet, enet)
         seq_df['risk'] = qdist[0]
         return seq_df
 
@@ -392,4 +395,4 @@ def predict_irat_emergence(ha_risk:float, na_risk:float) -> Tuple[float, float,
     irat_emergence_low = emergence_low_model['intercept'] + emergence_low_model['slope'] * x
     irat_emergence_high = emergence_high_model['intercept'] + emergence_high_model['slope'] * x
     return irat_emergence, irat_emergence_low, irat_emergence_high
-
+

emergenet.egg-info/PKG-INFO

@@ -1,9 +1,9 @@
 Metadata-Version: 2.1
 Name: emergenet
-Version: 0.4.2
+Version: 0.4.3
 Summary: Superfast Risk Estimation of Emerging Pathogens
 Home-page: https://github.com/zeroknowledgediscovery/emergenet
-Download-URL: https://github.com/zeroknowledgediscovery/emergenet/archive/0.4.2.tar.gz
+Download-URL: https://github.com/zeroknowledgediscovery/emergenet/archive/0.4.3.tar.gz
 Author: zed.uchicago.edu
 Author-email: [email protected]
 License: LICENSE