From 0580e428516fd6b7135ae7866dd8f2ccab5c07d4 Mon Sep 17 00:00:00 2001 From: ishanuc Date: Fri, 28 Jun 2024 22:36:05 -0500 Subject: [PATCH] updated --- build/lib/emergenet/__init__.py | 19 +++++++++++++++++++ build/lib/emergenet/emergenet.py | 7 +++++-- emergenet.egg-info/PKG-INFO | 4 ++-- tex/overleaf | 1 + 4 files changed, 27 insertions(+), 4 deletions(-) create mode 160000 tex/overleaf diff --git a/build/lib/emergenet/__init__.py b/build/lib/emergenet/__init__.py index e69de29b..c29dd3e6 100644 --- a/build/lib/emergenet/__init__.py +++ b/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 + +""" diff --git a/build/lib/emergenet/emergenet.py b/build/lib/emergenet/emergenet.py index 515a5c06..e1e30485 100644 --- a/build/lib/emergenet/emergenet.py +++ b/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 - \ No newline at end of file + diff --git a/emergenet.egg-info/PKG-INFO b/emergenet.egg-info/PKG-INFO index 2cdaa43e..99ed7923 100644 --- a/emergenet.egg-info/PKG-INFO +++ b/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: ishanu@uchicago.edu License: LICENSE diff --git a/tex/overleaf b/tex/overleaf new file mode 160000 index 00000000..735e0cc4 --- /dev/null +++ b/tex/overleaf @@ -0,0 +1 @@ +Subproject commit 735e0cc45f6bc2222291f1c0f3dfd5b8d39356db