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Encoding.py
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Encoding.py
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import numpy as np
import pandas as pd
import pickle
import os
import sys
from sklearn.preprocessing import StandardScaler
# This section of code is copied from ProFET (Ofer & Linial, DOI: 10.1093/bioinformatics/btv345)
# Original comment by the ProFET authors: 'Acquired from georgiev's paper of
# AAscales using helper script "GetTextData.py". + RegEx cleaning DOI: 10.1089/cmb.2008.0173'
gg_1 = {'Q': -2.54, 'L': 2.72, 'T': -0.65, 'C': 2.66, 'I': 3.1, 'G': 0.15, 'V': 2.64, 'K': -3.89, 'M': 1.89, 'F': 3.12, 'N': -2.02, 'R': -2.8, 'H': -0.39, 'E': -3.08, 'W': 1.89, 'A': 0.57, 'D': -2.46, 'Y': 0.79, 'S': -1.1, 'P': -0.58}
gg_2 = {'Q': 1.82, 'L': 1.88, 'T': -1.6, 'C': -1.52, 'I': 0.37, 'G': -3.49, 'V': 0.03, 'K': 1.47, 'M': 3.88, 'F': 0.68, 'N': -1.92, 'R': 0.31, 'H': 1, 'E': 3.45, 'W': -0.09, 'A': 3.37, 'D': -0.66, 'Y': -2.62, 'S': -2.05, 'P': -4.33}
gg_3 = {'Q': -0.82, 'L': 1.92, 'T': -1.39, 'C': -3.29, 'I': 0.26, 'G': -2.97, 'V': -0.67, 'K': 1.95, 'M': -1.57, 'F': 2.4, 'N': 0.04, 'R': 2.84, 'H': -0.63, 'E': 0.05, 'W': 4.21, 'A': -3.66, 'D': -0.57, 'Y': 4.11, 'S': -2.19, 'P': -0.02}
gg_4 = {'Q': -1.85, 'L': 5.33, 'T': 0.63, 'C': -3.77, 'I': 1.04, 'G': 2.06, 'V': 2.34, 'K': 1.17, 'M': -3.58, 'F': -0.35, 'N': -0.65, 'R': 0.25, 'H': -3.49, 'E': 0.62, 'W': -2.77, 'A': 2.34, 'D': 0.14, 'Y': -0.63, 'S': 1.36, 'P': -0.21}
gg_5 = {'Q': 0.09, 'L': 0.08, 'T': 1.35, 'C': 2.96, 'I': -0.05, 'G': 0.7, 'V': 0.64, 'K': 0.53, 'M': -2.55, 'F': -0.88, 'N': 1.61, 'R': 0.2, 'H': 0.05, 'E': -0.49, 'W': 0.72, 'A': -1.07, 'D': 0.75, 'Y': 1.89, 'S': 1.78, 'P': -8.31}
gg_6 = {'Q': 0.6, 'L': 0.09, 'T': -2.45, 'C': -2.23, 'I': -1.18, 'G': 7.47, 'V': -2.01, 'K': 0.1, 'M': 2.07, 'F': 1.62, 'N': 2.08, 'R': -0.37, 'H': 0.41, 'E': 0, 'W': 0.86, 'A': -0.4, 'D': 0.24, 'Y': -0.53, 'S': -3.36, 'P': -1.82}
gg_7 = {'Q': 0.25, 'L': 0.27, 'T': -0.65, 'C': 0.44, 'I': -0.21, 'G': 0.41, 'V': -0.33, 'K': 4.01, 'M': 0.84, 'F': -0.15, 'N': 0.4, 'R': 3.81, 'H': 1.61, 'E': -5.66, 'W': -1.07, 'A': 1.23, 'D': -5.15, 'Y': -1.3, 'S': 1.39, 'P': -0.12}
gg_8 = {'Q': 2.11, 'L': -4.06, 'T': 3.43, 'C': -3.49, 'I': 3.45, 'G': 1.62, 'V': 3.93, 'K': -0.01, 'M': 1.85, 'F': -0.41, 'N': -2.47, 'R': 0.98, 'H': -0.6, 'E': -0.11, 'W': -1.66, 'A': -2.32, 'D': -1.17, 'Y': 1.31, 'S': -1.21, 'P': -1.18}
gg_9 = {'Q': -1.92, 'L': 0.43, 'T': 0.34, 'C': 2.22, 'I': 0.86, 'G': -0.47, 'V': -0.21, 'K': -0.26, 'M': -2.05, 'F': 4.2, 'N': -0.07, 'R': 2.43, 'H': 3.55, 'E': 1.49, 'W': -5.87, 'A': -2.01, 'D': 0.73, 'Y': -0.56, 'S': -2.83, 'P': 0}
gg_10 = {'Q': -1.67, 'L': -1.2, 'T': 0.24, 'C': -3.78, 'I': 1.98, 'G': -2.9, 'V': 1.27, 'K': -1.66, 'M': 0.78, 'F': 0.73, 'N': 7.02, 'R': -0.99, 'H': 1.52, 'E': -2.26, 'W': -0.66, 'A': 1.31, 'D': 1.5, 'Y': -0.95, 'S': 0.39, 'P': -0.66}
gg_11 = {'Q': 0.7, 'L': 0.67, 'T': -0.53, 'C': 1.98, 'I': 0.89, 'G': -0.98, 'V': 0.43, 'K': 5.86, 'M': 1.53, 'F': -0.56, 'N': 1.32, 'R': -4.9, 'H': -2.28, 'E': -1.62, 'W': -2.49, 'A': -1.14, 'D': 1.51, 'Y': 1.91, 'S': -2.92, 'P': 0.64}
gg_12 = {'Q': -0.27, 'L': -0.29, 'T': 1.91, 'C': -0.43, 'I': -1.67, 'G': -0.62, 'V': -1.71, 'K': -0.06, 'M': 2.44, 'F': 3.54, 'N': -2.44, 'R': 2.09, 'H': -3.12, 'E': -3.97, 'W': -0.3, 'A': 0.19, 'D': 5.61, 'Y': -1.26, 'S': 1.27, 'P': -0.92}
gg_13 = {'Q': -0.99, 'L': -2.47, 'T': 2.66, 'C': -1.03, 'I': -1.02, 'G': -0.11, 'V': -2.93, 'K': 1.38, 'M': -0.26, 'F': 5.25, 'N': 0.37, 'R': -3.08, 'H': -1.45, 'E': 2.3, 'W': -0.5, 'A': 1.66, 'D': -3.85, 'Y': 1.57, 'S': 2.86, 'P': -0.37}
gg_14 = {'Q': -1.56, 'L': -4.79, 'T': -3.07, 'C': 0.93, 'I': -1.21, 'G': 0.15, 'V': 4.22, 'K': 1.78, 'M': -3.09, 'F': 1.73, 'N': -0.89, 'R': 0.82, 'H': -0.77, 'E': -0.06, 'W': 1.64, 'A': 4.39, 'D': 1.28, 'Y': 0.2, 'S': -1.88, 'P': 0.17}
gg_15 = {'Q': 6.22, 'L': 0.8, 'T': 0.2, 'C': 1.43, 'I': -1.78, 'G': -0.53, 'V': 1.06, 'K': -2.71, 'M': -1.39, 'F': 2.14, 'N': 3.13, 'R': 1.32, 'H': -4.18, 'E': -0.35, 'W': -0.72, 'A': 0.18, 'D': -1.98, 'Y': -0.76, 'S': -2.42, 'P': 0.36}
gg_16 = {'Q': -0.18, 'L': -1.43, 'T': -2.2, 'C': 1.45, 'I': 5.71, 'G': 0.35, 'V': -1.31, 'K': 1.62, 'M': -1.02, 'F': 1.1, 'N': 0.79, 'R': 0.69, 'H': -2.91, 'E': 1.51, 'W': 1.75, 'A': -2.6, 'D': 0.05, 'Y': -5.19, 'S': 1.75, 'P': 0.08}
gg_17 = {'Q': 2.72, 'L': 0.63, 'T': 3.73, 'C': -1.15, 'I': 1.54, 'G': 0.3, 'V': -1.97, 'K': 0.96, 'M': -4.32, 'F': 0.68, 'N': -1.54, 'R': -2.62, 'H': 3.37, 'E': -2.29, 'W': 2.73, 'A': 1.49, 'D': 0.9, 'Y': -2.56, 'S': -2.77, 'P': 0.16}
gg_18 = {'Q': 4.35, 'L': -0.24, 'T': -5.46, 'C': -1.64, 'I': 2.11, 'G': 0.32, 'V': -1.21, 'K': -1.09, 'M': -1.34, 'F': 1.46, 'N': -1.71, 'R': -1.49, 'H': 1.87, 'E': -1.47, 'W': -2.2, 'A': 0.46, 'D': 1.38, 'Y': 2.87, 'S': 3.36, 'P': -0.34}
gg_19 = {'Q': 0.92, 'L': 1.01, 'T': -0.73, 'C': -1.05, 'I': -4.18, 'G': 0.05, 'V': 4.77, 'K': 1.36, 'M': 0.09, 'F': 2.33, 'N': -0.25, 'R': -2.57, 'H': 2.17, 'E': 0.15, 'W': 0.9, 'A': -4.22, 'D': -0.03, 'Y': -3.43, 'S': 2.67, 'P': 0.04}
# Package all georgiev parameters
georgiev_parameters = [gg_1, gg_2, gg_3, gg_4, gg_5, gg_6, gg_7, gg_8, gg_9,
gg_10, gg_11, gg_12, gg_13, gg_14, gg_15, gg_16, gg_17,
gg_18, gg_19]
########################
########################
def feature_single(variant,encoding):
# four physicochemical descriptors for AA
Feature = []
if encoding=='AA':
AAvolume = {'A':88.6, 'R':173.4, 'D':111.1, 'N':114.1, 'C':108.5, 'E':138.4, 'Q':143.8, 'G':60.1, 'H':153.2, 'I':166.7, 'L':166.7, 'K':168.6, 'M':162.9, 'F':189.9, 'P':112.7, 'S':89., 'T':116.1, 'W':227.8, 'Y':193.6, 'V':140. }
AAhydropathy = {'A':1.8, 'R':-4.5, 'N':-3.5, 'D': -3.5, 'C': 2.5, 'E':-3.5, 'Q':-3.5, 'G':-0.4, 'H':-3.2, 'I':4.5, 'L':3.8, 'K':-3.9, 'M':1.9, 'F':2.8, 'P':-1.6, 'S':-0.8, 'T':-0.7, 'W':-0.9, 'Y':-1.3, 'V':4.2}
AAarea = {'A':115.,'R':225.,'D':150.,'N':160.,'C':135.,'E':190.,'Q':180.,'G':75.,'H':195.,'I':175.,'L':170.,'K':200.,'M':185.,'F':210.,'P':145.,'S':115.,'T':140.,'W':255.,'Y':230.,'V':155.}
AAweight = {'A':89.094,'R':174.203,'N':132.119,'D':133.104,'C':121.154,'E':147.131,'Q':146.146,'G':75.067,'H':155.156,'I':131.175,'L':131.175,'K':146.189,'M':149.208,'F':165.192,'P':115.132,'S':105.093,'T':119.12,'W':204.228,'Y':181.191,'V':117.148}
for AA in variant:
Feature.append([AAvolume[AA],AAhydropathy[AA],AAarea[AA],AAweight[AA]])
Feature=np.asarray(Feature)
elif encoding=='Georgiev':
Feature=[[georgiev_param[character] for georgiev_param
in georgiev_parameters] for character in variant]
Feature=np.asarray(Feature)
elif encoding == 'onehot':
aalist=list(gg_1.keys())
for AA in variant:
Feature.append([AA==aa for aa in aalist])
Feature=np.asarray(Feature).astype(float)
return Feature
def RunEncoding(input_dir,Variants,encoding):
Feature=[]
for i in range(len(Variants)):
variant=Variants[i]
feature=feature_single(variant,encoding)
Feature.append(feature)
Feature=np.asarray(Feature)
# normalize data
if encoding =='onehot':
Feature_normalized=Feature
else:
Feature_normalized =np.zeros(Feature.shape)
for i in range(Feature.shape[1]):
for j in range(Feature.shape[2]):
scalers= StandardScaler()
tmp=Feature[:, i, j].reshape(-1,1)
if tmp.max()==1.0 and tmp.min()==0.0:
Feature_normalized[:,i,j] = tmp.reshape(len(tmp))
else:
tmp2=scalers.fit_transform(tmp)
Feature_normalized[:, i, j] = tmp2.reshape(len(tmp2))
# create ComboToIndex file
ComboToIndex ={Variants[i]:i for i in range(len(Variants))}
return Feature,Feature_normalized,ComboToIndex
def saveEncoding(input_dir,save_dir,dataset,encoding):
data=pd.read_excel(os.path.join(input_dir,dataset+'.xlsx'))
Variants = data['Variants'].values
Feature,Feature_normalized,ComboToIndex = RunEncoding(input_dir, Variants, encoding)
np.save(os.path.join(save_dir, dataset+'_'+encoding+ '.npy'), Feature)
np.save(os.path.join(save_dir, dataset+'_'+encoding + '_normalized.npy'), Feature_normalized)
with open(os.path.join(save_dir, 'ComboToIndex' + '_'+dataset +'_'+ encoding+ '.pkl'), 'wb') as f:
pickle.dump(ComboToIndex, f)
##########################################################################################
##########################################################################################
if __name__ == "__main__":
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('--save_dir', help="Directory for Output Encoding Files. Default value is 'Input/' which store all input files for CLADE", default='Input/')
parser.add_argument("--dataset", help = "Name of the data set. Options: 1. GB1; 2. PhoQ. It will load file DATASET.xlsx", default = 'GB1')
parser.add_argument("--encoding", help = "Name of the encoding method; Options: 1. AA; 2. Georgiev. Default: AA",default='AA')
parser.add_argument('--input_dir',help="Directory for Input Files (directory for xlsx files for combinatorial library). Default: Input",default='Input/')
args = parser.parse_args()
save_dir = args.save_dir
dataset = args.dataset
encoding = args.encoding
input_dir = args.input_dir
if len(save_dir)==0:
from time import strftime
time = strftime("%Y%m%d-%H%M%S")
save_dir = time + '/'
if not os.path.exists(save_dir):
os.mkdir(save_dir)
saveEncoding(input_dir,save_dir, dataset, encoding)