biopipen 0.21.0__py3-none-any.whl → 0.34.26__py3-none-any.whl

biopipen/scripts/tcr/GIANA/GIANA4.py

@@ -24,7 +24,6 @@
 import sys, os, re, resource
 from os import path
 import numpy as np
-from Bio.SubsMat.MatrixInfo import blosum62
 import time
 from time import gmtime, strftime
 from operator import itemgetter
@@ -36,255 +35,585 @@ from sklearn.decomposition import PCA
 from sklearn.manifold import MDS
 import faiss
 from query import *
+try:
+    from Bio.Align import substitution_matrices
+    blosum62 = substitution_matrices.load("BLOSUM62")
+    _tmp = {}
+    for ab1 in blosum62.alphabet:
+        for ab2 in blosum62.alphabet:
+            _tmp[(ab1, ab2)] = int(blosum62[(ab1, ab2)])
+    blosum62 = _tmp
+except ModuleNotFoundError:
+    from Bio.SubsMat.MatrixInfo import blosum62
 
-AAstring='ACDEFGHIKLMNPQRSTVWY'
-AAstringList=list(AAstring)
-cur_dir=os.path.dirname(os.path.realpath(__file__))+'/'
+AAstring = "ACDEFGHIKLMNPQRSTVWY"
+AAstringList = list(AAstring)
+cur_dir = os.path.dirname(os.path.realpath(__file__)) + "/"
 
-blosum62n={}
+blosum62n = {}
 for kk in blosum62:
-    a1=kk[0]
-    a2=kk[1]
-    vv=blosum62[kk]
-    if vv>4:
-        vv=4
-    blosum62n[(a1,a2)]=vv
+    a1 = kk[0]
+    a2 = kk[1]
+    vv = blosum62[kk]
+    if vv > 4:
+        vv = 4
+    blosum62n[(a1, a2)] = vv
     if a1 != a2:
-        blosum62n[(a2,a1)]=vv
-
-bl62={'A':[4,-1,-2,-2,0,-1,-1,0,-2,-1,-1,-1,-1,-2,-1,1,0,-3,-2,0],
-      'R':[-1,4,0,-2,-3,1,0,-2,0,-3,-2,2,-1,-3,-2,-1,-1,-3,-2,-3],
-      'N':[-2,0,4,1,-3,0,0,0,1,-3,-3,0,-2,-3,-2,1,0,-4,-2,-3],
-      'D':[-2,-2,1,4,-3,0,2,-1,-1,-3,-4,-1,-3,-3,-1,0,-1,-4,-3,-3],
-      'C':[0,-3,-3,-3,4,-3,-4,-3,-3,-1,-1,-3,-1,-2,-3,-1,-1,-2,-2,-1],
-      'Q':[-1,1,0,0,-3,4,2,-2,0,-3,-2,1,0,-3,-1,0,-1,-2,-1,-2],
-      'E':[-1,0,0,2,-4,2,4,-2,0,-3,-3,1,-2,-3,-1,0,-1,-3,-2,-2],
-      'G':[0,-2,0,-1,-3,-2,-2,4,-2,-4,-4,-2,-3,-3,-2,0,-2,-2,-3,-3],
-      'H':[-2,0,1,-1,-3,0,0,-2,4,-3,-3,-1,-2,-1,-2,-1,-2,-2,2,-3],
-      'I':[-1,-3,-3,-3,-1,-3,-3,-4,-3,4,2,-3,1,0,-3,-2,-1,-3,-1,3],
-      'L':[-1,-2,-3,-4,-1,-2,-3,-4,-3,2,4,-2,2,0,-3,-2,-1,-2,-1,1],
-      'K':[-1,2,0,-1,-3,1,1,-2,-1,-3,-2,4,-1,-3,-1,0,-1,-3,-2,-2],
-      'M':[-1,-1,-2,-3,-1,0,-2,-3,-2,1,2,-1,4,0,-2,-1,-1,-1,-1,1],
-      'F':[-2,-3,-3,-3,-2,-3,-3,-3,-1,0,0,-3,0,4,-4,-2,-2,1,3,-1],
-      'P':[-1,-2,-2,-1,-3,-1,-1,-2,-2,-3,-3,-1,-2,-4,4,-1,-1,-4,-3,-2],
-      'S':[1,-1,1,0,-1,0,0,0,-1,-2,-2,0,-1,-2,-1,4,1,-3,-2,-2],
-      'T':[0,-1,0,-1,-1,-1,-1,-2,-2,-1,-1,-1,-1,-2,-1,1,4,-2,-2,0],
-      'W':[-3,-3,-4,-4,-2,-2,-3,-2,-2,-3,-2,-3,-1,1,-4,-3,-2,4,2,-3],
-      'Y':[-2,-2,-2,-3,-2,-1,-2,-3,2,-1,-1,-2,-1,3,-3,-2,-2,2,4,-1],
-      'V':[0,-3,-3,-3,-1,-2,-2,-3,-3,3,1,-2,1,-1,-2,-2,0,-3,-1,4]}
-
-bl62c=np.array([np.array(x) for x in list(bl62.values())])
-bl62c=4-bl62c
-
-embedding=MDS(n_components=13, n_init=100, max_iter=1000, eps=0.00001, dissimilarity='precomputed')
-X=embedding.fit_transform(bl62c) 
-
-bl62np={}
-vkk=list(bl62.keys())
+        blosum62n[(a2, a1)] = vv
+
+bl62 = {
+    "A": [4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3, -2, 0],
+    "R": [-1, 4, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3, -2, -3],
+    "N": [-2, 0, 4, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2, -3],
+    "D": [-2, -2, 1, 4, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4, -3, -3],
+    "C": [0, -3, -3, -3, 4, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2, -2, -1],
+    "Q": [-1, 1, 0, 0, -3, 4, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1, -2],
+    "E": [-1, 0, 0, 2, -4, 2, 4, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2, -2],
+    "G": [0, -2, 0, -1, -3, -2, -2, 4, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2, -3, -3],
+    "H": [-2, 0, 1, -1, -3, 0, 0, -2, 4, -3, -3, -1, -2, -1, -2, -1, -2, -2, 2, -3],
+    "I": [-1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3, -1, 3],
+    "L": [-1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2, -1, 1],
+    "K": [-1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 4, -1, -3, -1, 0, -1, -3, -2, -2],
+    "M": [-1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 4, 0, -2, -1, -1, -1, -1, 1],
+    "F": [-2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 4, -4, -2, -2, 1, 3, -1],
+    "P": [
+        -1,
+        -2,
+        -2,
+        -1,
+        -3,
+        -1,
+        -1,
+        -2,
+        -2,
+        -3,
+        -3,
+        -1,
+        -2,
+        -4,
+        4,
+        -1,
+        -1,
+        -4,
+        -3,
+        -2,
+    ],
+    "S": [1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2, -2],
+    "T": [0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 4, -2, -2, 0],
+    "W": [-3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2, 4, 2, -3],
+    "Y": [-2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2, 4, -1],
+    "V": [0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3, -1, 4],
+}
+
+bl62c = np.array([np.array(x) for x in list(bl62.values())])
+bl62c = 4 - bl62c
+
+embedding = MDS(
+    n_components=13, n_init=100, max_iter=1000, eps=0.00001, dissimilarity="precomputed"
+)
+X = embedding.fit_transform(bl62c)
+
+bl62np = {}
+vkk = list(bl62.keys())
 for ii in range(20):
-    kk=vkk[ii]
-    bl62np[kk]=np.array(list(X[ii,])+[0]*17)
+    kk = vkk[ii]
+    bl62np[kk] = np.array(list(X[ii,]) + [0] * 17)
 
-   
-AAencodingDict={}
+
+AAencodingDict = {}
 for ii in range(len(AAstringList)):
-    aa=AAstringList[ii]
-    CODE=[0]*(ii)+[1]+[0]*(20-ii)
-    AAencodingDict[aa]=np.array(CODE)
-
-Ndim=16  ## optimized for isometric embedding
-n0=Ndim*6
-#M0=np.concatenate((np.concatenate((ZERO,M1),axis=1),np.concatenate((M1, ZERO),axis=1)))
-ZERO=np.zeros((Ndim,Ndim))
-II=np.eye(Ndim)
-M0=np.concatenate((np.concatenate((ZERO,ZERO, II),axis=1),np.concatenate((II, ZERO, ZERO),axis=1),np.concatenate((ZERO,II, ZERO),axis=1)))
+    aa = AAstringList[ii]
+    CODE = [0] * (ii) + [1] + [0] * (20 - ii)
+    AAencodingDict[aa] = np.array(CODE)
+
+Ndim = 16  ## optimized for isometric embedding
+n0 = Ndim * 6
+# M0=np.concatenate((np.concatenate((ZERO,M1),axis=1),np.concatenate((M1, ZERO),axis=1)))
+ZERO = np.zeros((Ndim, Ndim))
+II = np.eye(Ndim)
+M0 = np.concatenate(
+    (
+        np.concatenate((ZERO, ZERO, II), axis=1),
+        np.concatenate((II, ZERO, ZERO), axis=1),
+        np.concatenate((ZERO, II, ZERO), axis=1),
+    )
+)
 ## Construct 6-th order cyclic group
-ZERO45=np.zeros((Ndim*3,Ndim*3))
-M6=np.concatenate((np.concatenate((ZERO45,M0),axis=1),np.concatenate((M0, ZERO45),axis=1)))
-
-X=np.array([[-0.31230882, -0.53572156, -0.01949946, -0.12211268, -0.70947917,
-        -0.42211092,  0.02783931,  0.02637933, -0.41760305,  0.21809875,
-         0.53532768,  0.04833016,  0.07877711,  0.50464914, -0.26972087,
-        -0.52416842],
-       [ 0.29672002,  0.29005364,  0.18176298, -0.05103382, -0.34686519,
-         0.58024228, -0.49282931,  0.62304281, -0.09575202,  0.30115555,
-         0.09913529,  0.1577466 , -0.94391939, -0.10505925,  0.05482389,
-         0.38409897],
-       [-0.42212537,  0.12225749,  0.16279646,  0.60099009,  0.19734216,
-         0.42819919, -0.33562418,  0.17036334,  0.4234109 ,  0.46681561,
-        -0.50347222, -0.37936876,  0.1494825 ,  0.32176759,  0.28584684,
-         0.68469861],
-       [ 0.18599294, -0.44017825, -0.4476952 ,  0.34340976,  0.44603553,
-         0.40974629, -0.60045935, -0.09056728,  0.22147919, -0.33029418,
-         0.55635594, -0.54149972,  0.05459062,  0.57334159, -0.06227118,
-         0.65299872],
-       [-0.19010428,  0.64418792, -0.85286762,  0.21380295,  0.37639516,
-        -0.67753593,  0.38751609,  0.55746524,  0.01443766,  0.1776535 ,
-         0.62853954, -0.15048523,  0.55100206, -0.21426656,  0.3644061 ,
-        -0.0018255 ],
-       [ 0.7350723 ,  0.10111267,  0.55640019, -0.18226966,  0.51658102,
-        -0.19321508, -0.46599027, -0.02989911,  0.4036196 , -0.11978213,
-        -0.29837524, -0.30232765, -0.36738065, -0.1379793 ,  0.04362871,
-         0.33553714],
-       [ 0.41134047,  0.13512443,  0.62492322, -0.10120261, -0.03093491,
-         0.23751917, -0.68338694,  0.05124762,  0.41533821,  0.46669353,
-         0.31467277, -0.02427587,  0.15361135,  0.70595112, -0.27952632,
-         0.32408931],
-       [-0.33041265, -0.43860065, -0.5509376 , -0.04380843, -0.35160935,
-         0.25134855,  0.53409314,  0.54850824,  0.59490287,  0.32669345,
-        -0.45355268, -0.56317041, -0.55416297,  0.18117841, -0.71600849,
-        -0.08989825],
-       [-0.40366849,  0.10978974,  0.0280101 , -0.46667987, -0.45607028,
-         0.54114052, -0.77552923, -0.10720425,  0.55252091, -0.34397153,
-        -0.59813694,  0.15567728,  0.03071009, -0.02176143,  0.34442719,
-         0.14681541],
-       [ 0.19280422,  0.35777863,  0.06139255,  0.20081699, -0.30546596,
-        -0.56901549, -0.15290953, -0.31181573, -0.74523217,  0.22296016,
-        -0.39143832, -0.16474685,  0.58064427, -0.77386654,  0.19713107,
-        -0.49477418],
-       [-0.16133903,  0.22112761, -0.53162136,  0.34764073, -0.08522381,
-        -0.2510216 ,  0.04699411, -0.25702389, -0.8739765 , -0.24171728,
-        -0.24370533,  0.42193635,  0.41056913, -0.60378211, -0.65756832,
-         0.0845203 ],
-       [-0.34792144,  0.18450939,  0.77038332,  0.63868511, -0.06221681,
-         0.11930421,  0.04895523, -0.22463059, -0.03268844, -0.58941354,
-         0.11640045,  0.32384901, -0.42952779,  0.58119471,  0.07288662,
-         0.26669673],
-       [ 0.01834555, -0.16367754,  0.34900298,  0.45087949,  0.47073855,
-        -0.37377404,  0.0606911 ,  0.2455703 , -0.55182937, -0.20261009,
-         0.28325423, -0.04741146,  0.30565238, -0.62090653,  0.17528413,
-        -0.60434975],
-       [-0.55464981,  0.50918784, -0.21371646, -0.63996967, -0.37656862,
-         0.27852662,  0.3287838 , -0.56800869,  0.23260763, -0.20653106,
-         0.63261439, -0.22666691,  0.00726302, -0.60125196,  0.07139961,
-        -0.35086639],
-       [ 0.94039731, -0.25999326,  0.43922549, -0.485738  , -0.20492235,
-        -0.26005626,  0.68776626,  0.57826888, -0.05973995, -0.1193658 ,
-        -0.12102433, -0.22091354,  0.43427913,  0.71447886,  0.32745991,
-         0.03466398],
-       [-0.13194625, -0.12262688,  0.18029209,  0.16555524,  0.39594125,
-        -0.58110665,  0.16161717,  0.0839783 ,  0.0911945 ,  0.34546976,
-        -0.29415349,  0.29891936, -0.60834721,  0.5943593 , -0.29473819,
-         0.4864154 ],
-       [ 0.40850093, -0.4638894 , -0.39732987, -0.01972861,  0.51189582,
-         0.10176704,  0.37528519, -0.41479418, -0.1932531 ,  0.54732221,
-        -0.11876511,  0.32843973, -0.259283  ,  0.59500132,  0.35168375,
-        -0.21733727],
-       [-0.50627723, -0.1973602 , -0.02339884, -0.66846048,  0.62696606,
-         0.60049717,  0.69143364, -0.48053591,  0.17812208, -0.58481821,
-        -0.23551415, -0.06229112,  0.20993116, -0.72485884,  0.34375662,
-        -0.23539168],
-       [-0.51388312, -0.2788953 ,  0.00859533, -0.5247195 , -0.18021544,
-         0.28372911,  0.10791359,  0.13033494,  0.34294013, -0.70310089,
-        -0.13245433,  0.48661081,  0.08451644, -0.69990992,  0.0408274 ,
-        -0.47204888],
-       [ 0.68546275,  0.22581365, -0.32571833,  0.34394298, -0.43232367,
-        -0.5041842 ,  0.04784017, -0.53067936, -0.50049908,  0.36874221,
-         0.22429186,  0.4616482 ,  0.11159174, -0.26827959, -0.39372848,
-        -0.40987423]])
-
-bl62np={}
-vkk=list(bl62.keys())
+ZERO45 = np.zeros((Ndim * 3, Ndim * 3))
+M6 = np.concatenate(
+    (np.concatenate((ZERO45, M0), axis=1), np.concatenate((M0, ZERO45), axis=1))
+)
+
+X = np.array(
+    [
+        [
+            -0.31230882,
+            -0.53572156,
+            -0.01949946,
+            -0.12211268,
+            -0.70947917,
+            -0.42211092,
+            0.02783931,
+            0.02637933,
+            -0.41760305,
+            0.21809875,
+            0.53532768,
+            0.04833016,
+            0.07877711,
+            0.50464914,
+            -0.26972087,
+            -0.52416842,
+        ],
+        [
+            0.29672002,
+            0.29005364,
+            0.18176298,
+            -0.05103382,
+            -0.34686519,
+            0.58024228,
+            -0.49282931,
+            0.62304281,
+            -0.09575202,
+            0.30115555,
+            0.09913529,
+            0.1577466,
+            -0.94391939,
+            -0.10505925,
+            0.05482389,
+            0.38409897,
+        ],
+        [
+            -0.42212537,
+            0.12225749,
+            0.16279646,
+            0.60099009,
+            0.19734216,
+            0.42819919,
+            -0.33562418,
+            0.17036334,
+            0.4234109,
+            0.46681561,
+            -0.50347222,
+            -0.37936876,
+            0.1494825,
+            0.32176759,
+            0.28584684,
+            0.68469861,
+        ],
+        [
+            0.18599294,
+            -0.44017825,
+            -0.4476952,
+            0.34340976,
+            0.44603553,
+            0.40974629,
+            -0.60045935,
+            -0.09056728,
+            0.22147919,
+            -0.33029418,
+            0.55635594,
+            -0.54149972,
+            0.05459062,
+            0.57334159,
+            -0.06227118,
+            0.65299872,
+        ],
+        [
+            -0.19010428,
+            0.64418792,
+            -0.85286762,
+            0.21380295,
+            0.37639516,
+            -0.67753593,
+            0.38751609,
+            0.55746524,
+            0.01443766,
+            0.1776535,
+            0.62853954,
+            -0.15048523,
+            0.55100206,
+            -0.21426656,
+            0.3644061,
+            -0.0018255,
+        ],
+        [
+            0.7350723,
+            0.10111267,
+            0.55640019,
+            -0.18226966,
+            0.51658102,
+            -0.19321508,
+            -0.46599027,
+            -0.02989911,
+            0.4036196,
+            -0.11978213,
+            -0.29837524,
+            -0.30232765,
+            -0.36738065,
+            -0.1379793,
+            0.04362871,
+            0.33553714,
+        ],
+        [
+            0.41134047,
+            0.13512443,
+            0.62492322,
+            -0.10120261,
+            -0.03093491,
+            0.23751917,
+            -0.68338694,
+            0.05124762,
+            0.41533821,
+            0.46669353,
+            0.31467277,
+            -0.02427587,
+            0.15361135,
+            0.70595112,
+            -0.27952632,
+            0.32408931,
+        ],
+        [
+            -0.33041265,
+            -0.43860065,
+            -0.5509376,
+            -0.04380843,
+            -0.35160935,
+            0.25134855,
+            0.53409314,
+            0.54850824,
+            0.59490287,
+            0.32669345,
+            -0.45355268,
+            -0.56317041,
+            -0.55416297,
+            0.18117841,
+            -0.71600849,
+            -0.08989825,
+        ],
+        [
+            -0.40366849,
+            0.10978974,
+            0.0280101,
+            -0.46667987,
+            -0.45607028,
+            0.54114052,
+            -0.77552923,
+            -0.10720425,
+            0.55252091,
+            -0.34397153,
+            -0.59813694,
+            0.15567728,
+            0.03071009,
+            -0.02176143,
+            0.34442719,
+            0.14681541,
+        ],
+        [
+            0.19280422,
+            0.35777863,
+            0.06139255,
+            0.20081699,
+            -0.30546596,
+            -0.56901549,
+            -0.15290953,
+            -0.31181573,
+            -0.74523217,
+            0.22296016,
+            -0.39143832,
+            -0.16474685,
+            0.58064427,
+            -0.77386654,
+            0.19713107,
+            -0.49477418,
+        ],
+        [
+            -0.16133903,
+            0.22112761,
+            -0.53162136,
+            0.34764073,
+            -0.08522381,
+            -0.2510216,
+            0.04699411,
+            -0.25702389,
+            -0.8739765,
+            -0.24171728,
+            -0.24370533,
+            0.42193635,
+            0.41056913,
+            -0.60378211,
+            -0.65756832,
+            0.0845203,
+        ],
+        [
+            -0.34792144,
+            0.18450939,
+            0.77038332,
+            0.63868511,
+            -0.06221681,
+            0.11930421,
+            0.04895523,
+            -0.22463059,
+            -0.03268844,
+            -0.58941354,
+            0.11640045,
+            0.32384901,
+            -0.42952779,
+            0.58119471,
+            0.07288662,
+            0.26669673,
+        ],
+        [
+            0.01834555,
+            -0.16367754,
+            0.34900298,
+            0.45087949,
+            0.47073855,
+            -0.37377404,
+            0.0606911,
+            0.2455703,
+            -0.55182937,
+            -0.20261009,
+            0.28325423,
+            -0.04741146,
+            0.30565238,
+            -0.62090653,
+            0.17528413,
+            -0.60434975,
+        ],
+        [
+            -0.55464981,
+            0.50918784,
+            -0.21371646,
+            -0.63996967,
+            -0.37656862,
+            0.27852662,
+            0.3287838,
+            -0.56800869,
+            0.23260763,
+            -0.20653106,
+            0.63261439,
+            -0.22666691,
+            0.00726302,
+            -0.60125196,
+            0.07139961,
+            -0.35086639,
+        ],
+        [
+            0.94039731,
+            -0.25999326,
+            0.43922549,
+            -0.485738,
+            -0.20492235,
+            -0.26005626,
+            0.68776626,
+            0.57826888,
+            -0.05973995,
+            -0.1193658,
+            -0.12102433,
+            -0.22091354,
+            0.43427913,
+            0.71447886,
+            0.32745991,
+            0.03466398,
+        ],
+        [
+            -0.13194625,
+            -0.12262688,
+            0.18029209,
+            0.16555524,
+            0.39594125,
+            -0.58110665,
+            0.16161717,
+            0.0839783,
+            0.0911945,
+            0.34546976,
+            -0.29415349,
+            0.29891936,
+            -0.60834721,
+            0.5943593,
+            -0.29473819,
+            0.4864154,
+        ],
+        [
+            0.40850093,
+            -0.4638894,
+            -0.39732987,
+            -0.01972861,
+            0.51189582,
+            0.10176704,
+            0.37528519,
+            -0.41479418,
+            -0.1932531,
+            0.54732221,
+            -0.11876511,
+            0.32843973,
+            -0.259283,
+            0.59500132,
+            0.35168375,
+            -0.21733727,
+        ],
+        [
+            -0.50627723,
+            -0.1973602,
+            -0.02339884,
+            -0.66846048,
+            0.62696606,
+            0.60049717,
+            0.69143364,
+            -0.48053591,
+            0.17812208,
+            -0.58481821,
+            -0.23551415,
+            -0.06229112,
+            0.20993116,
+            -0.72485884,
+            0.34375662,
+            -0.23539168,
+        ],
+        [
+            -0.51388312,
+            -0.2788953,
+            0.00859533,
+            -0.5247195,
+            -0.18021544,
+            0.28372911,
+            0.10791359,
+            0.13033494,
+            0.34294013,
+            -0.70310089,
+            -0.13245433,
+            0.48661081,
+            0.08451644,
+            -0.69990992,
+            0.0408274,
+            -0.47204888,
+        ],
+        [
+            0.68546275,
+            0.22581365,
+            -0.32571833,
+            0.34394298,
+            -0.43232367,
+            -0.5041842,
+            0.04784017,
+            -0.53067936,
+            -0.50049908,
+            0.36874221,
+            0.22429186,
+            0.4616482,
+            0.11159174,
+            -0.26827959,
+            -0.39372848,
+            -0.40987423,
+        ],
+    ]
+)
+
+bl62np = {}
+vkk = list(bl62.keys())
 for ii in range(20):
-    kk=vkk[ii]
-    bl62np[kk]=np.array(list(X[ii,])+[0]*Ndim*5)
+    kk = vkk[ii]
+    bl62np[kk] = np.array(list(X[ii,]) + [0] * Ndim * 5)
+
 
 def EncodingCDR3(s, M, n0):
-    sL=list(s)
-    x=np.array([0]*n0)
+    sL = list(s)
+    x = np.array([0] * n0)
     for ii in range(len(sL)):
-        x = np.dot(M, (x+bl62np[sL[ii]]))
+        x = np.dot(M, (x + bl62np[sL[ii]]))
     return x
 
+
 def BuildLengthDict(seqs, sIDs, vGene=[], INFO=[]):
-    LLs=[10,11,12,13,14,15,16,17,18,19,20,21,22,23,24]
-    LengthD={}
-    SeqD={}
-    VgeneD={}
-    InfoD={}
-    AAs=set(list(AAencodingDict.keys()))
-    NAs=len(AAencodingDict)
-    cNAs=0
+    LLs = [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]
+    LengthD = {}
+    SeqD = {}
+    VgeneD = {}
+    InfoD = {}
+    AAs = set(list(AAencodingDict.keys()))
+    NAs = len(AAencodingDict)
+    cNAs = 0
     for ii in range(len(seqs)):
-        ID=sIDs[ii]
-        ss=seqs[ii]
-        ssAA=set(list(ss))
-        TMP=list(ssAA | AAs)
+        ID = sIDs[ii]
+        ss = seqs[ii]
+        ssAA = set(list(ss))
+        TMP = list(ssAA | AAs)
         if len(TMP) > NAs:
             ## CDR3 containing non amino acid letter
-            #print('Warning: CDR3: '+ss + ' contains non amino acid letter!')
-            cNAs+=1
+            # print('Warning: CDR3: '+ss + ' contains non amino acid letter!')
+            cNAs += 1
             continue
-        if len(vGene)>0:
-            vv=vGene[ii]
-        if len(INFO)>0:
-            info=INFO[ii]
-        L=len(ss)
+        if len(vGene) > 0:
+            vv = vGene[ii]
+        if len(INFO) > 0:
+            info = INFO[ii]
+        L = len(ss)
         if L not in LLs:
             continue
         if L not in LengthD:
-            LengthD[L]=[ID]
-            SeqD[L]=[ss]
-            if len(vGene)>0:
-                VgeneD[L]=[vv]
-            if len(INFO)>0:
-                InfoD[L]=[info]
+            LengthD[L] = [ID]
+            SeqD[L] = [ss]
+            if len(vGene) > 0:
+                VgeneD[L] = [vv]
+            if len(INFO) > 0:
+                InfoD[L] = [info]
         else:
             LengthD[L].append(ID)
             SeqD[L].append(ss)
-            if len(vGene)>0:
+            if len(vGene) > 0:
                 VgeneD[L].append(vv)
-            if len(INFO)>0:
+            if len(INFO) > 0:
                 InfoD[L].append(info)
-    if cNAs>0:
-        print("Warning: Skipped %d sequences with non AA letter!" %(cNAs))
+    if cNAs > 0:
+        print("Warning: Skipped %d sequences with non AA letter!" % (cNAs))
     return LengthD, VgeneD, InfoD, SeqD
 
+
 def CollapseUnique(LD, VD, ID, SD):
-    kks=LD.keys()
-    LDu={}
-    VDu={}
-    IDu={}
-    SDu={}
+    kks = LD.keys()
+    LDu = {}
+    VDu = {}
+    IDu = {}
+    SDu = {}
     for kk in kks:
-        vvL=list(LD[kk])
-        if len(VD)>0:
-            vvV=list(VD[kk])
+        vvL = list(LD[kk])
+        if len(VD) > 0:
+            vvV = list(VD[kk])
         else:
-            vvV=['TRBV2-1*01']*len(vvL)
-        vvI=list(ID[kk])
-        vvS=list(SD[kk])
-        zz=zip(vvL, vvS, vvV, vvI)
-        zzs=sorted(zz, key = lambda x: (x[1], x[2]))
-        nz=len(zzs)
-        pointer_pre=0
-        pointer_cur=1
-        s_pre=zzs[pointer_pre][1]
-        v_pre=zzs[pointer_pre][2]
-        uS=[s_pre]
-        uV=[v_pre]
-        uI=[[zzs[pointer_pre][3]]]
+            vvV = ["TRBV2-1*01"] * len(vvL)
+        vvI = list(ID[kk])
+        vvS = list(SD[kk])
+        zz = zip(vvL, vvS, vvV, vvI)
+        zzs = sorted(zz, key=lambda x: (x[1], x[2]))
+        nz = len(zzs)
+        pointer_pre = 0
+        pointer_cur = 1
+        s_pre = zzs[pointer_pre][1]
+        v_pre = zzs[pointer_pre][2]
+        uS = [s_pre]
+        uV = [v_pre]
+        uI = [[zzs[pointer_pre][3]]]
         while pointer_cur < nz:
-            s_cur=zzs[pointer_cur][1]
-            v_cur=zzs[pointer_cur][2]
+            s_cur = zzs[pointer_cur][1]
+            v_cur = zzs[pointer_cur][2]
             if s_cur == s_pre and v_cur == v_pre:
-                uI[len(uI)-1].append(zzs[pointer_cur][3])
+                uI[len(uI) - 1].append(zzs[pointer_cur][3])
                 pointer_cur += 1
                 continue
             else:
                 uS.append(s_cur)
                 uV.append(v_cur)
                 uI.append([zzs[pointer_cur][3]])
-                s_pre=s_cur
-                v_pre=v_cur
-                pointer_pre=pointer_cur
+                s_pre = s_cur
+                v_pre = v_cur
+                pointer_pre = pointer_cur
                 pointer_cur += 1
-        uL=[x for x in range(len(uS))]
-        LDu[kk]=uL
-        SDu[kk]=uS
-        if len(VD)>0:
-            VDu[kk]=uV
-        IDu[kk]=uI
+        uL = [x for x in range(len(uS))]
+        LDu[kk] = uL
+        SDu[kk] = uS
+        if len(VD) > 0:
+            VDu[kk] = uV
+        IDu[kk] = uI
     return LDu, VDu, IDu, SDu
 
 
@@ -296,14 +625,15 @@ class CDR3:
         ## KS: Kmer size
         ## st: the first 0:(st-1) amino acids will not be included in K-merization
         ## ed: the last L-ed amino acids will be skipped
-        self.s=s
-        self.ID=sID
-        L=len(s)
-        self.L=L
-        sub_s=s[st: (L-ed)]
-        Ls=len(sub_s)
-        Kmer=[sub_s[x:(x+KS)] for x in range(0,Ls-KS+1)]
-        self.Kmer=Kmer
+        self.s = s
+        self.ID = sID
+        L = len(s)
+        self.L = L
+        sub_s = s[st : (L - ed)]
+        Ls = len(sub_s)
+        Kmer = [sub_s[x : (x + KS)] for x in range(0, Ls - KS + 1)]
+        self.Kmer = Kmer
+
 
 class KmerSet:
     ## Kmer set for fast read searching based on mismatch-allowed Kmer index
@@ -312,263 +642,277 @@ class KmerSet:
         ## Seqs and sIDs must have the same length
         if len(Seqs) != len(sIDs):
             raise "Sequence and ID lists have different length. Please check input."
-        KmerDict={}
-        N=len(Seqs)
-        self.N=N
-        CDR3Dict={}
-        LLs=[]
-        for ii in range(0,N):
-            s=Seqs[ii]
-            sID=sIDs[ii]
-            cc=CDR3(s,sID,KS,st,ed)
-            CDR3Dict[cc.ID]=cc.Kmer
-            KK=cc.Kmer
+        KmerDict = {}
+        N = len(Seqs)
+        self.N = N
+        CDR3Dict = {}
+        LLs = []
+        for ii in range(0, N):
+            s = Seqs[ii]
+            sID = sIDs[ii]
+            cc = CDR3(s, sID, KS, st, ed)
+            CDR3Dict[cc.ID] = cc.Kmer
+            KK = cc.Kmer
             LLs.append(cc.L)
             for kk in KK:
                 if kk not in KmerDict:
-                    KmerDict[kk]=[sID]
+                    KmerDict[kk] = [sID]
                 else:
                     KmerDict[kk].append(sID)
-        self.KD=KmerDict
-        self.KS=KS
-        self.CD=CDR3Dict
-        self.LL=LLs
-    def FindKmerNeighbor(self,kk):
-        KS=self.KS
-        KS_n1=[]
+        self.KD = KmerDict
+        self.KS = KS
+        self.CD = CDR3Dict
+        self.LL = LLs
+
+    def FindKmerNeighbor(self, kk):
+        KS = self.KS
+        KS_n1 = []
         for jj in range(KS):
-            kk_pre=[kk[0:jj]]*20
-            kk_suf=[kk[(jj+1):KS]]*20
-            kkn=list(zip(kk_pre,AAstringList,kk_suf))
-            KS_n1+=[''.join(list(x)) for x in kkn]
+            kk_pre = [kk[0:jj]] * 20
+            kk_suf = [kk[(jj + 1) : KS]] * 20
+            kkn = list(zip(kk_pre, AAstringList, kk_suf))
+            KS_n1 += ["".join(list(x)) for x in kkn]
         return KS_n1
-    def FindKmerNeighbor2(self,kk):
+
+    def FindKmerNeighbor2(self, kk):
         ## KS>=6, allowing 2 mismatches. CDR3 length must be >= 10
-        KS=self.KS
-        KS_n1=[]
+        KS = self.KS
+        KS_n1 = []
         for jj in range(KS):
             for ii in range(KS):
-                if ii<=jj:
+                if ii <= jj:
                     continue
-                kk_pre=[kk[0:jj]]*20
-                kk_mid=[kk[(jj+1):ii]]*20
-                kk_suf=[kk[(ii+1):KS]]*400
-                kkn=list(zip(kk_pre,AAstringList,kk_mid))
-                kkn=[''.join(list(x)) for x in kkn]
-                kkn=[[x]*20 for x in kkn]
-                kkn=list(chain(*kkn))
-                kkn2=list(zip(kkn, AAstringList*20, kk_suf))
-                kkn2=[''.join(list(x)) for x in kkn2]
-                KS_n1+=kkn2
+                kk_pre = [kk[0:jj]] * 20
+                kk_mid = [kk[(jj + 1) : ii]] * 20
+                kk_suf = [kk[(ii + 1) : KS]] * 400
+                kkn = list(zip(kk_pre, AAstringList, kk_mid))
+                kkn = ["".join(list(x)) for x in kkn]
+                kkn = [[x] * 20 for x in kkn]
+                kkn = list(chain(*kkn))
+                kkn2 = list(zip(kkn, AAstringList * 20, kk_suf))
+                kkn2 = ["".join(list(x)) for x in kkn2]
+                KS_n1 += kkn2
         return KS_n1
+
     def KmerIndex(self):
         ## For each K-mer, find its nearest neighbor with 1 character mismatch
-        KKs=list(self.KD.keys())
-        KS=self.KS
-        KKs_set=set(KKs)
-        Skk='_'.join(KKs)
-        KI_Dict={}
+        KKs = list(self.KD.keys())
+        KS = self.KS
+        KKs_set = set(KKs)
+        Skk = "_".join(KKs)
+        KI_Dict = {}
         for kk in KKs:
-##            kk_neighbor=[]
-##            for jj in range(KS):
-##                kk_pre=kk[0:jj]
-##                kk_suf=kk[(jj+1):KS]
-##                pat=kk_pre+'['+AAstring+']{1}'+kk_suf
-##                p=re.compile(pat)
-##                mm=[m.group() for m in p.finditer(Skk)]
-##                kk_neighbor+=mm
-            KS_n=set(self.FindKmerNeighbor(kk))
+            ##            kk_neighbor=[]
+            ##            for jj in range(KS):
+            ##                kk_pre=kk[0:jj]
+            ##                kk_suf=kk[(jj+1):KS]
+            ##                pat=kk_pre+'['+AAstring+']{1}'+kk_suf
+            ##                p=re.compile(pat)
+            ##                mm=[m.group() for m in p.finditer(Skk)]
+            ##                kk_neighbor+=mm
+            KS_n = set(self.FindKmerNeighbor(kk))
             kk_neighbor = KS_n & KKs_set
-            KI_Dict[kk]=list(kk_neighbor)
+            KI_Dict[kk] = list(kk_neighbor)
         return KI_Dict
+
     def updateKD(self, KI):
         ## group sequences sharing motifs with 1-2 mismatches
-        KD=self.KD
-        KDnew={}
+        KD = self.KD
+        KDnew = {}
         for kk in KD:
-            kkm=KI[kk]
-            vvL=itemgetter(*kkm)(KD)
-            if isinstance(vvL[0],list):
-                vvL=list(chain(*vvL))
-            KDnew[kk]=vvL
+            kkm = KI[kk]
+            vvL = itemgetter(*kkm)(KD)
+            if isinstance(vvL[0], list):
+                vvL = list(chain(*vvL))
+            KDnew[kk] = vvL
         return KDnew
 
-def GenerateMotifGraph(mD,seqs,seqID):
-    SeqShareGraph={}
-    mDL={}
+
+def GenerateMotifGraph(mD, seqs, seqID):
+    SeqShareGraph = {}
+    mDL = {}
     for kk in mD:
-        vv=mD[kk]
-        LL=[]
+        vv = mD[kk]
+        LL = []
         for v in vv:
             LL.append(len(seqs[v]))
-        mDL[kk]=LL
+        mDL[kk] = LL
     for kk in mD:
-        vv=mD[kk]
-        LL=mDL[kk]
-        nv=len(vv)
-        for ii in range(0,nv):
-            id_1=vv[ii]
-            L1=LL[ii]
-            for jj in range(ii,nv):
-                if jj==ii:
+        vv = mD[kk]
+        LL = mDL[kk]
+        nv = len(vv)
+        for ii in range(0, nv):
+            id_1 = vv[ii]
+            L1 = LL[ii]
+            for jj in range(ii, nv):
+                if jj == ii:
                     continue
-                id_2=vv[jj]
-                L2=LL[jj]
+                id_2 = vv[jj]
+                L2 = LL[jj]
                 if L2 != L1:
                     continue
                 if id_1 not in SeqShareGraph:
-                    SeqShareGraph[id_1]=[id_2]
+                    SeqShareGraph[id_1] = [id_2]
                 elif id_2 not in SeqShareGraph[id_1]:
                     SeqShareGraph[id_1].append(id_2)
                 if id_2 not in SeqShareGraph:
-                    SeqShareGraph[id_2]=[id_1]
+                    SeqShareGraph[id_2] = [id_1]
                 elif id_1 not in SeqShareGraph[id_2]:
                     SeqShareGraph[id_2].append(id_1)
     return SeqShareGraph
 
+
 def generateSSG(Kset, CDR3s, k_thr=2):
-    KD=Kset.KD
-    KI=Kset.KmerIndex()
-    KDnew=Kset.updateKD(KI)
-    CD=Kset.CD
-    LL=np.array(Kset.LL)
-    SSG={}
+    KD = Kset.KD
+    KI = Kset.KmerIndex()
+    KDnew = Kset.updateKD(KI)
+    CD = Kset.CD
+    LL = np.array(Kset.LL)
+    SSG = {}
     for kk in CD:
-        vv=itemgetter(*CD[kk])(KDnew)
-        if isinstance(vv[0],list):
-            vv=list(chain(*vv))
-        vv1=[]
-        c=Counter(vv)
+        vv = itemgetter(*CD[kk])(KDnew)
+        if isinstance(vv[0], list):
+            vv = list(chain(*vv))
+        vv1 = []
+        c = Counter(vv)
         for k in c:
-            if c[k]>=k_thr:
+            if c[k] >= k_thr:
                 vv1.append(k)
-        vv1=np.array(vv1)
-        if len(vv1)==0:
+        vv1 = np.array(vv1)
+        if len(vv1) == 0:
             continue
-        cdr3=CDR3s[kk]
-        L0=len(cdr3)
-        idx=np.where(LL[vv1]==L0)[0]
-        if len(idx)==0:
+        cdr3 = CDR3s[kk]
+        L0 = len(cdr3)
+        idx = np.where(LL[vv1] == L0)[0]
+        if len(idx) == 0:
             continue
-        vvs=list(vv1[idx])
+        vvs = list(vv1[idx])
         vvs.remove(kk)
-        if len(vvs)>0:
-            SSG[kk]=vvs
+        if len(vvs) > 0:
+            SSG[kk] = vvs
     return SSG
 
-def SeqComparison(s1,s2,gap=-6):
-    n=len(s1)
-    CorList=[]
-    score=0
-    for kk in range(0,n):
-        aa=s1[kk]
-        bb=s2[kk]
-        if aa in ['.','-','*'] or bb in ['.','-','*']:
-            if aa!=bb:
+
+def SeqComparison(s1, s2, gap=-6):
+    n = len(s1)
+    CorList = []
+    score = 0
+    for kk in range(0, n):
+        aa = s1[kk]
+        bb = s2[kk]
+        if aa in [".", "-", "*"] or bb in [".", "-", "*"]:
+            if aa != bb:
                 score += gap
             continue
-        if aa==bb:
-#            score += min(4,blosum62[(aa,aa)])
-            score += blosum62n[(aa,aa)]
+        if aa == bb:
+            #            score += min(4,blosum62[(aa,aa)])
+            score += blosum62n[(aa, aa)]
             continue
-        KEY=(aa,bb)
-#        if KEY not in blosum62:
-#            KEY=(bb,aa)
-#        if KEY not in blosum62:
-#            raise "Non-standard amino acid coding!"
-        score+=blosum62n[KEY]
+        KEY = (aa, bb)
+        #        if KEY not in blosum62:
+        #            KEY=(bb,aa)
+        #        if KEY not in blosum62:
+        #            raise "Non-standard amino acid coding!"
+        score += blosum62n[KEY]
     return score
 
-def NHLocalAlignment(Seq1,Seq2,gap_thr=1,gap=-6):
-    n1=len(Seq1)
-    n2=len(Seq2)
-    if n1<n2:
-        Seq=Seq1
-        Seq1=Seq2
-        Seq2=Seq
-        nn=n2-n1
+
+def NHLocalAlignment(Seq1, Seq2, gap_thr=1, gap=-6):
+    n1 = len(Seq1)
+    n2 = len(Seq2)
+    if n1 < n2:
+        Seq = Seq1
+        Seq1 = Seq2
+        Seq2 = Seq
+        nn = n2 - n1
     else:
-        nn=n1-n2
-    if nn>gap_thr:
+        nn = n1 - n2
+    if nn > gap_thr:
         return -1
-    SeqList1=[Seq1]
-    SeqList2=InsertGap(Seq2,nn)
-    alns=[]
-    SCOREList=[]
+    SeqList1 = [Seq1]
+    SeqList2 = InsertGap(Seq2, nn)
+    alns = []
+    SCOREList = []
     for s1 in SeqList1:
         for s2 in SeqList2:
-                SCOREList.append(SeqComparison(s1,s2,gap))
-    maxS=max(SCOREList)
+            SCOREList.append(SeqComparison(s1, s2, gap))
+    maxS = max(SCOREList)
     return maxS
 
-def InsertGap(Seq,n):
+
+def InsertGap(Seq, n):
     ## Insert n gaps to Seq; n<=2
-    if n==0:
+    if n == 0:
         return [Seq]
-    ns=len(Seq)
-    SeqList=[]
-    if(n==1):
-        for kk in range(0,ns+1):
-            SeqNew=Seq[0:kk]+'-'+Seq[kk:]
+    ns = len(Seq)
+    SeqList = []
+    if n == 1:
+        for kk in range(0, ns + 1):
+            SeqNew = Seq[0:kk] + "-" + Seq[kk:]
             SeqList.append(SeqNew)
-    if(n==2):
-        for kk in range(0,ns+1):
-            SeqNew=Seq[0:kk]+'-'+Seq[kk:]
-            for jj in range(0,ns+2):
-                SeqNew0=SeqNew[0:jj]+'-'+SeqNew[jj:]
+    if n == 2:
+        for kk in range(0, ns + 1):
+            SeqNew = Seq[0:kk] + "-" + Seq[kk:]
+            for jj in range(0, ns + 2):
+                SeqNew0 = SeqNew[0:jj] + "-" + SeqNew[jj:]
                 SeqList.append(SeqNew0)
     return SeqList
 
-def falign(s1, s2, V1, V2 ,st,VScore={}, UseV=True, gapn=1, gap=-6):
-    mid1=s1[st:-2]
-    mid2=s2[st:-2]
+
+def falign(s1, s2, V1, V2, st, VScore={}, UseV=True, gapn=1, gap=-6):
+    mid1 = s1[st:-2]
+    mid2 = s2[st:-2]
     if UseV:
-        if V2==V1:
-            V_score=4
+        if V2 == V1:
+            V_score = 4
         else:
-            Vkey=(V1,V2)
+            Vkey = (V1, V2)
             if Vkey not in VScore:
-                Vkey=(V2,V1)
+                Vkey = (V2, V1)
             if Vkey not in VScore:
-                #print("V gene not found!")
+                # print("V gene not found!")
                 return 0
             else:
-                V_score=VScore[Vkey]/20.0
+                V_score = VScore[Vkey] / 20.0
     else:
-        V_score=4.0
-    aln=NHLocalAlignment(mid1,mid2,gapn,gap)
-    score=aln/float(max(len(mid1),len(mid2)))+V_score
+        V_score = 4.0
+    aln = NHLocalAlignment(mid1, mid2, gapn, gap)
+    score = aln / float(max(len(mid1), len(mid2))) + V_score
     return score
 
+
 def UpdateSSG(SSG, seqs, Vgenes, Vscore={}, UseV=True, gap=-6, gapn=1, cutoff=7.5):
-    SSGnew={}
-    count=0
-    t1=time.time()
-    N=len(list(chain(*list(SSG.values()))))
-#    print("Number of pairs to be processed: %d" %N)
+    SSGnew = {}
+    count = 0
+    t1 = time.time()
+    N = len(list(chain(*list(SSG.values()))))
+    #    print("Number of pairs to be processed: %d" %N)
     for kk in SSG:
-        s1=seqs[kk]
-        V1=Vgenes[kk]
-        VV=SSG[kk]
+        s1 = seqs[kk]
+        V1 = Vgenes[kk]
+        VV = SSG[kk]
         for vv in VV:
-            s2=seqs[vv]
-            V2=Vgenes[vv]
-            score=falign(s1, s2, V1, V2, st=3, VScore=Vscore, UseV=UseV, gap=-6, gapn=1)
-            count+=1
-            if count % 1000000 ==0:
-                t2=time.time()
-#                print("Processed %d pairs. Elapsed time %f" %(count, t2-t1))
-            if score>=cutoff:
+            s2 = seqs[vv]
+            V2 = Vgenes[vv]
+            score = falign(
+                s1, s2, V1, V2, st=3, VScore=Vscore, UseV=UseV, gap=-6, gapn=1
+            )
+            count += 1
+            if count % 1000000 == 0:
+                t2 = time.time()
+            #                print("Processed %d pairs. Elapsed time %f" %(count, t2-t1))
+            if score >= cutoff:
                 if kk not in SSGnew:
-                    SSGnew[kk]=[vv]
+                    SSGnew[kk] = [vv]
                 else:
                     SSGnew[kk].append(vv)
     return SSGnew
 
+
 def dfs(graph, start):
-    '''
+    """
     Non-resursive depth first search
-    '''
+    """
     visited = set()
     stack = [start]
     while stack:
@@ -576,443 +920,503 @@ def dfs(graph, start):
         if vertex not in visited:
             visited.add(vertex)
             stack.extend(set(graph[vertex]) - visited)
-    
+
     return visited
 
+
 def IdentifyMotifCluster(SSG):
     ## Input SeqShareGraph dictionary representation of sparse matrix
-    POS=set(SSG.keys())
-    NP=len(POS)
-    ClusterList=[]
-    tmpL=set(chain(*ClusterList))
-    count=0
+    POS = set(SSG.keys())
+    NP = len(POS)
+    ClusterList = []
+    tmpL = set(chain(*ClusterList))
+    count = 0
     while 1:
-            xx=POS ^ tmpL
-            if len(xx)==0:
-                break
-            for ii in xx:
-#            STACK=LoadComm([],ii)
-                STACK=dfs(SSG,ii)
-                tmpL = tmpL | STACK
-                ClusterList.append(list(STACK))
-#                tmpL=set(chain(*ClusterList))
-                count+=1
-                if count % 200 ==0:
-                    print ("    Solved %d clusters" %(count))
-                break
+        xx = POS ^ tmpL
+        if len(xx) == 0:
+            break
+        for ii in xx:
+            #            STACK=LoadComm([],ii)
+            STACK = dfs(SSG, ii)
+            tmpL = tmpL | STACK
+            ClusterList.append(list(STACK))
+            #                tmpL=set(chain(*ClusterList))
+            count += 1
+            if count % 200 == 0:
+                print("    Solved %d clusters" % (count))
+            break
     return ClusterList
 
+
 def IdentifyVgeneCluster(sMat):
     ## Input Vgene score matrix
-    vG={}
-    n=len(sMat)
-    IDs=[x for x in range(n)]
+    vG = {}
+    n = len(sMat)
+    IDs = [x for x in range(n)]
     for kk in IDs:
-        LL=sMat[:,kk]
-        vL=np.where(LL>=thr_v)[0]
-        if len(vL)>0:
-            vG[kk]=vL
-    CL=IdentifyMotifCluster(vG)
+        LL = sMat[:, kk]
+        vL = np.where(LL >= thr_v)[0]
+        if len(vL) > 0:
+            vG[kk] = vL
+    CL = IdentifyMotifCluster(vG)
     return CL
-    
+
+
 def ParseFa(fname):
-    InputStr=open(fname).readlines()
-    FaDict={}
-    seq=''
+    InputStr = open(fname).readlines()
+    FaDict = {}
+    seq = ""
     for line in InputStr:
-        if line.startswith('>'):
-            if len(seq)>0:
-                FaDict[seqHead]=seq
-                seq=''
-            seqHead=line.strip()
+        if line.startswith(">"):
+            if len(seq) > 0:
+                FaDict[seqHead] = seq
+                seq = ""
+            seqHead = line.strip()
         else:
-            seq+=line.strip()
+            seq += line.strip()
     if seqHead not in FaDict:
-        FaDict[seqHead]=seq
+        FaDict[seqHead] = seq
     return FaDict
 
+
 def PreCalculateVgeneDist(VgeneFa="Imgt_Human_TRBV.fasta"):
     ## Only run one time if needed
-    FaDict=ParseFa(cur_dir+VgeneFa)
-    VScore={}
-    CDR1Dict={}
-    CDR2Dict={}
+    FaDict = ParseFa(cur_dir + VgeneFa)
+    VScore = {}
+    CDR1Dict = {}
+    CDR2Dict = {}
     for kk in FaDict:
-        if '|' in kk:
-            VV=kk.split('|')[1]
+        if "|" in kk:
+            VV = kk.split("|")[1]
         else:
-            VV=kk[1:]
-        CDR1Dict[VV]=FaDict[kk][26:37]  ## Imgt CDR1: 27 - 38
-        CDR2Dict[VV]=FaDict[kk][55:64]  ## Imgt CDR2: 56 - 65
-    Vkeys=list(CDR1Dict.keys())
-    nn=len(Vkeys)
-    for ii in range(0,nn):
-        V1=Vkeys[ii]
-        s1_CDR1=CDR1Dict[V1]
-        s1_CDR2=CDR2Dict[V1]
-        for jj in range(ii,nn):
-            V2=Vkeys[jj]
-            s2_CDR1=CDR1Dict[V2]
-            s2_CDR2=CDR2Dict[V2]
-            score1=SeqComparison(s1_CDR1,s2_CDR1)
-            score2=SeqComparison(s2_CDR2,s2_CDR2)
-            #print score1+score2
-            VScore[(V1,V2)]=score1+score2
-    gg=open('VgeneScores.txt','w')
+            VV = kk[1:]
+        CDR1Dict[VV] = FaDict[kk][26:37]  ## Imgt CDR1: 27 - 38
+        CDR2Dict[VV] = FaDict[kk][55:64]  ## Imgt CDR2: 56 - 65
+    Vkeys = list(CDR1Dict.keys())
+    nn = len(Vkeys)
+    for ii in range(0, nn):
+        V1 = Vkeys[ii]
+        s1_CDR1 = CDR1Dict[V1]
+        s1_CDR2 = CDR2Dict[V1]
+        for jj in range(ii, nn):
+            V2 = Vkeys[jj]
+            s2_CDR1 = CDR1Dict[V2]
+            s2_CDR2 = CDR2Dict[V2]
+            score1 = SeqComparison(s1_CDR1, s2_CDR1)
+            score2 = SeqComparison(s2_CDR2, s2_CDR2)
+            # print score1+score2
+            VScore[(V1, V2)] = score1 + score2
+    gg = open("VgeneScores.txt", "w")
     for kk in VScore:
-        vv=VScore[kk]
-        line=kk[0]+'\t'+kk[1]+'\t'+str(vv)+'\n'
+        vv = VScore[kk]
+        line = kk[0] + "\t" + kk[1] + "\t" + str(vv) + "\n"
         gg.write(line)
     gg.close()
 
-def EncodeRepertoire(inputfile, outdir, outfile='',exact=True, ST=3, thr_v=3.7, thr_s=3.5, VDict={},Vgene=True,thr_iso=10, gap=-6, GPU=False,Mat=False, verbose=False):
+
+def EncodeRepertoire(
+    inputfile,
+    outdir,
+    outfile="",
+    exact=True,
+    ST=3,
+    thr_v=3.7,
+    thr_s=3.5,
+    VDict={},
+    Vgene=True,
+    thr_iso=10,
+    gap=-6,
+    GPU=False,
+    Mat=False,
+    verbose=False,
+):
     ## No V gene version
     ## Encode CDR3 sequences into 96 dimensional space and perform k-means clustering
     ## If exact is True, SW alignment will be performed within each cluster after isometric encoding and clustering
-    h=open(inputfile)
-    t1=time.time()
-    alines=h.readlines()
-    ww=alines[0].strip().split('\t')
-    if not ww[0].startswith('C'):
+    h = open(inputfile)
+    t1 = time.time()
+    alines = h.readlines()
+    ww = alines[0].strip().split("\t")
+    if not ww[0].startswith("C"):
         ## header line
-        hline=alines[0]
-        alines=alines[1:]        
-    elif 'CDR3' in ww[0]:
-        hline=alines[0]
-        alines=alines[1:]
+        hline = alines[0]
+        alines = alines[1:]
+    elif "CDR3" in ww[0]:
+        hline = alines[0]
+        alines = alines[1:]
     else:
-        hline='CDR3\t'+'\t'.join(['Info'+str(x) for x in range(len(ww)-1)])        
-    seqs=[]
-    vgs=[]
-    infoList=[]
-    count=0
+        hline = "CDR3\t" + "\t".join(["Info" + str(x) for x in range(len(ww) - 1)])
+    seqs = []
+    vgs = []
+    infoList = []
+    count = 0
     if verbose:
-        print('Creating CDR3 list')
+        print("Creating CDR3 list")
     for ll in alines:
-        ww=ll.strip().split('\t')
-        cdr3=ww[0]
-        if '*' in cdr3:
+        ww = ll.strip().split("\t")
+        cdr3 = ww[0]
+        if "*" in cdr3:
             continue
-        if '_' in cdr3:
+        if "_" in cdr3:
             continue
         seqs.append(ww[0])
         if Vgene:
             vgs.append(ww[1])
-            infoList.append('\t'.join(ww[1:]))
+            infoList.append("\t".join(ww[1:]))
         else:
-            infoList.append('\t'.join(ww[1:]))
-        count+=1
-    if len(outfile)==0:
-        outfile=inputfile.split('/')
-        outfile=outfile[len(outfile)-1]
-        outfile=outdir+'/'+re.sub('\\.[txcsv]+','',outfile)+'-'+'-RotationEncodingBL62.txt'
-    g=open(outfile,'w')
-    tm=strftime("%Y-%m-%d %H:%M:%S", gmtime())
-    InfoLine='##TIME:'+tm+'|cmd: '+sys.argv[0]+'|'+inputfile+'|IsometricDistance_Thr='+str(thr_iso)+'|thr_v='+str(thr_v)+'|thr_s='+str(thr_s)+'|exact='+str(exact)+'|Vgene='+str(Vgene)+'|ST='+str(ST)
-    g.write(InfoLine+'\n')
-    g.write("##Column Info: CDR3 aa sequence, cluster id, other information in the input file\n")
-    gr=0
+            infoList.append("\t".join(ww[1:]))
+        count += 1
+    if len(outfile) == 0:
+        outfile = inputfile.split("/")
+        outfile = outfile[len(outfile) - 1]
+        outfile = (
+            outdir
+            + "/"
+            + re.sub("\\.[txcsv]+", "", outfile)
+            + "-"
+            + "-RotationEncodingBL62.txt"
+        )
+    g = open(outfile, "w")
+    tm = strftime("%Y-%m-%d %H:%M:%S", gmtime())
+    InfoLine = (
+        "##TIME:"
+        + tm
+        + "|cmd: "
+        + sys.argv[0]
+        + "|"
+        + inputfile
+        + "|IsometricDistance_Thr="
+        + str(thr_iso)
+        + "|thr_v="
+        + str(thr_v)
+        + "|thr_s="
+        + str(thr_s)
+        + "|exact="
+        + str(exact)
+        + "|Vgene="
+        + str(Vgene)
+        + "|ST="
+        + str(ST)
+    )
+    g.write(InfoLine + "\n")
+    g.write(
+        "##Column Info: CDR3 aa sequence, cluster id, other information in the input file\n"
+    )
+    gr = 0
     ## Split into different lengths
-    LD,VD, ID,SD= BuildLengthDict(seqs, vGene=vgs,INFO=infoList,sIDs=[x for x in range(len(seqs))])
+    LD, VD, ID, SD = BuildLengthDict(
+        seqs, vGene=vgs, INFO=infoList, sIDs=[x for x in range(len(seqs))]
+    )
     LDu, VDu, IDu, SDu = CollapseUnique(LD, VD, ID, SD)
     if Mat:
-        Mfile=outfile+'_EncodingMatrix.txt'
-        h=open(Mfile, 'w')
+        Mfile = outfile + "_EncodingMatrix.txt"
+        h = open(Mfile, "w")
     for kk in LDu:
         if verbose:
-            print("---Process CDR3s with length %d ---" %(kk))
-        vSD=LDu[kk]
-        vSD0=[x for x in range(len(vSD))]
-        vss=SDu[kk]
-        vInfo=IDu[kk]
-        flagL=[len(x)-1 for x in vInfo]
+            print("---Process CDR3s with length %d ---" % (kk))
+        vSD = LDu[kk]
+        vSD0 = [x for x in range(len(vSD))]
+        vss = SDu[kk]
+        vInfo = IDu[kk]
+        flagL = [len(x) - 1 for x in vInfo]
         if verbose:
-            print(' Performing CDR3 encoding')
-        dM=np.array([EncodingCDR3(x[ST:-2], M6, n0) for x in vss])
-        dM=dM.astype("float32")
+            print(" Performing CDR3 encoding")
+        dM = np.array([EncodingCDR3(x[ST:-2], M6, n0) for x in vss])
+        dM = dM.astype("float32")
         if verbose:
-            print(" The number of sequences is %d" %(dM.shape[0]))
+            print(" The number of sequences is %d" % (dM.shape[0]))
         if Mat:
             for ii in range(len(vss)):
-                line=vss[ii]+'\t'+vInfo[ii][0]+'\t'
-                NUMs=[str(xx) for xx in dM[ii,:]]
-                line += '\t'.join(NUMs) + '\n'
+                line = vss[ii] + "\t" + vInfo[ii][0] + "\t"
+                NUMs = [str(xx) for xx in dM[ii, :]]
+                line += "\t".join(NUMs) + "\n"
                 h.write(line)
-        sID=[x for x in range(dM.shape[0])]
-        t2=time.time()
+        sID = [x for x in range(dM.shape[0])]
+        t2 = time.time()
         if verbose:
-            print(' Done! Total time elapsed %f' %(t2-t1))
-        Cls = ClusterCDR3(dM, flagL, thr=thr_iso - 0.5*(15-kk), verbose=verbose)  ## change cutoff with different lengths
+            print(" Done! Total time elapsed %f" % (t2 - t1))
+        Cls = ClusterCDR3(
+            dM, flagL, thr=thr_iso - 0.5 * (15 - kk), verbose=verbose
+        )  ## change cutoff with different lengths
         if verbose:
             print("     Handling identical CDR3 groups")
-        Cls_u=[]
+        Cls_u = []
         for ii in range(len(Cls)):
-            cc=Cls[ii]
+            cc = Cls[ii]
             if len(cc) == 1:
                 ## Handle identical CDR3 groups first
-                if flagL[cc[0]]>0:
+                if flagL[cc[0]] > 0:
                     gr += 1
-                    jj=cc[0]
+                    jj = cc[0]
                     for v_info in vInfo[jj]:
-                        line=vss[jj]+'\t'+str(gr)+'\t'+v_info+'\n'
-                        _=g.write(line)
+                        line = vss[jj] + "\t" + str(gr) + "\t" + v_info + "\n"
+                        _ = g.write(line)
             else:
                 Cls_u.append(cc)
-        Cls=Cls_u
-        t2=time.time()
+        Cls = Cls_u
+        t2 = time.time()
         if verbose:
-            print(' Done! Total time elapsed %f' %(t2-t1))
+            print(" Done! Total time elapsed %f" % (t2 - t1))
         if Vgene:
-            vVgene=VDu[kk]
+            vVgene = VDu[kk]
             if verbose:
-                print('     Matching variable genes')
-            Cls_v=[]
+                print("     Matching variable genes")
+            Cls_v = []
             for cc in Cls:
-                Nc=len(cc)
-                sMat={}
+                Nc = len(cc)
+                sMat = {}
                 for ii in range(Nc):
-                    v1=vVgene[cc[ii]]
-                    for jj in range(ii,Nc):
-                        if jj==ii:
+                    v1 = vVgene[cc[ii]]
+                    for jj in range(ii, Nc):
+                        if jj == ii:
                             continue
-                        v2=vVgene[cc[jj]]
+                        v2 = vVgene[cc[jj]]
                         if (v1, v2) not in VDict:
                             if v1 == v2:
                                 if ii not in sMat:
-                                    sMat[ii]=[jj]
+                                    sMat[ii] = [jj]
                                 else:
                                     sMat[ii].append(jj)
                                 if jj not in sMat:
-                                    sMat[jj]=[ii]
+                                    sMat[jj] = [ii]
                                 else:
                                     sMat[jj].append(ii)
                             continue
-                        if VDict[(v1,v2)] >= thr_v:
-                                if ii not in sMat:
-                                    sMat[ii]=[jj]
-                                else:
-                                    sMat[ii].append(jj)
-                                if jj not in sMat:
-                                    sMat[jj]=[ii]
-                                else:
-                                    sMat[jj].append(ii)
-                vCL=IdentifyMotifCluster(sMat)
-                vCL_List=list(chain(*vCL))
+                        if VDict[(v1, v2)] >= thr_v:
+                            if ii not in sMat:
+                                sMat[ii] = [jj]
+                            else:
+                                sMat[ii].append(jj)
+                            if jj not in sMat:
+                                sMat[jj] = [ii]
+                            else:
+                                sMat[jj].append(ii)
+                vCL = IdentifyMotifCluster(sMat)
+                vCL_List = list(chain(*vCL))
                 for ii in range(Nc):
-                    uu=flagL[cc[ii]]
-                    if uu>0 and ii not in vCL_List:
+                    uu = flagL[cc[ii]]
+                    if uu > 0 and ii not in vCL_List:
                         vCL.append([ii])
                 for vcc in vCL:
                     Cls_v.append(list(np.array(cc)[np.array(vcc)]))
-            Cls=[]
+            Cls = []
             for ii in range(len(Cls_v)):
-                cc=Cls_v[ii]
+                cc = Cls_v[ii]
                 if len(cc) == 1:
                     ## Handle identical CDR3 groups first
                     gr += 1
-                    jj=cc[0]
+                    jj = cc[0]
                     for v_info in vInfo[jj]:
-                        line=vss[jj]+'\t'+str(gr)+'\t'+v_info+'\n'
-                        _=g.write(line)
+                        line = vss[jj] + "\t" + str(gr) + "\t" + v_info + "\n"
+                        _ = g.write(line)
                 else:
                     Cls.append(cc)
         if exact:
             if verbose:
-                print(' Performing Smith-Waterman alignment')
-            Cls_s=[]
+                print(" Performing Smith-Waterman alignment")
+            Cls_s = []
             for cc in Cls:
-                Nc=len(cc)
-                if len(cc)<=3:
-                    sMat=np.zeros((Nc,Nc))
+                Nc = len(cc)
+                if len(cc) <= 3:
+                    sMat = np.zeros((Nc, Nc))
                     for ii in range(Nc):
-                        s1=vss[cc[ii]]
-                        for jj in range(ii,Nc):
-                            if jj==ii:
+                        s1 = vss[cc[ii]]
+                        for jj in range(ii, Nc):
+                            if jj == ii:
                                 continue
-                            s2=vss[cc[jj]]
+                            s2 = vss[cc[jj]]
                             if len(s1) != len(s2):
                                 continue
-                            if len(s1)<=5:
+                            if len(s1) <= 5:
                                 continue
-                            sw=SeqComparison(s1[ST:-2],s2[ST:-2],gap=gap)
-                            sw=sw/(len(s1)-ST-2)
-                            sMat[ii,jj]=sw
-                            sMat[jj,ii]=sw
-                    s_max=[]
+                            sw = SeqComparison(s1[ST:-2], s2[ST:-2], gap=gap)
+                            sw = sw / (len(s1) - ST - 2)
+                            sMat[ii, jj] = sw
+                            sMat[jj, ii] = sw
+                    s_max = []
                     for ii in range(Nc):
-                        s_max.append(np.max(sMat[:,ii]))
-                    cc_new=[]
+                        s_max.append(np.max(sMat[:, ii]))
+                    cc_new = []
                     for ii in range(Nc):
-                        if s_max[ii]>=thr_s:
+                        if s_max[ii] >= thr_s:
                             cc_new.append(cc[ii])
-                    if len(cc_new)>1:
+                    if len(cc_new) > 1:
                         Cls_s.append(cc_new)
                     else:
                         for ii in range(Nc):
-                            uu=flagL[cc[ii]]
-                            if uu>0:
+                            uu = flagL[cc[ii]]
+                            if uu > 0:
                                 Cls_s.append([cc[ii]])
-#                    print(Cls_s)
-                    Cls_sList=list(chain(*Cls_s))
+                    #                    print(Cls_s)
+                    Cls_sList = list(chain(*Cls_s))
                     for ii in range(len(cc)):
-                        uu=flagL[cc[ii]]
-                        if uu>0 and cc[ii] not in Cls_sList:
+                        uu = flagL[cc[ii]]
+                        if uu > 0 and cc[ii] not in Cls_sList:
                             Cls_s.append([cc[ii]])
                 else:
-                    CDR3s=[vss[x] for x in cc]
-                    sIDs=np.array([vSD0[x] for x in cc])
-                    sIDs0=[x for x in range(len(cc))]
-                    Kset=KmerSet(CDR3s, sIDs0, KS=5, st=ST, ed=2)
-                    SSG=generateSSG(Kset, CDR3s, k_thr=1)
-                    tmpVgenes=['TRBV2']*len(CDR3s)
-                    SSGnew=UpdateSSG(SSG, CDR3s, tmpVgenes, Vscore=VDict, cutoff=thr_s+4)
-                    CLall=IdentifyMotifCluster(SSGnew)
-                    CLall_list=list(chain(*CLall))
+                    CDR3s = [vss[x] for x in cc]
+                    sIDs = np.array([vSD0[x] for x in cc])
+                    sIDs0 = [x for x in range(len(cc))]
+                    Kset = KmerSet(CDR3s, sIDs0, KS=5, st=ST, ed=2)
+                    SSG = generateSSG(Kset, CDR3s, k_thr=1)
+                    tmpVgenes = ["TRBV2"] * len(CDR3s)
+                    SSGnew = UpdateSSG(
+                        SSG, CDR3s, tmpVgenes, Vscore=VDict, cutoff=thr_s + 4
+                    )
+                    CLall = IdentifyMotifCluster(SSGnew)
+                    CLall_list = list(chain(*CLall))
                     for ii in range(len(cc)):
-                        uu=flagL[cc[ii]]
-                        if uu>0 and ii not in CLall_list:
+                        uu = flagL[cc[ii]]
+                        if uu > 0 and ii not in CLall_list:
                             CLall.append([ii])
                     for cl in CLall:
-                        ccs=list(sIDs[np.array(cl)])
+                        ccs = list(sIDs[np.array(cl)])
                         Cls_s.append(ccs)
-            Cls=Cls_s
+            Cls = Cls_s
         if verbose:
-            print(' Writing results into file')
+            print(" Writing results into file")
         for ii in range(len(Cls)):
-#            if ii % 100000 == 0 and ii>0:
-                #print('      %d sequences written' %(ii))
-            cc=Cls[ii]
-            gr+=1
+            #            if ii % 100000 == 0 and ii>0:
+            # print('      %d sequences written' %(ii))
+            cc = Cls[ii]
+            gr += 1
             for jj in cc:
                 for v_info in vInfo[jj]:
-                    line=vss[jj]+'\t'+str(gr)+'\t'+v_info+'\n'
-                    _=g.write(line)
+                    line = vss[jj] + "\t" + str(gr) + "\t" + v_info + "\n"
+                    _ = g.write(line)
     g.close()
     if Mat:
         h.close()
 
+
 def OrderUnique(Ig):
-    vv=list(Ig.values())
-    kk=list(Ig.keys())
-    LL=[len(x[1]) for x in vv]
-    v0=[x[0][0] for x in vv]
-    v1=[x[0][1] for x in vv]
-    zkk=zip(kk,v0,v1,LL)
-    zkks=sorted(zkk,key=lambda x: (x[1],x[3]))
-    nk=len(zkks)
-    keep_id=[0]
-    ii=1
-    n_pre=str(zkks[0][1])+'_'+str(zkks[0][2])
-    while ii<nk:
-        n_cur=str(zkks[ii][1])+'_'+str(zkks[ii][2])
-        if n_cur==n_pre:
-            ii+=1
+    vv = list(Ig.values())
+    kk = list(Ig.keys())
+    LL = [len(x[1]) for x in vv]
+    v0 = [x[0][0] for x in vv]
+    v1 = [x[0][1] for x in vv]
+    zkk = zip(kk, v0, v1, LL)
+    zkks = sorted(zkk, key=lambda x: (x[1], x[3]))
+    nk = len(zkks)
+    keep_id = [0]
+    ii = 1
+    n_pre = str(zkks[0][1]) + "_" + str(zkks[0][2])
+    while ii < nk:
+        n_cur = str(zkks[ii][1]) + "_" + str(zkks[ii][2])
+        if n_cur == n_pre:
+            ii += 1
             continue
         else:
             keep_id.append(ii)
-            n_pre=n_cur
-            ii+=1
+            n_pre = n_cur
+            ii += 1
             continue
-    nid=[x[0] for x in zkks]
-    filtered_id=np.array(nid)[np.array(keep_id)]
-    Igs={}
+    nid = [x[0] for x in zkks]
+    filtered_id = np.array(nid)[np.array(keep_id)]
+    Igs = {}
     for ii in filtered_id:
-        Igs[kk[ii]]=vv[ii]
+        Igs[kk[ii]] = vv[ii]
     return Igs, filtered_id
 
+
 def ClusterCDR3(dM, flagL, thr=10, GPU=False, verbose=False):
     ## flagL: flag vector for identical CDR3 groups, >0 for grouped non-identical CDR3s
-    Cls=[]
-    flag=0
-    dM1=dM
-    flagL=np.array(flagL)
+    Cls = []
+    flag = 0
+    dM1 = dM
+    flagL = np.array(flagL)
     if GPU:
         res = faiss.StandardGpuResources()
     while 1:
-#        print("     %d number of clusters, with %d sequences" %(len(Cls),dM1.shape[0]))
+        #        print("     %d number of clusters, with %d sequences" %(len(Cls),dM1.shape[0]))
         if verbose:
-            print('=',end='')
-        index = faiss.IndexFlatL2(Ndim*6)
+            print("=", end="")
+        index = faiss.IndexFlatL2(Ndim * 6)
         if GPU:
             index = faiss.index_cpu_to_gpu(res, 0, index)
         index.add(dM1)
-        if flag==0:
+        if flag == 0:
             D, I = index.search(dM1, 2)
-            vv=np.where((D[:,1]<=thr))[0]
-            vv0=np.where((D[:,1]>thr) & (flagL>0))[0]
+            vv = np.where((D[:, 1] <= thr))[0]
+            vv0 = np.where((D[:, 1] > thr) & (flagL > 0))[0]
             for v in vv0:
                 Cls.append([v])
-            tmp_dM=np.zeros((len(vv),Ndim*6))
-            Ig_new={}
+            tmp_dM = np.zeros((len(vv), Ndim * 6))
+            Ig_new = {}
             for ii in range(len(vv)):
-                v=vv[ii]
-                Idx=I[v,]
+                v = vv[ii]
+                Idx = I[v,]
                 if v not in Idx:
-                    Idx[0]=v
-                Ig_new[ii]=(sorted(list(set(Idx))),sorted(list(set(Idx))))
-                tmp_dM[ii,]=(dM1[Idx[0],]+dM1[Idx[1],])/2
-            if len(Ig_new)==0:
+                    Idx[0] = v
+                Ig_new[ii] = (sorted(list(set(Idx))), sorted(list(set(Idx))))
+                tmp_dM[ii,] = (dM1[Idx[0],] + dM1[Idx[1],]) / 2
+            if len(Ig_new) == 0:
                 if verbose:
-                    print('type 0 break')
+                    print("type 0 break")
                 break
-#                print('%d of sequence left at cycle %d' %(len(Ig_new),flag))
-            Igs, fid=OrderUnique(Ig_new)
-            tmp_dM=tmp_dM[fid,]
-            Ig_new=Igs
+            #                print('%d of sequence left at cycle %d' %(len(Ig_new),flag))
+            Igs, fid = OrderUnique(Ig_new)
+            tmp_dM = tmp_dM[fid,]
+            Ig_new = Igs
         else:
-            D, I = index.search(dM1,2)
-            vv=np.where(D[:,1]<=thr)[0]
-            vv0=np.where(D[:,1]>thr)[0]
+            D, I = index.search(dM1, 2)
+            vv = np.where(D[:, 1] <= thr)[0]
+            vv0 = np.where(D[:, 1] > thr)[0]
             ## move groups in vv0 to Cls
-            kkg=list(Ig.keys())
+            kkg = list(Ig.keys())
             for v in vv0:
-                ng=list(Ig[kkg[v]][1])
-    #            if ng not in Cls:
+                ng = list(Ig[kkg[v]][1])
+                #            if ng not in Cls:
                 Cls.append(ng)
-            tmp_dM=np.zeros((len(vv),Ndim*6))
-            Ig_new={}
+            tmp_dM = np.zeros((len(vv), Ndim * 6))
+            Ig_new = {}
             for ii in range(len(vv)):
-                v=vv[ii]
-                idx1=I[v,0]
-                idx2=I[v,1]
+                v = vv[ii]
+                idx1 = I[v, 0]
+                idx2 = I[v, 1]
                 if v not in I[v,]:
-                    idx1=v
-#                Ig_new[ii]=sorted(list(set(list(Ig[kkg[idx1]])+list(Ig[kkg[idx2]]))))
-                Ig_new[ii]=(sorted(list(set([idx1,idx2]))),  ## First entry records the relative index of a sequence clique
-                            sorted(list(set(list(Ig[kkg[idx1]][1])+list(Ig[kkg[idx2]][1])))))  ## Second entry records the absolute index of a sequence
-                tmp_dM[ii,]=(dM1[idx1,]+dM1[idx2,])/2
-            if len(Ig_new)==0:
+                    idx1 = v
+                #                Ig_new[ii]=sorted(list(set(list(Ig[kkg[idx1]])+list(Ig[kkg[idx2]]))))
+                Ig_new[ii] = (
+                    sorted(
+                        list(set([idx1, idx2]))
+                    ),  ## First entry records the relative index of a sequence clique
+                    sorted(list(set(list(Ig[kkg[idx1]][1]) + list(Ig[kkg[idx2]][1])))),
+                )  ## Second entry records the absolute index of a sequence
+                tmp_dM[ii,] = (dM1[idx1,] + dM1[idx2,]) / 2
+            if len(Ig_new) == 0:
                 if verbose:
                     print("\ntype I break")
-                kkg=list(Ig.keys())
+                kkg = list(Ig.keys())
                 for kk in kkg:
-                    ng=list(Ig[kk][1])
+                    ng = list(Ig[kk][1])
                     if ng not in Cls:
                         Cls.append(ng)
                 break
-#            print('%d of sequence left at cycle %d' %(len(Ig_new),flag))
-            Igs, fid=OrderUnique(Ig_new)
-            tmp_dM=tmp_dM[fid,]
-            Ig_new=Igs
-        if flag>0:
+            #            print('%d of sequence left at cycle %d' %(len(Ig_new),flag))
+            Igs, fid = OrderUnique(Ig_new)
+            tmp_dM = tmp_dM[fid,]
+            Ig_new = Igs
+        if flag > 0:
             if Ig == Ig_new:
                 if verbose:
                     print("\ntype II break")
-                kkg=list(Ig.keys())
+                kkg = list(Ig.keys())
                 for kk in kkg:
-                    ng=list(Ig[kk][1])
+                    ng = list(Ig[kk][1])
                     if ng in Cls:
                         continue
                     Cls.append(ng)
                 break
-        Ig=Ig_new
-        tmp_dM=tmp_dM.astype('float32')
-        dM1=tmp_dM
-        flag+=1
+        Ig = Ig_new
+        tmp_dM = tmp_dM.astype("float32")
+        dM1 = tmp_dM
+        flag += 1
     return Cls
 
-def ClusterCDR3r(dM, flagL, thr = 10, verbose = False):
-    index = faiss.IndexFlatL2(Ndim*6)
+
+def ClusterCDR3r(dM, flagL, thr=10, verbose=False):
+    index = faiss.IndexFlatL2(Ndim * 6)
     index.add(dM)
     lims, D, I = index.range_search(dM, thr)
     # with open('cdr3.npy', 'wb') as f:
@@ -1020,53 +1424,70 @@ def ClusterCDR3r(dM, flagL, thr = 10, verbose = False):
     #     np.save(f, D)
     #     np.save(f, I)
     #     np.save(f, dM)
-    
+
     # now clustering results
     N = dM.shape[0]
-    neighborSize = np.array([lims[cur_idx_i+1] - lims[cur_idx_i] for cur_idx_i in range(N)])
+    neighborSize = np.array(
+        [lims[cur_idx_i + 1] - lims[cur_idx_i] for cur_idx_i in range(N)]
+    )
     # to_cluster = np.ones( (N,))
     clusterNo = 0
-    cluster = - np.ones( (N, ),  dtype = np.int32)
+    cluster = -np.ones((N,), dtype=np.int32)
     idx = np.where(cluster < 0)[0]
     unclustered = [np.argmax(neighborSize[idx])]
     depth = 0
     while True:
-        if len(unclustered) == 0: break
+        if len(unclustered) == 0:
+            break
         # cur_idx = unclustered[0] # first unclustered index
         cur_idx = unclustered
-        cluster[cur_idx] = clusterNo # assign cluster
-   
-        neighbor = np.unique(np.array(list(chain (* [I[(lims[cur_idx_i]): lims[cur_idx_i+1]] for cur_idx_i in cur_idx]))))
+        cluster[cur_idx] = clusterNo  # assign cluster
+
+        neighbor = np.unique(
+            np.array(
+                list(
+                    chain(
+                        *[
+                            I[(lims[cur_idx_i]) : lims[cur_idx_i + 1]]
+                            for cur_idx_i in cur_idx
+                        ]
+                    )
+                )
+            )
+        )
         # find those unclusterred
         idx = np.where(cluster[neighbor] < 0)[0]
         if len(idx) == 0:
             depth = 0
             clusterNo += 1
             idx = np.where(cluster < 0)[0]
-            if len(idx) == 0: break
+            if len(idx) == 0:
+                break
             unclustered = [idx[np.argmax(neighborSize[idx])]]
-           
+
         else:
             if depth > 3:
                 depth = 0
                 clusterNo += 1
             unclustered = neighbor[idx]
             depth += 1
-#    print('clusterNo = ', clusterNo)
-    Cls = [ [] for i in range(clusterNo)]
+    #    print('clusterNo = ', clusterNo)
+    Cls = [[] for i in range(clusterNo)]
     for idx, i in enumerate(cluster):
-            Cls[i].append(idx)
-#    print("Cls[:5] = ", Cls[:5])
-#    print("len(Cls) = ", len(Cls),
-#          ', #elem=', sum([len(i) for i in Cls]),
-#          ', #single=', sum([len(i) for i in Cls if len(i) == 1]),
-#          ', #non_single=', sum([len(i) for i in Cls if len(i) != 1]),          
-#          ', #max=', max([len(i) for i in Cls]))
+        Cls[i].append(idx)
+    #    print("Cls[:5] = ", Cls[:5])
+    #    print("len(Cls) = ", len(Cls),
+    #          ', #elem=', sum([len(i) for i in Cls]),
+    #          ', #single=', sum([len(i) for i in Cls if len(i) == 1]),
+    #          ', #non_single=', sum([len(i) for i in Cls if len(i) != 1]),
+    #          ', #max=', max([len(i) for i in Cls]))
     return Cls
 
+
 def CommandLineParser():
-    parser=OptionParser()
-    print ('''
+    parser = OptionParser()
+    print(
+        """
 GIANA: Geometric Isometry based ANtigen-specific tcr Alignment
 Ultrafast short peptide alignment exclusively designed for large-scale adaptome analysis
 
@@ -1079,130 +1500,282 @@ Input columns:
 
 !!! ALL amino acid letters must be CAPITAL !!!
 
-''')
-    parser.add_option("-d","--directory",dest="Directory",help="Input repertoire sequencing file directory. Please make sure that all the files in the directory are input files.",default="")
-    parser.add_option("-f","--file",dest="File",default='',help="Input single file of CDR3 sequences for grouping")
-    parser.add_option("-F","--fileList",dest="files",default='',help='Alternative input: a file containing the full path to all the files. If given, overwrite -d and -f option')
-    parser.add_option("-t","--threshold",dest="thr",default=7,help="Isometric distance threshold for calling similar CDR3 groups. Without -E, smaller value will increase speed. With -E, smaller value will increase specificity. Must be smaller than 12.")
-    parser.add_option("-S","--threshold_score",dest="thr_s",default=3.6, help="Threshold for Smith-Waterman alignment score (normalized by CDR3 length). Default 3.6")
-    parser.add_option("-G","--threshold_vgene",dest="thr_v",default=3.7,help="Threshold for variable gene comparison. Default 3.7.")
-    parser.add_option("-o","--output",dest="OutDir",default='./',help="Output directory for intermediate and final outputs.")
-    parser.add_option("-O","--outfile",dest="OutFile",default='',help="Output file name. If not given, a file with --RotationEncoding will be added to the input file as the output file name.")
-    parser.add_option("-T","--startPosition",dest='ST',default=3, help="Starting position of CDR3 sequence. The first ST letters are omitted. CDR3 sequence length L must be >= ST+7 ")
-    parser.add_option("-g","--GapPenalty",dest="Gap",default= -6,help="Gap penalty,default= -6. Not used.")
-    parser.add_option("-n","--GapNumber",dest="GapN",default=1,help="Maximum number of gaps allowed when performing alignment. Max=1, default=1. Not used.")
-    parser.add_option("-V","--VariableGeneFa",dest="VFa",default="Imgt_Human_TRBV.fasta",help="IMGT Human beta variable gene sequences")
-    parser.add_option("-v","--VariableGene",dest="V",default=True,action="store_false",help="If False, GIANA will omit variable gene information and use CDR3 sequences only. This will yield reduced specificity. The cut-off will automatically become the current value-4.0")
-    parser.add_option("-e","--Exact",dest="E",default=True,action="store_false",help="If False, GIANA will not perform Smith-Waterman alignment after isometric encoding.")
-    parser.add_option("-N","--NumberOfThreads",dest="NN",default=1,help="Number of threads for multiple processing. Not working so well.")
-    parser.add_option("-M","--EncodingMatrix", dest="Mat", default=False,action="store_true", help="If true, GIANA will export the isometric encoding matrix for each TCR. Default: False.")
-    parser.add_option("-U","--UseGPU",dest="GPU", default=False, action="store_true",help="Use GPU for Faiss indexing. Must be CUDA GPUs.")
-    parser.add_option("-q","--queryFile",dest="Query",default='',help="Input query file, if given, GIANA will run in query mode, also need to provide -r option.")
-    parser.add_option("-r","--refFile",dest="ref", default='',help="Input reference file. Query model required.")
-    parser.add_option("-b","--Verbose", dest='v', default=False, action="store_true", help="Verbose option: if given, GIANA will print intermediate messages.")
+"""
+    )
+    parser.add_option(
+        "-d",
+        "--directory",
+        dest="Directory",
+        help="Input repertoire sequencing file directory. Please make sure that all the files in the directory are input files.",
+        default="",
+    )
+    parser.add_option(
+        "-f",
+        "--file",
+        dest="File",
+        default="",
+        help="Input single file of CDR3 sequences for grouping",
+    )
+    parser.add_option(
+        "-F",
+        "--fileList",
+        dest="files",
+        default="",
+        help="Alternative input: a file containing the full path to all the files. If given, overwrite -d and -f option",
+    )
+    parser.add_option(
+        "-t",
+        "--threshold",
+        dest="thr",
+        default=7,
+        help="Isometric distance threshold for calling similar CDR3 groups. Without -E, smaller value will increase speed. With -E, smaller value will increase specificity. Must be smaller than 12.",
+    )
+    parser.add_option(
+        "-S",
+        "--threshold_score",
+        dest="thr_s",
+        default=3.6,
+        help="Threshold for Smith-Waterman alignment score (normalized by CDR3 length). Default 3.6",
+    )
+    parser.add_option(
+        "-G",
+        "--threshold_vgene",
+        dest="thr_v",
+        default=3.7,
+        help="Threshold for variable gene comparison. Default 3.7.",
+    )
+    parser.add_option(
+        "-o",
+        "--output",
+        dest="OutDir",
+        default="./",
+        help="Output directory for intermediate and final outputs.",
+    )
+    parser.add_option(
+        "-O",
+        "--outfile",
+        dest="OutFile",
+        default="",
+        help="Output file name. If not given, a file with --RotationEncoding will be added to the input file as the output file name.",
+    )
+    parser.add_option(
+        "-T",
+        "--startPosition",
+        dest="ST",
+        default=3,
+        help="Starting position of CDR3 sequence. The first ST letters are omitted. CDR3 sequence length L must be >= ST+7 ",
+    )
+    parser.add_option(
+        "-g",
+        "--GapPenalty",
+        dest="Gap",
+        default=-6,
+        help="Gap penalty,default= -6. Not used.",
+    )
+    parser.add_option(
+        "-n",
+        "--GapNumber",
+        dest="GapN",
+        default=1,
+        help="Maximum number of gaps allowed when performing alignment. Max=1, default=1. Not used.",
+    )
+    parser.add_option(
+        "-V",
+        "--VariableGeneFa",
+        dest="VFa",
+        default="Imgt_Human_TRBV.fasta",
+        help="IMGT Human beta variable gene sequences",
+    )
+    parser.add_option(
+        "-v",
+        "--VariableGene",
+        dest="V",
+        default=True,
+        action="store_false",
+        help="If False, GIANA will omit variable gene information and use CDR3 sequences only. This will yield reduced specificity. The cut-off will automatically become the current value-4.0",
+    )
+    parser.add_option(
+        "-e",
+        "--Exact",
+        dest="E",
+        default=True,
+        action="store_false",
+        help="If False, GIANA will not perform Smith-Waterman alignment after isometric encoding.",
+    )
+    parser.add_option(
+        "-N",
+        "--NumberOfThreads",
+        dest="NN",
+        default=1,
+        help="Number of threads for multiple processing. Not working so well.",
+    )
+    parser.add_option(
+        "-M",
+        "--EncodingMatrix",
+        dest="Mat",
+        default=False,
+        action="store_true",
+        help="If true, GIANA will export the isometric encoding matrix for each TCR. Default: False.",
+    )
+    parser.add_option(
+        "-U",
+        "--UseGPU",
+        dest="GPU",
+        default=False,
+        action="store_true",
+        help="Use GPU for Faiss indexing. Must be CUDA GPUs.",
+    )
+    parser.add_option(
+        "-q",
+        "--queryFile",
+        dest="Query",
+        default="",
+        help="Input query file, if given, GIANA will run in query mode, also need to provide -r option.",
+    )
+    parser.add_option(
+        "-r",
+        "--refFile",
+        dest="ref",
+        default="",
+        help="Input reference file. Query model required.",
+    )
+    parser.add_option(
+        "-b",
+        "--Verbose",
+        dest="v",
+        default=False,
+        action="store_true",
+        help="Verbose option: if given, GIANA will print intermediate messages.",
+    )
     return parser.parse_args()
 
+
 def main():
-    (opt,_)=CommandLineParser()
-    cutoff=float(opt.thr)
-    OutDir=opt.OutDir
-    thr_s=float(opt.thr_s)
+    (opt, _) = CommandLineParser()
+    cutoff = float(opt.thr)
+    OutDir = opt.OutDir
+    thr_s = float(opt.thr_s)
     ## Check if query mode first
-    qFile=opt.Query
-    if len(qFile)>0:
+    qFile = opt.Query
+    if len(qFile) > 0:
         ## query mode
-        t1=time.time()
-        if qFile.endswith('/'):
+        t1 = time.time()
+        if qFile.endswith("/"):
             ## input query is a directory
-            qFs=os.listdir(qFile)
-            qFileList=[]
+            qFs = os.listdir(qFile)
+            qFileList = []
             for ff in qFs:
-                qFileList.append(qFile+ff)
+                qFileList.append(qFile + ff)
         else:
-            qFileList=[qFile]
-        rFile=opt.ref
-        if len(rFile)==0:
-            raise("Must provide reference file in query mode!")
+            qFileList = [qFile]
+        rFile = opt.ref
+        if len(rFile) == 0:
+            raise ("Must provide reference file in query mode!")
         else:
             ## check if reference cluster file exists
-            rFile0=re.sub('\\.txt','',rFile)
-            refClusterFile=rFile0+'--RotationEncodingBL62.txt'
+            rFile0 = re.sub("\\.txt", "", rFile)
+            refClusterFile = rFile0 + "--RotationEncodingBL62.txt"
             if not os.path.exists(refClusterFile):
-                raise("Must run clustering on reference file first! Did you forget to put the clustering file in this directory?")
-            rData=CreateReference(rFile)
-            t2=time.time()
-            print("Reference created. Elapsed %f" %(t2-t1))
+                raise (
+                    "Must run clustering on reference file first! Did you forget to put the clustering file in this directory?"
+                )
+            rData = CreateReference(rFile)
+            t2 = time.time()
+            print("Reference created. Elapsed %f" % (t2 - t1))
             for qf in qFileList:
-                t2_0=time.time()
-                print("Querying "+qf)
-                qf_s=qf.split('/')[-1]
-                #outFile=re.sub('\\.txt','',qf_s)+'_query_'+rFile0+'.txt'
-                outFile=os.path.splitext(qf_s)[0]+'_query_'+os.path.basename(rFile0)+'.txt'
-                of=OutDir+'/'+outFile
+                t2_0 = time.time()
+                print("Querying " + qf)
+                qf_s = qf.split("/")[-1]
+                # outFile=re.sub('\\.txt','',qf_s)+'_query_'+rFile0+'.txt'
+                outFile = (
+                    os.path.splitext(qf_s)[0]
+                    + "_query_"
+                    + os.path.basename(rFile0)
+                    + ".txt"
+                )
+                of = OutDir + "/" + outFile
                 if path.exists(of):
-                    print(of+' already exits. Skipping.')
+                    print(of + " already exits. Skipping.")
                     continue
                 MakeQuery(qf, rData, thr=cutoff, thr_s=thr_s)
-                t2=time.time()
-                print("     Build query clustering file. Elapsed %f" %(t2-t1))
+                t2 = time.time()
+                print("     Build query clustering file. Elapsed %f" % (t2 - t1))
                 print("Now mering with reference cluster")
-                MergeExist(refClusterFile, OutDir+'/'+outFile)
-                t2=time.time()
-                print("         Time of elapsed for query %s: %f" %(qf, t2-t2_0))
+                MergeExist(refClusterFile, OutDir + "/" + outFile)
+                t2 = time.time()
+                print("         Time of elapsed for query %s: %f" % (qf, t2 - t2_0))
     else:
         ## regular clustering mode
-        FileDir=opt.Directory
-        if len(FileDir)>0:
-                files=os.listdir(FileDir)
-                files0=[]
-                for ff in files:
-                        ff=FileDir+'/'+ff
-                        files0.append(ff)
-                files=files0
+        FileDir = opt.Directory
+        if len(FileDir) > 0:
+            files = os.listdir(FileDir)
+            files0 = []
+            for ff in files:
+                ff = FileDir + "/" + ff
+                files0.append(ff)
+            files = files0
         else:
-                files=[]
-        File=opt.File
-        if len(File)>0:
-                files=[File]
-        FileList=opt.files
-        if len(FileList)>0:
-                files=[]
-                fL=open(FileList)
-                for ff in fL.readlines():
-                        files.append(ff.strip())
-        VFa=opt.VFa
+            files = []
+        File = opt.File
+        if len(File) > 0:
+            files = [File]
+        FileList = opt.files
+        if len(FileList) > 0:
+            files = []
+            fL = open(FileList)
+            for ff in fL.readlines():
+                files.append(ff.strip())
+        VFa = opt.VFa
         PreCalculateVgeneDist(VFa)
-        vf=open('./VgeneScores.txt')  ## Use tcrDist's Vgene 80-score calculation
-        VScore={}
-        VV=opt.V
-        EE=opt.E
-        Mat=opt.Mat
-        ST=int(opt.ST)
-        thr_v=float(opt.thr_v)
-        verbose=opt.v
+        vf = open("./VgeneScores.txt")  ## Use tcrDist's Vgene 80-score calculation
+        VScore = {}
+        VV = opt.V
+        EE = opt.E
+        Mat = opt.Mat
+        ST = int(opt.ST)
+        thr_v = float(opt.thr_v)
+        verbose = opt.v
         if VV:
             while 1:
-                line=vf.readline()
-                if len(line)==0:
+                line = vf.readline()
+                if len(line) == 0:
                     break
-                ww=line.strip().split('\t')
-                VScore[(ww[0],ww[1])]=int(ww[2])/20
-                VScore[(ww[1],ww[0])]=int(ww[2])/20
-        Gap=int(opt.Gap)
-        Gapn=int(opt.GapN)
-        OutFile=opt.OutFile
-        GPU=opt.GPU
-        st=3
-        ed=1
-        NT=int(opt.NN)
+                ww = line.strip().split("\t")
+                VScore[(ww[0], ww[1])] = int(ww[2]) / 20
+                VScore[(ww[1], ww[0])] = int(ww[2]) / 20
+        Gap = int(opt.Gap)
+        Gapn = int(opt.GapN)
+        OutFile = opt.OutFile
+        GPU = opt.GPU
+        st = 3
+        ed = 1
+        NT = int(opt.NN)
         faiss.omp_set_num_threads(NT)
         for ff in files:
-            print("Processing %s" %ff)
-            EncodeRepertoire(ff, OutDir, OutFile, ST=ST, thr_s=thr_s, thr_v=thr_v, exact=EE,VDict=VScore, Vgene=VV, thr_iso=cutoff, gap=Gap, GPU=GPU, Mat=Mat, verbose=verbose)
-        
+            print("Processing %s" % ff)
+            EncodeRepertoire(
+                ff,
+                OutDir,
+                OutFile,
+                ST=ST,
+                thr_s=thr_s,
+                thr_v=thr_v,
+                exact=EE,
+                VDict=VScore,
+                Vgene=VV,
+                thr_iso=cutoff,
+                gap=Gap,
+                GPU=GPU,
+                Mat=Mat,
+                verbose=verbose,
+            )
+
+
 if __name__ == "__main__":
-    t0=time.time()
+    t0 = time.time()
     main()
-    print ("Total time elapsed: %f" %(time.time()-t0))
-    print ("Maximum memory usage: %f MB" %(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss/1000000))
-
+    print("Total time elapsed: %f" % (time.time() - t0))
+    print(
+        "Maximum memory usage: %f MB"
+        % (resource.getrusage(resource.RUSAGE_SELF).ru_maxrss / 1000000)
+    )