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Commit a3dd565d authored by Patrick J. Lawrence's avatar Patrick J. Lawrence
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Removed scripts relating to pssm

parent 2fdb501e
1 merge request!1Recover lost data
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mhc_rank/PSSM.py deleted 100644 → 0
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− 200
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from __future__ import (
print_function,
division,
absolute_import,
)
import pandas as pd
import numpy as np
import amino_acid
class PSSM(object):
"""
Class to retrieve PSSM scores for peptides length 8-15 and the n and c terminal
flanks up to length 5. These were calculated from MS observed hits in MHCflurry 2.0
data set (MULTIALLELIC-OLD)
"""
def define_scores(self): # Define the PSSM score CSVs for various kmers
scores = {
'8': pd.read_csv('../pssm_csvs/eight.csv', index_col=0),
'9': pd.read_csv('../pssm_csvs/nine.csv', index_col=0),
'10': pd.read_csv('../pssm_csvs/ten.csv', index_col=0),
'11': pd.read_csv('../pssm_csvs/eleven.csv', index_col=0),
'12': pd.read_csv('../pssm_csvs/twelve.csv', index_col=0),
'13': pd.read_csv('../pssm_csvs/thirteen.csv', index_col=0),
'14': pd.read_csv('../pssm_csvs/fourteen.csv', index_col=0),
'15': pd.read_csv('../pssm_csvs/fifteen.csv', index_col=0),
'n_flank': pd.read_csv('../pssm_csvs/n_flank.csv', index_col=0),
'c_flank': pd.read_csv('../pssm_csvs/c_flank.csv', index_col=0)
}
return scores
def __init__(self):
self.scores = self.define_scores()
self.score_types = list(self.scores.keys())
# create assertion function to confirm supplied score_type in valid options
def assert_type(self, score_type):
assert score_type in self.score_types, \
"Valid types: ['8', '9', '10', '11', '12', '13', '14', '15', 'n_flank', 'c_flank']"
def show_scores(self, score_type):
"""
Retrieve df containing PSSM specific for supplied peptide k-mer or flank
Parameters:
score_type (str): K-mer from which to pull PSSMs
Valid options: 8, 9, 10, 11, 12, 13, 14,
15, n_flank, c_flank
Returns:
pandas.core.frame.DataFrame: contains scores for the given type
"""
self.assert_type(score_type)
return self.scores[score_type]
def score_lookup(self, residue, position, score_type):
"""
Retrieve normalized PSSM score for a specific residue at
a given position in the supplied peptide k-mer or flank
Parameters:
score_type (str): K-mer from which to pull PSSMs
Valid options: 8, 9, 10, 11, 12, 13, 14,
15, n_flank, c_flank
residue (str): Amino acid that needs to be scores
position (int): Position of the amino acid within the k-mer
Returns:
float: PSSM score for residue at given position in k-mer
"""
self.assert_type(score_type)
df = self.scores[score_type]
assert int(position) < len(df.columns), "Supplied position exceeds sequence length"
return df.iloc[:,position][residue]
def seq_score(self, seq, score_type, max_length=15):
"""
Retrieve the normalized PSSMs for all the residues in a sequence of a specific k-mer
Parameters:
seq (str): Sequence for which to obtain PSSM score
score_type (str): K-mer from which to pull PSSMs
Valid options: 8, 9, 10, 11, 12, 13, 14,
15, n_flank, c_flank
max_length (int): Max length supplied sequence. (Default=15)
Returns:
list: contains the PSSM score for each of the amino acids
in the provided sequence.
"""
self.assert_type(score_type)
assert type(seq) is str, "Seq must be a str defining amino acids"
if 'flank' in score_type:
assert len(seq) == max_length, "Must first unify flank lengths to match max"
seq_score = []
# since flanks can vary in length (max 5) and the PSSMs dont change, need to
# retrieve PSSM scores of residues closest to the cleavage site (idx = 4) and
# move further away (toward idx=0). Once values obtained, list is reversed again
# to return correct order.
if score_type == 'n_flank':
seq = seq[::-1] # reverse sequence
for pos, res in enumerate(seq):
if res.upper() not in amino_acid.AMINO_ACIDS:
res = 'X'
# define position in flank starting from closest to cleave site and
# move further away (toward n terminus)
pos = -(pos + 1)
seq_score.append(self.score_lookup(res, pos, score_type))
seq_score.reverse()
else: # for c_flank and peptides, can go left to right
for pos, res in enumerate(seq):
if res.upper() not in amino_acid.AMINO_ACIDS:
res = 'X'
seq_score.append(self.score_lookup(res, pos, score_type))
length = len(seq_score)
diff = max_length - length
# identify peptides which are shorter than the max length to pad center
if score_type != 'c_flank' and diff > 0:
split = length // 2
if length % 2 != 0: # if length of peptide is odd
split += 1 # make larger end the n terminal end
xpad = []
# create pad that includes the PSSM for 'X' at the middle of the max len
# peptide, where pad is equal to the diff btwn max len and actual len
for i in range(diff):
position = split + i
xpad.append(self.score_lookup('X', position, str(max_length)))
seq_score = seq_score[:split] + xpad + seq_score[split:] # put pad in mid
elif score_type != 'c_flank' and diff < 0:
split1 = split2 = max_length // 2 # calc length that should be kept
if max_length % 2 != 0: # from each end of peptide
split1 += 1 # if max_length is odd, keep 1 more from n term side
seq_score= seq_score[:split1] + seq_score[-split2:] # trim
return seq_score
def get_flank(self, sequences, max_length=5):
"""
Retrieve all the PSSM scores for supplied flank sequences
of a uniform length given by max length
Parameters:
sequences (pd.Series): Flank sequences that need to have PSSM scores obtained
max_length (int): Max length supplied sequence
Returns:
np.array: each element of the series is an array containing the PSSMs for
all the residues in a flank sequence
"""
score_type = sequences.name #
assert 'flank' in score_type, "Must be obtaining PSSMs for either n_flank or c_flank"
return np.asarray([self.seq_score(seq, score_type, max_length) for seq in sequences])
def get_peptide(self, sequences, max_length=9):
"""
Retrieve all the PSSM scores for supplied peptide sequences. The k-mer for each
peptide in the list is determined by calculating its length
Parameters:
sequences (pd.Series): Sequences that need to have PSSM scores obtained
max_length (int): Max length supplied sequence
Returns:
np.array: each element of the series is a list containing the PSSMs for
all the residues in a peptide sequence
"""
assert sequences.name == 'peptide'
sequence_scores = []
for idx, sequence in enumerate(sequences):
score_type = str(len(sequence))
self.assert_type(score_type)
sequence_scores.append(self.seq_score(sequence, score_type, max_length))
return np.asarray(sequence_scores)
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mhc_rank/pssm_lookup.py deleted 100644 → 0
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pssm_csvs/c_flank.csv deleted 100644 → 0
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,0,1,2,3,4
A,0.819402985,0.865834633,0.830357143,0.914670659,0.929012346
C,0.32238806,0.28549142,0.272321429,0.398203593,0.320987654
D,0.595522388,0.588143526,0.629464286,0.658682635,0.663580247
E,0.794029851,0.840873635,0.816964286,0.848802395,0.780864198
F,0.531343284,0.55226209,0.498511905,0.55988024,0.5
G,0.71641791,0.689547582,0.595238095,0.729041916,0.722222222
H,0.371641791,0.358814353,0.401785714,0.402694611,0.313271605
I,0.641791045,0.691107644,0.610119048,0.520958084,0.458333333
K,0.770149254,0.755070203,0.77827381,0.785928144,0.675925926
L,1,1,1,1,1
M,0.373134328,0.391575663,0.360119048,0.444610778,0.345679012
N,0.525373134,0.524180967,0.607142857,0.624251497,0.549382716
P,0.608955224,0.63650546,0.443452381,0.335329341,0.160493827
Q,0.631343284,0.669266771,0.680059524,0.72754491,0.591049383
R,0.7,0.72074883,0.806547619,0.751497006,0.714506173
S,0.791044776,0.814352574,0.837797619,0.913173653,0.890432099
T,0.656716418,0.68798752,0.705357143,0.74251497,0.561728395
V,0.768656716,0.812792512,0.797619048,0.754491018,0.600308642
W,0,0,0,0,0
Y,0.423880597,0.432137285,0.446428571,0.491017964,0.418209877
X,0.602089552,0.615834633,0.605877976,0.630164671,0.559799383
\ No newline at end of file
pssm_csvs/eight.csv deleted 100644 → 0
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,0,1,2,3,4,5,6,7
A,0.931670282,0.972508591,0.841158841,0.743005181,0.934443288,0.851590106,0.945492662,0.552508751
C,0,0,0,0,0,0,0.199161426,0
D,0.776572668,0.708762887,1,0.65388601,0.430801249,0.447585395,0.520964361,0.250875146
E,0.644251627,1,0.609390609,0.894300518,0.616024974,0.790341578,1,0.26487748
F,0.939262473,0.684707904,0.894105894,0.591709845,1,0.660777385,0.594339623,0.737456243
G,0.571583514,0.679553265,0.808191808,0.647668394,0.939646202,0.574793875,0.715932914,0.149941657
H,0.729934924,0.569587629,0.653346653,0.524352332,0.786680541,0.817432273,0.690775681,0.314469078
I,0.913232104,0.717353952,0.821178821,0.855958549,0.890738814,0.825677267,0.679245283,0.729288215
K,0.789587852,0.382302405,0.795204795,0.923316062,0.783558793,0.790341578,0.971698113,0.603850642
L,0.963123644,0.798969072,0.923076923,1,0.924037461,1,0.970649895,1
M,0.572668113,0.420103093,0.498501499,0.328497409,0.393340271,0.386336867,0.448637317,0.621936989
N,0.64208243,0.60395189,0.658341658,0.63626943,0.518210198,0.727915194,0.737945493,0.124270712
P,0.428416486,0.894329897,0.811188811,0.884974093,0.890738814,0.944640754,0.597484277,0.253208868
Q,0.556399132,0.770618557,0.633366633,0.696373057,0.623309053,0.810365135,0.80293501,0.242707118
R,0.810195228,0.66838488,0.681318681,0.767875648,0.764828304,0.885747939,0.805031447,0.574095683
S,0.976138829,0.902920962,0.748251748,0.76373057,0.831425598,0.895170789,0.962264151,0.248541424
T,0.844902386,0.786941581,0.713286713,0.819689119,0.764828304,0.857479388,0.912997904,0.35764294
V,1,0.75,0.843156843,0.956476684,0.994797086,0.989399293,0.975890985,0.782963827
W,0.111713666,0.141752577,0.420579421,0.117098446,0.136316337,0.241460542,0,0.526254376
Y,0.876355748,0.645189003,0.883116883,0.497409326,0.785639958,0.573616019,0.596436059,0.710618436
X,0.703904555,0.654896907,0.711838162,0.665129534,0.700468262,0.703533569,0.70639413,0.452275379
\ No newline at end of file
pssm_csvs/eleven.csv deleted 100644 → 0
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,0,1,2,3,4,5,6,7,8,9,10
A,0.963585434,0.812903226,0.874524715,0.827263267,0.951247166,0.892938497,0.961916462,0.840144231,0.783333333,0.884279476,0.671149966
C,0,0,0,0,0,0,0,0,0,0.163755459,0
D,0.567693744,0.31797235,0.742712294,1,0.867346939,0.907744875,0.84029484,0.606971154,0.54047619,0.438864629,0.315400134
E,0.764705882,0.919815668,0.57287706,0.971904266,0.970521542,0.945330296,0.921375921,0.735576923,0.729761905,0.800218341,0.432414257
F,0.713352007,0.464516129,0.884664132,0.506763788,0.580498866,0.555808656,0.546683047,0.637019231,0.603571429,0.631004367,0.899798252
G,0.81512605,0.521658986,0.466413181,0.889698231,0.914965986,0.981776765,1,0.897836538,0.632142857,0.778384279,0.326160054
H,0.663865546,0.481105991,0.342205323,0.443288241,0.504535147,0.54214123,0.536855037,0.423076923,0.579761905,0.542576419,0.357094822
I,0.732026144,0.655299539,0.874524715,0.554630593,0.731292517,0.767653759,0.76044226,0.832932692,0.79047619,0.588427948,0.665770007
K,0.936507937,0.309677419,0.662864385,0.719042664,0.725623583,0.833712984,0.852579853,0.752403846,0.65952381,0.855895197,0.874243443
L,0.823529412,0.918894009,1,0.829344433,0.921768707,0.945330296,0.964373464,1,1,1,1
M,0.541549953,0.423041475,0.513307985,0.271592092,0.325396825,0.313211845,0.291154791,0.295673077,0.43452381,0.385371179,0.579690652
N,0.524743231,0.252534562,0.518377693,0.669094693,0.790249433,0.719817768,0.697788698,0.651442308,0.61547619,0.63209607,0.290517821
P,0.318394024,0.848847926,0.556400507,0.985431842,1,0.898633257,0.836609337,0.728365385,0.545238095,0.59279476,0.339609953
Q,0.64799253,0.621198157,0.54626109,0.697190427,0.744897959,0.72095672,0.721130221,0.651442308,0.780952381,0.804585153,0.345662408
R,1,1,0.575411914,0.598335068,0.598639456,0.700455581,0.642506143,0.625,0.71547619,0.779475983,0.855413584
S,0.940242764,0.840552995,0.747782003,0.911550468,0.952380952,1,0.963144963,0.810096154,0.810714286,0.945414847,0.371217216
T,0.779645191,0.865437788,0.401774398,0.729448491,0.784580499,0.854214123,0.821867322,0.724759615,0.777380952,0.915938865,0.37995965
V,0.790849673,0.875576037,0.761723701,0.662851197,0.861678005,0.834851936,0.861179361,0.830528846,0.897619048,0.854803493,0.716879623
W,0.081232493,0.087557604,0.321926489,0.129032258,0.156462585,0.0523918,0.015970516,0,0.169047619,0,0.793544048
Y,0.672268908,0.630414747,0.747782003,0.465140479,0.48185941,0.422551253,0.465601966,0.461538462,0.470238095,0.641921397,0.886348352
X,0.663865546,0.59235023,0.605576679,0.643080125,0.693197279,0.694476082,0.68507371,0.625240385,0.626785714,0.661790393,0.555043712
\ No newline at end of file
pssm_csvs/fifteen.csv deleted 100644 → 0
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,0,1,2,3,4,5,6,7,8,9,10,11,12,13,14
A,0.914438503,0.909287257,0.967121091,0.825870647,0.912835249,0.851769912,0.903943377,0.866805411,0.888994307,0.941591138,0.839814815,0.911708253,0.942016807,0.95,0.774846086
C,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
D,0.598039216,0.718142549,0.897353649,0.891542289,0.828544061,0.744469027,0.814964611,0.813735692,0.862428843,0.84592145,0.84537037,0.798464491,0.78487395,0.816,0.733509235
E,0.676470588,0.812095032,0.948676824,0.898507463,0.850574713,0.849557522,0.88372093,0.902185224,0.858633776,0.846928499,0.894444444,0.880998081,0.948739496,0.898,0.89533861
F,0.647950089,0.623110151,0.920609463,0.635820896,0.659961686,0.585176991,0.634984833,0.662851197,0.512333966,0.582074522,0.575,0.666986564,0.728571429,0.647,0.884784521
G,0.901960784,1,1,1,1,1,1,1,1,1,1,1,1,0.963,0.744942832
H,0.780748663,0.427645788,0.546110666,0.525373134,0.495210728,0.475663717,0.434782609,0.605619147,0.498102467,0.599194361,0.596296296,0.527831094,0.643697479,0.526,0.437994723
I,0.663101604,0.75161987,0.897353649,0.711442786,0.781609195,0.740044248,0.699696663,0.686784599,0.736242884,0.725075529,0.74537037,0.692898273,0.841176471,0.794,0.539138083
K,0.751336898,0.585313175,0.865276664,0.694527363,0.696360153,0.721238938,0.70677452,0.781477627,0.709677419,0.789526687,0.799074074,0.716890595,0.823529412,0.843,0.990325418
L,0.770053476,0.980561555,0.943865277,0.827860697,0.868773946,0.873893805,0.869565217,0.975026015,0.865275142,0.833836858,0.812962963,0.842610365,0.948739496,1,0.944591029
M,0.446524064,0.455723542,0.563753007,0.254726368,0.457854406,0.403761062,0.440849343,0.340270552,0.383301708,0.319234642,0.47037037,0.439539347,0.468067227,0.344,0.537379068
N,0.608734403,0.630669546,0.743384122,0.63880597,0.74137931,0.64159292,0.684529828,0.711758585,0.720113852,0.715005035,0.712037037,0.706333973,0.742857143,0.713,0.72823219
P,0.53030303,0.962203024,0.932638332,0.846766169,0.880268199,0.836283186,0.845298281,0.964620187,0.837760911,0.90835851,0.865740741,0.861804223,0.85210084,0.894,0.569920844
Q,0.511586453,0.761339093,0.847634322,0.712437811,0.722222222,0.678097345,0.783619818,0.783558793,0.726755218,0.700906344,0.706481481,0.695777351,0.819327731,0.759,0.678979771
R,0.786987522,0.943844492,0.811547715,0.595024876,0.631226054,0.585176991,0.572295248,0.696149844,0.634724858,0.572004028,0.634259259,0.661228407,0.805042017,0.768,1
S,1,0.976241901,0.910986367,0.862686567,0.907088123,0.911504425,0.923154702,0.983350676,0.861480076,0.939577039,0.92962963,0.931861804,0.976470588,0.98,0.772207564
T,0.899286988,0.853131749,0.824378508,0.760199005,0.776819923,0.82079646,0.823053589,0.82830385,0.758064516,0.813695871,0.737962963,0.770633397,0.917647059,0.878,0.649076517
V,0.782531194,0.928725702,0.855653569,0.812935323,0.888888889,0.838495575,0.804853387,0.849115505,0.79886148,0.825780463,0.875,0.780230326,0.937815126,0.934,0.669305189
W,0.092691622,0.153347732,0.450681636,0.237810945,0.229885057,0,0.062689585,0.079084287,0.189753321,0.07653575,0.200925926,0.121880998,0.226890756,0.087,0.591908531
Y,0.642602496,0.601511879,0.812349639,0.608955224,0.712643678,0.544247788,0.564206269,0.62226847,0.625237192,0.597180262,0.512037037,0.665067179,0.667226891,0.58,0.922603342
X,0.65026738,0.703725702,0.786968725,0.667064677,0.70210728,0.655088496,0.672649141,0.707648283,0.673387097,0.681621349,0.687638889,0.683637236,0.753739496,0.7187,0.703254178
\ No newline at end of file
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,0,1,2,3,4,5,6,7,8,9,10,11,12,13
A,0.898859316,0.907763259,0.960111317,0.827380952,0.938547486,0.861087866,0.870333988,0.879310345,0.889784946,0.854779412,0.876404494,0.828804348,0.933106576,0.788492707
C,0,0,0,0,0,0,0,0,0,0,0,0,0,0
D,0.634220532,0.794004612,0.924860853,0.895408163,0.814711359,0.908786611,0.816306483,0.875478927,0.858422939,0.817095588,0.737487232,0.641304348,0.639455782,0.719611021
E,0.753612167,0.873174481,0.95825603,0.900510204,0.872439479,0.890376569,0.888998035,0.946360153,0.846774194,0.870404412,0.86721144,0.876358696,0.924036281,0.846839546
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G,0.873764259,0.930822444,0.974953618,1,1,1,1,1,1,1,1,0.914402174,0.882086168,0.744732577
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I,0.709505703,0.774788624,0.896103896,0.714285714,0.800744879,0.756485356,0.650294695,0.731800766,0.67562724,0.657169118,0.728294178,0.680706522,0.780045351,0.553484603
K,0.77338403,0.764027671,0.815398887,0.707482993,0.732774674,0.744769874,0.756385069,0.784482759,0.834229391,0.730698529,0.676200204,0.710597826,0.824263039,0.988654781
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M,0.519391635,0.480399693,0.572356215,0.385204082,0.49255121,0.533891213,0.362475442,0.324712644,0.392473118,0.367647059,0.3340143,0.213315217,0.299319728,0.471636953
N,0.641825095,0.686395081,0.689239332,0.716836735,0.629422719,0.769037657,0.714145383,0.754789272,0.71953405,0.669117647,0.741573034,0.625,0.697278912,0.671799028
P,0.559695817,0.950038432,0.930426716,0.87755102,0.907821229,0.848535565,0.876227898,0.880268199,0.887096774,0.854779412,0.835546476,0.64673913,0.833333333,0.569692058
Q,0.586311787,0.811683321,0.827458256,0.729591837,0.765363128,0.759832636,0.73870334,0.744252874,0.764336918,0.725183824,0.705822268,0.725543478,0.792517007,0.669367909
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S,1,0.970023059,0.932282004,0.892857143,0.945065177,0.972384937,0.918467583,0.963601533,0.896953405,0.914522059,0.865168539,1,1,0.773905997
T,0.926235741,0.914681015,0.908163265,0.75085034,0.846368715,0.876150628,0.859528487,0.818965517,0.785842294,0.835477941,0.765066394,0.828804348,0.878684807,0.611831442
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Y,0.641825095,0.763259032,0.865491651,0.603741497,0.662011173,0.605857741,0.607072692,0.574712644,0.598566308,0.533088235,0.575076609,0.309782609,0.548752834,0.995137763
X,0.683840304,0.75622598,0.803200371,0.68422619,0.714571695,0.725104603,0.687573674,0.699760536,0.696415771,0.670818015,0.664300306,0.634578804,0.681122449,0.70834684
\ No newline at end of file
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,0,1,2,3,4
A,0.988984088,0.855051245,0.886255924,0.842662632,0.856012658
C,0.522643819,0.29136164,0.249605055,0.323751891,0.262658228
D,0.625458996,0.701317716,0.701421801,0.680786687,0.735759494
E,0.755201958,0.799414348,0.872037915,0.836611195,0.900316456
F,0.521419829,0.469985359,0.58135861,0.549167927,0.561708861
G,0.835985312,0.8477306,0.812006319,0.810892587,0.824367089
H,0.619339045,0.376281113,0.458135861,0.428139183,0.416139241
I,0.494492044,0.63250366,0.592417062,0.686838124,0.675632911
K,0.958384333,0.881405564,0.778830964,0.792738275,0.830696203
L,0.898408813,1,1,1,1
M,0.476132191,0.409956076,0.314375987,0.340393343,0.324367089
N,0.70624235,0.651537335,0.600315956,0.621785174,0.620253165
P,0.620563035,0.631039531,0.628751975,0.768532526,0.786392405
Q,0.801713586,0.70863836,0.690363349,0.691376702,0.731012658
R,0.929008568,0.840409956,0.726698262,0.736762481,0.789556962
S,1,0.865300146,0.892575039,0.854765507,0.89556962
T,0.7625459,0.693997072,0.70300158,0.703479576,0.716772152
V,0.76499388,0.74670571,0.733017378,0.797276853,0.789556962
W,0,0,0,0,0
Y,0.496940024,0.364568082,0.423380727,0.443267776,0.414556962
X,0.688922889,0.638360176,0.632227488,0.645461422,0.656566456
\ No newline at end of file
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,0,1,2,3,4,5,6,7,8
A,0.990142388,0.937293729,0.978843441,0.813137033,0.837086093,0.787564767,0.785202864,0.9375,0.63756773
C,0,0,0,0,0,0,0,0.1875,0
D,0.525739321,0.358085809,0.915373766,0.929784824,0.654304636,0.414507772,0.446300716,0.426339286,0.003612282
E,0.732749179,0.918316832,0.509167842,1,0.761589404,0.590673575,0.754176611,0.934151786,0.17037929
F,0.864184009,0.636138614,0.888575458,0.554926387,0.789403974,0.738341969,0.637231504,0.643973214,0.835039133
G,0.771084337,0.520627063,0.500705219,0.857304643,0.862251656,0.733160622,0.402147971,0.722098214,0.125827815
H,0.654983571,0.578382838,0.537376587,0.472253681,0.668874172,0.450777202,0.650357995,0.604910714,0.388922336
I,0.801752464,0.77310231,0.915373766,0.611551529,0.904635762,0.932642487,0.782816229,0.588169643,0.751956653
K,0.941949617,0.369636964,0.791255289,0.791619479,0.891390728,0.651554404,0.621718377,0.872767857,0.7128236
L,0.903614458,1,1,0.835787089,1,1,1,0.941964286,1
M,0.576122673,0.603960396,0.54583921,0.252548131,0.332450331,0.327720207,0.349642005,0.370535714,0.633353402
N,0.623220153,0.334158416,0.730606488,0.672706682,0.774834437,0.534974093,0.595465394,0.676339286,0.062010837
P,0.071193866,0.881188119,0.71932299,0.993204983,0.892715232,0.788860104,0.737470167,0.597098214,0.304635762
Q,0.641840088,0.737623762,0.598025388,0.69988675,0.674172185,0.64119171,0.705250597,0.808035714,0.153521975
R,0.948521358,0.947194719,0.650211566,0.638731597,0.82781457,0.647668394,0.664677804,0.768973214,0.705599037
S,1,0.839933993,0.84203103,0.857304643,0.847682119,0.769430052,0.776849642,1,0.217940999
T,0.796276013,0.847359736,0.648801128,0.696489241,0.786754967,0.791450777,0.786396181,0.950892857,0.32871764
V,0.853231106,0.874587459,0.819464034,0.693091733,0.98013245,0.948186528,0.88424821,0.876116071,0.818181818
W,0.116100767,0.171617162,0.244005642,0.182332956,0.260927152,0.037564767,0.238663484,0,0.606863335
Y,0.813800657,0.722772277,0.791255289,0.429218573,0.601324503,0.448186528,0.528639618,0.637276786,0.822396147
X,0.681325301,0.65259901,0.681311707,0.649093998,0.717417219,0.611722798,0.617362768,0.677232143,0.463967489
\ No newline at end of file
pssm_csvs/ten.csv deleted 100644 → 0
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View file @ 2fdb501e
,0,1,2,3,4,5,6,7,8,9
A,0.991561181,0.8,0.901146132,0.782886335,0.874471086,0.852777778,0.735969388,0.835800808,0.908323281,0.676985195
C,0,0,0,0,0,0,0,0,0.138721351,0
D,0.494725738,0.294495413,0.775071633,0.979565773,0.812411848,0.718055556,0.557397959,0.520861373,0.431845597,0.200538358
E,0.797468354,0.977981651,0.510028653,1,0.857545839,0.805555556,0.654336735,0.796769852,0.858866104,0.283983849
F,0.803797468,0.562385321,0.905444126,0.476372925,0.715091678,0.6125,0.698979592,0.554508748,0.674306393,0.897711978
G,0.839662447,0.490825688,0.475644699,0.88633461,1,0.919444444,0.860969388,0.574697174,0.816646562,0.239569314
H,0.667721519,0.467889908,0.359598854,0.378033206,0.486600846,0.469444444,0.410714286,0.566621803,0.529553679,0.338492598
I,0.759493671,0.706422018,0.888252149,0.528735632,0.765867419,0.8375,0.789540816,0.799461642,0.580217129,0.708613728
K,0.952531646,0.331192661,0.630372493,0.729246488,0.708039492,0.816666667,0.704081633,0.650067295,0.849215923,0.837146703
L,0.882911392,0.983486239,1,0.802043423,0.961918195,1,1,1,1,1
M,0.564345992,0.543119266,0.517191977,0.181353768,0.242595205,0.304166667,0.331632653,0.372812921,0.316043426,0.605652759
N,0.523206751,0.232110092,0.574498567,0.647509579,0.706629055,0.618055556,0.628826531,0.65141319,0.652593486,0.182368775
P,0.19092827,0.866055046,0.659025788,0.957854406,0.919605078,0.894444444,0.802295918,0.69179004,0.598311218,0.286002692
Q,0.63185654,0.665137615,0.462750716,0.694763729,0.606488011,0.672222222,0.581632653,0.737550471,0.763570567,0.224764468
R,1,1,0.532951289,0.575989783,0.564174894,0.673611111,0.602040816,0.65141319,0.776839566,0.786675639
S,0.950421941,0.828440367,0.720630372,0.882503193,0.847672779,0.893055556,0.721938776,0.837146703,0.998793727,0.282637954
T,0.767932489,0.87706422,0.505730659,0.679438059,0.695345557,0.841666667,0.68622449,0.846567968,0.943305187,0.407806191
V,0.796413502,0.872477064,0.779369628,0.593869732,0.840620592,0.886111111,0.793367347,0.946164199,0.828709288,0.778600269
W,0.103375527,0.151376147,0.219197708,0.005108557,0.063469676,0.006944444,0.028061224,0.083445491,0,0.743606999
Y,0.733122363,0.626605505,0.766475645,0.407407407,0.459802539,0.45,0.452806122,0.444145357,0.667068758,0.886944818
X,0.67257384,0.613853211,0.609169054,0.60945083,0.656417489,0.663611111,0.602040816,0.628061911,0.666646562,0.518405114
\ No newline at end of file
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View file @ 2fdb501e
,0,1,2,3,4,5,6,7,8,9,10,11,12
A,0.990393013,0.820512821,0.848816029,0.843564356,0.93161435,0.88852459,0.887154862,0.887931034,0.877118644,0.950113379,0.850613155,0.893203883,0.743289745
C,0,0,0,0,0,0,0,0,0,0,0,0.114347357,0
D,0.691703057,0.615384615,0.870673953,0.991089109,0.862107623,0.90273224,0.951980792,0.825431034,0.800847458,0.700680272,0.643255295,0.551240561,0.584308328
E,0.755458515,0.841025641,0.845173042,0.940594059,0.966367713,0.957377049,0.93637455,0.793103448,0.92690678,0.826530612,0.816053512,0.842502697,0.764624914
F,0.715283843,0.577777778,0.951730419,0.576237624,0.607623318,0.547540984,0.4969988,0.600215517,0.620762712,0.659863946,0.62541806,0.622437972,0.905024088
G,0.912663755,0.774358974,0.806921676,1,1,1,1,1,1,1,0.88851728,0.846817691,0.641431521
H,0.758078603,0.383760684,0.475409836,0.44950495,0.465246637,0.476502732,0.454981993,0.454741379,0.574152542,0.461451247,0.525083612,0.510248112,0.485203028
I,0.752838428,0.690598291,0.897996357,0.672277228,0.764573991,0.766120219,0.75270108,0.672413793,0.668432203,0.790249433,0.801560758,0.64832794,0.611837577
K,0.939737991,0.512820513,0.733151184,0.694059406,0.670403587,0.797814208,0.779111645,0.712284483,0.854872881,0.755102041,0.678929766,0.817691478,0.924294563
L,0.820087336,0.927350427,1,0.852475248,0.912556054,0.901639344,0.968787515,0.869612069,0.833686441,0.934240363,1,1,0.971094288
M,0.539737991,0.452136752,0.630236794,0.327722772,0.372197309,0.363934426,0.234093637,0.245689655,0.278601695,0.386621315,0.554069119,0.374325782,0.60220234
N,0.56768559,0.505982906,0.649362477,0.663366337,0.633408072,0.689617486,0.733493397,0.663793103,0.718220339,0.639455782,0.65328874,0.645091694,0.617343427
P,0.655895197,0.865811966,0.77140255,0.955445545,0.980941704,0.856830601,0.865546218,0.859913793,0.850635593,0.843537415,0.674470457,0.731391586,0.52512044
Q,0.663755459,0.671794872,0.704918033,0.705940594,0.717488789,0.784699454,0.763505402,0.699353448,0.738347458,0.700680272,0.754738016,0.809061489,0.621472815
R,0.982532751,1,0.743169399,0.597029703,0.618834081,0.654644809,0.572629052,0.591594828,0.688559322,0.645124717,0.80490524,0.742179072,0.915347557
S,1,0.911111111,0.79417122,0.922772277,0.945067265,0.998907104,0.93637455,0.924568966,0.924788136,0.890022676,0.914158305,0.94390507,0.622161046
T,0.931004367,0.888034188,0.697632058,0.798019802,0.815022422,0.866666667,0.807923169,0.82112069,0.771186441,0.821995465,0.84057971,0.90399137,0.534755678
V,0.836681223,0.881196581,0.829690346,0.708910891,0.918161435,0.852459016,0.836734694,0.800646552,0.796610169,0.87755102,0.905239688,0.870550162,0.687543014
W,0.080349345,0.209401709,0.545537341,0.194059406,0.118834081,0.240437158,0.015606242,0.101293103,0.109110169,0.100907029,0.205128205,0,0.81761872
Y,0.71441048,0.704273504,0.839708561,0.504950495,0.548206278,0.589071038,0.527010804,0.412715517,0.465042373,0.540816327,0.460423634,0.57605178,1
X,0.715414847,0.661666667,0.731785064,0.66990099,0.692432735,0.706775956,0.67605042,0.646821121,0.674894068,0.676247166,0.679821628,0.672168285,0.678733655
\ No newline at end of file
pssm_csvs/twelve.csv deleted 100644 → 0
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View file @ 2fdb501e
,0,1,2,3,4,5,6,7,8,9,10,11
A,1,0.808492201,0.912100457,0.807770961,0.937573616,0.902073733,0.866336634,0.931222707,0.941176471,0.871915394,0.87345679,0.680486061
C,0,0,0,0,0,0,0,0,0,0,0.181069959,0
D,0.635496183,0.5,0.810502283,1,0.842167256,1,0.85049505,0.793668122,0.694373402,0.659224442,0.505144033,0.539671194
E,0.819656489,0.878682842,0.735159817,0.933537832,0.903415783,0.976958525,0.873267327,0.86790393,0.832480818,0.810810811,0.778806584,0.644031451
F,0.727099237,0.567590988,0.960045662,0.525562372,0.631330978,0.559907834,0.510891089,0.532751092,0.676470588,0.663924794,0.602880658,0.934953538
G,0.878816794,0.649913345,0.728310502,0.935582822,0.961130742,0.99078341,1,1,0.996163683,0.856639248,0.808641975,0.517512509
H,0.675572519,0.451473137,0.382420091,0.435582822,0.404004711,0.451612903,0.532673267,0.490174672,0.418158568,0.599294947,0.50617284,0.44031451
I,0.757633588,0.678509532,0.907534247,0.563394683,0.787985866,0.73156682,0.672277228,0.698689956,0.864450128,0.821386604,0.667695473,0.620443174
K,0.939885496,0.455805893,0.756849315,0.689161554,0.630153121,0.806451613,0.838613861,0.812227074,0.795396419,0.745005875,0.797325103,0.962115797
L,0.83778626,0.92287695,1,0.806748466,0.989399293,0.929723502,0.881188119,0.875545852,1,1,1,1
M,0.51240458,0.413344887,0.586757991,0.261758691,0.335689046,0.314516129,0.35049505,0.286026201,0.28516624,0.485311398,0.390946502,0.586132952
N,0.536259542,0.435875217,0.525114155,0.667689162,0.676089517,0.729262673,0.711881188,0.659388646,0.691815857,0.67920094,0.625514403,0.458184417
P,0.43129771,0.851819757,0.649543379,0.933537832,1,0.8640553,0.86039604,0.802401747,0.8657289,0.659224442,0.616255144,0.477483917
Q,0.634541985,0.632582322,0.614155251,0.691206544,0.731448763,0.728110599,0.723762376,0.723799127,0.727621483,0.803760282,0.764403292,0.523230879
R,1,1,0.690639269,0.534764826,0.553592462,0.658986175,0.632673267,0.620087336,0.643222506,0.761457109,0.74691358,0.884203002
S,0.977099237,0.883882149,0.751141553,0.938650307,0.959952886,0.989631336,0.917821782,0.894104803,0.913043478,0.916568743,0.943415638,0.531808435
T,0.889312977,0.880415945,0.626712329,0.761758691,0.823321555,0.861751152,0.795049505,0.810043668,0.87084399,0.890716804,0.889917695,0.497498213
V,0.823473282,0.880415945,0.840182648,0.688139059,0.885747939,0.851382488,0.827722772,0.798034934,0.875959079,0.947121034,0.866255144,0.677626876
W,0.041984733,0.079722704,0.478310502,0.103271984,0.111896349,0.080645161,0.12970297,0.175764192,0.125319693,0.286721504,0,0.852037169
Y,0.723282443,0.597920277,0.821917808,0.467280164,0.577149588,0.459677419,0.496039604,0.40720524,0.462915601,0.524089307,0.577160494,0.962830593
X,0.692080153,0.628466205,0.688869863,0.637269939,0.687102473,0.694354839,0.673564356,0.658951965,0.684015345,0.699118684,0.657098765,0.639528234
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