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annotate plotWheels/core.py @ 2:e9fb56f44c35 draft default tip

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author cpt
date Fri, 05 Jan 2024 05:52:58 +0000
parents 9b276485c94a
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1 # -*- coding: utf-8 -*-
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2 """
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3 .. currentmodule:: modlamp.core
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4
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5 .. moduleauthor:: modlab Alex Mueller ETH Zurich <alex.mueller@pharma.ethz.ch>
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7 Core helper functions and classes for other modules. The two main classes are:
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8
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9 ============================= =======================================================================================
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10 Class Characteristics
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11 ============================= =======================================================================================
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12 :py:class:`BaseSequence` Base class inheriting to all sequence classes in the module :py:mod:`modlamp.sequences`
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13 :py:class:`BaseDescriptor` Base class inheriting to the two descriptor classes in :py:mod:`modlamp.descriptors`
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14 ============================= =======================================================================================
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15 """
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16
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17 import os
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18 import random
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19 import re
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20
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21 import numpy as np
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22 import pandas as pd
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23 import collections
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24 import operator
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25 from scipy.spatial import distance
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26 from sklearn.preprocessing import MinMaxScaler, StandardScaler
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27 from sklearn.utils import shuffle
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28
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29 __author__ = "Alex Müller, Gisela Gabernet"
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30 __docformat__ = "restructuredtext en"
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32
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33 class BaseSequence(object):
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34 """Base class for sequence classes in the module :mod:`modlamp.sequences`.
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35 It contains amino acid probabilities for different sequence generation classes.
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36
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37 The following amino acid probabilities are used: (extracted from the
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38 `APD3 <http://aps.unmc.edu/AP/statistic/statistic.php>`_, March 17, 2016)
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39
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40 === ==== ====== ========= ==========
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41 AA rand AMP AMPnoCM randnoCM
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42 === ==== ====== ========= ==========
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43 A 0.05 0.0766 0.0812275 0.05555555
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44 C 0.05 0.071 0.0 0.0
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45 D 0.05 0.026 0.0306275 0.05555555
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46 E 0.05 0.0264 0.0310275 0.05555555
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47 F 0.05 0.0405 0.0451275 0.05555555
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48 G 0.05 0.1172 0.1218275 0.05555555
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49 H 0.05 0.021 0.0256275 0.05555555
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50 I 0.05 0.061 0.0656275 0.05555555
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51 K 0.05 0.0958 0.1004275 0.05555555
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52 L 0.05 0.0838 0.0884275 0.05555555
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53 M 0.05 0.0123 0.0 0.0
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54 N 0.05 0.0386 0.0432275 0.05555555
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55 P 0.05 0.0463 0.0509275 0.05555555
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56 Q 0.05 0.0251 0.0297275 0.05555555
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57 R 0.05 0.0545 0.0591275 0.05555555
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58 S 0.05 0.0613 0.0659275 0.05555555
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59 T 0.05 0.0455 0.0501275 0.05555555
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60 V 0.05 0.0572 0.0618275 0.05555555
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61 W 0.05 0.0155 0.0201275 0.05555555
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62 Y 0.05 0.0244 0.0290275 0.05555555
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63 === ==== ====== ========= ==========
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64
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65 """
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66
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67 def __init__(self, seqnum, lenmin=7, lenmax=28):
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68 """
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69 :param seqnum: number of sequences to generate
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70 :param lenmin: minimal length of the generated sequences
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71 :param lenmax: maximal length of the generated sequences
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72 :return: attributes :py:attr:`seqnum`, :py:attr:`lenmin` and :py:attr:`lenmax`.
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73 :Example:
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74
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75 >>> b = BaseSequence(10, 7, 28)
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76 >>> b.seqnum
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77 10
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78 >>> b.lenmin
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79 7
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80 >>> b.lenmax
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81 28
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82 """
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83 self.sequences = list()
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84 self.names = list()
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85 self.lenmin = int(lenmin)
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86 self.lenmax = int(lenmax)
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87 self.seqnum = int(seqnum)
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88
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89 # AA classes:
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90 self.AA_hyd = ["G", "A", "L", "I", "V"]
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91 self.AA_basic = ["K", "R"]
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92 self.AA_acidic = ["D", "E"]
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93 self.AA_aroma = ["W", "Y", "F"]
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94 self.AA_polar = ["S", "T", "Q", "N"]
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95 # AA labels:
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96 self.AAs = [
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97 "A",
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98 "C",
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99 "D",
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100 "E",
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101 "F",
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102 "G",
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103 "H",
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104 "I",
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105 "K",
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106 "L",
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107 "M",
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108 "N",
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109 "P",
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110 "Q",
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111 "R",
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112 "S",
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113 "T",
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114 "V",
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115 "W",
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116 "Y",
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117 ]
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118 # AA probability from the APD3 database:
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119 self.prob_AMP = [
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
120 0.0766,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
121 0.071,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
122 0.026,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
123 0.0264,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
124 0.0405,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
125 0.1172,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
126 0.021,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
127 0.061,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
128 0.0958,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
129 0.0838,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
130 0.0123,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
131 0.0386,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
132 0.0463,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
133 0.0251,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
134 0.0545,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
135 0.0613,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
136 0.0455,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
137 0.0572,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
138 0.0155,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
139 0.0244,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
140 ]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
141 # AA probability from the APD2 database without Cys and Met (synthesis reasons)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
142 self.prob_AMPnoCM = [
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
143 0.081228,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
144 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
145 0.030627,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
146 0.031027,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
147 0.045128,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
148 0.121828,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
149 0.025627,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
150 0.065628,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
151 0.100428,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
152 0.088428,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
153 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
154 0.043228,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
155 0.050928,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
156 0.029728,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
157 0.059128,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
158 0.065927,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
159 0.050128,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
160 0.061828,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
161 0.020128,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
162 0.029028,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
163 ]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
164 # equal AA probabilities:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
165 self.prob = [
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
166 0.05,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
167 0.05,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
168 0.05,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
169 0.05,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
170 0.05,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
171 0.05,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
172 0.05,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
173 0.05,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
174 0.05,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
175 0.05,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
176 0.05,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
177 0.05,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
178 0.05,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
179 0.05,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
180 0.05,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
181 0.05,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
182 0.05,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
183 0.05,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
184 0.05,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
185 0.05,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
186 ]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
187 # equal AA probabilities but 0 for Cys and Met:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
188 self.prob_randnoCM = [
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
189 0.05555555555,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
190 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
191 0.05555555555,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
192 0.05555555555,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
193 0.05555555555,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
194 0.05555555555,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
195 0.05555555555,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
196 0.05555555555,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
197 0.05555555555,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
198 0.05555555555,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
199 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
200 0.05555555555,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
201 0.05555555555,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
202 0.05555555555,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
203 0.05555555555,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
204 0.05555555555,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
205 0.05555555555,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
206 0.05555555555,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
207 0.05555555555,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
208 0.05555555555,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
209 ]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
210
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
211 # AA probability from the linear CancerPPD peptides:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
212 self.prob_ACP = [
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
213 0.14526966,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
214 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
215 0.00690031,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
216 0.00780824,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
217 0.06991102,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
218 0.04957327,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
219 0.01725077,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
220 0.05647358,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
221 0.27637552,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
222 0.17759216,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
223 0.00998729,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
224 0.00798983,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
225 0.01307427,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
226 0.00381333,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
227 0.02941711,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
228 0.02651171,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
229 0.0154349,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
230 0.04013074,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
231 0.0406755,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
232 0.00581079,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
233 ]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
234
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
235 # AA probabilities for perfect amphipathic helix of different arc sizes
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
236 self.prob_amphihel = [
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
237 [
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
238 0.04545455,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
239 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
240 0.04545454,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
241 0.04545455,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
242 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
243 0.04545455,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
244 0.04545455,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
245 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
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9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
630 0.01612903,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
631 0.20967742,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
632 0.16129032,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
633 0.01612903,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
634 0.0483871,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
635 0.33870968,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
636 0.16129032,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
637 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
638 0.14516129,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
639 0.25,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
640 0.11111111,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
641 0.01960784,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
642 0.02,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
643 0.21951219,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
644 0.22222222,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
645 ],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
646 [
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
647 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
648 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
649 0.12903226,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
650 0.01612903,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
651 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
652 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
653 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
654 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
655 0.01612903,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
656 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
657 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
658 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
659 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
660 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
661 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
662 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
663 0.02439024,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
664 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
665 ],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
666 [
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
667 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
668 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
669 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
670 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
671 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
672 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
673 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
674 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
675 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
676 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
677 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
678 0.01612903,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
679 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
680 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
681 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
682 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
683 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
684 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
685 ],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
686 ]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
687 )
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
688
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
689 def save_fasta(self, filename, names=False):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
690 """Method to save generated sequences in a ``.FASTA`` formatted file.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
691
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
692 :param filename: output filename in which the sequences from :py:attr:`sequences` are safed in fasta format.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
693 :param names: {bool} whether sequence names from :py:attr:`names` should be saved as sequence identifiers
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
694 :return: a FASTA formatted file containing the generated sequences
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
695 :Example:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
696
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
697 >>> b = BaseSequence(2)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
698 >>> b.sequences = ['KLLSLSLALDLLS', 'KLPERTVVNSSDF']
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
699 >>> b.names = ['Sequence1', 'Sequence2']
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
700 >>> b.save_fasta('/location/of/fasta/file.fasta', names=True)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
701 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
702 if names:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
703 save_fasta(filename, self.sequences, self.names)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
704 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
705 save_fasta(filename, self.sequences)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
706
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
707 def mutate_AA(self, nr, prob):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
708 """Method to mutate with **prob** probability a **nr** of positions per sequence randomly.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
709
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
710 :param nr: number of mutations to perform per sequence
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
711 :param prob: probability of mutating a sequence
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
712 :return: mutated sequences in the attribute :py:attr:`sequences`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
713 :Example:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
714
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
715 >>> b = BaseSequence(1)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
716 >>> b.sequences = ['IAKAGRAIIK']
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
717 >>> b.mutate_AA(3, 1.)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
718 >>> b.sequences
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
719 ['NAKAGRAWIK']
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
720 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
721 for s in range(len(self.sequences)):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
722 # mutate: yes or no? prob = mutation probability
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
723 mutate = np.random.choice([1, 0], 1, p=[prob, 1 - float(prob)])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
724 if mutate == 1:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
725 seq = list(self.sequences[s])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
726 cnt = 0
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
727 while cnt < nr: # mutate "nr" AA
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
728 seq[random.choice(range(len(seq)))] = random.choice(self.AAs)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
729 cnt += 1
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
730 self.sequences[s] = "".join(seq)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
731
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
732 def filter_duplicates(self):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
733 """Method to filter duplicates in the sequences from the class attribute :py:attr:`sequences`
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
734
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
735 :return: filtered sequences list in the attribute :py:attr:`sequences` and corresponding names.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
736 :Example:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
737
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
738 >>> b = BaseSequence(4)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
739 >>> b.sequences = ['KLLKLLKKLLKLLK', 'KLLKLLKKLLKLLK', 'KLAKLAKKLAKLAK', 'KLAKLAKKLAKLAK']
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
740 >>> b.filter_duplicates()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
741 >>> b.sequences
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
742 ['KLLKLLKKLLKLLK', 'KLAKLAKKLAKLAK']
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
743
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
744 .. versionadded:: v2.2.5
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
745 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
746 if not self.names:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
747 self.names = ["Seq_" + str(i) for i in range(len(self.sequences))]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
748 df = pd.DataFrame(
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
749 list(zip(self.sequences, self.names)), columns=["Sequences", "Names"]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
750 )
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
751 df = df.drop_duplicates(
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
752 "Sequences", "first"
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cpt
parents:
diff changeset
753 ) # keep first occurrence of duplicate
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cpt
parents:
diff changeset
754 self.sequences = df["Sequences"].get_values().tolist()
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cpt
parents:
diff changeset
755 self.names = df["Names"].get_values().tolist()
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cpt
parents:
diff changeset
756
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cpt
parents:
diff changeset
757 def keep_natural_aa(self):
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parents:
diff changeset
758 """Method to filter out sequences that do not contain natural amino acids. If the sequence contains a character
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cpt
parents:
diff changeset
759 that is not in ``['A','C','D,'E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y']``.
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cpt
parents:
diff changeset
760
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cpt
parents:
diff changeset
761 :return: filtered sequence list in the attribute :py:attr:`sequences`. The other attributes are also filtered
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cpt
parents:
diff changeset
762 accordingly (if present).
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cpt
parents:
diff changeset
763 :Example:
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cpt
parents:
diff changeset
764
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cpt
parents:
diff changeset
765 >>> b = BaseSequence(2)
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cpt
parents:
diff changeset
766 >>> b.sequences = ['BBBsdflUasUJfBJ', 'GLFDIVKKVVGALGSL']
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
767 >>> b.keep_natural_aa()
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cpt
parents:
diff changeset
768 >>> b.sequences
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cpt
parents:
diff changeset
769 ['GLFDIVKKVVGALGSL']
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cpt
parents:
diff changeset
770 """
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cpt
parents:
diff changeset
771 natural_aa = [
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cpt
parents:
diff changeset
772 "A",
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cpt
parents:
diff changeset
773 "C",
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cpt
parents:
diff changeset
774 "D",
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cpt
parents:
diff changeset
775 "E",
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cpt
parents:
diff changeset
776 "F",
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cpt
parents:
diff changeset
777 "G",
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parents:
diff changeset
778 "H",
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parents:
diff changeset
779 "I",
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parents:
diff changeset
780 "K",
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cpt
parents:
diff changeset
781 "L",
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cpt
parents:
diff changeset
782 "M",
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cpt
parents:
diff changeset
783 "N",
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cpt
parents:
diff changeset
784 "P",
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cpt
parents:
diff changeset
785 "Q",
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cpt
parents:
diff changeset
786 "R",
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cpt
parents:
diff changeset
787 "S",
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cpt
parents:
diff changeset
788 "T",
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cpt
parents:
diff changeset
789 "V",
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cpt
parents:
diff changeset
790 "W",
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cpt
parents:
diff changeset
791 "Y",
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parents:
diff changeset
792 ]
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cpt
parents:
diff changeset
793
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cpt
parents:
diff changeset
794 seqs = []
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cpt
parents:
diff changeset
795 names = []
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cpt
parents:
diff changeset
796
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cpt
parents:
diff changeset
797 for i, s in enumerate(self.sequences):
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cpt
parents:
diff changeset
798 seq = list(s.upper())
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cpt
parents:
diff changeset
799 if all(c in natural_aa for c in seq):
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cpt
parents:
diff changeset
800 seqs.append(s.upper())
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cpt
parents:
diff changeset
801 if hasattr(self, "names") and self.names:
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cpt
parents:
diff changeset
802 names.append(self.names[i])
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cpt
parents:
diff changeset
803
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cpt
parents:
diff changeset
804 self.sequences = seqs
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cpt
parents:
diff changeset
805 self.names = names
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cpt
parents:
diff changeset
806
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cpt
parents:
diff changeset
807 def filter_aa(self, amino_acids):
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cpt
parents:
diff changeset
808 """Method to filter out corresponding names and descriptor values of sequences with given amino acids in the
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
809 argument list *aminoacids*.
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cpt
parents:
diff changeset
810
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cpt
parents:
diff changeset
811 :param amino_acids: {list} amino acids to be filtered
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cpt
parents:
diff changeset
812 :return: filtered list of sequences names in the corresponding attributes.
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cpt
parents:
diff changeset
813 :Example:
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cpt
parents:
diff changeset
814
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cpt
parents:
diff changeset
815 >>> b = BaseSequence(3)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
816 >>> b.sequences = ['AAALLLIIIKKK', 'CCEERRT', 'LLVVIIFFFQQ']
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cpt
parents:
diff changeset
817 >>> b.filter_aa(['C'])
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cpt
parents:
diff changeset
818 >>> b.sequences
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cpt
parents:
diff changeset
819 ['AAALLLIIIKKK', 'LLVVIIFFFQQ']
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cpt
parents:
diff changeset
820 """
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cpt
parents:
diff changeset
821
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cpt
parents:
diff changeset
822 pattern = re.compile("|".join(amino_acids))
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cpt
parents:
diff changeset
823 seqs = []
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cpt
parents:
diff changeset
824 names = []
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cpt
parents:
diff changeset
825
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cpt
parents:
diff changeset
826 for i, s in enumerate(self.sequences):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
827 if not pattern.search(s):
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cpt
parents:
diff changeset
828 seqs.append(s)
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cpt
parents:
diff changeset
829 if hasattr(self, "names") and self.names:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
830 names.append(self.names[i])
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cpt
parents:
diff changeset
831
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cpt
parents:
diff changeset
832 self.sequences = seqs
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cpt
parents:
diff changeset
833 self.names = names
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cpt
parents:
diff changeset
834
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cpt
parents:
diff changeset
835 def clean(self):
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cpt
parents:
diff changeset
836 """Method to clean / clear / empty the attributes :py:attr:`sequences` and :py:attr:`names`.
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cpt
parents:
diff changeset
837
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cpt
parents:
diff changeset
838 :return: freshly initialized, empty class attributes.
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cpt
parents:
diff changeset
839 """
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cpt
parents:
diff changeset
840 self.__init__(self.seqnum, self.lenmin, self.lenmax)
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cpt
parents:
diff changeset
841
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cpt
parents:
diff changeset
842
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cpt
parents:
diff changeset
843 class BaseDescriptor(object):
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cpt
parents:
diff changeset
844 """
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cpt
parents:
diff changeset
845 Base class inheriting to both peptide descriptor classes :py:class:`modlamp.descriptors.GlobalDescriptor` and
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cpt
parents:
diff changeset
846 :py:class:`modlamp.descriptors.PeptideDescriptor`.
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cpt
parents:
diff changeset
847 """
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cpt
parents:
diff changeset
848
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cpt
parents:
diff changeset
849 def __init__(self, seqs):
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cpt
parents:
diff changeset
850 """
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cpt
parents:
diff changeset
851 :param seqs: a ``.FASTA`` file with sequences, a list / array of sequences or a single sequence as string to
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
852 calculate the descriptor values for.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
853 :return: initialized attributes :py:attr:`sequences` and :py:attr:`names`.
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cpt
parents:
diff changeset
854 :Example:
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cpt
parents:
diff changeset
855
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cpt
parents:
diff changeset
856 >>> AMP = BaseDescriptor('KLLKLLKKLLKLLK','pepCATS')
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cpt
parents:
diff changeset
857 >>> AMP.sequences
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cpt
parents:
diff changeset
858 ['KLLKLLKKLLKLLK']
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cpt
parents:
diff changeset
859 >>> seqs = BaseDescriptor('/Path/to/file.fasta', 'eisenberg') # load sequences from .fasta file
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cpt
parents:
diff changeset
860 >>> seqs.sequences
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cpt
parents:
diff changeset
861 ['AFDGHLKI','KKLQRSDLLRTK','KKLASCNNIPPR'...]
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cpt
parents:
diff changeset
862 """
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cpt
parents:
diff changeset
863 if type(seqs) == list and seqs[0].isupper():
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
864 self.sequences = [s.strip() for s in seqs]
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cpt
parents:
diff changeset
865 self.names = []
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cpt
parents:
diff changeset
866 elif type(seqs) == np.ndarray and seqs[0].isupper():
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cpt
parents:
diff changeset
867 self.sequences = [s.strip() for s in seqs.tolist()]
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cpt
parents:
diff changeset
868 self.names = []
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cpt
parents:
diff changeset
869 elif type(seqs) == str and seqs.isupper():
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cpt
parents:
diff changeset
870 self.sequences = [seqs.strip()]
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cpt
parents:
diff changeset
871 self.names = []
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parents:
diff changeset
872 elif os.path.isfile(seqs):
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cpt
parents:
diff changeset
873 if seqs.endswith(".fasta"): # read .fasta file
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
874 self.sequences, self.names = read_fasta(seqs)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
875 elif seqs.endswith(".csv"): # read .csv file with sequences every line
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
876 with open(seqs) as f:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
877 self.sequences = list()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
878 cntr = 0
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
879 self.names = []
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
880 for line in f:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
881 if line.isupper():
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
882 self.sequences.append(line.strip())
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
883 self.names.append("seq_" + str(cntr))
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
884 cntr += 1
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
885 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
886 print("Sorry, currently only .fasta or .csv files can be read!")
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
887 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
888 print(
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
889 "%s does not exist, is not a valid list of AA sequences or is not a valid sequence string"
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
890 % seqs
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
891 )
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
892
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
893 self.descriptor = np.array([[]])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
894 self.target = np.array([], dtype="int")
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
895 self.scaler = None
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
896 self.featurenames = []
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
897
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
898 def read_fasta(self, filename):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
899 """Method for loading sequences from a ``.FASTA`` formatted file into the attributes :py:attr:`sequences` and
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
900 :py:attr:`names`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
901
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
902 :param filename: {str} ``.FASTA`` file with sequences and headers to read
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
903 :return: {list} sequences in the attribute :py:attr:`sequences` with corresponding sequence names in
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
904 :py:attr:`names`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
905 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
906 self.sequences, self.names = read_fasta(filename)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
907
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
908 def save_fasta(self, filename, names=False):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
909 """Method for saving sequences from :py:attr:`sequences` to a ``.FASTA`` formatted file.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
910
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
911 :param filename: {str} filename of the output ``.FASTA`` file
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
912 :param names: {bool} whether sequence names from self.names should be saved as sequence identifiers
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
913 :return: a FASTA formatted file containing the generated sequences
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
914 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
915 if names:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
916 save_fasta(filename, self.sequences, self.names)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
917 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
918 save_fasta(filename, self.sequences)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
919
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
920 def count_aa(self, scale="relative", average=False, append=False):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
921 """Method for producing the amino acid distribution for the given sequences as a descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
922
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
923 :param scale: {'absolute' or 'relative'} defines whether counts or frequencies are given for each AA
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
924 :param average: {boolean} whether the averaged amino acid counts for all sequences should be returned
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
925 :param append: {boolean} whether the produced descriptor values should be appended to the existing ones in the
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
926 attribute :py:attr:`descriptor`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
927 :return: the amino acid distributions for every sequence individually in the attribute :py:attr:`descriptor`
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
928 :Example:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
929
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
930 >>> AMP = PeptideDescriptor('ACDEFGHIKLMNPQRSTVWY') # aa_count() does not depend on the descriptor scale
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
931 >>> AMP.count_aa()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
932 >>> AMP.descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
933 array([[ 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, ... ]])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
934 >>> AMP.descriptor.shape
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
935 (1, 20)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
936
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
937 .. seealso:: :py:func:`modlamp.core.count_aa()`
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
938 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
939 desc = list()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
940 for seq in self.sequences:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
941 od = count_aas(seq, scale)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
942 desc.append(list(od.values()))
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
943
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
944 desc = np.array(desc)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
945 self.featurenames = list(od.keys())
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
946
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
947 if append:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
948 self.descriptor = np.hstack((self.descriptor, desc))
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
949 elif average:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
950 self.descriptor = np.mean(desc, axis=0)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
951 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
952 self.descriptor = desc
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
953
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
954 def count_ngrams(self, n):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
955 """Method for producing n-grams of all sequences in self.sequences
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
956
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
957 :param n: {int or list of ints} defines whether counts or frequencies are given for each AA
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
958 :return: {dict} dictionary with n-grams as keys and their counts in the sequence as values in :py:attr:`descriptor`
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
959 :Example:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
960
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
961 >>> D = PeptideDescriptor('GLLDFLSLAALSLDKLVKKGALS')
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
962 >>> D.count_ngrams([2, 3])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
963 >>> D.descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
964 {'LS': 3, 'LD': 2, 'LSL': 2, 'AL': 2, ..., 'LVK': 1}
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
965
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
966 .. seealso:: :py:func:`modlamp.core.count_ngrams()`
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
967 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
968 ngrams = dict()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
969 for seq in self.sequences:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
970 d = count_ngrams(seq, n)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
971 for k, v in d.items():
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
972 if k in ngrams.keys():
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
973 ngrams[k] += v
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
974 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
975 ngrams[k] = v
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
976 self.descriptor = ngrams
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
977
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
978 def feature_scaling(self, stype="standard", fit=True):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
979 """Method for feature scaling of the calculated descriptor matrix.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
980
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
981 :param stype: {'standard' or 'minmax'} type of scaling to be used
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
982 :param fit: {boolean} defines whether the used scaler is first fitting on the data (True) or
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
983 whether the already fitted scaler in :py:attr:`scaler` should be used to transform (False).
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
984 :return: scaled descriptor values in :py:attr:`descriptor`
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
985 :Example:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
986
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
987 >>> D.descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
988 array([[0.155],[0.34],[0.16235294],[-0.08842105],[0.116]])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
989 >>> D.feature_scaling(type='minmax',fit=True)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
990 array([[0.56818182],[1.],[0.5853447],[0.],[0.47714988]])
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cpt
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991 """
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992 if stype in ["standard", "minmax"]:
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diff changeset
993 if stype == "standard":
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diff changeset
994 self.scaler = StandardScaler()
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995 elif stype == "minmax":
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diff changeset
996 self.scaler = MinMaxScaler()
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diff changeset
997
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diff changeset
998 if fit:
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parents:
diff changeset
999 self.descriptor = self.scaler.fit_transform(self.descriptor)
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diff changeset
1000 else:
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diff changeset
1001 self.descriptor = self.scaler.transform(self.descriptor)
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diff changeset
1002 else:
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1003 print("Unknown scaler type!\nAvailable: 'standard', 'minmax'")
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diff changeset
1004
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diff changeset
1005 def feature_shuffle(self):
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diff changeset
1006 """Method for shuffling feature columns randomly.
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cpt
parents:
diff changeset
1007
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cpt
parents:
diff changeset
1008 :return: descriptor matrix with shuffled feature columns in :py:attr:`descriptor`
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parents:
diff changeset
1009 :Example:
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parents:
diff changeset
1010
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diff changeset
1011 >>> D.descriptor
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1012 array([[0.80685625,167.05234375,39.56818125,-0.26338667,155.16888667,33.48778]])
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parents:
diff changeset
1013 >>> D.feature_shuffle()
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parents:
diff changeset
1014 array([[155.16888667,-0.26338667,167.05234375,0.80685625,39.56818125,33.48778]])
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diff changeset
1015 """
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parents:
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1016 self.descriptor = shuffle(self.descriptor.transpose()).transpose()
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parents:
diff changeset
1017
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parents:
diff changeset
1018 def sequence_order_shuffle(self):
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parents:
diff changeset
1019 """Method for shuffling sequence order in the attribute :py:attr:`sequences`.
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cpt
parents:
diff changeset
1020
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parents:
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1021 :return: sequences in :py:attr:`sequences` with shuffled order in the list.
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parents:
diff changeset
1022 :Example:
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parents:
diff changeset
1023
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parents:
diff changeset
1024 >>> D.sequences
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parents:
diff changeset
1025 ['LILRALKGAARALKVA','VKIAKIALKIIKGLG','VGVRLIKGIGRVARGAI','LRGLRGVIRGGKAIVRVGK','GGKLVRLIARIGKGV']
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cpt
parents:
diff changeset
1026 >>> D.sequence_order_shuffle()
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parents:
diff changeset
1027 >>> D.sequences
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cpt
parents:
diff changeset
1028 ['VGVRLIKGIGRVARGAI','LILRALKGAARALKVA','LRGLRGVIRGGKAIVRVGK','GGKLVRLIARIGKGV','VKIAKIALKIIKGLG']
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cpt
parents:
diff changeset
1029 """
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cpt
parents:
diff changeset
1030 self.sequences = shuffle(self.sequences)
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cpt
parents:
diff changeset
1031
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cpt
parents:
diff changeset
1032 def random_selection(self, num):
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parents:
diff changeset
1033 """Method to randomly select a specified number of sequences (with names and descriptors if present) out of a given
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cpt
parents:
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1034 descriptor instance.
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cpt
parents:
diff changeset
1035
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cpt
parents:
diff changeset
1036 :param num: {int} number of entries to be randomly selected
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cpt
parents:
diff changeset
1037 :return: updated instance
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cpt
parents:
diff changeset
1038 :Example:
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cpt
parents:
diff changeset
1039
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cpt
parents:
diff changeset
1040 >>> h = Helices(7, 28, 100)
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cpt
parents:
diff changeset
1041 >>> h.generate_helices()
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cpt
parents:
diff changeset
1042 >>> desc = PeptideDescriptor(h.sequences, 'eisenberg')
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cpt
parents:
diff changeset
1043 >>> desc.calculate_moment()
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cpt
parents:
diff changeset
1044 >>> len(desc.sequences)
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cpt
parents:
diff changeset
1045 100
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cpt
parents:
diff changeset
1046 >>> len(desc.descriptor)
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cpt
parents:
diff changeset
1047 100
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cpt
parents:
diff changeset
1048 >>> desc.random_selection(10)
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cpt
parents:
diff changeset
1049 >>> len(desc.descriptor)
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cpt
parents:
diff changeset
1050 10
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cpt
parents:
diff changeset
1051 >>> len(desc.descriptor)
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cpt
parents:
diff changeset
1052 10
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cpt
parents:
diff changeset
1053
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cpt
parents:
diff changeset
1054 .. versionadded:: v2.2.3
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parents:
diff changeset
1055 """
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cpt
parents:
diff changeset
1056
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cpt
parents:
diff changeset
1057 sel = np.random.choice(len(self.sequences), size=num, replace=False)
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cpt
parents:
diff changeset
1058 self.sequences = np.array(self.sequences)[sel].tolist()
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cpt
parents:
diff changeset
1059 if hasattr(self, "descriptor") and self.descriptor.size:
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cpt
parents:
diff changeset
1060 self.descriptor = self.descriptor[sel]
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cpt
parents:
diff changeset
1061 if hasattr(self, "names") and self.names:
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cpt
parents:
diff changeset
1062 self.names = np.array(self.names)[sel].tolist()
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cpt
parents:
diff changeset
1063 if hasattr(self, "target") and self.target.size:
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cpt
parents:
diff changeset
1064 self.target = self.target[sel]
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cpt
parents:
diff changeset
1065
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cpt
parents:
diff changeset
1066 def minmax_selection(self, iterations, distmetric="euclidean", seed=0):
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cpt
parents:
diff changeset
1067 """Method to select a specified number of sequences according to the minmax algorithm.
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cpt
parents:
diff changeset
1068
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cpt
parents:
diff changeset
1069 :param iterations: {int} Number of sequences to retrieve.
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cpt
parents:
diff changeset
1070 :param distmetric: Distance metric to calculate the distances between the sequences in descriptor space.
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cpt
parents:
diff changeset
1071 Choose from 'euclidean' or 'minkowsky'.
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cpt
parents:
diff changeset
1072 :param seed: {int} Set a random seed for numpy to pick the first sequence.
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cpt
parents:
diff changeset
1073 :return: updated instance
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cpt
parents:
diff changeset
1074
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cpt
parents:
diff changeset
1075 .. seealso:: **SciPy** http://docs.scipy.org/doc/scipy/reference/spatial.distance.html
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parents:
diff changeset
1076 """
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cpt
parents:
diff changeset
1077
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cpt
parents:
diff changeset
1078 # Storing M into pool, where selections get deleted
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cpt
parents:
diff changeset
1079 pool = self.descriptor # Store pool where selections get deleted
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cpt
parents:
diff changeset
1080 minmaxidx = list() # Store original indices of selections to return
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cpt
parents:
diff changeset
1081
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cpt
parents:
diff changeset
1082 # Randomly selecting first peptide into the sele
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cpt
parents:
diff changeset
1083 np.random.seed(seed)
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cpt
parents:
diff changeset
1084 idx = int(np.random.random_integers(0, len(pool), 1))
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cpt
parents:
diff changeset
1085 sele = pool[idx : idx + 1, :]
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cpt
parents:
diff changeset
1086 minmaxidx.append(
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cpt
parents:
diff changeset
1087 int(*np.where(np.all(self.descriptor == pool[idx : idx + 1, :], axis=1)))
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cpt
parents:
diff changeset
1088 )
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cpt
parents:
diff changeset
1089
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cpt
parents:
diff changeset
1090 # Deleting peptide in selection from pool
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cpt
parents:
diff changeset
1091 pool = np.delete(pool, idx, axis=0)
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cpt
parents:
diff changeset
1092
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cpt
parents:
diff changeset
1093 for i in range(iterations - 1):
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cpt
parents:
diff changeset
1094 # Calculating distance from sele to the rest of the peptides
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cpt
parents:
diff changeset
1095 dist = distance.cdist(pool, sele, distmetric)
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cpt
parents:
diff changeset
1096
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cpt
parents:
diff changeset
1097 # Choosing maximal distances for every sele instance
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cpt
parents:
diff changeset
1098 maxidx = np.argmax(dist, axis=0)
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cpt
parents:
diff changeset
1099 maxcols = np.max(dist, axis=0)
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cpt
parents:
diff changeset
1100
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cpt
parents:
diff changeset
1101 # Choosing minimal distance among the maximal distances
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cpt
parents:
diff changeset
1102 minmax = np.argmin(maxcols)
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cpt
parents:
diff changeset
1103 maxidx = int(maxidx[minmax])
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cpt
parents:
diff changeset
1104
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cpt
parents:
diff changeset
1105 # Adding it to selection and removing from pool
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cpt
parents:
diff changeset
1106 sele = np.append(sele, pool[maxidx : maxidx + 1, :], axis=0)
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cpt
parents:
diff changeset
1107 pool = np.delete(pool, maxidx, axis=0)
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parents:
diff changeset
1108 minmaxidx.append(
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cpt
parents:
diff changeset
1109 int(
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cpt
parents:
diff changeset
1110 *np.where(
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cpt
parents:
diff changeset
1111 np.all(self.descriptor == pool[maxidx : maxidx + 1, :], axis=1)
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parents:
diff changeset
1112 )
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parents:
diff changeset
1113 )
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parents:
diff changeset
1114 )
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cpt
parents:
diff changeset
1115
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cpt
parents:
diff changeset
1116 self.sequences = np.array(self.sequences)[minmaxidx].tolist()
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cpt
parents:
diff changeset
1117 if hasattr(self, "descriptor") and self.descriptor.size:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1118 self.descriptor = self.descriptor[minmaxidx]
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cpt
parents:
diff changeset
1119 if hasattr(self, "names") and self.names:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1120 self.names = np.array(self.names)[minmaxidx].tolist()
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cpt
parents:
diff changeset
1121 if hasattr(self, "target") and self.target.size:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1122 self.target = self.descriptor[minmaxidx]
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cpt
parents:
diff changeset
1123
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cpt
parents:
diff changeset
1124 def filter_sequences(self, sequences):
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parents:
diff changeset
1125 """Method to filter out entries for given sequences in *sequences* out of a descriptor instance. All
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1126 corresponding attribute values of these sequences (e.g. in :py:attr:`descriptor`, :py:attr:`name`) are deleted
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parents:
diff changeset
1127 as well. The method returns an updated descriptor instance.
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cpt
parents:
diff changeset
1128
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parents:
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1129 :param sequences: {list} sequences to be filtered out of the whole instance, including corresponding data
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parents:
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1130 :return: updated instance without filtered sequences
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parents:
diff changeset
1131 :Example:
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parents:
diff changeset
1132
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parents:
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1133 >>> sequences = ['KLLKLLKKLLKLLK', 'ACDEFGHIK', 'GLFDIVKKVV', 'GLFDIVKKVVGALG', 'GLFDIVKKVVGALGSL']
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parents:
diff changeset
1134 >>> desc = PeptideDescriptor(sequences, 'pepcats')
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parents:
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1135 >>> desc.calculate_crosscorr(7)
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parents:
diff changeset
1136 >>> len(desc.descriptor)
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parents:
diff changeset
1137 5
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parents:
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1138 >>> desc.filter_sequences('KLLKLLKKLLKLLK')
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cpt
parents:
diff changeset
1139 >>> len(desc.descriptor)
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parents:
diff changeset
1140 4
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parents:
diff changeset
1141 >>> desc.sequences
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parents:
diff changeset
1142 ['ACDEFGHIK', 'GLFDIVKKVV', 'GLFDIVKKVVGALG', 'GLFDIVKKVVGALGSL']
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parents:
diff changeset
1143 """
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parents:
diff changeset
1144 indices = list()
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parents:
diff changeset
1145 if isinstance(
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parents:
diff changeset
1146 sequences, str
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parents:
diff changeset
1147 ): # check if sequences is only one sequence string and convert it to a list
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cpt
parents:
diff changeset
1148 sequences = [sequences]
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cpt
parents:
diff changeset
1149 for s in sequences: # get indices of queried sequences
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parents:
diff changeset
1150 indices.append(self.sequences.index(s))
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cpt
parents:
diff changeset
1151
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cpt
parents:
diff changeset
1152 self.sequences = np.delete(np.array(self.sequences), indices, 0).tolist()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1153 if hasattr(self, "descriptor") and self.descriptor.size:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1154 self.descriptor = np.delete(self.descriptor, indices, 0)
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cpt
parents:
diff changeset
1155 if hasattr(self, "names") and self.names:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1156 self.names = np.delete(np.array(self.names), indices, 0).tolist()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1157 if hasattr(self, "target") and self.target.size:
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cpt
parents:
diff changeset
1158 self.target = np.delete(self.target, indices, 0)
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cpt
parents:
diff changeset
1159
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cpt
parents:
diff changeset
1160 def filter_values(self, values, operator="=="):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1161 """Method to filter the descriptor matrix in the attribute :py:attr:`descriptor` for a given list of values (same
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1162 size as the number of features in the descriptor matrix!) The operator option tells the method whether to
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1163 filter for values equal, lower, higher ect. to the given values in the *values* array.
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cpt
parents:
diff changeset
1164
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parents:
diff changeset
1165 :param values: {list} values to filter the attribute :py:attr:`descriptor` for
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
diff changeset
1166 :param operator: {str} filter criterion, available the operators ``==``, ``<``, ``>``, ``<=``and ``>=``.
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cpt
parents:
diff changeset
1167 :return: descriptor matrix and updated sequences containing only entries with descriptor values given in
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1168 *values* in the corresponding attributes.
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cpt
parents:
diff changeset
1169 :Example:
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cpt
parents:
diff changeset
1170
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parents:
diff changeset
1171 >>> desc.descriptor # desc = BaseDescriptor instance
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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parents:
diff changeset
1172 array([[ 0.7666517 ],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1173 [ 0.38373498]])
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cpt
parents:
diff changeset
1174 >>> desc.filter_values([0.5], '<')
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parents:
diff changeset
1175 >>> desc.descriptor
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parents:
diff changeset
1176 array([[ 0.38373498]])
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parents:
diff changeset
1177 """
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parents:
diff changeset
1178 dim = self.descriptor.shape[1]
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cpt
parents:
diff changeset
1179 for d in range(dim): # for all the features in self.descriptor
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1180 if operator == "==":
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cpt
parents:
diff changeset
1181 indices = np.where(self.descriptor[:, d] == values[d])[0]
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cpt
parents:
diff changeset
1182 elif operator == "<":
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cpt
parents:
diff changeset
1183 indices = np.where(self.descriptor[:, d] < values[d])[0]
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cpt
parents:
diff changeset
1184 elif operator == ">":
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cpt
parents:
diff changeset
1185 indices = np.where(self.descriptor[:, d] > values[d])[0]
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cpt
parents:
diff changeset
1186 elif operator == "<=":
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1187 indices = np.where(self.descriptor[:, d] <= values[d])[0]
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cpt
parents:
diff changeset
1188 elif operator == ">=":
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1189 indices = np.where(self.descriptor[:, d] >= values[d])[0]
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parents:
diff changeset
1190 else:
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parents:
diff changeset
1191 raise KeyError(
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parents:
diff changeset
1192 "available operators: ``==``, ``<``, ``>``, ``<=``and ``>=``"
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cpt
parents:
diff changeset
1193 )
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cpt
parents:
diff changeset
1194
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cpt
parents:
diff changeset
1195 # filter descriptor matrix, sequence list and names list according to obtained indices
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cpt
parents:
diff changeset
1196 self.sequences = np.array(self.sequences)[indices].tolist()
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cpt
parents:
diff changeset
1197 if hasattr(self, "descriptor") and self.descriptor.size:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1198 self.descriptor = self.descriptor[indices]
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cpt
parents:
diff changeset
1199 if hasattr(self, "names") and self.names:
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cpt
parents:
diff changeset
1200 self.names = np.array(self.names)[indices].tolist()
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cpt
parents:
diff changeset
1201 if hasattr(self, "target") and self.target.size:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1202 self.target = self.target[indices]
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cpt
parents:
diff changeset
1203
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parents:
diff changeset
1204 def filter_aa(self, amino_acids):
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parents:
diff changeset
1205 """Method to filter out corresponding names and descriptor values of sequences with given amino acids in the
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1206 argument list *aminoacids*.
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cpt
parents:
diff changeset
1207
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cpt
parents:
diff changeset
1208 :param amino_acids: list of amino acids to be filtered
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cpt
parents:
diff changeset
1209 :return: filtered list of sequences, descriptor values, target values and names in the corresponding attributes.
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parents:
diff changeset
1210 :Example:
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parents:
diff changeset
1211
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parents:
diff changeset
1212 >>> b = BaseSequence(3)
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parents:
diff changeset
1213 >>> b.sequences = ['AAALLLIIIKKK', 'CCEERRT', 'LLVVIIFFFQQ']
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cpt
parents:
diff changeset
1214 >>> b.filter_aa(['C'])
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parents:
diff changeset
1215 >>> b.sequences
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parents:
diff changeset
1216 ['AAALLLIIIKKK', 'LLVVIIFFFQQ']
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parents:
diff changeset
1217 """
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parents:
diff changeset
1218
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parents:
diff changeset
1219 pattern = re.compile("|".join(amino_acids))
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cpt
parents:
diff changeset
1220 seqs = []
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cpt
parents:
diff changeset
1221 desc = []
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cpt
parents:
diff changeset
1222 names = []
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1223 target = []
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1224
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1225 for i, s in enumerate(self.sequences):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1226 if not pattern.search(s):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1227 seqs.append(s)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1228 if hasattr(self, "descriptor") and self.descriptor.size:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1229 desc.append(self.descriptor[i])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1230 if hasattr(self, "names") and self.names:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1231 names.append(self.names[i])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1232 if hasattr(self, "target") and self.target.size:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1233 target.append(self.target[i])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1234
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cpt
parents:
diff changeset
1235 self.sequences = seqs
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1236 self.names = names
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1237 self.descriptor = np.array(desc)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1238 self.target = np.array(target, dtype="int")
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1239
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cpt
parents:
diff changeset
1240 def filter_duplicates(self):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1241 """Method to filter duplicates in the sequences from the class attribute :py:attr:`sequences`
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1242
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cpt
parents:
diff changeset
1243 :return: filtered sequences list in the attribute :py:attr:`sequences` and corresponding names.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1244 :Example:
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cpt
parents:
diff changeset
1245
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cpt
parents:
diff changeset
1246 >>> b = BaseDescriptor(['KLLKLLKKLLKLLK', 'KLLKLLKKLLKLLK', 'KLAKLAKKLAKLAK', 'KLAKLAKKLAKLAK'])
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cpt
parents:
diff changeset
1247 >>> b.filter_duplicates()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1248 >>> b.sequences
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1249 ['KLLKLLKKLLKLLK', 'KLAKLAKKLAKLAK']
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1250
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1251 .. versionadded:: v2.2.5
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1252 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1253 if not self.names:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1254 self.names = ["Seq_" + str(i) for i in range(len(self.sequences))]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1255 if not self.target:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1256 self.target = [0] * len(self.sequences)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1257 if not self.descriptor:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1258 self.descriptor = np.zeros(len(self.sequences))
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1259 df = pd.DataFrame(
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1260 np.array([self.sequences, self.names, self.descriptor, self.target]).T,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1261 columns=["Sequences", "Names", "Descriptor", "Target"],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1262 )
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1263 df = df.drop_duplicates(
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1264 "Sequences", "first"
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1265 ) # keep first occurrence of duplicate
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1266 self.sequences = df["Sequences"].get_values().tolist()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1267 self.names = df["Names"].get_values().tolist()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1268 self.descriptor = df["Descriptor"].get_values()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1269 self.target = df["Target"].get_values()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1270
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1271 def keep_natural_aa(self):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1272 """Method to filter out sequences that do not contain natural amino acids. If the sequence contains a character
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1273 that is not in ['A','C','D,'E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y'].
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1274
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1275 :return: filtered sequence list in the attribute :py:attr:`sequences`. The other attributes are also filtered
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1276 accordingly (if present).
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1277 :Example:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1278
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1279 >>> b = BaseSequence(2)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1280 >>> b.sequences = ['BBBsdflUasUJfBJ', 'GLFDIVKKVVGALGSL']
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1281 >>> b.keep_natural_aa()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1282 >>> b.sequences
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1283 ['GLFDIVKKVVGALGSL']
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1284 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1285
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cpt
parents:
diff changeset
1286 natural_aa = [
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1287 "A",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1288 "C",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1289 "D",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1290 "E",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1291 "F",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1292 "G",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1293 "H",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1294 "I",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1295 "K",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1296 "L",
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cpt
parents:
diff changeset
1297 "M",
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cpt
parents:
diff changeset
1298 "N",
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cpt
parents:
diff changeset
1299 "P",
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cpt
parents:
diff changeset
1300 "Q",
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cpt
parents:
diff changeset
1301 "R",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1302 "S",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1303 "T",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1304 "V",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1305 "W",
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cpt
parents:
diff changeset
1306 "Y",
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cpt
parents:
diff changeset
1307 ]
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cpt
parents:
diff changeset
1308
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cpt
parents:
diff changeset
1309 seqs = []
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1310 desc = []
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1311 names = []
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1312 target = []
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cpt
parents:
diff changeset
1313
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cpt
parents:
diff changeset
1314 for i, s in enumerate(self.sequences):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1315 seq = list(s.upper())
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1316 if all(c in natural_aa for c in seq):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1317 seqs.append(s.upper())
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1318 if hasattr(self, "descriptor") and self.descriptor.size:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1319 desc.append(self.descriptor[i])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1320 if hasattr(self, "names") and self.names:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1321 names.append(self.names[i])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1322 if hasattr(self, "target") and self.target.size:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1323 target.append(self.target[i])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1324
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1325 self.sequences = seqs
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1326 self.names = names
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1327 self.descriptor = np.array(desc)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1328 self.target = np.array(target, dtype="int")
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1329
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cpt
parents:
diff changeset
1330 def load_descriptordata(
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1331 self, filename, delimiter=",", targets=False, skip_header=0
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1332 ):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1333 """Method to load any data file with sequences and descriptor values and save it to a new insatnce of the
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1334 class :class:`modlamp.descriptors.PeptideDescriptor`.
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cpt
parents:
diff changeset
1335
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1336 .. note:: Headers are not considered. To skip initial lines in the file, use the *skip_header* option.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1337
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1338 :param filename: {str} filename of the data file to be loaded
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1339 :param delimiter: {str} column delimiter
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1340 :param targets: {boolean} whether last column in the file contains a target class vector
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1341 :param skip_header: {int} number of initial lines to skip in the file
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1342 :return: loaded sequences, descriptor values and targets in the corresponding attributes.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1343 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1344 data = np.genfromtxt(filename, delimiter=delimiter, skip_header=skip_header)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1345 data = data[:, 1:] # skip sequences as they are "nan" when read as float
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1346 seqs = np.genfromtxt(filename, delimiter=delimiter, dtype="str")
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1347 seqs = seqs[:, 0]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1348 if targets:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1349 self.target = np.array(data[:, -1], dtype="int")
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1350 self.sequences = seqs
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1351 self.descriptor = data
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1352
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1353 def save_descriptor(self, filename, delimiter=",", targets=None, header=None):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1354 """Method to save the descriptor values to a .csv/.txt file
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1355
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1356 :param filename: filename of the output file
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1357 :param delimiter: column delimiter
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1358 :param targets: target class vector to be added to descriptor (same length as :py:attr:`sequences`)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1359 :param header: {str} header to be written at the beginning of the file (if ``None``: feature names are taken)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1360 :return: output file with peptide names and descriptor values
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1361 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1362 seqs = np.array(self.sequences, dtype="|S80")[:, np.newaxis]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1363 ids = np.array(self.names, dtype="|S80")[:, np.newaxis]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1364 if ids.shape == seqs.shape:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1365 names = np.hstack((ids, seqs))
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1366 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1367 names = seqs
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1368 if targets and len(targets) == len(self.sequences):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1369 target = np.array(targets)[:, np.newaxis]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1370 data = np.hstack((names, self.descriptor, target))
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1371 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1372 data = np.hstack((names, self.descriptor))
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1373 if not header:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1374 featurenames = [["Sequence"]] + self.featurenames
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1375 header = ", ".join([f[0] for f in featurenames])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1376 np.savetxt(filename, data, delimiter=delimiter, fmt="%s", header=header)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1377
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1378
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1379 def load_scale(scalename):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1380 """Method to load scale values for a given amino acid scale
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1381
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1382 :param scalename: amino acid scale name, for available scales see the
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1383 :class:`modlamp.descriptors.PeptideDescriptor()` documentation.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1384 :return: amino acid scale values in dictionary format.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1385 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1386 # predefined amino acid scales dictionary
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1387 scales = {
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1388 "aasi": {
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1389 "A": [1.89],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1390 "C": [1.73],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1391 "D": [3.13],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1392 "E": [3.14],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1393 "F": [1.53],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1394 "G": [2.67],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1395 "H": [3],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1396 "I": [1.97],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1397 "K": [2.28],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1398 "L": [1.74],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1399 "M": [2.5],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1400 "N": [2.33],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1401 "P": [0.22],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1402 "Q": [3.05],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1403 "R": [1.91],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1404 "S": [2.14],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1405 "T": [2.18],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1406 "V": [2.37],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1407 "W": [2],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1408 "Y": [2.01],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1409 },
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1410 "abhprk": {
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1411 "A": [0, 0, 0, 0, 0, 0],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1412 "C": [0, 0, 0, 0, 0, 0],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1413 "D": [1, 0, 0, 1, 0, 0],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1414 "E": [1, 0, 0, 1, 0, 0],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1415 "F": [0, 0, 1, 0, 1, 0],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1416 "G": [0, 0, 0, 0, 0, 0],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1417 "H": [0, 0, 0, 1, 1, 0],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1418 "I": [0, 0, 1, 0, 0, 0],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1419 "K": [0, 1, 0, 1, 0, 0],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1420 "L": [0, 0, 1, 0, 0, 0],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1421 "M": [0, 0, 1, 0, 0, 0],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1422 "N": [0, 0, 0, 1, 0, 0],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1423 "P": [0, 0, 0, 0, 0, 1],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1424 "Q": [0, 0, 0, 1, 0, 0],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1425 "R": [0, 1, 0, 1, 0, 0],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1426 "S": [0, 0, 0, 1, 0, 0],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1427 "T": [0, 0, 0, 1, 0, 0],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1428 "V": [0, 0, 1, 0, 0, 0],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1429 "W": [0, 0, 1, 0, 1, 0],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1430 "Y": [0, 0, 0, 1, 1, 0],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1431 },
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1432 "argos": {
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1433 "I": [0.77],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1434 "F": [1.2],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1435 "V": [0.14],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1436 "L": [2.3],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1437 "W": [0.07],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1438 "M": [2.3],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1439 "A": [0.64],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1440 "G": [-0.48],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1441 "C": [0.25],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1442 "Y": [-0.41],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1443 "P": [-0.31],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1444 "T": [-0.13],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1445 "S": [-0.25],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1446 "H": [-0.87],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1447 "E": [-0.94],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1448 "N": [-0.89],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1449 "Q": [-0.61],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1450 "D": [-1],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1451 "K": [-1],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1452 "R": [-0.68],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1453 },
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1454 "bulkiness": {
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1455 "A": [0.443],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1456 "C": [0.551],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1457 "D": [0.453],
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1977 ],
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1987 -1.2098,
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1998 ],
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9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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2309 "R": [0.626851634],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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2313 "W": [1],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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2314 "Y": [0.741359041],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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2315 },
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2316 "t_scale": {
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2317 "A": [-8.4, -8.01, -3.73, -3.65, -6.12, -1.59, 1.56],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
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9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
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9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2320 "E": [-6.5, 16.2, 17.28, 3.11, -4.75, -2.54, 4.72],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2321 "F": [21.59, -5.73, 1.03, -3.3, 2.64, -5.02, 1.7],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2322 "G": [-8.48, -10.37, -5.14, -6.51, -11.84, -3.6, 2.01],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2323 "H": [15.28, -3.67, 6.72, -6.38, 4.12, -1.55, -2.85],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2324 "I": [-2.97, 4.64, -0.77, 11, 3.26, -4.36, -7.88],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2325 "K": [2.7, 13.46, -14.03, -2.55, 2.77, 0.15, 3.19],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2326 "L": [2.61, 5.96, 1.97, 2.59, -4.77, -4.84, -5.44],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2327 "M": [3.38, 12.43, -4.77, 0.45, -1.55, -0.6, 3.26],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2328 "N": [-3.11, -1.22, 6.26, -9.38, 9.94, 7.66, -4.81],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2329 "P": [-5.35, -9.07, -1.52, -8.79, -8.73, 4.29, -9.91],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2330 "Q": [-5.31, 15.64, 8.44, 1.03, -4.32, -4.4, -0.52],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2331 "R": [-2.27, 18.9, -18.24, -3.47, 3.03, 6.64, 0.45],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2332 "S": [-15.88, -11.21, -2.44, -3.61, 3.46, -0.37, 8.98],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2333 "T": [-17.81, -13.64, -5.19, 10.57, 6.91, -4.43, 3.49],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2334 "V": [-5.8, -6.15, -2.26, 9.87, 5.28, -1.49, -7.54],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2335 "W": [21.68, -8.78, -2.53, 15.53, -8.15, 11.98, 3.23],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2336 "Y": [23.9, -6.47, 0.31, -4.14, 4.08, -7.28, 3.59],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2337 },
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2338 "tm_tend": {
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2339 "A": [0.38],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2340 "C": [-0.3],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2341 "D": [-3.27],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2342 "E": [-2.9],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2343 "F": [1.98],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2344 "G": [-0.19],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2345 "H": [-1.44],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2346 "I": [1.97],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2347 "K": [-3.46],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2348 "L": [1.82],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
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diff changeset
2349 "M": [1.4],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2350 "N": [-1.62],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2351 "P": [-1.44],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2352 "Q": [-1.84],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2353 "R": [-2.57],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2354 "S": [-0.53],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2355 "T": [-0.32],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2356 "V": [1.46],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2357 "W": [1.53],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2358 "Y": [0.49],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
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diff changeset
2359 },
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2360 "z3": {
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
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diff changeset
2361 "A": [0.07, -1.73, 0.09],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
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diff changeset
2362 "C": [0.71, -0.97, 4.13],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
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diff changeset
2363 "D": [3.64, 1.13, 2.36],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
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diff changeset
2364 "E": [3.08, 0.39, -0.07],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
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diff changeset
2365 "F": [-4.92, 1.3, 0.45],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
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diff changeset
2366 "G": [2.23, -5.36, 0.3],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
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diff changeset
2367 "H": [2.41, 1.74, 1.11],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
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diff changeset
2368 "I": [-4.44, -1.68, -1.03],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2369 "K": [2.84, 1.41, -3.14],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2370 "L": [-4.19, -1.03, -0.98],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2371 "M": [-2.49, -0.27, -0.41],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
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diff changeset
2372 "N": [3.22, 1.45, 0.84],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
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diff changeset
2373 "P": [-1.22, 0.88, 2.23],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
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diff changeset
2374 "Q": [2.18, 0.53, -1.14],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
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diff changeset
2375 "R": [2.88, 2.52, -3.44],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
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diff changeset
2376 "S": [1.96, -1.63, 0.57],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2377 "T": [0.92, -2.09, -1.4],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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diff changeset
2378 "V": [-2.69, -2.53, -1.29],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
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diff changeset
2379 "W": [-4.75, 3.65, 0.85],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
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diff changeset
2380 "Y": [-1.39, 2.32, 0.01],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2381 },
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2382 "z5": {
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
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diff changeset
2383 "A": [0.24, -2.32, 0.6, -0.14, 1.3],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2384 "C": [0.84, -1.67, 3.71, 0.18, -2.65],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2385 "D": [3.98, 0.93, 1.93, -2.46, 0.75],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2386 "E": [3.11, 0.26, -0.11, -3.04, -0.25],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2387 "F": [-4.22, 1.94, 1.06, 0.54, -0.62],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2388 "G": [2.05, -4.06, 0.36, -0.82, -0.38],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2389 "H": [2.47, 1.95, 0.26, 3.9, 0.09],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2390 "I": [-3.89, -1.73, -1.71, -0.84, 0.26],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
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diff changeset
2391 "K": [2.29, 0.89, -2.49, 1.49, 0.31],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2392 "L": [-4.28, -1.3, -1.49, -0.72, 0.84],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2393 "M": [-2.85, -0.22, 0.47, 1.94, -0.98],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2394 "N": [3.05, 1.62, 1.04, -1.15, 1.61],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2395 "P": [-1.66, 0.27, 1.84, 0.7, 2],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2396 "Q": [1.75, 0.5, -1.44, -1.34, 0.66],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2397 "R": [3.52, 2.5, -3.5, 1.99, -0.17],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2398 "S": [2.39, -1.07, 1.15, -1.39, 0.67],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2399 "T": [0.75, -2.18, -1.12, -1.46, -0.4],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2400 "V": [-2.59, -2.64, -1.54, -0.85, -0.02],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2401 "W": [-4.36, 3.94, 0.59, 3.44, -1.59],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2402 "Y": [-2.54, 2.44, 0.43, 0.04, -1.47],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2403 },
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2404 }
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2405 if scalename == "all":
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2406 d = {
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2407 "I": [],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2408 "F": [],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2409 "V": [],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2410 "L": [],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2411 "W": [],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2412 "M": [],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2413 "A": [],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2414 "G": [],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2415 "C": [],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2416 "Y": [],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2417 "P": [],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2418 "T": [],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2419 "S": [],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2420 "H": [],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2421 "E": [],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2422 "N": [],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2423 "Q": [],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2424 "D": [],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2425 "K": [],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2426 "R": [],
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2427 }
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2428 for scale in scales.keys():
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2429 for k, v in scales[scale].items():
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2430 d[k].extend(v)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2431 return "all", d
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2432
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2433 elif scalename == "instability":
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2434 d = {
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2435 "A": {
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2436 "A": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2437 "C": 44.94,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2438 "E": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2439 "D": -7.49,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2440 "G": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2441 "F": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2442 "I": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2443 "H": -7.49,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2444 "K": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2445 "M": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2446 "L": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2447 "N": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2448 "Q": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2449 "P": 20.26,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2450 "S": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2451 "R": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2452 "T": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2453 "W": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2454 "V": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2455 "Y": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2456 },
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2457 "C": {
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2458 "A": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2459 "C": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2460 "E": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2461 "D": 20.26,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2462 "G": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2463 "F": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2464 "I": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2465 "H": 33.6,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2466 "K": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2467 "M": 33.6,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2468 "L": 20.26,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2469 "N": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2470 "Q": -6.54,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2471 "P": 20.26,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2472 "S": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2473 "R": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2474 "T": 33.6,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2475 "W": 24.68,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2476 "V": -6.54,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2477 "Y": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2478 },
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2479 "E": {
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2480 "A": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2481 "C": 44.94,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2482 "E": 33.6,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2483 "D": 20.26,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2484 "G": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2485 "F": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2486 "I": 20.26,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2487 "H": -6.54,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2488 "K": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2489 "M": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2490 "L": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2491 "N": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2492 "Q": 20.26,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2493 "P": 20.26,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2494 "S": 20.26,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2495 "R": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2496 "T": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2497 "W": -14.03,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2498 "V": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2499 "Y": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2500 },
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2501 "D": {
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2502 "A": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2503 "C": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2504 "E": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2505 "D": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2506 "G": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2507 "F": -6.54,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2508 "I": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2509 "H": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2510 "K": -7.49,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2511 "M": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2512 "L": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2513 "N": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2514 "Q": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2515 "P": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2516 "S": 20.26,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2517 "R": -6.54,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2518 "T": -14.03,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2519 "W": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2520 "V": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2521 "Y": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2522 },
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2523 "G": {
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2524 "A": -7.49,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2525 "C": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2526 "E": -6.54,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2527 "D": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2528 "G": 13.34,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2529 "F": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2530 "I": -7.49,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2531 "H": 1.0,
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2775 "M": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2776 "L": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2777 "N": 13.34,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2778 "Q": 20.26,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2779 "P": 20.26,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2780 "S": 44.94,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2781 "R": 58.28,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2782 "T": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2783 "W": 58.28,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2784 "V": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2785 "Y": -6.54,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2786 },
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2787 "T": {
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2788 "A": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2789 "C": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2790 "E": 20.26,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2791 "D": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2792 "G": -7.49,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2793 "F": 13.34,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2794 "I": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2795 "H": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2796 "K": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2797 "M": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2798 "L": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2799 "N": -14.03,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2800 "Q": -6.54,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2801 "P": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2802 "S": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2803 "R": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2804 "T": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2805 "W": -14.03,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2806 "V": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2807 "Y": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2808 },
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2809 "W": {
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2810 "A": -14.03,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2811 "C": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2812 "E": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2813 "D": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2814 "G": -9.37,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2815 "F": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2816 "I": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2817 "H": 24.68,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2818 "K": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2819 "M": 24.68,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2820 "L": 13.34,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2821 "N": 13.34,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2822 "Q": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2823 "P": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2824 "S": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2825 "R": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2826 "T": -14.03,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2827 "W": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2828 "V": -7.49,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2829 "Y": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2830 },
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2831 "V": {
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2832 "A": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2833 "C": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2834 "E": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2835 "D": -14.03,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2836 "G": -7.49,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2837 "F": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2838 "I": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2839 "H": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2840 "K": -1.88,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2841 "M": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2842 "L": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2843 "N": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2844 "Q": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2845 "P": 20.26,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2846 "S": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2847 "R": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2848 "T": -7.49,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2849 "W": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2850 "V": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2851 "Y": -6.54,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2852 },
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2853 "Y": {
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2854 "A": 24.68,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2855 "C": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2856 "E": -6.54,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2857 "D": 24.68,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2858 "G": -7.49,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2859 "F": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2860 "I": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2861 "H": 13.34,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2862 "K": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2863 "M": 44.94,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2864 "L": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2865 "N": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2866 "Q": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2867 "P": 13.34,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2868 "S": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2869 "R": -15.91,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2870 "T": -7.49,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2871 "W": -9.37,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2872 "V": 1.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2873 "Y": 13.34,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2874 },
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2875 }
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2876 return "instability", d
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2877
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2878 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2879 return scalename, scales[scalename]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2880
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2881
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2882 def read_fasta(inputfile):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2883 """Method for loading sequences from a FASTA formatted file into :py:attr:`sequences` & :py:attr:`names`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2884 This method is used by the base class :class:`modlamp.descriptors.PeptideDescriptor` if the input is a FASTA file.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2885
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2886 :param inputfile: .fasta file with sequences and headers to read
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2887 :return: list of sequences in the attribute :py:attr:`sequences` with corresponding sequence names in
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2888 :py:attr:`names`.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2889 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2890 names = list() # list for storing names
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2891 sequences = list() # list for storing sequences
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2892 seq = str()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2893 with open(inputfile) as f:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2894 all = f.readlines()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2895 last = all[-1]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2896 for line in all:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2897 if line.startswith(">"):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2898 names.append(
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2899 line.split(" ")[0][1:].strip()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2900 ) # add FASTA name without description as molecule name
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2901 sequences.append(seq.strip())
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2902 seq = str()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2903 elif line == last:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2904 seq += line.strip() # remove potential white space
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2905 sequences.append(seq.strip())
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2906 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2907 seq += line.strip() # remove potential white space
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2908 return sequences[1:], names
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2909
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2910
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2911 def save_fasta(filename, sequences, names=None):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2912 """Method for saving sequences in the instance :py:attr:`sequences` to a file in FASTA format.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2913
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2914 :param filename: {str} output filename (ending .fasta)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2915 :param sequences: {list} sequences to be saved to file
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2916 :param names: {list} whether sequence names from self.names should be saved as sequence identifiers
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2917 :return: a FASTA formatted file containing the generated sequences
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2918 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2919 if os.path.exists(filename):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2920 os.remove(filename) # remove outputfile, it it exists
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2921
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2922 with open(filename, "w") as o:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2923 for n, seq in enumerate(sequences):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2924 if names:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2925 o.write(">" + str(names[n]) + "\n")
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2926 else:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2927 o.write(">Seq_" + str(n) + "\n")
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2928 o.write(seq + "\n")
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2929
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2930
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2931 def aa_weights():
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2932 """Function holding molecular weight data on all natural amino acids.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2933
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2934 :return: dictionary with amino acid letters and corresponding weights
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2935
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2936 .. versionadded:: v2.4.1
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2937 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2938 weights = {
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2939 "A": 89.093,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2940 "C": 121.158,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2941 "D": 133.103,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2942 "E": 147.129,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2943 "F": 165.189,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2944 "G": 75.067,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2945 "H": 155.155,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2946 "I": 131.173,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2947 "K": 146.188,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2948 "L": 131.173,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2949 "M": 149.211,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2950 "N": 132.118,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2951 "P": 115.131,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2952 "Q": 146.145,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2953 "R": 174.20,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2954 "S": 105.093,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2955 "T": 119.119,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2956 "V": 117.146,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2957 "W": 204.225,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2958 "Y": 181.189,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2959 }
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2960 return weights
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2961
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2962
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2963 def count_aas(seq, scale="relative"):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2964 """Function to count the amino acids occuring in a given sequence.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2965
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2966 :param seq: {str} amino acid sequence
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2967 :param scale: {'absolute' or 'relative'} defines whether counts or frequencies are given for each AA
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2968 :return: {dict} dictionary with amino acids as keys and their counts in the sequence as values.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2969 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2970 if seq == "": # error if len(seq) == 0
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2971 seq = " "
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2972 aas = [
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2973 "A",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2974 "C",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2975 "D",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2976 "E",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2977 "F",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2978 "G",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2979 "H",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2980 "I",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2981 "K",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2982 "L",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2983 "M",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2984 "N",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2985 "P",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2986 "Q",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2987 "R",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2988 "S",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2989 "T",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2990 "V",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2991 "W",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2992 "Y",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2993 ]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2994 scl = 1.0
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2995 if scale == "relative":
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2996 scl = len(seq)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2997 aa = {a: (float(seq.count(a)) / scl) for a in aas}
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2998 aa = collections.OrderedDict(sorted(list(aa.items())))
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2999 return aa
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3000
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3001
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3002 def count_ngrams(seq, n):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3003 """Function to count the n-grams of an amino acid sequence. N can be one integer or a list of integers
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3004
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3005 :param seq: {str} amino acid sequence
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3006 :param n: {int or list of ints} defines whether counts or frequencies are given for each AA
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3007 :return: {dict} dictionary with n-grams as keys and their counts in the sequence as values.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3008 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3009 if seq == "":
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3010 seq = " "
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3011 if isinstance(n, int):
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3012 n = [n]
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3013 ngrams = list()
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3014 for i in n:
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3015 ngrams.extend([seq[j : j + i] for j in range(len(seq) - (i - 1))])
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3016 counts = {g: (seq.count(g)) for g in set(ngrams)}
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3017 counts = collections.OrderedDict(
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3018 sorted(counts.items(), key=operator.itemgetter(1), reverse=True)
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3019 )
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3020 return counts
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3021
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3022
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3023 def aa_energies():
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3024 """Function holding free energies of transfer between cyclohexane and water for all natural amino acids.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3025 H. G. Boman, D. Wade, I. a Boman, B. Wåhlin, R. B. Merrifield, *FEBS Lett*. **1989**, *259*, 103–106.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3026
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3027 :return: dictionary with amino acid letters and corresponding energies.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3028 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3029 energies = {
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3030 "L": -4.92,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3031 "I": -4.92,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3032 "V": -4.04,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3033 "F": -2.98,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3034 "M": -2.35,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3035 "W": -2.33,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3036 "A": -1.81,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3037 "C": -1.28,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3038 "G": -0.94,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3039 "Y": 0.14,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3040 "T": 2.57,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3041 "S": 3.40,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3042 "H": 4.66,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3043 "Q": 5.54,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3044 "K": 5.55,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3045 "N": 6.64,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3046 "E": 6.81,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3047 "D": 8.72,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3048 "R": 14.92,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3049 "P": 0.0,
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3050 }
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3051 return energies
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3052
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3053
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3054 def ngrams_apd():
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3055 """Function returning the most frequent 2-, 3- and 4-grams from all sequences in the `APD3
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3056 <http://aps.unmc.edu/AP/>`_, version August 2016 with 2727 sequences.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3057 For all 2, 3 and 4grams, all possible ngrams were generated from all sequences and the top 50 most frequent
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3058 assembled into a list. Finally, leading and tailing spaces were striped and duplicates as well as ngrams containing
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3059 spaces were removed.
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3060
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3061 :return: numpy.array containing most frequent ngrams
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3062 """
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3063 return np.array(
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3064 [
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3065 "AGK",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3066 "CKI",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3067 "RR",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3068 "YGGG",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3069 "LSGL",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3070 "RG",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3071 "YGGY",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3072 "PRP",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3073 "LGGG",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3074 "GV",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3075 "GT",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3076 "GS",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3077 "GR",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3078 "IAG",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3079 "GG",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3080 "GF",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3081 "GC",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3082 "GGYG",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3083 "GA",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3084 "GL",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3085 "GK",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3086 "GI",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3087 "IPC",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3088 "KAA",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3089 "LAK",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3090 "GLGG",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3091 "GGLG",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3092 "CKIT",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3093 "GAGK",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3094 "LLSG",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3095 "LKK",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3096 "FLP",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3097 "LSG",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3098 "SCK",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3099 "LLS",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3100 "GETC",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3101 "VLG",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3102 "GKLL",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3103 "LLG",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3104 "C",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3105 "KCKI",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3106 "G",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3107 "VGK",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3108 "CSC",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3109 "TKKC",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3110 "GCS",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3111 "GKA",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3112 "IGK",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3113 "GESC",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3114 "KVCY",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3115 "KKL",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3116 "KKI",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3117 "KKC",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3118 "LGGL",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3119 "GLL",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3120 "CGE",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3121 "GGYC",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3122 "GLLS",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3123 "GLF",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3124 "AKK",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3125 "GKAA",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3126 "ESCV",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3127 "GLP",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3128 "CGES",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3129 "PCGE",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3130 "FL",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3131 "CGET",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3132 "GLW",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3133 "KGAA",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3134 "KAAL",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3135 "GGY",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3136 "GGG",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3137 "IKG",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3138 "LKG",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3139 "GGL",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3140 "CK",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3141 "GTC",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3142 "CG",
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
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3143 "SKKC",
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parents:
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3144 "CS",
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parents:
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3145 "CR",
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parents:
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3146 "KC",
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parents:
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3147 "AGKA",
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parents:
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3148 "KA",
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parents:
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3149 "KG",
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3150 "LKCK",
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parents:
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3151 "SCKL",
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parents:
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3152 "KK",
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parents:
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3153 "KI",
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parents:
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3154 "KN",
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parents:
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3155 "KL",
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3156 "SK",
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3157 "KV",
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parents:
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3158 "SL",
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3159 "SC",
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parents:
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3160 "SG",
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3161 "AAA",
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3162 "VAK",
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3163 "AAL",
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3164 "AAK",
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3165 "GGGG",
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parents:
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3166 "KNVA",
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parents:
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3167 "GGGL",
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parents:
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3168 "GYG",
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3169 "LG",
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3170 "LA",
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3171 "LL",
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3172 "LK",
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3173 "LS",
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3174 "LP",
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3175 "GCSC",
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3176 "TC",
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3177 "GAA",
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3178 "AA",
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3179 "VA",
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3180 "VC",
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3181 "AG",
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3182 "VG",
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3183 "AI",
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3184 "AK",
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3185 "VL",
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3186 "AL",
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3187 "TPGC",
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3188 "IK",
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3189 "IA",
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3190 "IG",
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3191 "YGG",
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3192 "LGK",
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3193 "CSCK",
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3194 "GYGG",
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3195 "LGG",
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3196 "KGA",
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3197 ]
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3198 )
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3199
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3200
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3201 def aa_formulas():
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3202 """
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3203 Function returning the molecular formulas of all amino acids. All amino acids are considered in the neutral form
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3204 (uncharged).
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3205 """
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3206 formulas = {
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3207 "A": {"C": 3, "H": 7, "N": 1, "O": 2, "S": 0},
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3208 "C": {"C": 3, "H": 7, "N": 1, "O": 2, "S": 1},
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3209 "D": {"C": 4, "H": 7, "N": 1, "O": 4, "S": 0},
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3210 "E": {"C": 5, "H": 9, "N": 1, "O": 4, "S": 0},
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3211 "F": {"C": 9, "H": 11, "N": 1, "O": 2, "S": 0},
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3212 "G": {"C": 2, "H": 5, "N": 1, "O": 2, "S": 0},
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3213 "H": {"C": 6, "H": 9, "N": 3, "O": 2, "S": 0},
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3214 "I": {"C": 6, "H": 13, "N": 1, "O": 2, "S": 0},
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3215 "K": {"C": 6, "H": 14, "N": 2, "O": 2, "S": 0},
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3216 "L": {"C": 6, "H": 13, "N": 1, "O": 2, "S": 0},
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3217 "M": {"C": 5, "H": 11, "N": 1, "O": 2, "S": 1},
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3218 "N": {"C": 4, "H": 8, "N": 2, "O": 3, "S": 0},
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3219 "P": {"C": 5, "H": 9, "N": 1, "O": 2, "S": 0},
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3220 "Q": {"C": 5, "H": 10, "N": 2, "O": 3, "S": 0},
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3221 "R": {"C": 6, "H": 14, "N": 4, "O": 2, "S": 0},
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3222 "S": {"C": 3, "H": 7, "N": 1, "O": 3, "S": 0},
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3223 "T": {"C": 4, "H": 9, "N": 1, "O": 3, "S": 0},
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3224 "V": {"C": 5, "H": 11, "N": 1, "O": 2, "S": 0},
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3225 "W": {"C": 11, "H": 12, "N": 2, "O": 2, "S": 0},
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3226 "Y": {"C": 9, "H": 11, "N": 1, "O": 3, "S": 0},
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3227 }
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3228 return formulas