Mercurial > repos > abims-sbr > mutcount

annotate scripts/S01b_study_seq_composition_aa.py @ 7:f1e24200e5ae draft

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planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit b7a3030ea134b5dfad89b1a869db659d72d1145c
author abims-sbr
date Wed, 28 Feb 2018 10:39:41 -0500
parents 0ba551449008
children 04a9ada73cc4
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1 #!/usr/bin/env python
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2 # -*- coding: ascii -*-
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3 ## Author: Eric FONTANILLAS
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4 ## Date: 21.12.10
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5 ## Last Version : 12/2017 by Victor Mataigne
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6 ## Object: Test for compositional bias in genome and proteome as marker of thermal adaptation (comparison between 2 "hot" species: Ap and Ps and two "cold" species: Pg, Pp)
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8 import sys,os,shutil,subprocess,string, itertools
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9 from functions import simplify_fasta_name, dico
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11 script_path = os.path.dirname(sys.argv[0])
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13 ##################
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14 ###### DEF2 ######
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15 ##################
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16 def base_composition(seq):
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17 count_A=string.count(seq, "A")
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18 count_T=string.count(seq, "T")
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19 count_C=string.count(seq, "C")
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20 count_G=string.count(seq, "G")
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23 CG = count_C+count_G
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24 AT = count_T+count_A
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26 AG = count_A+count_G
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27 TC = count_T+count_C
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29 ## 1 ## Search for compositional bias in genome as marker of thermal adaptation: CG vs AT
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30 ratio_CG_AT=float(CG)/float(AT)
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32 ## 2 ## Search for compositional bias in genome as marker of thermal adaptation: AG vs TC
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33 ratio_purine_pyrimidine=float(AG)/float(TC)
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35 ## 3 ## Nucleotide proportion
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36 ln = len(seq)
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37 prop_A = float(count_A)/float(ln)
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38 prop_T = float(count_T)/float(ln)
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39 prop_C = float(count_C)/float(ln)
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40 prop_G = float(count_G)/float(ln)
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43 return(ratio_CG_AT, ratio_purine_pyrimidine, prop_A, prop_T, prop_C, prop_G)
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44 ##############################################
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47 ##################
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48 ###### DEF3 ######
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49 ##################
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50 def aa_composition1(seq):
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52 ## 1 ## count occurence of AA
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53 count_K=string.count(seq,"K")
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54 count_R=string.count(seq,"R")
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55 count_A=string.count(seq,"A")
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56 count_F=string.count(seq,"F")
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57 count_I=string.count(seq,"I")
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58 count_L=string.count(seq,"L")
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59 count_M=string.count(seq,"M")
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60 count_V=string.count(seq,"V")
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61 count_W=string.count(seq,"W")
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62 count_N=string.count(seq,"N")
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63 count_Q=string.count(seq,"Q")
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64 count_S=string.count(seq,"S")
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65 count_T=string.count(seq,"T")
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66 count_H=string.count(seq,"H")
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67 count_Y=string.count(seq,"Y")
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68 count_C=string.count(seq,"C")
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69 count_D=string.count(seq,"D")
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70 count_E=string.count(seq,"E")
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71 count_P=string.count(seq,"P")
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72 count_G=string.count(seq,"G")
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76 ## 2 ## compute relative proportion
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77 TOTAL=count_K+count_R+count_A+count_F+count_I+count_L+count_M+count_V+count_W+count_N+count_Q+count_S+count_T+count_H+count_Y+count_C+count_D+count_E+count_P+count_G
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78 if (TOTAL!=0):
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79 ln = TOTAL
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81 prop_K=float(count_K)/float(ln)
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82 prop_R=float(count_R)/float(ln)
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83 prop_A=float(count_A)/float(ln)
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84 prop_F=float(count_F)/float(ln)
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85 prop_I=float(count_I)/float(ln)
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86 prop_L=float(count_L)/float(ln)
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87 prop_M=float(count_M)/float(ln)
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88 prop_V=float(count_V)/float(ln)
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89 prop_W=float(count_W)/float(ln)
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90 prop_N=float(count_N)/float(ln)
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91 prop_Q=float(count_Q)/float(ln)
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92 prop_S=float(count_S)/float(ln)
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93 prop_T=float(count_T)/float(ln)
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94 prop_H=float(count_H)/float(ln)
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95 prop_Y=float(count_Y)/float(ln)
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96 prop_C=float(count_C)/float(ln)
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97 prop_D=float(count_D)/float(ln)
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98 prop_E=float(count_E)/float(ln)
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99 prop_P=float(count_P)/float(ln)
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100 prop_G=float(count_G)/float(ln)
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101 else:
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102 prop_K=0
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103 prop_R=0
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104 prop_A=0
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105 prop_F=0
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106 prop_I=0
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107 prop_L=0
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108 prop_M=0
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109 prop_V=0
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110 prop_W=0
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111 prop_N=0
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112 prop_Q=0
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113 prop_S=0
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114 prop_T=0
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115 prop_H=0
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116 prop_Y=0
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117 prop_C=0
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118 prop_D=0
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119 prop_E=0
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120 prop_P=0
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121 prop_G=0
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122
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123
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124
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125
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126 return(prop_K,prop_R,prop_A,prop_F,prop_I,prop_L,prop_M,prop_V,prop_W,prop_N,prop_Q,prop_S,prop_T,prop_H,prop_Y,prop_C,prop_D,prop_E,prop_P,prop_G)
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127
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128 ##################
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129 ###### DEF4 ######
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130 ##################
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131 def aa_composition2(seq):
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132
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133 ## 1 ## count occurence of AA
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134 count_K=string.count(seq,"K")
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135 count_R=string.count(seq,"R")
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136 count_A=string.count(seq,"A")
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137 count_F=string.count(seq,"F")
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138 count_I=string.count(seq,"I")
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139 count_L=string.count(seq,"L")
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140 count_M=string.count(seq,"M")
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141 count_V=string.count(seq,"V")
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142 count_W=string.count(seq,"W")
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143 count_N=string.count(seq,"N")
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144 count_Q=string.count(seq,"Q")
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145 count_S=string.count(seq,"S")
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146 count_T=string.count(seq,"T")
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147 count_H=string.count(seq,"H")
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148 count_Y=string.count(seq,"Y")
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149 count_C=string.count(seq,"C")
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150 count_D=string.count(seq,"D")
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151 count_E=string.count(seq,"E")
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152 count_P=string.count(seq,"P")
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153 count_G=string.count(seq,"G")
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154
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155
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156
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157 ## 2 ## compute seq length
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158 TOTAL=count_K+count_R+count_A+count_F+count_I+count_L+count_M+count_V+count_W+count_N+count_Q+count_S+count_T+count_H+count_Y+count_C+count_D+count_E+count_P+count_G
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159 if (TOTAL!=0):
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160
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161 ln = TOTAL
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162 ##3 Famous Hyperthermophile Prokaryotes criterias
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163
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164 # 3.1. IVYWREL estimator => positivelly correlated with otpimal growth
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165 count_IVYWREL = count_I+count_V+count_Y+count_W+count_R+count_E+count_L
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166 prop_IVYWREL = float(count_IVYWREL)/float(ln)
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167
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168 # 3.2. ERK estimator (i.e. ERK vs DNQTSHA) => positivelly correlated with optimal growth temperature
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169 # ERK alone
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170 count_ERK = count_E + count_R + count_K
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171 prop_ERK = float(count_ERK)/float(ln)
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172 # DNQTSHA alone
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173 count_DNQTSH = count_D+count_N+count_Q+count_T+count_S+count_H
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174 prop_DNQTSH=float(count_DNQTSH)/float(ln)
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175 # ERK vs DNQTSH
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176 if count_DNQTSH != 0:
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177 ratio_ERK_vs_DNQTSH = float(count_ERK)/float(count_DNQTSH)
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178 else:
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179 ratio_ERK_vs_DNQTSH=-1
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180 # EK/QH estimator
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181 count_EK = count_E+count_K
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182 count_QH = count_Q+count_H
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183
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184 prop_EK = float(count_EK)/float(ln)
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185 prop_QH = float(count_QH)/float(ln)
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186
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187 if count_QH != 0:
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188 ratio_EK_vs_QH = float(count_EK)/float(count_QH)
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189 else:
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190 ratio_EK_vs_QH=-1 ## "-1" will indicate the impossibility to compute the ratio (coz the numerator)
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191
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192 ## 4 ## Mutationnal bias hypothesis => AT rich: favor FYMINK // GC rich: favor GARP
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193 ## The mutational bias model predict a linear relationship between GARP vs FYMINK ==> so if outliers to that, it means that the excess of GARP or FYMINK are not explained by the mutationnal bias model but by other thing ... selection!!???
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194 count_FYMINK=count_F+count_Y+count_M+count_I+count_N+count_K
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195 prop_FYMINK = float(count_FYMINK)/float(ln)
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196
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197 count_GARP=count_G+count_A+count_R+count_P
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198 prop_GARP=float(count_GARP)/float(ln)
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199
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200 ## 5 ## Hydophobicity hypothesis [should INCREASE with thermal adaptation]
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201 ## 5.1. AL
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202 count_AVLIMFYW = count_A+count_V+count_L+count_I+count_F+count_Y+count_W+count_M
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203 prop_AVLIMFYW=float(count_AVLIMFYW)/float(ln)
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204 ## 5.2. Only non-aromatic
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205 count_AVLIM = count_A+count_V+count_L+count_I+count_M
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206 prop_AVLIM=float(count_AVLIM)/float(ln)
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207 ## 5.3. Only aromatic (have they higher residus volume?? in such case opposite hypothesis based on residu volume, predict DECREASE for these aa in composition)
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208 count_FYW = count_F+count_Y+count_W
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209 prop_FYW=float(count_FYW)/float(ln)
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210
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211 ## 6 ## Charged hypothesis => positivelly correlated with optimal growth temperature
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212 # All charged
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213 count_RHKDE = count_R + count_H +count_K + count_D + count_E
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214 prop_RHKDE = float(count_RHKDE)/float(ln)
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215 # Only positive
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216 count_RHK = count_R + count_H +count_K
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217 prop_RHK = float(count_RHK)/float(ln)
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218 # Only negative
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219 count_DE = count_D + count_E
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220 prop_DE = float(count_DE)/float(ln)
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221
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222 ## 7 ## Neutral polar hypothesis [should DECREASE with thermal adaptation]
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223 count_STNQ = count_S+count_T+count_N+count_Q
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224 prop_STNQ=float(count_STNQ)/float(ln)
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225
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226
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227 ## 9 ## PAYRE VS MGDS (FONTANILLAS CRITERIA)
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228 ## 9.1 ## Didier's criteria 1 = SMALL / BIG
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229 count_PAYRE = count_A+count_Y+count_P+count_R+count_E
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230 prop_PAYRE=float(count_PAYRE)/float(ln)
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231 count_MVGDS = count_V+count_M+count_S+count_G+count_D
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232 prop_MVGDS=float(count_MVGDS)/float(ln)
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233 if count_MVGDS!= 0:
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234 ratio_PAYRE_vs_MVGDS = float(count_PAYRE)/float(count_MVGDS)
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235 else:
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236 ratio_PAYRE_vs_MVGDS=-1 ## "-1" will indicate the impossibility to compute the ratio (coz the numerator)
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237
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238 ## 9.2 ## Didier's criteria 2 = VERY SMALL / BIG
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239 count_AC = count_A+count_C
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240 prop_AC=float(count_AC)/float(ln)
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241
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242 #count_VLIM = count_V+count_L+count_I+count_M
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243 if count_MVGDS != 0:
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244 ratio_AC_vs_MVGDS = float(count_AC)/float(count_MVGDS)
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245 else:
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246 ratio_AC_vs_MVGDS=-1 ## "-1" will indicate the impossibility to compute the ratio (coz the numerator)
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247 else:
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248 count_IVYWREL=0
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249 prop_IVYWREL=0
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250 count_ERK=0
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251 prop_ERK=0
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252 count_DNQTSH=0
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253 prop_DNQTSH=0
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254 ratio_ERK_vs_DNQTSH=0
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255 count_EK=0
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256 prop_EK=0
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257 count_QH=0
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258 prop_QH=0
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259 ratio_EK_vs_QH=0
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260 count_FYMINK=0
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261 prop_FYMINK=0
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262 count_GARP=0
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263 prop_GARP=0
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264 count_AVLIMFYW=0
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265 prop_AVLIMFYW=0
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266 count_AVLIM=0
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267 prop_AVLIM=0
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268 count_FYW=0
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269 prop_FYW=0
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270 count_STNQ=0
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271 prop_STNQ=0
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272 count_MVGDS=0
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273 prop_MVGDS=0
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274 count_PAYRE=0
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275 prop_PAYRE=0
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276 count_AC=0
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277 prop_AC=0
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278 ratio_PAYRE_vs_MVGDS=0
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279 ratio_AC_vs_MVGDS=0
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280 count_RHKDE=0
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281 prop_RHKDE=0
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282 count_RHK=0
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283 prop_RHK=0
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284 count_DE=0
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285 prop_DE=0
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286
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287 return(count_IVYWREL,prop_IVYWREL,count_ERK,prop_ERK,count_DNQTSH,prop_DNQTSH,ratio_ERK_vs_DNQTSH,count_EK,prop_EK,count_QH,prop_QH,ratio_EK_vs_QH,count_FYMINK,prop_FYMINK,count_GARP,prop_GARP,count_AVLIMFYW, prop_AVLIMFYW,count_AVLIM,prop_AVLIM,count_FYW,prop_FYW,count_STNQ, prop_STNQ, count_MVGDS,prop_MVGDS, count_PAYRE,prop_PAYRE, count_AC,prop_AC, ratio_PAYRE_vs_MVGDS, ratio_AC_vs_MVGDS, count_RHKDE,prop_RHKDE,count_RHK,prop_RHK,count_DE,prop_DE)
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288 #####################
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289
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290
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291 ##################
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292 ###### DEF5 ######
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293 ##################
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294 def aa_properties(fileIN_aaProperties):
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295 next = fileIN_aaProperties.readline() ## JUMP HEADERS
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296
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297 bash_aa_properties={}
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298
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299 while 1:
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300 next = fileIN_aaProperties.readline()
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301 if not next:
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302 break
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303
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304 S1 = string.split(next, ",")
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305
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306 aa_name = S1[1]
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307 S2 = string.split(aa_name, "/")
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308 aa_code = S2[1][:-1]
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309
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310 frequencies = S1[2][:-1]
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311 Residue_Weight = S1[5]
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312 Residue_Volume = S1[6]
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313 Partial_specific_volume = S1[7]
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314 Hydration = S1[8]
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315
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316 bash_aa_properties[aa_code] = [frequencies,Residue_Weight,Residue_Volume,Partial_specific_volume,Hydration]
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317
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318 return(bash_aa_properties)
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319
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320
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321 ##################
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322 ###### DEF6 ######
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323 ##################
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324 def sequence_properties_from_aa_properties(seq, bash_properties):
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325
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326 ## 1 ## count occurence of AA
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327 count_K=string.count(seq,"K")
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328 count_R=string.count(seq,"R")
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329 count_A=string.count(seq,"A")
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330 count_F=string.count(seq,"F")
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331 count_I=string.count(seq,"I")
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332 count_L=string.count(seq,"L")
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333 count_M=string.count(seq,"M")
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334 count_V=string.count(seq,"V")
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335 count_W=string.count(seq,"W")
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336 count_N=string.count(seq,"N")
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337 count_Q=string.count(seq,"Q")
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338 count_S=string.count(seq,"S")
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339 count_T=string.count(seq,"T")
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340 count_H=string.count(seq,"H")
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341 count_Y=string.count(seq,"Y")
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342 count_C=string.count(seq,"C")
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343 count_D=string.count(seq,"D")
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344 count_E=string.count(seq,"E")
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345 count_P=string.count(seq,"P")
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346 count_G=string.count(seq,"G")
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347
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348 TOTAL=count_K+count_R+count_A+count_F+count_I+count_L+count_M+count_V+count_W+count_N+count_Q+count_S+count_T+count_H+count_Y+count_C+count_D+count_E+count_P+count_G
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349
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350 if (TOTAL!=0):
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351
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352
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353 ## 2 ## Compute properties 1: Residue Weight (Mr) (UNIT:Daltons):
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354
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355 Total_Residue_Weight = count_K*float(bash_properties["K"][1]) + count_R*float(bash_properties["R"][1]) + count_A*float(bash_properties["A"][1]) + count_F*float(bash_properties["F"][1]) + count_I*float(bash_properties["I"][1]) + count_L*float(bash_properties["L"][1]) + count_M*float(bash_properties["M"][1]) + count_V*float(bash_properties["V"][1]) + count_W*float(bash_properties["W"][1]) + count_N*float(bash_properties["N"][1]) + count_Q*float(bash_properties["Q"][1]) + count_S*float(bash_properties["S"][1]) + count_T*float(bash_properties["T"][1]) + count_H*float(bash_properties["H"][1]) + count_Y*float(bash_properties["Y"][1]) + count_C*float(bash_properties["C"][1]) + count_D*float(bash_properties["D"][1]) + count_E*float(bash_properties["E"][1]) + count_P*float(bash_properties["P"][1]) + count_G*float(bash_properties["G"][1])
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356 Total_Residue_Volume = count_K*float(bash_properties["K"][2]) + count_R*float(bash_properties["R"][2]) + count_A*float(bash_properties["A"][2]) + count_F*float(bash_properties["F"][2]) + count_I*float(bash_properties["I"][2]) + count_L*float(bash_properties["L"][2]) + count_M*float(bash_properties["M"][2]) + count_V*float(bash_properties["V"][2]) + count_W*float(bash_properties["W"][2]) + count_N*float(bash_properties["N"][2]) + count_Q*float(bash_properties["Q"][2]) + count_S*float(bash_properties["S"][2]) + count_T*float(bash_properties["T"][2]) + count_H*float(bash_properties["H"][2]) + count_Y*float(bash_properties["Y"][2]) + count_C*float(bash_properties["C"][2]) + count_D*float(bash_properties["D"][2]) + count_E*float(bash_properties["E"][2]) + count_P*float(bash_properties["P"][2]) + count_G*float(bash_properties["G"][2])
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357 Total_Partial_specific_volume = count_K*float(bash_properties["K"][3]) + count_R*float(bash_properties["R"][3]) + count_A*float(bash_properties["A"][3]) + count_F*float(bash_properties["F"][3]) + count_I*float(bash_properties["I"][3]) + count_L*float(bash_properties["L"][3]) + count_M*float(bash_properties["M"][3]) + count_V*float(bash_properties["V"][3]) + count_W*float(bash_properties["W"][3]) + count_N*float(bash_properties["N"][3]) + count_Q*float(bash_properties["Q"][3]) + count_S*float(bash_properties["S"][3]) + count_T*float(bash_properties["T"][3]) + count_H*float(bash_properties["H"][3]) + count_Y*float(bash_properties["Y"][3]) + count_C*float(bash_properties["C"][3]) + count_D*float(bash_properties["D"][3]) + count_E*float(bash_properties["E"][3]) + count_P*float(bash_properties["P"][3]) + count_G*float(bash_properties["G"][3])
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358 Total_Hydration = count_K*float(bash_properties["K"][4]) + count_R*float(bash_properties["R"][4]) + count_A*float(bash_properties["A"][4]) + count_F*float(bash_properties["F"][4]) + count_I*float(bash_properties["I"][4]) + count_L*float(bash_properties["L"][4]) + count_M*float(bash_properties["M"][4]) + count_V*float(bash_properties["V"][4]) + count_W*float(bash_properties["W"][4]) + count_N*float(bash_properties["N"][4]) + count_Q*float(bash_properties["Q"][4]) + count_S*float(bash_properties["S"][4]) + count_T*float(bash_properties["T"][4]) + count_H*float(bash_properties["H"][4]) + count_Y*float(bash_properties["Y"][4]) + count_C*float(bash_properties["C"][4]) + count_D*float(bash_properties["D"][4]) + count_E*float(bash_properties["E"][4]) + count_P*float(bash_properties["P"][4]) + count_G*float(bash_properties["G"][4])
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359 else:
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360 Total_Residue_Weight=0
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361 Total_Residue_Volume=0
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362 Total_Partial_specific_volume=0
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363 Total_Hydration=0
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364
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365 return(Total_Residue_Weight,Total_Residue_Volume,Total_Partial_specific_volume,Total_Hydration)
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366
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367 ########################################################
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368
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369
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370
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371 ###################
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372 ### RUN RUN RUN ###
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373 ###################
1
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374
0
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375
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376 ##Create specific folders
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377 Path_IN_loci_NUC = "./IN_AA"
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378 outpath= "./OUT"
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379 os.makedirs(Path_IN_loci_NUC)
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380 os.makedirs(outpath)
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381
1
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382 infiles = str.split(sys.argv[1], ",")
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383 for file in infiles:
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384 os.system("cp %s %s" %(file, Path_IN_loci_NUC))
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385
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386 ## 1 ## List taxa
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387 LT=[]
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388 cmd="grep '>' %s" % sys.argv[2]
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389 result = subprocess.check_output(cmd, shell=True)
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390 result=result.split('\n')
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391 for i in result:
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392 sp=i[1:]
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393 if sp !='':
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394 LT.append(sp)
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395 print LT
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396
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397
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398 ## 2 ## PathIN
1
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399 fileIN_properties = open("amino_acid_properties.csv", "r")
0
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400 Path_IN_loci_AA = "./IN_AA"
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401 #Path_IN_loci_AA = "02_CDS_No_Missing_Data_aa_CDS_withM"
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402 Lloci_AA = os.listdir(Path_IN_loci_AA)
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403
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404 ## 3 ## PathOUT
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405
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406 ## 3.1 ## PROT composition
1
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407 fileOUT_PROT_ALL=open("./OUT/prot_compositions_All_AA.csv","w")
0
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408 fileOUT_PROT_ALL.write("LOCUS,")
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409 for taxa in LT[0:-1]:
0
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410 fileOUT_PROT_ALL.write("%s_prop_K,%s_prop_R,%s_prop_A,%s_prop_F,%s_prop_I,%s_prop_L,%s_prop_M,%s_prop_V,%s_prop_W,%s_prop_N,%s_prop_Q,%s_prop_S,%s_prop_T,%s_prop_H,%s_prop_Y,%s_prop_C,%s_prop_D,%s_prop_E,%s_prop_P,%s_prop_G," %(taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa))
5
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411 fileOUT_PROT_ALL.write("%s_prop_K,%s_prop_R,%s_prop_A,%s_prop_F,%s_prop_I,%s_prop_L,%s_prop_M,%s_prop_V,%s_prop_W,%s_prop_N,%s_prop_Q,%s_prop_S,%s_prop_T,%s_prop_H,%s_prop_Y,%s_prop_C,%s_prop_D,%s_prop_E,%s_prop_P,%s_prop_G" %(LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1]))
0
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412 fileOUT_PROT_ALL.write("\n")
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413
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414 ## 3.2 ## PROT IVYWREL
1
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415 fileOUT_IVYWREL=open("./OUT/IVYWREL.csv","w")
0
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416 fileOUT_IVYWREL.write("LOCUS,")
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417 for taxa in LT[0:-1]:
0
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418 fileOUT_IVYWREL.write("%s_count_IVYWREL,%s_prop_IVYWREL," %(taxa,taxa))
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419 fileOUT_IVYWREL.write("%s_count_IVYWREL,%s_prop_IVYWREL" %(LT[-1],LT[-1]))
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420 fileOUT_IVYWREL.write("\n")
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421
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422 ## 3.3 ## PROT ERK_DNQTSHA
1
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423 fileOUT_ERK_DNQTSH=open("./OUT/ERK_DNQTSH.csv","w")
0
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424 fileOUT_ERK_DNQTSH.write("LOCUS,")
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425 for taxa in LT[0:-1]:
0
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426 fileOUT_ERK_DNQTSH.write("%s_count_ERK,%s_prop_ERK,%s_count_DNQTSH,%s_prop_DNQTSH,%s_ratio_ERK_vs_DNQTSH," %(taxa,taxa,taxa,taxa,taxa))
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427 fileOUT_ERK_DNQTSH.write("%s_count_ERK,%s_prop_ERK,%s_count_DNQTSH,%s_prop_DNQTSH,%s_ratio_ERK_vs_DNQTSH" %(LT[-1],LT[-1],LT[-1],LT[-1],LT[-1]))
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428 fileOUT_ERK_DNQTSH.write("\n")
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429
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430 ## 3.4 ## PROT EK_QH
1
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431 fileOUT_EK_QH=open("./OUT/EK_QH.csv","w")
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432 fileOUT_EK_QH.write("LOCUS,")
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433 for taxa in LT[0:-1]:
0
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434 fileOUT_EK_QH.write("%s_count_EK,%s_prop_EK,%s_count_QH,%s_prop_QH,%s_ratio_EK_vs_QH," %(taxa,taxa,taxa,taxa,taxa))
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435 fileOUT_EK_QH.write("%s_count_EK,%s_prop_EK,%s_count_QH,%s_prop_QH,%s_ratio_EK_vs_QH" %(LT[-1],LT[-1],LT[-1],LT[-1],LT[-1]))
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436 fileOUT_EK_QH.write("\n")
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437
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438 ## 3.5 ## PROT FYMINK_GARP
1
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439 fileOUT_FYMINK_GARP=open("./OUT/FYMINK_GARP.csv","w")
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440 fileOUT_FYMINK_GARP.write("LOCUS,")
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441 for taxa in LT[0:-1]:
0
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442 fileOUT_FYMINK_GARP.write("%s_count_FYMINK,%s_prop_FYMINK,%s_count_GARP,%s_prop_GARP," %(taxa,taxa,taxa,taxa))
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443 fileOUT_FYMINK_GARP.write("%s_count_FYMINK,%s_prop_FYMINK,%s_count_GARP,%s_prop_GARP" %(LT[-1],LT[-1],LT[-1],LT[-1]))
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444 fileOUT_FYMINK_GARP.write("\n")
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445
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446 ## 3.6 ## PROT AVLIMFYW
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447 fileOUT_AVLIMFYW=open("./OUT/AVLIMFYW.csv","w")
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448 fileOUT_AVLIMFYW.write("LOCUS,")
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449 for taxa in LT[0:-1]:
0
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450 fileOUT_AVLIMFYW.write("%s_count_AVLIMFYW,%s_prop_AVLIMFYW,%s_count_AVLIM,%s_prop_AVLIM,%s_count_FYW,%s_prop_FYW," %(taxa,taxa,taxa,taxa,taxa,taxa))
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451 fileOUT_AVLIMFYW.write("%s_count_AVLIMFYW,%s_prop_AVLIMFYW,%s_count_AVLIM,%s_prop_AVLIM,%s_count_FYW,%s_prop_FYW" %(LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1]))
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452 fileOUT_AVLIMFYW.write("\n")
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453
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454 ## 3.7 ## PROT STNQ
1
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abims-sbr
parents: 0
diff changeset
455 fileOUT_STNQ=open("./OUT/STNQ.csv","w")
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
456 fileOUT_STNQ.write("LOCUS,")
5
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abims-sbr
parents: 4
diff changeset
457 for taxa in LT[0:-1]:
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
458 fileOUT_STNQ.write("%s_count_STNQ,%s_prop_STNQ," %(taxa,taxa))
5
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
459 fileOUT_STNQ.write("%s_count_STNQ,%s_prop_STNQ" %(LT[-1],LT[-1]))
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
460 fileOUT_STNQ.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
461
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
462 ## 3.8 ## PROT RHKDE
1
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abims-sbr
parents: 0
diff changeset
463 fileOUT_RHKDE=open("./OUT/RHKDE.csv","w")
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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diff changeset
464 fileOUT_RHKDE.write("LOCUS,")
5
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abims-sbr
parents: 4
diff changeset
465 for taxa in LT[0:-1]:
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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diff changeset
466 fileOUT_RHKDE.write("%s_count_RHKDE,%s_prop_RHKDE,%s_count_RHK,%s_prop_RHK,%s_count_DE,%s_prop_DE," %(taxa,taxa,taxa,taxa,taxa,taxa))
5
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
467 fileOUT_RHKDE.write("%s_count_RHKDE,%s_prop_RHKDE,%s_count_RHK,%s_prop_RHK,%s_count_DE,%s_prop_DE" %(LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1]))
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
468 fileOUT_RHKDE.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
469
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
470 ## 3.9 ## PROT DIDER CRITERIA
1
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diff changeset
471 fileOUT_PAYRE=open("./OUT/PAYRE-MVGDS.csv","w")
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
472 fileOUT_PAYRE.write("LOCUS,")
5
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abims-sbr
parents: 4
diff changeset
473 for taxa in LT[0:-1]:
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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diff changeset
474 fileOUT_PAYRE.write("%s_count_PAYRE,%s_prop_PAYRE,%s_count_AC,%s_prop_AC,%s_count_MVGDS,%s_prop_MVGDS,%s_ratio_PAYRE_vs_MVGDS,%s_ratio_AC_vs_MVGDS," %(taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa))
5
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abims-sbr
parents: 4
diff changeset
475 fileOUT_PAYRE.write("%s_count_PAYRE,%s_prop_PAYRE,%s_count_AC,%s_prop_AC,%s_count_MVGDS,%s_prop_MVGDS,%s_ratio_PAYRE_vs_MVGDS,%s_ratio_AC_vs_MVGDS" %(LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1]))
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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parents:
diff changeset
476 fileOUT_PAYRE.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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parents:
diff changeset
477
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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diff changeset
478 ## 3.10 ## PROT Total residue weight
1
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diff changeset
479 fileOUT_TotalResidueWeight=open("./OUT/TotalResidueWeight.csv","w")
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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diff changeset
480 fileOUT_TotalResidueWeight.write("LOCUS,")
5
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abims-sbr
parents: 4
diff changeset
481 for taxa in LT[0:-1]:
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
482 fileOUT_TotalResidueWeight.write("%s_Total_Residue_Weight," %taxa)
5
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abims-sbr
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diff changeset
483 fileOUT_TotalResidueWeight.write("%s_Total_Residue_Weight" %LT[-1])
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
484 fileOUT_TotalResidueWeight.write("\n")
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diff changeset
485
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
486 ## 3.11 ## PROT Total residue volume
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
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diff changeset
487 fileOUT_TotalResidueVolume=open("./OUT/TotalResidueVolume.csv","w")
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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diff changeset
488 fileOUT_TotalResidueVolume.write("LOCUS,")
5
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abims-sbr
parents: 4
diff changeset
489 for taxa in LT[0:-1]:
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
490 fileOUT_TotalResidueVolume.write("%s_Total_Residue_Volume," %taxa)
5
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abims-sbr
parents: 4
diff changeset
491 fileOUT_TotalResidueVolume.write("%s_Total_Residue_Volume" %LT[-1])
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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diff changeset
492 fileOUT_TotalResidueVolume.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
493
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
494 ## 3.12 ## PROT Total partial specific volume
1
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abims-sbr
parents: 0
diff changeset
495 fileOUT_TotalPartialSpecificVolume=open("./OUT/TotalPartialSpecificVolume.csv","w")
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
496 fileOUT_TotalPartialSpecificVolume.write("LOCUS,")
5
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abims-sbr
parents: 4
diff changeset
497 for taxa in LT[0:-1]:
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
498 fileOUT_TotalPartialSpecificVolume.write("%s_Total_Partial_Specific_Volume," %taxa)
5
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abims-sbr
parents: 4
diff changeset
499 fileOUT_TotalPartialSpecificVolume.write("%s_Total_Partial_Specific_Volume" %LT[-1])
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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diff changeset
500 fileOUT_TotalPartialSpecificVolume.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
501
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
502 ## 3.13 ## PROT Total hydratation
1
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abims-sbr
parents: 0
diff changeset
503 fileOUT_TotalHydratation=open("./OUT/TotalHydratation.csv","w")
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
504 fileOUT_TotalHydratation.write("LOCUS,")
5
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abims-sbr
parents: 4
diff changeset
505 for taxa in LT[0:-1]:
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
506 fileOUT_TotalHydratation.write("%s_Total_Hydratation," %taxa)
5
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abims-sbr
parents: 4
diff changeset
507 fileOUT_TotalHydratation.write("%s_Total_Hydratation" %LT[-1])
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
508 fileOUT_TotalHydratation.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
509
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
510 #####################
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
511 ## 4 ## Process Loci
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
512 #####################
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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diff changeset
513 bash_aa_properties = aa_properties(fileIN_properties)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
514
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
515 for locus in Lloci_AA:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
516 print locus
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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parents:
diff changeset
517 path_locus = "%s/%s" %(Path_IN_loci_AA, locus)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
518 bash = dico(path_locus,LT)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
519
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
520 #print bash
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
521
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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parents:
diff changeset
522 fileOUT_PROT_ALL.write("%s," %locus)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
523 fileOUT_IVYWREL.write("%s," %locus)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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parents:
diff changeset
524 fileOUT_ERK_DNQTSH.write("%s," %locus)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
525 fileOUT_EK_QH.write("%s," %locus)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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parents:
diff changeset
526 fileOUT_FYMINK_GARP.write("%s," %locus)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
527 fileOUT_AVLIMFYW.write("%s," %locus)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
528 fileOUT_STNQ.write("%s," %locus)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
529 fileOUT_RHKDE.write("%s," %locus)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
530 fileOUT_PAYRE.write("%s," %locus)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
531 fileOUT_TotalResidueWeight.write("%s," %locus)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
532 fileOUT_TotalResidueVolume.write("%s," %locus)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
533 fileOUT_TotalPartialSpecificVolume.write("%s," %locus)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
534 fileOUT_TotalHydratation.write("%s," %locus)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
535
5
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
536 for taxa in LT[0:-1]:
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
537 if taxa in bash.keys():
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
538 seq = bash[taxa]
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
539 prop_K,prop_R,prop_A,prop_F,prop_I,prop_L,prop_M,prop_V,prop_W,prop_N,prop_Q,prop_S,prop_T,prop_H,prop_Y,prop_C,prop_D,prop_E,prop_P,prop_G = aa_composition1(seq) ### DEF3 ###
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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parents:
diff changeset
540 count_IVYWREL,prop_IVYWREL,count_ERK,prop_ERK,count_DNQTSH,prop_DNQTSH,ratio_ERK_vs_DNQTSH,count_EK,prop_EK,count_QH,prop_QH,ratio_EK_vs_QH,count_FYMINK,prop_FYMINK,count_GARP,prop_GARP,count_AVLIMFYW,prop_AVLIMFYW,count_AVLIM,prop_AVLIM,count_FYW,prop_FYW,count_STNQ,prop_STNQ, count_MVGDS,prop_MVGDS, count_PAYRE,prop_PAYRE, count_AC,prop_AC, ratio_PAYRE_vs_MVGDS, ratio_AC_vs_MVGDS,count_RHKDE,prop_RHKDE,count_RHK,prop_RHK,count_DE,prop_DE = aa_composition2(seq) ### DEF4 ###
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
541 Total_Residue_Weight,Total_Residue_Volume,Total_Partial_Specific_Volume,Total_Hydration = sequence_properties_from_aa_properties(seq, bash_aa_properties) ### DEF6 ###
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
542
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
543 fileOUT_PROT_ALL.write("%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f," %(prop_K,prop_R,prop_A,prop_F,prop_I,prop_L,prop_M,prop_V,prop_W,prop_N,prop_Q,prop_S,prop_T,prop_H,prop_Y,prop_C,prop_D,prop_E,prop_P,prop_G))
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
544 fileOUT_IVYWREL.write("%.5f,%.5f," %(count_IVYWREL, prop_IVYWREL))
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
545 fileOUT_ERK_DNQTSH.write("%.5f,%.5f,%.5f,%.5f,%.5f," %(count_ERK,prop_ERK,count_DNQTSH,prop_DNQTSH,ratio_ERK_vs_DNQTSH))
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
546 fileOUT_EK_QH.write("%.5f,%.5f,%.5f,%.5f,%.5f," %(count_EK,prop_EK,count_QH,prop_QH,ratio_EK_vs_QH))
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
547 fileOUT_FYMINK_GARP.write("%.5f,%.5f,%.5f,%.5f," %(count_FYMINK,prop_FYMINK,count_GARP,prop_GARP))
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
548 fileOUT_AVLIMFYW.write("%.5f,%.5f,%.5f,%.5f,%.5f,%.5f," %(count_AVLIMFYW,prop_AVLIMFYW,count_AVLIM,prop_AVLIM,count_FYW,prop_FYW))
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
549 fileOUT_STNQ.write("%.5f,%.5f," %(count_STNQ,prop_STNQ))
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
550 fileOUT_RHKDE.write("%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,"%(count_RHKDE,prop_RHKDE,count_RHK,prop_RHK,count_DE,prop_DE))
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
551 fileOUT_PAYRE.write("%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f," %(count_PAYRE,prop_PAYRE,count_AC,prop_AC,count_MVGDS,prop_MVGDS,ratio_PAYRE_vs_MVGDS,ratio_AC_vs_MVGDS))
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
552 fileOUT_TotalResidueWeight.write("%.5f," %Total_Residue_Weight)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
553 fileOUT_TotalResidueVolume.write("%.5f," %Total_Residue_Volume)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
554 fileOUT_TotalPartialSpecificVolume.write("%.5f," %(Total_Partial_Specific_Volume))
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
555 fileOUT_TotalHydratation.write("%.5f," % Total_Hydration)
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
556 else:
4
5766f80370e7 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 17acd02c547bd1f7661a846661aa99de9743efe9
abims-sbr
parents: 2
diff changeset
557 fileOUT_PROT_ALL.write("%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s," %("NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA"))
5766f80370e7 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 17acd02c547bd1f7661a846661aa99de9743efe9
abims-sbr
parents: 2
diff changeset
558 fileOUT_IVYWREL.write("%s,%s," %("NA", "NA"))
5766f80370e7 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 17acd02c547bd1f7661a846661aa99de9743efe9
abims-sbr
parents: 2
diff changeset
559 fileOUT_ERK_DNQTSH.write("%s,%s,%s,%s,%s," %("NA","NA","NA","NA","NA"))
5766f80370e7 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 17acd02c547bd1f7661a846661aa99de9743efe9
abims-sbr
parents: 2
diff changeset
560 fileOUT_EK_QH.write("%s,%s,%s,%s,%s," %("NA","NA","NA","NA","NA"))
5766f80370e7 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 17acd02c547bd1f7661a846661aa99de9743efe9
abims-sbr
parents: 2
diff changeset
561 fileOUT_FYMINK_GARP.write("%s,%s,%s,%s," %("NA","NA","NA","NA"))
5766f80370e7 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 17acd02c547bd1f7661a846661aa99de9743efe9
abims-sbr
parents: 2
diff changeset
562 fileOUT_AVLIMFYW.write("%s,%s,%s,%s,%s,%s," %("NA","NA","NA","NA","NA","NA"))
5766f80370e7 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 17acd02c547bd1f7661a846661aa99de9743efe9
abims-sbr
parents: 2
diff changeset
563 fileOUT_STNQ.write("%s,%s," %("NA","NA"))
5766f80370e7 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 17acd02c547bd1f7661a846661aa99de9743efe9
abims-sbr
parents: 2
diff changeset
564 fileOUT_RHKDE.write("%s,%s,%s,%s,%s,%s,"%("NA","NA","NA","NA","NA","NA"))
5766f80370e7 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 17acd02c547bd1f7661a846661aa99de9743efe9
abims-sbr
parents: 2
diff changeset
565 fileOUT_PAYRE.write("%s,%s,%s,%s,%s,%s,%s,%s," %("NA","NA","NA","NA","NA","NA","NA","NA"))
5766f80370e7 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 17acd02c547bd1f7661a846661aa99de9743efe9
abims-sbr
parents: 2
diff changeset
566 fileOUT_TotalResidueWeight.write("%s," %"NA")
5766f80370e7 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 17acd02c547bd1f7661a846661aa99de9743efe9
abims-sbr
parents: 2
diff changeset
567 fileOUT_TotalResidueVolume.write("%s," %"NA")
5766f80370e7 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 17acd02c547bd1f7661a846661aa99de9743efe9
abims-sbr
parents: 2
diff changeset
568 fileOUT_TotalPartialSpecificVolume.write("%s," %"NA")
5766f80370e7 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 17acd02c547bd1f7661a846661aa99de9743efe9
abims-sbr
parents: 2
diff changeset
569 fileOUT_TotalHydratation.write("%s," %"NA")
5
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
570
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
571 if LT[-1] in bash.keys():
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
572 seq = bash[LT[-1]]
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
573 prop_K,prop_R,prop_A,prop_F,prop_I,prop_L,prop_M,prop_V,prop_W,prop_N,prop_Q,prop_S,prop_T,prop_H,prop_Y,prop_C,prop_D,prop_E,prop_P,prop_G = aa_composition1(seq) ### DEF3 ###
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
574 count_IVYWREL,prop_IVYWREL,count_ERK,prop_ERK,count_DNQTSH,prop_DNQTSH,ratio_ERK_vs_DNQTSH,count_EK,prop_EK,count_QH,prop_QH,ratio_EK_vs_QH,count_FYMINK,prop_FYMINK,count_GARP,prop_GARP,count_AVLIMFYW,prop_AVLIMFYW,count_AVLIM,prop_AVLIM,count_FYW,prop_FYW,count_STNQ,prop_STNQ, count_MVGDS,prop_MVGDS, count_PAYRE,prop_PAYRE, count_AC,prop_AC, ratio_PAYRE_vs_MVGDS, ratio_AC_vs_MVGDS,count_RHKDE,prop_RHKDE,count_RHK,prop_RHK,count_DE,prop_DE = aa_composition2(seq) ### DEF4 ###
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
575 Total_Residue_Weight,Total_Residue_Volume,Total_Partial_Specific_Volume,Total_Hydration = sequence_properties_from_aa_properties(seq, bash_aa_properties) ### DEF6 ###
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
576
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
577 fileOUT_PROT_ALL.write("%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f" %(prop_K,prop_R,prop_A,prop_F,prop_I,prop_L,prop_M,prop_V,prop_W,prop_N,prop_Q,prop_S,prop_T,prop_H,prop_Y,prop_C,prop_D,prop_E,prop_P,prop_G))
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
578 fileOUT_IVYWREL.write("%.5f,%.5f" %(count_IVYWREL, prop_IVYWREL))
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
579 fileOUT_ERK_DNQTSH.write("%.5f,%.5f,%.5f,%.5f,%.5f" %(count_ERK,prop_ERK,count_DNQTSH,prop_DNQTSH,ratio_ERK_vs_DNQTSH))
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
580 fileOUT_EK_QH.write("%.5f,%.5f,%.5f,%.5f,%.5f" %(count_EK,prop_EK,count_QH,prop_QH,ratio_EK_vs_QH))
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
581 fileOUT_FYMINK_GARP.write("%.5f,%.5f,%.5f,%.5f" %(count_FYMINK,prop_FYMINK,count_GARP,prop_GARP))
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
582 fileOUT_AVLIMFYW.write("%.5f,%.5f,%.5f,%.5f,%.5f,%.5f" %(count_AVLIMFYW,prop_AVLIMFYW,count_AVLIM,prop_AVLIM,count_FYW,prop_FYW))
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
583 fileOUT_STNQ.write("%.5f,%.5f" %(count_STNQ,prop_STNQ))
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
584 fileOUT_RHKDE.write("%.5f,%.5f,%.5f,%.5f,%.5f,%.5f"%(count_RHKDE,prop_RHKDE,count_RHK,prop_RHK,count_DE,prop_DE))
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
585 fileOUT_PAYRE.write("%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f" %(count_PAYRE,prop_PAYRE,count_AC,prop_AC,count_MVGDS,prop_MVGDS,ratio_PAYRE_vs_MVGDS,ratio_AC_vs_MVGDS))
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
586 fileOUT_TotalResidueWeight.write("%.5f" %Total_Residue_Weight)
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
587 fileOUT_TotalResidueVolume.write("%.5f" %Total_Residue_Volume)
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
588 fileOUT_TotalPartialSpecificVolume.write("%.5f" %(Total_Partial_Specific_Volume))
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
589 fileOUT_TotalHydratation.write("%.5f" % Total_Hydration)
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
590 else:
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
591 fileOUT_PROT_ALL.write("%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s" %("NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA"))
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
592 fileOUT_IVYWREL.write("%s,%s" %("NA", "NA"))
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
593 fileOUT_ERK_DNQTSH.write("%s,%s,%s,%s,%s" %("NA","NA","NA","NA","NA"))
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
594 fileOUT_EK_QH.write("%s,%s,%s,%s,%s" %("NA","NA","NA","NA","NA"))
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
595 fileOUT_FYMINK_GARP.write("%s,%s,%s,%s" %("NA","NA","NA","NA"))
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
596 fileOUT_AVLIMFYW.write("%s,%s,%s,%s,%s,%s" %("NA","NA","NA","NA","NA","NA"))
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
597 fileOUT_STNQ.write("%s,%s" %("NA","NA"))
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
598 fileOUT_RHKDE.write("%s,%s,%s,%s,%s,%s"%("NA","NA","NA","NA","NA","NA"))
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
599 fileOUT_PAYRE.write("%s,%s,%s,%s,%s,%s,%s,%s" %("NA","NA","NA","NA","NA","NA","NA","NA"))
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
600 fileOUT_TotalResidueWeight.write("%s" %"NA")
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
601 fileOUT_TotalResidueVolume.write("%s" %"NA")
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
602 fileOUT_TotalPartialSpecificVolume.write("%s" %"NA")
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
603 fileOUT_TotalHydratation.write("%s" %"NA")
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
604
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
605 ## END LINE
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
606 fileOUT_PROT_ALL.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
607 fileOUT_IVYWREL.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
608 fileOUT_ERK_DNQTSH.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
609 fileOUT_EK_QH.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
610 fileOUT_FYMINK_GARP.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
611 fileOUT_AVLIMFYW.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
612 fileOUT_STNQ.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
613 fileOUT_RHKDE.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
614 fileOUT_PAYRE.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
615 fileOUT_TotalResidueWeight.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
616 fileOUT_TotalResidueVolume.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
617 fileOUT_TotalPartialSpecificVolume.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
618 fileOUT_TotalHydratation.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
619