Mercurial > repos > abims-sbr > mutcount

annotate scripts/S01b_study_seq_composition_aa.py @ 0:78dd6454f6f0 draft

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planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
author abims-sbr
date Tue, 02 May 2017 04:20:51 -0400
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children 8de21b6eb110
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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 ## 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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6 import sys, os
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7 script_path = os.path.dirname(sys.argv[0])
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9 #############
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10 ### DEF 0 ###
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11 #############
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12 def simplify_fasta_name(fasta_name,LT):
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14 for abbreviation in LT:
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15 if abbreviation in fasta_name:
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16 new_fasta_name = abbreviation
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18 return(new_fasta_name)
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19 ##########################################
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21 ###########
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22 ## DEF1 ##
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23 ###########
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24 ## Generates bash, with key = fasta name; value = sequence (WITH GAP, IF ANY, REMOVED IN THIS FUNCTION)
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26 def dico(fasta_file,LT):
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28 count_fastaName=0
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29 F1 = open(fasta_file, "r")
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31 bash1 = {}
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32 while 1:
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33 nextline = F1.readline()
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34 #print nextline
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35 if not nextline :
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36 break
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38 if nextline[0] == ">":
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39 count_fastaName = count_fastaName + 1
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40 fasta_name = nextline[1:-1]
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41 nextline = F1.readline()
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42 sequence = nextline[:-1]
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44 if fasta_name not in bash1.keys():
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45 fasta_name = simplify_fasta_name(fasta_name,LT) ### DEF 0 ###
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46 bash1[fasta_name] = sequence
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47 else:
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48 print fasta_name
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50 # Find alignment length
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51 kk = bash1.keys()
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52 key0 = kk[0]
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53 seq0 = bash1[key0]
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54 ln_seq = len(seq0)
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56 F1.close()
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58 return(bash1)
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59 #####################################
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63 ##################
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64 ###### DEF2 ######
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65 ##################
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66 def base_composition(seq):
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67 count_A=string.count(seq, "A")
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68 count_T=string.count(seq, "T")
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69 count_C=string.count(seq, "C")
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70 count_G=string.count(seq, "G")
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73 CG = count_C+count_G
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74 AT = count_T+count_A
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76 AG = count_A+count_G
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77 TC = count_T+count_C
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79 ## 1 ## Search for compositional bias in genome as marker of thermal adaptation: CG vs AT
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80 ratio_CG_AT=float(CG)/float(AT)
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82 ## 2 ## Search for compositional bias in genome as marker of thermal adaptation: AG vs TC
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83 ratio_purine_pyrimidine=float(AG)/float(TC)
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85 ## 3 ## Nucleotide proportion
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86 ln = len(seq)
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87 prop_A = float(count_A)/float(ln)
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88 prop_T = float(count_T)/float(ln)
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89 prop_C = float(count_C)/float(ln)
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90 prop_G = float(count_G)/float(ln)
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93 return(ratio_CG_AT, ratio_purine_pyrimidine, prop_A, prop_T, prop_C, prop_G)
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94 ##############################################
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97 ##################
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98 ###### DEF3 ######
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99 ##################
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100 def aa_composition1(seq):
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101
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102 ## 1 ## count occurence of AA
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103 count_K=string.count(seq,"K")
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104 count_R=string.count(seq,"R")
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105 count_A=string.count(seq,"A")
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106 count_F=string.count(seq,"F")
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107 count_I=string.count(seq,"I")
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108 count_L=string.count(seq,"L")
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109 count_M=string.count(seq,"M")
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110 count_V=string.count(seq,"V")
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111 count_W=string.count(seq,"W")
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112 count_N=string.count(seq,"N")
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113 count_Q=string.count(seq,"Q")
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114 count_S=string.count(seq,"S")
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115 count_T=string.count(seq,"T")
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116 count_H=string.count(seq,"H")
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117 count_Y=string.count(seq,"Y")
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118 count_C=string.count(seq,"C")
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119 count_D=string.count(seq,"D")
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120 count_E=string.count(seq,"E")
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121 count_P=string.count(seq,"P")
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122 count_G=string.count(seq,"G")
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123
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124
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125
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126 ## 2 ## compute relative proportion
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127 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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128 if (TOTAL!=0):
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129 ln = TOTAL
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130
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131 prop_K=float(count_K)/float(ln)
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132 prop_R=float(count_R)/float(ln)
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133 prop_A=float(count_A)/float(ln)
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134 prop_F=float(count_F)/float(ln)
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135 prop_I=float(count_I)/float(ln)
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136 prop_L=float(count_L)/float(ln)
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137 prop_M=float(count_M)/float(ln)
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138 prop_V=float(count_V)/float(ln)
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139 prop_W=float(count_W)/float(ln)
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140 prop_N=float(count_N)/float(ln)
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141 prop_Q=float(count_Q)/float(ln)
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142 prop_S=float(count_S)/float(ln)
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143 prop_T=float(count_T)/float(ln)
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144 prop_H=float(count_H)/float(ln)
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145 prop_Y=float(count_Y)/float(ln)
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146 prop_C=float(count_C)/float(ln)
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147 prop_D=float(count_D)/float(ln)
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148 prop_E=float(count_E)/float(ln)
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149 prop_P=float(count_P)/float(ln)
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150 prop_G=float(count_G)/float(ln)
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151 else:
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152 prop_K=0
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153 prop_R=0
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154 prop_A=0
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155 prop_F=0
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156 prop_I=0
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157 prop_L=0
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158 prop_M=0
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159 prop_V=0
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160 prop_W=0
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161 prop_N=0
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162 prop_Q=0
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163 prop_S=0
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164 prop_T=0
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165 prop_H=0
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166 prop_Y=0
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167 prop_C=0
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168 prop_D=0
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169 prop_E=0
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170 prop_P=0
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171 prop_G=0
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172
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173
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174
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175
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176 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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177
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178 ##################
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179 ###### DEF4 ######
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180 ##################
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181 def aa_composition2(seq):
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182
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183 ## 1 ## count occurence of AA
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184 count_K=string.count(seq,"K")
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185 count_R=string.count(seq,"R")
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186 count_A=string.count(seq,"A")
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187 count_F=string.count(seq,"F")
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188 count_I=string.count(seq,"I")
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189 count_L=string.count(seq,"L")
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190 count_M=string.count(seq,"M")
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191 count_V=string.count(seq,"V")
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192 count_W=string.count(seq,"W")
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193 count_N=string.count(seq,"N")
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194 count_Q=string.count(seq,"Q")
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195 count_S=string.count(seq,"S")
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196 count_T=string.count(seq,"T")
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197 count_H=string.count(seq,"H")
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198 count_Y=string.count(seq,"Y")
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199 count_C=string.count(seq,"C")
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200 count_D=string.count(seq,"D")
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201 count_E=string.count(seq,"E")
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202 count_P=string.count(seq,"P")
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203 count_G=string.count(seq,"G")
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204
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205
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206
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207 ## 2 ## compute seq length
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208 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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209 if (TOTAL!=0):
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210
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211 ln = TOTAL
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212 ##3 Famous Hyperthermophile Prokaryotes criterias
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213
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214 # 3.1. IVYWREL estimator => positivelly correlated with otpimal growth
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215 count_IVYWREL = count_I+count_V+count_Y+count_W+count_R+count_E+count_L
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216 prop_IVYWREL = float(count_IVYWREL)/float(ln)
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217
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218 # 3.2. ERK estimator (i.e. ERK vs DNQTSHA) => positivelly correlated with optimal growth temperature
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219 # ERK alone
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220 count_ERK = count_E + count_R + count_K
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221 prop_ERK = float(count_ERK)/float(ln)
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222 # DNQTSHA alone
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223 count_DNQTSH = count_D+count_N+count_Q+count_T+count_S+count_H
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224 prop_DNQTSH=float(count_DNQTSH)/float(ln)
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225 # ERK vs DNQTSH
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226 if count_DNQTSH != 0:
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227 ratio_ERK_vs_DNQTSH = float(count_ERK)/float(count_DNQTSH)
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228 else:
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229 ratio_ERK_vs_DNQTSH=-1
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230 # EK/QH estimator
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231 count_EK = count_E+count_K
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232 count_QH = count_Q+count_H
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233
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234 prop_EK = float(count_EK)/float(ln)
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235 prop_QH = float(count_QH)/float(ln)
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236
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237 if count_QH != 0:
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238 ratio_EK_vs_QH = float(count_EK)/float(count_QH)
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239 else:
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240 ratio_EK_vs_QH=-1 ## "-1" will indicate the impossibility to compute the ratio (coz the numerator)
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241
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242 ## 4 ## Mutationnal bias hypothesis => AT rich: favor FYMINK // GC rich: favor GARP
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243 ## 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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244 count_FYMINK=count_F+count_Y+count_M+count_I+count_N+count_K
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245 prop_FYMINK = float(count_FYMINK)/float(ln)
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246
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247 count_GARP=count_G+count_A+count_R+count_P
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248 prop_GARP=float(count_GARP)/float(ln)
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249
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250 ## 5 ## Hydophobicity hypothesis [should INCREASE with thermal adaptation]
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251 ## 5.1. AL
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252 count_AVLIMFYW = count_A+count_V+count_L+count_I+count_F+count_Y+count_W+count_M
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253 prop_AVLIMFYW=float(count_AVLIMFYW)/float(ln)
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254 ## 5.2. Only non-aromatic
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255 count_AVLIM = count_A+count_V+count_L+count_I+count_M
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256 prop_AVLIM=float(count_AVLIM)/float(ln)
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257 ## 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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258 count_FYW = count_F+count_Y+count_W
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259 prop_FYW=float(count_FYW)/float(ln)
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260
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261 ## 6 ## Charged hypothesis => positivelly correlated with optimal growth temperature
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262 # All charged
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263 count_RHKDE = count_R + count_H +count_K + count_D + count_E
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264 prop_RHKDE = float(count_RHKDE)/float(ln)
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265 # Only positive
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266 count_RHK = count_R + count_H +count_K
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267 prop_RHK = float(count_RHK)/float(ln)
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268 # Only negative
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269 count_DE = count_D + count_E
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270 prop_DE = float(count_DE)/float(ln)
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271
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272 ## 7 ## Neutral polar hypothesis [should DECREASE with thermal adaptation]
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273 count_STNQ = count_S+count_T+count_N+count_Q
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274 prop_STNQ=float(count_STNQ)/float(ln)
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275
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276
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277 ## 9 ## PAYRE VS MGDS (FONTANILLAS CRITERIA)
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278 ## 9.1 ## Didier's criteria 1 = SMALL / BIG
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279 count_PAYRE = count_A+count_Y+count_P+count_R+count_E
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280 prop_PAYRE=float(count_PAYRE)/float(ln)
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281 count_MVGDS = count_V+count_M+count_S+count_G+count_D
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282 prop_MVGDS=float(count_MVGDS)/float(ln)
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283 if count_MVGDS!= 0:
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284 ratio_PAYRE_vs_MVGDS = float(count_PAYRE)/float(count_MVGDS)
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285 else:
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286 ratio_PAYRE_vs_MVGDS=-1 ## "-1" will indicate the impossibility to compute the ratio (coz the numerator)
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287
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288 ## 9.2 ## Didier's criteria 2 = VERY SMALL / BIG
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289 count_AC = count_A+count_C
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290 prop_AC=float(count_AC)/float(ln)
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291
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292 #count_VLIM = count_V+count_L+count_I+count_M
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293 if count_MVGDS != 0:
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294 ratio_AC_vs_MVGDS = float(count_AC)/float(count_MVGDS)
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295 else:
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296 ratio_AC_vs_MVGDS=-1 ## "-1" will indicate the impossibility to compute the ratio (coz the numerator)
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297 else:
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298 count_IVYWREL=0
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299 prop_IVYWREL=0
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300 count_ERK=0
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301 prop_ERK=0
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302 count_DNQTSH=0
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303 prop_DNQTSH=0
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304 ratio_ERK_vs_DNQTSH=0
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305 count_EK=0
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306 prop_EK=0
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307 count_QH=0
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308 prop_QH=0
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309 ratio_EK_vs_QH=0
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310 count_FYMINK=0
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311 prop_FYMINK=0
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312 count_GARP=0
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313 prop_GARP=0
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314 count_AVLIMFYW=0
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315 prop_AVLIMFYW=0
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316 count_AVLIM=0
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317 prop_AVLIM=0
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318 count_FYW=0
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319 prop_FYW=0
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320 count_STNQ=0
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321 prop_STNQ=0
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322 count_MVGDS=0
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323 prop_MVGDS=0
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324 count_PAYRE=0
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325 prop_PAYRE=0
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326 count_AC=0
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327 prop_AC=0
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328 ratio_PAYRE_vs_MVGDS=0
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329 ratio_AC_vs_MVGDS=0
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330 count_RHKDE=0
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331 prop_RHKDE=0
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332 count_RHK=0
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333 prop_RHK=0
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334 count_DE=0
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335 prop_DE=0
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336
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337 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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338 #####################
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339
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340
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341 ##################
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342 ###### DEF5 ######
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343 ##################
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344 def aa_properties(fileIN_aaProperties):
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345 next = fileIN_aaProperties.readline() ## JUMP HEADERS
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346
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347 bash_aa_properties={}
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348
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349 while 1:
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350 next = fileIN_aaProperties.readline()
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351 if not next:
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352 break
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353
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354 S1 = string.split(next, ",")
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355
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356 aa_name = S1[1]
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357 S2 = string.split(aa_name, "/")
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358 aa_code = S2[1][:-1]
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359
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360 frequencies = S1[2][:-1]
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361 Residue_Weight = S1[5]
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362 Residue_Volume = S1[6]
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363 Partial_specific_volume = S1[7]
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364 Hydration = S1[8]
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365
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366 bash_aa_properties[aa_code] = [frequencies,Residue_Weight,Residue_Volume,Partial_specific_volume,Hydration]
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367
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368 return(bash_aa_properties)
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369
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370
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371 ##################
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372 ###### DEF6 ######
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373 ##################
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374 def sequence_properties_from_aa_properties(seq, bash_properties):
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375
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376 ## 1 ## count occurence of AA
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377 count_K=string.count(seq,"K")
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378 count_R=string.count(seq,"R")
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379 count_A=string.count(seq,"A")
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380 count_F=string.count(seq,"F")
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381 count_I=string.count(seq,"I")
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382 count_L=string.count(seq,"L")
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383 count_M=string.count(seq,"M")
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384 count_V=string.count(seq,"V")
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385 count_W=string.count(seq,"W")
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386 count_N=string.count(seq,"N")
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387 count_Q=string.count(seq,"Q")
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388 count_S=string.count(seq,"S")
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389 count_T=string.count(seq,"T")
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390 count_H=string.count(seq,"H")
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391 count_Y=string.count(seq,"Y")
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392 count_C=string.count(seq,"C")
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393 count_D=string.count(seq,"D")
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394 count_E=string.count(seq,"E")
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395 count_P=string.count(seq,"P")
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396 count_G=string.count(seq,"G")
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397
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398 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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399
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400 if (TOTAL!=0):
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401
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402
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403 ## 2 ## Compute properties 1: Residue Weight (Mr) (UNIT:Daltons):
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404
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405 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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406 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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407 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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408 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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409 else:
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410 Total_Residue_Weight=0
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411 Total_Residue_Volume=0
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412 Total_Partial_specific_volume=0
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413 Total_Hydration=0
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414
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415 return(Total_Residue_Weight,Total_Residue_Volume,Total_Partial_specific_volume,Total_Hydration)
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416
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417 ########################################################
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418
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419
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420
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421 ###################
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422 ### RUN RUN RUN ###
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423 ###################
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424 import sys,os,zipfile,shutil,subprocess,string
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425
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426 ##Create specific folders
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427 Path_IN_loci_NUC = "./IN_AA"
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428 outpath= "./OUT"
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429 os.makedirs(Path_IN_loci_NUC)
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430 os.makedirs(outpath)
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431
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432
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433 #Check if the file is a zip or fasta file
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434
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435 the_zip_file = zipfile.ZipFile(sys.argv[1])
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436 ret = the_zip_file.testzip()
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437
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438 if ret is not None:
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439 shutil.copy2(sys.argv[1], './IN_AA/input.fasta')
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440 else:
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441 cmd="unzip %s -d ./IN_AA"%(sys.argv[1])
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442 os.system(cmd)
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443
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444
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445
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446 ## 1 ## List taxa
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447 LT=[]
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448 cmd="grep '>' %s" % sys.argv[2]
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449 result = subprocess.check_output(cmd, shell=True)
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450 result=result.split('\n')
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451 for i in result:
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452 sp=i[1:]
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453 if sp !='':
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454 LT.append(sp)
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455 print LT
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456
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457
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458 ## 2 ## PathIN
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459 fileIN_properties = open("%s/01_AminoAcid_Properties2.csv"%(script_path), "r")
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460 Path_IN_loci_AA = "./IN_AA"
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461 #Path_IN_loci_AA = "02_CDS_No_Missing_Data_aa_CDS_withM"
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462 Lloci_AA = os.listdir(Path_IN_loci_AA)
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463
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464 ## 3 ## PathOUT
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465
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466 ## 3.1 ## PROT composition
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467 fileOUT_PROT_ALL=open("./OUT/13_prot_compositions_All_AA.csv","w")
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468 fileOUT_PROT_ALL.write("LOCUS,")
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469 for taxa in LT:
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470 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))
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471 fileOUT_PROT_ALL.write("\n")
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diff changeset
472
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
473 ## 3.2 ## PROT IVYWREL
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
474 fileOUT_IVYWREL=open("./OUT/14_IVYWREL.csv","w")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
475 fileOUT_IVYWREL.write("LOCUS,")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
476 for taxa in LT:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
477 fileOUT_IVYWREL.write("%s_count_IVYWREL,%s_prop_IVYWREL," %(taxa,taxa))
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
478 fileOUT_IVYWREL.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
479
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
480
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
481 ## 3.3 ## PROT ERK_DNQTSHA
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
482 fileOUT_ERK_DNQTSH=open("./OUT/15_ERK_DNQTSH.csv","w")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
483 fileOUT_ERK_DNQTSH.write("LOCUS,")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
484 for taxa in LT:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
485 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))
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
486 fileOUT_ERK_DNQTSH.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
487
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
488 ## 3.4 ## PROT EK_QH
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
489 fileOUT_EK_QH=open("./OUT/16_EK_QH.csv","w")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
490 fileOUT_EK_QH.write("LOCUS,")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
491 for taxa in LT:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
492 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))
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
493 fileOUT_EK_QH.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
494
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
495
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
496 ## 3.5 ## PROT FYMINK_GARP
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
497 fileOUT_FYMINK_GARP=open("./OUT/17_FYMINK_GARP.csv","w")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
498 fileOUT_FYMINK_GARP.write("LOCUS,")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
499 for taxa in LT:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
500 fileOUT_FYMINK_GARP.write("%s_count_FYMINK,%s_prop_FYMINK,%s_count_GARP,%s_prop_GARP," %(taxa,taxa,taxa,taxa))
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
501 fileOUT_FYMINK_GARP.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
502
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
503
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
504 ## 3.6 ## PROT AVLIMFYW
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
505 fileOUT_AVLIMFYW=open("./OUT/18_AVLIMFYW.csv","w")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
506 fileOUT_AVLIMFYW.write("LOCUS,")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
507 for taxa in LT:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
508 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))
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
509 fileOUT_AVLIMFYW.write("\n")
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 ## 3.7 ## PROT STNQ
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
512 fileOUT_STNQ=open("./OUT/19_STNQ.csv","w")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
513 fileOUT_STNQ.write("LOCUS,")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
514 for taxa in LT:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
515 fileOUT_STNQ.write("%s_count_STNQ,%s_prop_STNQ," %(taxa,taxa))
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
516 fileOUT_STNQ.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
517
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
518 ## 3.8 ## PROT RHKDE
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
519 fileOUT_RHKDE=open("./OUT/20_RHKDE.csv","w")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
520 fileOUT_RHKDE.write("LOCUS,")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
521 for taxa in LT:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
522 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))
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
523 fileOUT_RHKDE.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
524
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
525 ## 3.9 ## PROT DIDER CRITERIA
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
526 fileOUT_PAYRE=open("./OUT/21_PAYRE-MVGDS.csv","w")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
527 fileOUT_PAYRE.write("LOCUS,")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
528 for taxa in LT:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
529 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))
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
530 fileOUT_PAYRE.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
531
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
532 ## 3.10 ## PROT Total residue weight
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
533 fileOUT_TotalResidueWeight=open("./OUT/22_TotalResidueWeight.csv","w")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
534 fileOUT_TotalResidueWeight.write("LOCUS,")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
535 for taxa in LT:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
536 fileOUT_TotalResidueWeight.write("%s_Total_Residue_Weight," %taxa)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
537 fileOUT_TotalResidueWeight.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
538
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
539 ## 3.11 ## PROT Total residue volume
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
540 fileOUT_TotalResidueVolume=open("./OUT/23_TotalResidueVolume.csv","w")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
541 fileOUT_TotalResidueVolume.write("LOCUS,")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
542 for taxa in LT:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
543 fileOUT_TotalResidueVolume.write("%s_Total_Residue_Volume," %taxa)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
544 fileOUT_TotalResidueVolume.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
545
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
546 ## 3.12 ## PROT Total partial specific volume
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
547 fileOUT_TotalPartialSpecificVolume=open("./OUT/24_TotalPartialSpecificVolume.csv","w")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
548 fileOUT_TotalPartialSpecificVolume.write("LOCUS,")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
549 for taxa in LT:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
550 fileOUT_TotalPartialSpecificVolume.write("%s_Total_Partial_Specific_Volume," %taxa)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
551 fileOUT_TotalPartialSpecificVolume.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
552
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
553 ## 3.13 ## PROT Total hydratation
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
554 fileOUT_TotalHydratation=open("./OUT/25_TotalHydratation.csv","w")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
555 fileOUT_TotalHydratation.write("LOCUS,")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
556 for taxa in LT:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
557 fileOUT_TotalHydratation.write("%s_Total_Hydratation," %taxa)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
558 fileOUT_TotalHydratation.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
559
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
560
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
561 #####################
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
562 ## 4 ## Process Loci
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
563 #####################
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
564 bash_aa_properties = aa_properties(fileIN_properties)
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diff changeset
565
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diff changeset
566 for locus in Lloci_AA:
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567 print locus
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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568 path_locus = "%s/%s" %(Path_IN_loci_AA, locus)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
569 bash = dico(path_locus,LT)
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abims-sbr
parents:
diff changeset
570
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
571 #print bash
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abims-sbr
parents:
diff changeset
572
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
573 fileOUT_PROT_ALL.write("%s," %locus)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
574 fileOUT_IVYWREL.write("%s," %locus)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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diff changeset
575 fileOUT_ERK_DNQTSH.write("%s," %locus)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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diff changeset
576 fileOUT_EK_QH.write("%s," %locus)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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diff changeset
577 fileOUT_FYMINK_GARP.write("%s," %locus)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
578 fileOUT_AVLIMFYW.write("%s," %locus)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
579 fileOUT_STNQ.write("%s," %locus)
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diff changeset
580 fileOUT_RHKDE.write("%s," %locus)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
581 fileOUT_PAYRE.write("%s," %locus)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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diff changeset
582 fileOUT_TotalResidueWeight.write("%s," %locus)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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diff changeset
583 fileOUT_TotalResidueVolume.write("%s," %locus)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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diff changeset
584 fileOUT_TotalPartialSpecificVolume.write("%s," %locus)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
585 fileOUT_TotalHydratation.write("%s," %locus)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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parents:
diff changeset
586
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diff changeset
587 for taxa in LT:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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588 if taxa in bash.keys():
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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589 seq = bash[taxa]
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diff changeset
590 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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diff changeset
591 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 ###
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diff changeset
592 Total_Residue_Weight,Total_Residue_Volume,Total_Partial_Specific_Volume,Total_Hydration = sequence_properties_from_aa_properties(seq, bash_aa_properties) ### DEF6 ###
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diff changeset
593
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diff changeset
594 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))
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diff changeset
595 fileOUT_IVYWREL.write("%.5f,%.5f," %(count_IVYWREL, prop_IVYWREL))
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596 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
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597 fileOUT_EK_QH.write("%.5f,%.5f,%.5f,%.5f,%.5f," %(count_EK,prop_EK,count_QH,prop_QH,ratio_EK_vs_QH))
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598 fileOUT_FYMINK_GARP.write("%.5f,%.5f,%.5f,%.5f," %(count_FYMINK,prop_FYMINK,count_GARP,prop_GARP))
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599 fileOUT_AVLIMFYW.write("%.5f,%.5f,%.5f,%.5f,%.5f,%.5f," %(count_AVLIMFYW,prop_AVLIMFYW,count_AVLIM,prop_AVLIM,count_FYW,prop_FYW))
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600 fileOUT_STNQ.write("%.5f,%.5f," %(count_STNQ,prop_STNQ))
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601 fileOUT_RHKDE.write("%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,"%(count_RHKDE,prop_RHKDE,count_RHK,prop_RHK,count_DE,prop_DE))
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602 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))
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603 fileOUT_TotalResidueWeight.write("%.5f," %Total_Residue_Weight)
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diff changeset
604 fileOUT_TotalResidueVolume.write("%.5f," %Total_Residue_Volume)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
605 fileOUT_TotalPartialSpecificVolume.write("%.5f," %(Total_Partial_Specific_Volume))
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
606 fileOUT_TotalHydratation.write("%.5f," % Total_Hydration)
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diff changeset
607
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diff changeset
608 ## END LINE
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609 fileOUT_PROT_ALL.write("\n")
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diff changeset
610 fileOUT_IVYWREL.write("\n")
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diff changeset
611 fileOUT_ERK_DNQTSH.write("\n")
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diff changeset
612 fileOUT_EK_QH.write("\n")
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diff changeset
613 fileOUT_FYMINK_GARP.write("\n")
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diff changeset
614 fileOUT_AVLIMFYW.write("\n")
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diff changeset
615 fileOUT_STNQ.write("\n")
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diff changeset
616 fileOUT_RHKDE.write("\n")
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diff changeset
617 fileOUT_PAYRE.write("\n")
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diff changeset
618 fileOUT_TotalResidueWeight.write("\n")
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diff changeset
619 fileOUT_TotalResidueVolume.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
620 fileOUT_TotalPartialSpecificVolume.write("\n")
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diff changeset
621 fileOUT_TotalHydratation.write("\n")
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diff changeset
622
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623
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diff changeset
624
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625