Mercurial > repos > abims-sbr > mutcount
comparison scripts/S01b_study_seq_composition_aa.py @ 10:f62c76aab669 draft default tip
planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
| author | lecorguille |
|---|---|
| date | Mon, 24 Sep 2018 04:34:39 -0400 |
| parents | 04a9ada73cc4 |
| children |
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| 9:04a9ada73cc4 | 10:f62c76aab669 |
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| 1 #!/usr/bin/env python | |
| 2 # -*- coding: ascii -*- | |
| 3 ## Author: Eric FONTANILLAS | |
| 4 ## Date: 21.12.10 | |
| 5 ## Last Version : 12/2017 by Victor Mataigne | |
| 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) | |
| 7 | |
| 8 import sys,os,shutil,subprocess,string, itertools | |
| 9 from functions import simplify_fasta_name, dico | |
| 10 | |
| 11 script_path = os.path.dirname(sys.argv[0]) | |
| 12 | |
| 13 ################## | |
| 14 ###### DEF2 ###### | |
| 15 ################## | |
| 16 def base_composition(seq): | |
| 17 count_A=string.count(seq, "A") | |
| 18 count_T=string.count(seq, "T") | |
| 19 count_C=string.count(seq, "C") | |
| 20 count_G=string.count(seq, "G") | |
| 21 | |
| 22 | |
| 23 CG = count_C+count_G | |
| 24 AT = count_T+count_A | |
| 25 | |
| 26 AG = count_A+count_G | |
| 27 TC = count_T+count_C | |
| 28 | |
| 29 ## 1 ## Search for compositional bias in genome as marker of thermal adaptation: CG vs AT | |
| 30 ratio_CG_AT=float(CG)/float(AT) | |
| 31 | |
| 32 ## 2 ## Search for compositional bias in genome as marker of thermal adaptation: AG vs TC | |
| 33 ratio_purine_pyrimidine=float(AG)/float(TC) | |
| 34 | |
| 35 ## 3 ## Nucleotide proportion | |
| 36 ln = len(seq) | |
| 37 prop_A = float(count_A)/float(ln) | |
| 38 prop_T = float(count_T)/float(ln) | |
| 39 prop_C = float(count_C)/float(ln) | |
| 40 prop_G = float(count_G)/float(ln) | |
| 41 | |
| 42 | |
| 43 return(ratio_CG_AT, ratio_purine_pyrimidine, prop_A, prop_T, prop_C, prop_G) | |
| 44 ############################################## | |
| 45 | |
| 46 | |
| 47 ################## | |
| 48 ###### DEF3 ###### | |
| 49 ################## | |
| 50 def aa_composition1(seq): | |
| 51 | |
| 52 ## 1 ## count occurence of AA | |
| 53 count_K=string.count(seq,"K") | |
| 54 count_R=string.count(seq,"R") | |
| 55 count_A=string.count(seq,"A") | |
| 56 count_F=string.count(seq,"F") | |
| 57 count_I=string.count(seq,"I") | |
| 58 count_L=string.count(seq,"L") | |
| 59 count_M=string.count(seq,"M") | |
| 60 count_V=string.count(seq,"V") | |
| 61 count_W=string.count(seq,"W") | |
| 62 count_N=string.count(seq,"N") | |
| 63 count_Q=string.count(seq,"Q") | |
| 64 count_S=string.count(seq,"S") | |
| 65 count_T=string.count(seq,"T") | |
| 66 count_H=string.count(seq,"H") | |
| 67 count_Y=string.count(seq,"Y") | |
| 68 count_C=string.count(seq,"C") | |
| 69 count_D=string.count(seq,"D") | |
| 70 count_E=string.count(seq,"E") | |
| 71 count_P=string.count(seq,"P") | |
| 72 count_G=string.count(seq,"G") | |
| 73 | |
| 74 | |
| 75 | |
| 76 ## 2 ## compute relative proportion | |
| 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 | |
| 78 if (TOTAL!=0): | |
| 79 ln = TOTAL | |
| 80 | |
| 81 prop_K=float(count_K)/float(ln) | |
| 82 prop_R=float(count_R)/float(ln) | |
| 83 prop_A=float(count_A)/float(ln) | |
| 84 prop_F=float(count_F)/float(ln) | |
| 85 prop_I=float(count_I)/float(ln) | |
| 86 prop_L=float(count_L)/float(ln) | |
| 87 prop_M=float(count_M)/float(ln) | |
| 88 prop_V=float(count_V)/float(ln) | |
| 89 prop_W=float(count_W)/float(ln) | |
| 90 prop_N=float(count_N)/float(ln) | |
| 91 prop_Q=float(count_Q)/float(ln) | |
| 92 prop_S=float(count_S)/float(ln) | |
| 93 prop_T=float(count_T)/float(ln) | |
| 94 prop_H=float(count_H)/float(ln) | |
| 95 prop_Y=float(count_Y)/float(ln) | |
| 96 prop_C=float(count_C)/float(ln) | |
| 97 prop_D=float(count_D)/float(ln) | |
| 98 prop_E=float(count_E)/float(ln) | |
| 99 prop_P=float(count_P)/float(ln) | |
| 100 prop_G=float(count_G)/float(ln) | |
| 101 else: | |
| 102 prop_K=0 | |
| 103 prop_R=0 | |
| 104 prop_A=0 | |
| 105 prop_F=0 | |
| 106 prop_I=0 | |
| 107 prop_L=0 | |
| 108 prop_M=0 | |
| 109 prop_V=0 | |
| 110 prop_W=0 | |
| 111 prop_N=0 | |
| 112 prop_Q=0 | |
| 113 prop_S=0 | |
| 114 prop_T=0 | |
| 115 prop_H=0 | |
| 116 prop_Y=0 | |
| 117 prop_C=0 | |
| 118 prop_D=0 | |
| 119 prop_E=0 | |
| 120 prop_P=0 | |
| 121 prop_G=0 | |
| 122 | |
| 123 | |
| 124 | |
| 125 | |
| 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) | |
| 127 | |
| 128 ################## | |
| 129 ###### DEF4 ###### | |
| 130 ################## | |
| 131 def aa_composition2(seq): | |
| 132 | |
| 133 ## 1 ## count occurence of AA | |
| 134 count_K=string.count(seq,"K") | |
| 135 count_R=string.count(seq,"R") | |
| 136 count_A=string.count(seq,"A") | |
| 137 count_F=string.count(seq,"F") | |
| 138 count_I=string.count(seq,"I") | |
| 139 count_L=string.count(seq,"L") | |
| 140 count_M=string.count(seq,"M") | |
| 141 count_V=string.count(seq,"V") | |
| 142 count_W=string.count(seq,"W") | |
| 143 count_N=string.count(seq,"N") | |
| 144 count_Q=string.count(seq,"Q") | |
| 145 count_S=string.count(seq,"S") | |
| 146 count_T=string.count(seq,"T") | |
| 147 count_H=string.count(seq,"H") | |
| 148 count_Y=string.count(seq,"Y") | |
| 149 count_C=string.count(seq,"C") | |
| 150 count_D=string.count(seq,"D") | |
| 151 count_E=string.count(seq,"E") | |
| 152 count_P=string.count(seq,"P") | |
| 153 count_G=string.count(seq,"G") | |
| 154 | |
| 155 | |
| 156 | |
| 157 ## 2 ## compute seq length | |
| 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 | |
| 159 if (TOTAL!=0): | |
| 160 | |
| 161 ln = TOTAL | |
| 162 ##3 Famous Hyperthermophile Prokaryotes criterias | |
| 163 | |
| 164 # 3.1. IVYWREL estimator => positivelly correlated with otpimal growth | |
| 165 count_IVYWREL = count_I+count_V+count_Y+count_W+count_R+count_E+count_L | |
| 166 prop_IVYWREL = float(count_IVYWREL)/float(ln) | |
| 167 | |
| 168 # 3.2. ERK estimator (i.e. ERK vs DNQTSHA) => positivelly correlated with optimal growth temperature | |
| 169 # ERK alone | |
| 170 count_ERK = count_E + count_R + count_K | |
| 171 prop_ERK = float(count_ERK)/float(ln) | |
| 172 # DNQTSHA alone | |
| 173 count_DNQTSH = count_D+count_N+count_Q+count_T+count_S+count_H | |
| 174 prop_DNQTSH=float(count_DNQTSH)/float(ln) | |
| 175 # ERK vs DNQTSH | |
| 176 if count_DNQTSH != 0: | |
| 177 ratio_ERK_vs_DNQTSH = float(count_ERK)/float(count_DNQTSH) | |
| 178 else: | |
| 179 ratio_ERK_vs_DNQTSH=-1 | |
| 180 # EK/QH estimator | |
| 181 count_EK = count_E+count_K | |
| 182 count_QH = count_Q+count_H | |
| 183 | |
| 184 prop_EK = float(count_EK)/float(ln) | |
| 185 prop_QH = float(count_QH)/float(ln) | |
| 186 | |
| 187 if count_QH != 0: | |
| 188 ratio_EK_vs_QH = float(count_EK)/float(count_QH) | |
| 189 else: | |
| 190 ratio_EK_vs_QH=-1 ## "-1" will indicate the impossibility to compute the ratio (coz the numerator) | |
| 191 | |
| 192 ## 4 ## Mutationnal bias hypothesis => AT rich: favor FYMINK // GC rich: favor GARP | |
| 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!!??? | |
| 194 count_FYMINK=count_F+count_Y+count_M+count_I+count_N+count_K | |
| 195 prop_FYMINK = float(count_FYMINK)/float(ln) | |
| 196 | |
| 197 count_GARP=count_G+count_A+count_R+count_P | |
| 198 prop_GARP=float(count_GARP)/float(ln) | |
| 199 | |
| 200 ## 5 ## Hydophobicity hypothesis [should INCREASE with thermal adaptation] | |
| 201 ## 5.1. AL | |
| 202 count_AVLIMFYW = count_A+count_V+count_L+count_I+count_F+count_Y+count_W+count_M | |
| 203 prop_AVLIMFYW=float(count_AVLIMFYW)/float(ln) | |
| 204 ## 5.2. Only non-aromatic | |
| 205 count_AVLIM = count_A+count_V+count_L+count_I+count_M | |
| 206 prop_AVLIM=float(count_AVLIM)/float(ln) | |
| 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) | |
| 208 count_FYW = count_F+count_Y+count_W | |
| 209 prop_FYW=float(count_FYW)/float(ln) | |
| 210 | |
| 211 ## 6 ## Charged hypothesis => positivelly correlated with optimal growth temperature | |
| 212 # All charged | |
| 213 count_RHKDE = count_R + count_H +count_K + count_D + count_E | |
| 214 prop_RHKDE = float(count_RHKDE)/float(ln) | |
| 215 # Only positive | |
| 216 count_RHK = count_R + count_H +count_K | |
| 217 prop_RHK = float(count_RHK)/float(ln) | |
| 218 # Only negative | |
| 219 count_DE = count_D + count_E | |
| 220 prop_DE = float(count_DE)/float(ln) | |
| 221 | |
| 222 ## 7 ## Neutral polar hypothesis [should DECREASE with thermal adaptation] | |
| 223 count_STNQ = count_S+count_T+count_N+count_Q | |
| 224 prop_STNQ=float(count_STNQ)/float(ln) | |
| 225 | |
| 226 | |
| 227 ## 9 ## PAYRE VS MGDS (FONTANILLAS CRITERIA) | |
| 228 ## 9.1 ## Didier's criteria 1 = SMALL / BIG | |
| 229 count_PAYRE = count_A+count_Y+count_P+count_R+count_E | |
| 230 prop_PAYRE=float(count_PAYRE)/float(ln) | |
| 231 count_MVGDS = count_V+count_M+count_S+count_G+count_D | |
| 232 prop_MVGDS=float(count_MVGDS)/float(ln) | |
| 233 if count_MVGDS!= 0: | |
| 234 ratio_PAYRE_vs_MVGDS = float(count_PAYRE)/float(count_MVGDS) | |
| 235 else: | |
| 236 ratio_PAYRE_vs_MVGDS=-1 ## "-1" will indicate the impossibility to compute the ratio (coz the numerator) | |
| 237 | |
| 238 ## 9.2 ## Didier's criteria 2 = VERY SMALL / BIG | |
| 239 count_AC = count_A+count_C | |
| 240 prop_AC=float(count_AC)/float(ln) | |
| 241 | |
| 242 #count_VLIM = count_V+count_L+count_I+count_M | |
| 243 if count_MVGDS != 0: | |
| 244 ratio_AC_vs_MVGDS = float(count_AC)/float(count_MVGDS) | |
| 245 else: | |
| 246 ratio_AC_vs_MVGDS=-1 ## "-1" will indicate the impossibility to compute the ratio (coz the numerator) | |
| 247 else: | |
| 248 count_IVYWREL=0 | |
| 249 prop_IVYWREL=0 | |
| 250 count_ERK=0 | |
| 251 prop_ERK=0 | |
| 252 count_DNQTSH=0 | |
| 253 prop_DNQTSH=0 | |
| 254 ratio_ERK_vs_DNQTSH=0 | |
| 255 count_EK=0 | |
| 256 prop_EK=0 | |
| 257 count_QH=0 | |
| 258 prop_QH=0 | |
| 259 ratio_EK_vs_QH=0 | |
| 260 count_FYMINK=0 | |
| 261 prop_FYMINK=0 | |
| 262 count_GARP=0 | |
| 263 prop_GARP=0 | |
| 264 count_AVLIMFYW=0 | |
| 265 prop_AVLIMFYW=0 | |
| 266 count_AVLIM=0 | |
| 267 prop_AVLIM=0 | |
| 268 count_FYW=0 | |
| 269 prop_FYW=0 | |
| 270 count_STNQ=0 | |
| 271 prop_STNQ=0 | |
| 272 count_MVGDS=0 | |
| 273 prop_MVGDS=0 | |
| 274 count_PAYRE=0 | |
| 275 prop_PAYRE=0 | |
| 276 count_AC=0 | |
| 277 prop_AC=0 | |
| 278 ratio_PAYRE_vs_MVGDS=0 | |
| 279 ratio_AC_vs_MVGDS=0 | |
| 280 count_RHKDE=0 | |
| 281 prop_RHKDE=0 | |
| 282 count_RHK=0 | |
| 283 prop_RHK=0 | |
| 284 count_DE=0 | |
| 285 prop_DE=0 | |
| 286 | |
| 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) | |
| 288 ##################### | |
| 289 | |
| 290 | |
| 291 ################## | |
| 292 ###### DEF5 ###### | |
| 293 ################## | |
| 294 def aa_properties(fileIN_aaProperties): | |
| 295 next = fileIN_aaProperties.readline() ## JUMP HEADERS | |
| 296 | |
| 297 bash_aa_properties={} | |
| 298 | |
| 299 while 1: | |
| 300 next = fileIN_aaProperties.readline() | |
| 301 if not next: | |
| 302 break | |
| 303 | |
| 304 S1 = string.split(next, ",") | |
| 305 | |
| 306 aa_name = S1[1] | |
| 307 S2 = string.split(aa_name, "/") | |
| 308 aa_code = S2[1][:-1] | |
| 309 | |
| 310 frequencies = S1[2][:-1] | |
| 311 Residue_Weight = S1[5] | |
| 312 Residue_Volume = S1[6] | |
| 313 Partial_specific_volume = S1[7] | |
| 314 Hydration = S1[8] | |
| 315 | |
| 316 bash_aa_properties[aa_code] = [frequencies,Residue_Weight,Residue_Volume,Partial_specific_volume,Hydration] | |
| 317 | |
| 318 return(bash_aa_properties) | |
| 319 | |
| 320 | |
| 321 ################## | |
| 322 ###### DEF6 ###### | |
| 323 ################## | |
| 324 def sequence_properties_from_aa_properties(seq, bash_properties): | |
| 325 | |
| 326 ## 1 ## count occurence of AA | |
| 327 count_K=string.count(seq,"K") | |
| 328 count_R=string.count(seq,"R") | |
| 329 count_A=string.count(seq,"A") | |
| 330 count_F=string.count(seq,"F") | |
| 331 count_I=string.count(seq,"I") | |
| 332 count_L=string.count(seq,"L") | |
| 333 count_M=string.count(seq,"M") | |
| 334 count_V=string.count(seq,"V") | |
| 335 count_W=string.count(seq,"W") | |
| 336 count_N=string.count(seq,"N") | |
| 337 count_Q=string.count(seq,"Q") | |
| 338 count_S=string.count(seq,"S") | |
| 339 count_T=string.count(seq,"T") | |
| 340 count_H=string.count(seq,"H") | |
| 341 count_Y=string.count(seq,"Y") | |
| 342 count_C=string.count(seq,"C") | |
| 343 count_D=string.count(seq,"D") | |
| 344 count_E=string.count(seq,"E") | |
| 345 count_P=string.count(seq,"P") | |
| 346 count_G=string.count(seq,"G") | |
| 347 | |
| 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 | |
| 349 | |
| 350 if (TOTAL!=0): | |
| 351 | |
| 352 | |
| 353 ## 2 ## Compute properties 1: Residue Weight (Mr) (UNIT:Daltons): | |
| 354 | |
| 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]) | |
| 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]) | |
| 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]) | |
| 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]) | |
| 359 else: | |
| 360 Total_Residue_Weight=0 | |
| 361 Total_Residue_Volume=0 | |
| 362 Total_Partial_specific_volume=0 | |
| 363 Total_Hydration=0 | |
| 364 | |
| 365 return(Total_Residue_Weight,Total_Residue_Volume,Total_Partial_specific_volume,Total_Hydration) | |
| 366 | |
| 367 ######################################################## | |
| 368 | |
| 369 | |
| 370 | |
| 371 ################### | |
| 372 ### RUN RUN RUN ### | |
| 373 ################### | |
| 374 | |
| 375 ##Create specific folders | |
| 376 Path_IN_loci_NUC = "./IN_AA" | |
| 377 outpath= "./OUT" | |
| 378 os.makedirs(Path_IN_loci_NUC) | |
| 379 os.makedirs(outpath) | |
| 380 | |
| 381 infiles = [] | |
| 382 with open(sys.argv[2], 'r') as f: | |
| 383 for line in f.readlines(): | |
| 384 infiles.append(line.strip('\n')) | |
| 385 | |
| 386 for file in infiles: | |
| 387 os.system("cp %s %s" %(file, Path_IN_loci_NUC)) | |
| 388 | |
| 389 ## 1 ## List taxa | |
| 390 LT=[] | |
| 391 cmd="grep '>' {}".format(sys.argv[1]) | |
| 392 result = subprocess.check_output(cmd, shell=True) | |
| 393 result=result.split('\n') | |
| 394 for i in result: | |
| 395 sp=i[1:] | |
| 396 if sp !='': | |
| 397 LT.append(sp) | |
| 398 print LT | |
| 399 | |
| 400 | |
| 401 ## 2 ## PathIN | |
| 402 fileIN_properties = open("amino_acid_properties.csv", "r") | |
| 403 Path_IN_loci_AA = "./IN_AA" | |
| 404 #Path_IN_loci_AA = "02_CDS_No_Missing_Data_aa_CDS_withM" | |
| 405 Lloci_AA = os.listdir(Path_IN_loci_AA) | |
| 406 | |
| 407 ## 3 ## PathOUT | |
| 408 | |
| 409 ## 3.1 ## PROT composition | |
| 410 fileOUT_PROT_ALL=open("./OUT/prot_compositions_All_AA.csv","w") | |
| 411 fileOUT_PROT_ALL.write("LOCUS,") | |
| 412 for taxa in LT[0:-1]: | |
| 413 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)) | |
| 414 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])) | |
| 415 fileOUT_PROT_ALL.write("\n") | |
| 416 | |
| 417 ## 3.2 ## PROT IVYWREL | |
| 418 fileOUT_IVYWREL=open("./OUT/IVYWREL.csv","w") | |
| 419 fileOUT_IVYWREL.write("LOCUS,") | |
| 420 for taxa in LT[0:-1]: | |
| 421 fileOUT_IVYWREL.write("%s_count_IVYWREL,%s_prop_IVYWREL," %(taxa,taxa)) | |
| 422 fileOUT_IVYWREL.write("%s_count_IVYWREL,%s_prop_IVYWREL" %(LT[-1],LT[-1])) | |
| 423 fileOUT_IVYWREL.write("\n") | |
| 424 | |
| 425 ## 3.3 ## PROT ERK_DNQTSHA | |
| 426 fileOUT_ERK_DNQTSH=open("./OUT/ERK_DNQTSH.csv","w") | |
| 427 fileOUT_ERK_DNQTSH.write("LOCUS,") | |
| 428 for taxa in LT[0:-1]: | |
| 429 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)) | |
| 430 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])) | |
| 431 fileOUT_ERK_DNQTSH.write("\n") | |
| 432 | |
| 433 ## 3.4 ## PROT EK_QH | |
| 434 fileOUT_EK_QH=open("./OUT/EK_QH.csv","w") | |
| 435 fileOUT_EK_QH.write("LOCUS,") | |
| 436 for taxa in LT[0:-1]: | |
| 437 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)) | |
| 438 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])) | |
| 439 fileOUT_EK_QH.write("\n") | |
| 440 | |
| 441 ## 3.5 ## PROT FYMINK_GARP | |
| 442 fileOUT_FYMINK_GARP=open("./OUT/FYMINK_GARP.csv","w") | |
| 443 fileOUT_FYMINK_GARP.write("LOCUS,") | |
| 444 for taxa in LT[0:-1]: | |
| 445 fileOUT_FYMINK_GARP.write("%s_count_FYMINK,%s_prop_FYMINK,%s_count_GARP,%s_prop_GARP," %(taxa,taxa,taxa,taxa)) | |
| 446 fileOUT_FYMINK_GARP.write("%s_count_FYMINK,%s_prop_FYMINK,%s_count_GARP,%s_prop_GARP" %(LT[-1],LT[-1],LT[-1],LT[-1])) | |
| 447 fileOUT_FYMINK_GARP.write("\n") | |
| 448 | |
| 449 ## 3.6 ## PROT AVLIMFYW | |
| 450 fileOUT_AVLIMFYW=open("./OUT/AVLIMFYW.csv","w") | |
| 451 fileOUT_AVLIMFYW.write("LOCUS,") | |
| 452 for taxa in LT[0:-1]: | |
| 453 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)) | |
| 454 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])) | |
| 455 fileOUT_AVLIMFYW.write("\n") | |
| 456 | |
| 457 ## 3.7 ## PROT STNQ | |
| 458 fileOUT_STNQ=open("./OUT/STNQ.csv","w") | |
| 459 fileOUT_STNQ.write("LOCUS,") | |
| 460 for taxa in LT[0:-1]: | |
| 461 fileOUT_STNQ.write("%s_count_STNQ,%s_prop_STNQ," %(taxa,taxa)) | |
| 462 fileOUT_STNQ.write("%s_count_STNQ,%s_prop_STNQ" %(LT[-1],LT[-1])) | |
| 463 fileOUT_STNQ.write("\n") | |
| 464 | |
| 465 ## 3.8 ## PROT RHKDE | |
| 466 fileOUT_RHKDE=open("./OUT/RHKDE.csv","w") | |
| 467 fileOUT_RHKDE.write("LOCUS,") | |
| 468 for taxa in LT[0:-1]: | |
| 469 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)) | |
| 470 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])) | |
| 471 fileOUT_RHKDE.write("\n") | |
| 472 | |
| 473 ## 3.9 ## PROT DIDER CRITERIA | |
| 474 fileOUT_PAYRE=open("./OUT/PAYRE-MVGDS.csv","w") | |
| 475 fileOUT_PAYRE.write("LOCUS,") | |
| 476 for taxa in LT[0:-1]: | |
| 477 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)) | |
| 478 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])) | |
| 479 fileOUT_PAYRE.write("\n") | |
| 480 | |
| 481 ## 3.10 ## PROT Total residue weight | |
| 482 fileOUT_TotalResidueWeight=open("./OUT/TotalResidueWeight.csv","w") | |
| 483 fileOUT_TotalResidueWeight.write("LOCUS,") | |
| 484 for taxa in LT[0:-1]: | |
| 485 fileOUT_TotalResidueWeight.write("%s_Total_Residue_Weight," %taxa) | |
| 486 fileOUT_TotalResidueWeight.write("%s_Total_Residue_Weight" %LT[-1]) | |
| 487 fileOUT_TotalResidueWeight.write("\n") | |
| 488 | |
| 489 ## 3.11 ## PROT Total residue volume | |
| 490 fileOUT_TotalResidueVolume=open("./OUT/TotalResidueVolume.csv","w") | |
| 491 fileOUT_TotalResidueVolume.write("LOCUS,") | |
| 492 for taxa in LT[0:-1]: | |
| 493 fileOUT_TotalResidueVolume.write("%s_Total_Residue_Volume," %taxa) | |
| 494 fileOUT_TotalResidueVolume.write("%s_Total_Residue_Volume" %LT[-1]) | |
| 495 fileOUT_TotalResidueVolume.write("\n") | |
| 496 | |
| 497 ## 3.12 ## PROT Total partial specific volume | |
| 498 fileOUT_TotalPartialSpecificVolume=open("./OUT/TotalPartialSpecificVolume.csv","w") | |
| 499 fileOUT_TotalPartialSpecificVolume.write("LOCUS,") | |
| 500 for taxa in LT[0:-1]: | |
| 501 fileOUT_TotalPartialSpecificVolume.write("%s_Total_Partial_Specific_Volume," %taxa) | |
| 502 fileOUT_TotalPartialSpecificVolume.write("%s_Total_Partial_Specific_Volume" %LT[-1]) | |
| 503 fileOUT_TotalPartialSpecificVolume.write("\n") | |
| 504 | |
| 505 ## 3.13 ## PROT Total hydratation | |
| 506 fileOUT_TotalHydratation=open("./OUT/TotalHydratation.csv","w") | |
| 507 fileOUT_TotalHydratation.write("LOCUS,") | |
| 508 for taxa in LT[0:-1]: | |
| 509 fileOUT_TotalHydratation.write("%s_Total_Hydratation," %taxa) | |
| 510 fileOUT_TotalHydratation.write("%s_Total_Hydratation" %LT[-1]) | |
| 511 fileOUT_TotalHydratation.write("\n") | |
| 512 | |
| 513 ##################### | |
| 514 ## 4 ## Process Loci | |
| 515 ##################### | |
| 516 bash_aa_properties = aa_properties(fileIN_properties) | |
| 517 | |
| 518 for locus in Lloci_AA: | |
| 519 print locus | |
| 520 path_locus = "%s/%s" %(Path_IN_loci_AA, locus) | |
| 521 bash = dico(path_locus,LT) | |
| 522 | |
| 523 #print bash | |
| 524 | |
| 525 fileOUT_PROT_ALL.write("%s," %locus) | |
| 526 fileOUT_IVYWREL.write("%s," %locus) | |
| 527 fileOUT_ERK_DNQTSH.write("%s," %locus) | |
| 528 fileOUT_EK_QH.write("%s," %locus) | |
| 529 fileOUT_FYMINK_GARP.write("%s," %locus) | |
| 530 fileOUT_AVLIMFYW.write("%s," %locus) | |
| 531 fileOUT_STNQ.write("%s," %locus) | |
| 532 fileOUT_RHKDE.write("%s," %locus) | |
| 533 fileOUT_PAYRE.write("%s," %locus) | |
| 534 fileOUT_TotalResidueWeight.write("%s," %locus) | |
| 535 fileOUT_TotalResidueVolume.write("%s," %locus) | |
| 536 fileOUT_TotalPartialSpecificVolume.write("%s," %locus) | |
| 537 fileOUT_TotalHydratation.write("%s," %locus) | |
| 538 | |
| 539 for taxa in LT[0:-1]: | |
| 540 if taxa in bash.keys(): | |
| 541 seq = bash[taxa] | |
| 542 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 ### | |
| 543 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 ### | |
| 544 Total_Residue_Weight,Total_Residue_Volume,Total_Partial_Specific_Volume,Total_Hydration = sequence_properties_from_aa_properties(seq, bash_aa_properties) ### DEF6 ### | |
| 545 | |
| 546 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)) | |
| 547 fileOUT_IVYWREL.write("%.5f,%.5f," %(count_IVYWREL, prop_IVYWREL)) | |
| 548 fileOUT_ERK_DNQTSH.write("%.5f,%.5f,%.5f,%.5f,%.5f," %(count_ERK,prop_ERK,count_DNQTSH,prop_DNQTSH,ratio_ERK_vs_DNQTSH)) | |
| 549 fileOUT_EK_QH.write("%.5f,%.5f,%.5f,%.5f,%.5f," %(count_EK,prop_EK,count_QH,prop_QH,ratio_EK_vs_QH)) | |
| 550 fileOUT_FYMINK_GARP.write("%.5f,%.5f,%.5f,%.5f," %(count_FYMINK,prop_FYMINK,count_GARP,prop_GARP)) | |
| 551 fileOUT_AVLIMFYW.write("%.5f,%.5f,%.5f,%.5f,%.5f,%.5f," %(count_AVLIMFYW,prop_AVLIMFYW,count_AVLIM,prop_AVLIM,count_FYW,prop_FYW)) | |
| 552 fileOUT_STNQ.write("%.5f,%.5f," %(count_STNQ,prop_STNQ)) | |
| 553 fileOUT_RHKDE.write("%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,"%(count_RHKDE,prop_RHKDE,count_RHK,prop_RHK,count_DE,prop_DE)) | |
| 554 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)) | |
| 555 fileOUT_TotalResidueWeight.write("%.5f," %Total_Residue_Weight) | |
| 556 fileOUT_TotalResidueVolume.write("%.5f," %Total_Residue_Volume) | |
| 557 fileOUT_TotalPartialSpecificVolume.write("%.5f," %(Total_Partial_Specific_Volume)) | |
| 558 fileOUT_TotalHydratation.write("%.5f," % Total_Hydration) | |
| 559 else: | |
| 560 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")) | |
| 561 fileOUT_IVYWREL.write("%s,%s," %("NA", "NA")) | |
| 562 fileOUT_ERK_DNQTSH.write("%s,%s,%s,%s,%s," %("NA","NA","NA","NA","NA")) | |
| 563 fileOUT_EK_QH.write("%s,%s,%s,%s,%s," %("NA","NA","NA","NA","NA")) | |
| 564 fileOUT_FYMINK_GARP.write("%s,%s,%s,%s," %("NA","NA","NA","NA")) | |
| 565 fileOUT_AVLIMFYW.write("%s,%s,%s,%s,%s,%s," %("NA","NA","NA","NA","NA","NA")) | |
| 566 fileOUT_STNQ.write("%s,%s," %("NA","NA")) | |
| 567 fileOUT_RHKDE.write("%s,%s,%s,%s,%s,%s,"%("NA","NA","NA","NA","NA","NA")) | |
| 568 fileOUT_PAYRE.write("%s,%s,%s,%s,%s,%s,%s,%s," %("NA","NA","NA","NA","NA","NA","NA","NA")) | |
| 569 fileOUT_TotalResidueWeight.write("%s," %"NA") | |
| 570 fileOUT_TotalResidueVolume.write("%s," %"NA") | |
| 571 fileOUT_TotalPartialSpecificVolume.write("%s," %"NA") | |
| 572 fileOUT_TotalHydratation.write("%s," %"NA") | |
| 573 | |
| 574 if LT[-1] in bash.keys(): | |
| 575 seq = bash[LT[-1]] | |
| 576 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 ### | |
| 577 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 ### | |
| 578 Total_Residue_Weight,Total_Residue_Volume,Total_Partial_Specific_Volume,Total_Hydration = sequence_properties_from_aa_properties(seq, bash_aa_properties) ### DEF6 ### | |
| 579 | |
| 580 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)) | |
| 581 fileOUT_IVYWREL.write("%.5f,%.5f" %(count_IVYWREL, prop_IVYWREL)) | |
| 582 fileOUT_ERK_DNQTSH.write("%.5f,%.5f,%.5f,%.5f,%.5f" %(count_ERK,prop_ERK,count_DNQTSH,prop_DNQTSH,ratio_ERK_vs_DNQTSH)) | |
| 583 fileOUT_EK_QH.write("%.5f,%.5f,%.5f,%.5f,%.5f" %(count_EK,prop_EK,count_QH,prop_QH,ratio_EK_vs_QH)) | |
| 584 fileOUT_FYMINK_GARP.write("%.5f,%.5f,%.5f,%.5f" %(count_FYMINK,prop_FYMINK,count_GARP,prop_GARP)) | |
| 585 fileOUT_AVLIMFYW.write("%.5f,%.5f,%.5f,%.5f,%.5f,%.5f" %(count_AVLIMFYW,prop_AVLIMFYW,count_AVLIM,prop_AVLIM,count_FYW,prop_FYW)) | |
| 586 fileOUT_STNQ.write("%.5f,%.5f" %(count_STNQ,prop_STNQ)) | |
| 587 fileOUT_RHKDE.write("%.5f,%.5f,%.5f,%.5f,%.5f,%.5f"%(count_RHKDE,prop_RHKDE,count_RHK,prop_RHK,count_DE,prop_DE)) | |
| 588 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)) | |
| 589 fileOUT_TotalResidueWeight.write("%.5f" %Total_Residue_Weight) | |
| 590 fileOUT_TotalResidueVolume.write("%.5f" %Total_Residue_Volume) | |
| 591 fileOUT_TotalPartialSpecificVolume.write("%.5f" %(Total_Partial_Specific_Volume)) | |
| 592 fileOUT_TotalHydratation.write("%.5f" % Total_Hydration) | |
| 593 else: | |
| 594 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")) | |
| 595 fileOUT_IVYWREL.write("%s,%s" %("NA", "NA")) | |
| 596 fileOUT_ERK_DNQTSH.write("%s,%s,%s,%s,%s" %("NA","NA","NA","NA","NA")) | |
| 597 fileOUT_EK_QH.write("%s,%s,%s,%s,%s" %("NA","NA","NA","NA","NA")) | |
| 598 fileOUT_FYMINK_GARP.write("%s,%s,%s,%s" %("NA","NA","NA","NA")) | |
| 599 fileOUT_AVLIMFYW.write("%s,%s,%s,%s,%s,%s" %("NA","NA","NA","NA","NA","NA")) | |
| 600 fileOUT_STNQ.write("%s,%s" %("NA","NA")) | |
| 601 fileOUT_RHKDE.write("%s,%s,%s,%s,%s,%s"%("NA","NA","NA","NA","NA","NA")) | |
| 602 fileOUT_PAYRE.write("%s,%s,%s,%s,%s,%s,%s,%s" %("NA","NA","NA","NA","NA","NA","NA","NA")) | |
| 603 fileOUT_TotalResidueWeight.write("%s" %"NA") | |
| 604 fileOUT_TotalResidueVolume.write("%s" %"NA") | |
| 605 fileOUT_TotalPartialSpecificVolume.write("%s" %"NA") | |
| 606 fileOUT_TotalHydratation.write("%s" %"NA") | |
| 607 | |
| 608 ## END LINE | |
| 609 fileOUT_PROT_ALL.write("\n") | |
| 610 fileOUT_IVYWREL.write("\n") | |
| 611 fileOUT_ERK_DNQTSH.write("\n") | |
| 612 fileOUT_EK_QH.write("\n") | |
| 613 fileOUT_FYMINK_GARP.write("\n") | |
| 614 fileOUT_AVLIMFYW.write("\n") | |
| 615 fileOUT_STNQ.write("\n") | |
| 616 fileOUT_RHKDE.write("\n") | |
| 617 fileOUT_PAYRE.write("\n") | |
| 618 fileOUT_TotalResidueWeight.write("\n") | |
| 619 fileOUT_TotalResidueVolume.write("\n") | |
| 620 fileOUT_TotalPartialSpecificVolume.write("\n") | |
| 621 fileOUT_TotalHydratation.write("\n") | |
| 622 |