Mercurial > repos > abims-sbr > mutcount

annotate scripts/S02b_study_seq_composition_nuc.py @ 7:f1e24200e5ae draft

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planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit b7a3030ea134b5dfad89b1a869db659d72d1145c
author abims-sbr
date Wed, 28 Feb 2018 10:39:41 -0500
parents 0ba551449008
children 04a9ada73cc4
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1 #!/usr/bin/env python
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2 ## Author: Eric FONTANILLAS
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3 ## Date: 21.12.10
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4 ## Last Version : 12/2017 by Victor Mataigne
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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 one "cold" species: Pg)
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7 import sys,os,shutil,subprocess, string, itertools
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8 from functions import simplify_fasta_name, dico
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10 ##################
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11 ###### DEF2 ######
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12 ##################
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13 def base_composition(seq):
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14 count_A=string.count(seq, "A") + string.count(seq, "a")
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15 count_T=string.count(seq, "T") + string.count(seq, "t")
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16 count_C=string.count(seq, "C") + string.count(seq, "c")
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17 count_G=string.count(seq, "G") + string.count(seq, "g")
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18 ## 3 ## Nucleotide proportions
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19 ln = count_C+count_G+count_T+count_A
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20 if (ln!=0):
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22 CG = count_C+count_G
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23 AT = count_T+count_A
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25 AG = count_A+count_G
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26 TC = count_T+count_C
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28 ## 1 ## Search for compositional bias in genome as marker of thermal adaptation: CG vs AT
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29 ratio_CG_AT = float(CG)/float(AT)
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30 percent_CG = float(CG)/(float(AT) + float(CG))*100
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32 ## 2 ## Search for compositional bias in genome as marker of thermal adaptation: AG vs TC
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33 ratio_purine_pyrimidine=float(AG)/float(TC)
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34 percent_purine=float(AG)/(float(AG)+float(TC))*100
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37 prop_A = float(count_A)/float(ln)
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38 prop_T = float(count_T)/float(ln)
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39 prop_C = float(count_C)/float(ln)
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40 prop_G = float(count_G)/float(ln)
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41 else:
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42 percent_CG=0
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43 percent_purine=0
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44 prop_A=0
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45 prop_T=0
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46 prop_C=0
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47 prop_G=0
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49 return(percent_CG, percent_purine, prop_A, prop_T, prop_C, prop_G)
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50 ##############################################
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52 ##################
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53 ###### DEF3 ######
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54 ##################
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55 def purine_loading(seq):
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56 count_A=string.count(seq, "A") + string.count(seq, "a")
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57 count_T=string.count(seq, "T") + string.count(seq, "t")
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58 count_C=string.count(seq, "C") + string.count(seq, "c")
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59 count_G=string.count(seq, "G") + string.count(seq, "g")
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60 ## 3 ## Nucleotide proportions
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61 TOTAL = count_C+count_G+count_T+count_A
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62 if (TOTAL!=0):
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64 ## PLI : Purine loading indice (Forsdyke et al.)
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65 # (G-C)/N * 1000 et (A-T)/N * 1000
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67 DIFF_GC = count_G - count_C
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68 DIFF_AT = count_A - count_T
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70 # Per bp
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71 PLI_GC = float(DIFF_GC)/float(TOTAL)
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72 PLI_AT = float(DIFF_AT)/float(TOTAL)
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74 # Per 1000 bp
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75 PLI_GC_1000 = PLI_GC*1000
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76 PLI_AT_1000 = PLI_AT*1000
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77 else:
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78 DIFF_GC=0
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79 DIFF_AT=0
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80 PLI_GC=0
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81 PLI_AT=0
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82 PLI_GC_1000=0
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83 PLI_AT_1000=0
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85 return(TOTAL, DIFF_GC, DIFF_AT,PLI_GC,PLI_AT,PLI_GC_1000,PLI_AT_1000)
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86 ##############################################
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87
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88 ###################
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89 ### RUN RUN RUN ###
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90 ###################
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91
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92 ##Create specific folders
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93 Path_IN_loci_NUC = "./IN_NUC"
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94 outpath= "./OUT"
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95 os.makedirs(Path_IN_loci_NUC)
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96 os.makedirs(outpath)
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97
1
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98 infiles = str.split(sys.argv[1], ",")
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99 for file in infiles:
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100 os.system("cp %s %s" %(file, Path_IN_loci_NUC))
0
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101
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102 ## 1 ## List taxa
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103 LT=[]
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104 cmd="grep '>' %s" % sys.argv[2]
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105 result = subprocess.check_output(cmd, shell=True)
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106 result=result.split('\n')
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107 for i in result:
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108 sp=i[1:]
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109 if sp !='':
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110 LT.append(sp)
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111 print LT
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112
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113 #LT = ["Ap", "Ac", "Pg"]
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114 #os.system("grep '>' %s" %(sys.argv[1]))
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115
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116 ## 2 ## PathIN
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117 # fileIN_properties = open("01_AminoAcid_Properties2.csv", "r")
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118 Lloci_NUC = os.listdir(Path_IN_loci_NUC)
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119
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120
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121 ## 3 ## PathOUT
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122 ## 3.1 ## NUC composition
1
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123 fileOUT_NUC=open("./OUT/nuc_compositions.csv","w")
0
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124 fileOUT_NUC.write("LOCUS,")
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125 for taxa in LT[0:-1]:
0
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126 fileOUT_NUC.write("%s_prop_A,%s_prop_T,%s_prop_C,%s_prop_G," %(taxa,taxa,taxa,taxa))
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127 fileOUT_NUC.write("%s_prop_A,%s_prop_T,%s_prop_C,%s_prop_G" %(LT[-1],LT[-1],LT[-1],LT[-1]))
0
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128 fileOUT_NUC.write("\n")
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129
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130 ## 3.2 ## NUC percent_GC
1
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131 fileOUT_percent_GC=open("./OUT/percent_GC.csv","w")
0
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132 fileOUT_percent_GC.write("LOCUS,")
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133 for taxa in LT[0:-1]:
0
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134 fileOUT_percent_GC.write("%s_percent_GC," %(taxa))
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135 fileOUT_percent_GC.write("%s_percentGC" %(LT[-1]))
0
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136 fileOUT_percent_GC.write("\n")
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137
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138 ## 3.3 ## NUC percent_purine
1
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139 fileOUT_percent_purine=open("./OUT/percent_purine.csv","w")
0
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140 fileOUT_percent_purine.write("LOCUS,")
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141 for taxa in LT[0:-1]:
0
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142 fileOUT_percent_purine.write("%s_percent_purine," %(taxa))
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143 fileOUT_percent_purine.write("%s_percent_purine" %(LT[-1]))
0
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144 fileOUT_percent_purine.write("\n")
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145
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146 ## 3.4 ## Purine Load
1
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147 fileOUT_Purine_Load=open("./OUT/Purine_Load_Indice.csv", "w")
0
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148 fileOUT_Purine_Load.write("LOCUS,")
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149 for taxa in LT[0:-1]:
0
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150 fileOUT_Purine_Load.write("%s_TOTAL,%s_DIFF_GC,%s_DIFF_AT,%s_PLI_GC1000,%s_PLI_AT1000," %(taxa,taxa,taxa,taxa,taxa))
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151 fileOUT_Purine_Load.write("%s_TOTAL,%s_DIFF_GC,%s_DIFF_AT,%s_PLI_GC1000,%s_PLI_AT1000" %(LT[-1],LT[-1],LT[-1],LT[-1],LT[-1]))
0
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152 fileOUT_Purine_Load.write("\n")
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153
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154 #####################
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155 ## 4 ## Process Loci
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156 #####################
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157 for locus in Lloci_NUC:
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158 print locus
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159 path_locus = "%s/%s" %(Path_IN_loci_NUC, locus)
2
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160 bash = dico(path_locus,LT)
0
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161
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162 fileOUT_NUC.write("%s," %locus)
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163 fileOUT_percent_GC.write("%s," %locus)
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164 fileOUT_percent_purine.write("%s," %locus)
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165 fileOUT_Purine_Load.write("%s," %locus)
2
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166
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167 for taxa in LT[0:-1]:
2
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168 if taxa in bash.keys():
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169 seq = bash[taxa]
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170 percent_GC, percent_purine,prop_A, prop_T, prop_C, prop_G = base_composition(seq) ### DEF2 ###
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171 TOTAL, DIFF_GC, DIFF_AT,PLI_GC,PLI_AT,PLI_GC_1000,PLI_AT_1000 = purine_loading(seq) ### DEF3 ###
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172 fileOUT_NUC.write("%.5f,%.5f,%.5f,%.5f," %(prop_A,prop_T,prop_C,prop_G))
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173 fileOUT_percent_GC.write("%.5f," %percent_GC)
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174 fileOUT_percent_purine.write("%.5f," %percent_purine)
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175 fileOUT_Purine_Load.write("%d,%d,%d,%.5f,%.5f," %(TOTAL, DIFF_GC, DIFF_AT,PLI_GC_1000, PLI_AT_1000))
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176 else:
4
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177 fileOUT_NUC.write("%s,%s,%s,%s," %("NA","NA","NA","NA"))
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178 fileOUT_percent_GC.write("%s," %"NA")
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179 fileOUT_percent_purine.write("%s," %"NA")
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180 fileOUT_Purine_Load.write("%s,%s,%s,%s,%s," %("NA","NA","NA","NA","NA"))
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181
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182 if LT[-1] in bash.keys():
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183 seq = bash[LT[-1]]
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184 percent_GC, percent_purine,prop_A, prop_T, prop_C, prop_G = base_composition(seq) ### DEF2 ###
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185 TOTAL, DIFF_GC, DIFF_AT,PLI_GC,PLI_AT,PLI_GC_1000,PLI_AT_1000 = purine_loading(seq) ### DEF3 ###
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186 fileOUT_NUC.write("%.5f,%.5f,%.5f,%.5f" %(prop_A,prop_T,prop_C,prop_G))
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
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187 fileOUT_percent_GC.write("%.5f" %percent_GC)
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
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188 fileOUT_percent_purine.write("%.5f" %percent_purine)
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
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189 fileOUT_Purine_Load.write("%d,%d,%d,%.5f,%.5f" %(TOTAL, DIFF_GC, DIFF_AT,PLI_GC_1000, PLI_AT_1000))
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
190 else:
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
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191 fileOUT_NUC.write("%s,%s,%s,%s" %("NA","NA","NA","NA"))
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
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192 fileOUT_percent_GC.write("%s" %"NA")
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
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193 fileOUT_percent_purine.write("%s" %"NA")
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
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194 fileOUT_Purine_Load.write("%s,%s,%s,%s,%s" %("NA","NA","NA","NA","NA"))
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
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195
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
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196
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
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197 fileOUT_NUC.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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198 fileOUT_percent_GC.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
199 fileOUT_percent_purine.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
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200 fileOUT_Purine_Load.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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201 fileOUT_NUC.close()
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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parents:
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202 fileOUT_percent_GC.close()
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
203 fileOUT_percent_purine.close()
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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parents:
diff changeset
204 fileOUT_Purine_Load.close()