Mercurial > repos > abims-sbr > mutcount

annotate scripts/S02a_codon_counting.py @ 2:988467f963f0 draft

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planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
author abims-sbr
date Wed, 17 Jan 2018 08:57:49 -0500
parents 78dd6454f6f0
children 5766f80370e7
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988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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1 #!/usr/bin/env python
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2 # coding:utf-8
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4 # Command line : ./S02a_codon_counting.py <concatenation_file_from_phylogeny>
0
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6 #python codoncounting.py alignement_file
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7 #Warning!! alignement_file should always be preceded by a path, at least ./
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8 #Warning!! pairs.txt should be located in the same folder as alignement_file
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10 #the script counts the number of codons, amino acids, and types of amino acids in sequences, as well as the mutation bias from one item to another between 2 sequences
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11 #counting is then compared to empirical p-values, obtained from bootstrapped sequences obtained from a subset of sequences
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12 #the script takes as input the DNA alignment (fasta format): python codoncounting.py file_path.fasta
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13 #in the output files, the pvalues indicate the position of the observed data in a distribution of empirical countings obtained from a resample of the data. Values above 0.95 indicate a significantly higher counting, values under 0.05 a significantly lower counting
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15 #the script automatically reads the sequences to compare from a file that must be called pairs.txt and located with the .fasta file
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16 #in the pairs.txt file, sequences (let's assume X, Y, Z, U, V) pairs must be written as 'X Y\nU V\nZ V'
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17 #in this case, codoncounting will count the occurence of codons, amino acids, and types of amino acids in X, U, Z, and count the mutation bias from Y to X, V to U and V to Z
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18 #you can add comments in the pairs.txt file inbetween lines, beginning with '#'. E.G. 'X Y\n#This is my comment\nU V\nZ V'
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19 #X, Y, Z, U, V must be character strings contained in the sequences names in the .fasta file (and be specific to each of them)
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20 #in pairs.txt, you must write how should be built the bootstrapped resampling of sequences. This must be formated as:'X Y\nbackground: length iterration plusminus listofspecies\nU V\nZ V', explanation below
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21 #backgrounds must be excplicitely written in the pairs.txt file (the script still integers default parameters). This implies that the first line of pairs.txt should be a background line
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22 #by default, once the background has been determined, it will be applied to each subsequent analysis until another background is written
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23 #e.g. 'background: length1 iterration1 plusminus1 listofspecies1\nU V\nZ V\nbackground: length2 iterration2 plusminus2 listofspecies2\nX Y' the first background is applied to U V and Z V and the 2nd background to X Y
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26 #the script resamples random pairs of aligned codon to determine what countings can be expected under the hypothesis of an homogenous dataset
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27 #countings are performed on each generated random alignement, thousands of alignments allow to draw a gaussian distribution of the countings
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28 #then the script simply checks whether the observed data are within the 5% lowest or 5% highest values of the distribution
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29 #in background: length iterration plusminus listofspecies
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30 #-> length is the number of pairs of codons in each generated alignments (effect on the robustness on the countings performed on this alignement)
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31 #-> iterration is the number of alignments that will be generated (effect on the resolution of the gaussian distribution)
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32 #-> plusminus can be either '+' or '-', '+' indicates that the following species only must be resampled, '-' that the following species must be excluded from the resampling
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33 #-> listofspecies is the list of species (names contained in the sequences names from the fasta file) that must be included or excluded from the sampling. You can also write 'all' to include every species (in this case, plusminus parameter is ignored)
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34 #full example: background 5000 10000 + melanogaster elegans sapiens
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35 #iterration shouldn't be lower that 1000 to have a relatively smooth gaussian distribution, length shouldn't be lower as 1000 to detect codons with relatively low occurence (<1%)
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36 #for the list of species, you can try to form subgroups depending on the studied parameter (e.g. comparing a terrestrial species with a background composed of marine species)
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39 #added: also counts GC3 and IVYWREL
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40 #added: also counts GC12, CvP bias and EK/QH
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41 #added: also counts purine load and PAYRE/SDGM
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44 def viable(seqs,pos):
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45 r=0
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46 compt=0
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47 for i in range(len(seqs)):
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48 if i%2==1:
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49 if not '-' in seqs[i][pos:pos+3]:
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50 compt+=1
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51 if compt>1:
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52 r=1
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53 return r
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55 def substrcountings(table,pvalues):
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57 string=[]
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58 names=[]
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59 numbers=[]
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60 stats=['pvalues']
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61 for f in table:
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62 names.append(',%s' % f)
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63 numbers.append(',%f' % table[f])
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64 stats.append(',%f' % pvalues[f])
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65 names.append('\n')
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66 numbers.append('\n')
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67 stats.append('\n')
2
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68 string=names+numbers+stats
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70 return string
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72 def substrbiases(table,pvalues):
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74 string=[]
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75 names=[]
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76 numbers=[]
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77 stats=['pvalues']
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78 for f in table:
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79 for g in table[f]:
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80 names.append(',%s>%s' % (g,f))
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81 numbers.append(',%f' % table[f][g])
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82 stats.append(',%f' % pvalues[f][g])
0
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83 names.append('\n')
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84 numbers.append('\n')
2
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85 stats.append('\n')
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86 string=names+numbers+stats
0
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87
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88 return string
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90 def strcountings(codons, aa, classif,codonspvalues,aapvalues,classifpvalues,GC3,GC12,IVYWREL,EKQH,PAYRESDGM,purineload,CvP):
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91
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92 subcodons=['occurence of codons\n']+substrcountings(codons,codonspvalues)
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93 subaa=subcodons+['\noccurence of amino_acids\n']+substrcountings(aa,aapvalues)
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94 subclassif=subaa+['\noccurence of amino_acid types\n']+substrcountings(classif,classifpvalues)
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95
2
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96 string=subclassif+[('\nGC3 GC12 IVYWREL EK/QH PAYRE/SDGM Purine_load CvP\n%f,%f,%f,%f,%f,%f,%f\n' % (GC3, GC12, IVYWREL, EKQH, PAYRESDGM, purineload, CvP))]
0
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97
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98 return string
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99
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100
2
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101 def strbiases(codons, aa, classif,codonspvalues,aapvalues,classifpvalues,fileaa, fileaatype, p):
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102
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103 # Writing to files (tab separated; the tab characters are in the lists values)
0
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104
2
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105 aafreq, aapval = substrbiases(aa,aapvalues)[401:801], substrbiases(aa,aapvalues)[803:-1]
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106 aatypefreq, aatypepval = substrbiases(classif,classifpvalues)[17:33], substrbiases(classif,classifpvalues)[35:-1]
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107
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108 fileaa.write("%s>%s" %(p[1], p[0]))
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109 for value in aafreq:
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110 fileaa.write(str(value))
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111 fileaa.write("\n")
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112 fileaa.write("%s>%s_pvalue" %(p[1], p[0]))
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113 for value in aapval:
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114 fileaa.write(str(value))
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115 fileaa.write("\n")
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116
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117 fileaatype.write("%s>%s" %(p[1], p[0]))
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118 for value in aatypefreq:
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119 fileaatype.write(str(value))
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120 fileaatype.write("\n")
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121 fileaatype.write("%s>%s_pvalue" %(p[1], p[0]))
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122 for value in aatypepval:
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123 fileaatype.write(str(value))
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124 fileaatype.write("\n")
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125
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126 # Origin code
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127
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128 subcodons=['codons mutations biases\n']+substrbiases(codons,codonspvalues)
0
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129 subaa=subcodons+['\namino acids mutation biases\n']+substrbiases(aa,aapvalues)
2
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130 subclassif=subaa+['\ntypes of amino_acids mutation biasecodoncountingv22.pys\n']+substrbiases(classif,classifpvalues)
0
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131
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132 return subclassif
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133
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134 def testpvalue(bootstrap,value,iterration): #computes where the observed value is located in the expected counting distribution
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135
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136 maxval=iterration-1
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137 minval=0
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138 testval=(maxval+minval)/2
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139 while maxval-minval > 1:
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140 if value > bootstrap[testval]:
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141 minval=testval
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142 testval=(maxval+minval)/2
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143 elif value < bootstrap[testval]:
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144 maxval=testval
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145 testval=(maxval+minval)/2
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146 else:
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147 break
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148 pvalue=(testval+1)/float(iterration+1)
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149
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150 return pvalue
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151
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152 def gettables(content,reversecode,code,classif): #generates the tables contening all the countings
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153
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154 if content==[]:
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155 codonscount={k:[] for k in reversecode}
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156 aacount={k:[] for k in code}
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157 aaclassifcount={k:[] for k in classif}
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158
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159 codons={}
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160 for k in reversecode:
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161 codons[k]={}
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162 for q in reversecode:
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163 codons[k][q]=[]
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164 aa={}
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165 for k in code:
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166 aa[k]={}
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167 for q in code:
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168 aa[k][q]=[]
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169 aaclassif={}
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170 for k in classif:
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171 aaclassif[k]={}
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172 for q in classif:
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173 aaclassif[k][q]=[]
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174
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175 elif content==0:
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176 codonscount={k:0 for k in reversecode}
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177 aacount={k:0 for k in code}
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178 aaclassifcount={k:0 for k in classif}
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179
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180 codons={}
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181 for k in reversecode:
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182 codons[k]={}
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183 for q in reversecode:
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184 codons[k][q]=0
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185 aa={}
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186 for k in code:
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187 aa[k]={}
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188 for q in code:
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189 aa[k][q]=0
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190 aaclassif={}
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191 for k in classif:
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192 aaclassif[k]={}
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193 for q in classif:
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194 aaclassif[k][q]=0
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195
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196 return codonscount, aacount, aaclassifcount, codons, aa, aaclassif
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197
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198 def countings(seq1,seq2,code,classif,reversecode,reverseclassif):
2
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199 # COMPTAGES (output counts.txt) functions used : gettables()
0
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200 #countings actually counts occurence and mutation bias of codons, amino acids and types of amino acids
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201
2
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202 codonscount, aacount, aaclassifcount, codons, aa, aaclassif=gettables(0,reversecode,code,classif)
0
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203 codonscount2, aacount2, aaclassifcount2, _, _, _=gettables(0,reversecode,code,classif)
2
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204
0
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205 G12=0
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206 C12=0
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207 G3=0
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208 C3=0
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209 A=0
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210 T=0
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211
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212 i=0
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213 compcodons=0
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214 while i<len(seq1)-1:
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215 if not '-' in seq1[i:i+3]: #coutings of occurences is obtained from the maximum of full codons being in the sequence
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216 compcodons+=1
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217
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218 if (seq1[i]=='g'):
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219 G12+=1
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220 if (seq1[i]=='c'):
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221 C12+=1
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222 if (seq1[i+1]=='g'):
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223 G12+=1
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224 if (seq1[i+1]=='c'):
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225 C12+=1
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226 if (seq1[i+2]=='g'):
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227 G3+=1
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228 if (seq1[i+2]=='c'):
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229 C3+=1
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230
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231 if (seq1[i]=='a'):
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232 A+=1
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233 if (seq1[i]=='t'):
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234 T+=1
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235 if (seq1[i+1]=='a'):
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236 A+=1
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237 if (seq1[i+1]=='t'):
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238 T+=1
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239 if (seq1[i+2]=='a'):
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240 A+=1
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241 if (seq1[i+2]=='t'):
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242 T+=1
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243
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244 codonscount[seq1[i:i+3]]+=1
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245 aacount[reversecode[seq1[i:i+3]]]+=1
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246 aaclassifcount[reverseclassif[reversecode[seq1[i:i+3]]]]+=1
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247 if (not '-' in seq1[i:i+3]) and (not '-' in seq2[i:i+3]) and (not seq1[i:i+3]==seq2[i:i+3]): #mutation biases are count from non ambiguous pairs of codons in the 2 sequences
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248 codons[seq1[i:i+3]][seq2[i:i+3]]+=1
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249 codonscount2[seq2[i:i+3]]+=1
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250 aacount2[reversecode[seq2[i:i+3]]]+=1
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251 aaclassifcount2[reverseclassif[reversecode[seq2[i:i+3]]]]+=1
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252 i+=3
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253
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254 IVYWREL=aacount['ile']+aacount['val']+aacount['tyr']+aacount['trp']+aacount['arg']+aacount['glu']+aacount['leu']
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255 EKQH=(aacount['glu']+aacount['lys'])/max([float(aacount['gln']+aacount['his']),1])
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256 PAYRESDGM=(aacount['pro']+aacount['ala']+aacount['tyr']+aacount['arg']+aacount['glu'])/max([float(aacount['ser']+aacount['asp']+aacount['gly']+aacount['met']),1])
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257
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258 for i in codons:
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259 for j in codons[i]:
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260 if not reversecode[i]==reversecode[j]:
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261 aa[reversecode[i]][reversecode[j]]+=codons[i][j]
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262
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263 for i in aa:
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264 for j in aa[i]:
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265 if not reverseclassif[i]==reverseclassif[j]:
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266 aaclassif[reverseclassif[i]][reverseclassif[j]]+=aa[i][j]
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267
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268
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269 for f in codons: #mutations from codon C in sequence X to codon c in sequence Y are normalized by the total number of codons C in sequence X
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270 for g in codons[f]:
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271 codons[f][g]=codons[f][g]/float(max([codonscount2[g],1]))
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272 for f in aa:
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273 for g in aa[f]:
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274 aa[f][g]=aa[f][g]/float(max([aacount2[g],1]))
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275 for f in aaclassif:
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276 for g in aaclassif[f]:
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277 aaclassif[f][g]=aaclassif[f][g]/float(max([aaclassifcount2[g],1]))
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278 for f in codonscount: #occurences are normalized by the total number of non ambiguous codons in the sequence
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279 codonscount[f]=codonscount[f]/float(compcodons)
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280 for f in aacount:
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281 aacount[f]=aacount[f]/float(compcodons)
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282 for f in aaclassifcount:
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283 aaclassifcount[f]=aaclassifcount[f]/float(compcodons)
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284
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285 for f in codons:
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286 for g in codons[f]:
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287 if f==g:
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288 break
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289 if (codons[g][f]==0) and (codons[f][g])>0:
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290 codons[f][g]=1
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291 elif (codons[g][f]==0) and (codons[f][g])==0:
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292 codons[f][g]=0
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293 else:
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294 x=codons[f][g]/codons[g][f]
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295 codons[f][g]=-pow(2,1-x)+1
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296
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297 for f in aa:
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298 for g in aa[f]:
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299 if f==g:
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300 break
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301 if (aa[g][f]==0) and (aa[f][g])>0:
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302 aa[f][g]=1
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303 elif (aa[g][f]==0) and (aa[f][g])==0:
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304 aa[f][g]=0
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305 else:
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306 x=aa[f][g]/aa[g][f]
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307 aa[f][g]=-pow(2,1-x)+1
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308
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309 for f in aaclassif:
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310 for g in aaclassif[f]:
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311 if f==g:
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312 break
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313 if (aaclassif[g][f]==0) and (aaclassif[f][g])>0:
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314 aaclassif[f][g]=1
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315 elif (aaclassif[g][f]==0) and (aaclassif[f][g])==0:
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316 aaclassif[f][g]=0
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317 else:
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318 x=aaclassif[f][g]/aaclassif[g][f]
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319 aaclassif[f][g]=-pow(2,1-x)+1
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diff changeset
320
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diff changeset
321 GC3=(G3+C3)/float(compcodons)
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322 GC12=(G12+C12)/float(2*compcodons)
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diff changeset
323 purineload=(1000*(G12+G3+A-C12-C3-T))/float(3*compcodons)
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diff changeset
324 IVYWREL=IVYWREL/float(compcodons)
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diff changeset
325 CvP=aaclassifcount['charged']-aaclassifcount['polar']
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diff changeset
326
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diff changeset
327 return codonscount, aacount, aaclassifcount, codons, aa, aaclassif, GC3, GC12, IVYWREL, EKQH, PAYRESDGM, purineload, CvP
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diff changeset
328
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diff changeset
329 def sampling(inputfile,length,iterration,plusminus,species,code,classif,reversecode,reverseclassif):
2
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diff changeset
330 # functions used : gettables, countings
0
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331 #sampling provides 'iterations' pairs of sequences of 'length' non ambiguous codons obtained from the dataset specified by 'species' and 'plusminus'
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diff changeset
332 #sort of bootstrap
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333
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334 codonscount, aacount, aaclassifcount, codons, aa, aaclassif=gettables([],reversecode,code,classif)
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335
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diff changeset
336 inputfile.seek(0) #generates the bootstrapped sequences
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diff changeset
337 lines=[]
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diff changeset
338 comp=-1
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339 if species==['all']:
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340 while 1:
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341 line=inputfile.readline()[:-1]
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342 if not line:
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diff changeset
343 break
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diff changeset
344 lines.append(line)
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diff changeset
345 comp+=1
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346 else:
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diff changeset
347 if plusminus=='+':
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348 while 1:
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349 line1=inputfile.readline()[:-1]
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350 if not line1:
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351 break
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352 line2=inputfile.readline()[:-1]
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353 if any(spe in line1 for spe in species):
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diff changeset
354 lines.append(line1)
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diff changeset
355 lines.append(line2)
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diff changeset
356 comp+=2
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diff changeset
357 elif plusminus=='-':
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358 while 1:
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diff changeset
359 line1=inputfile.readline()[:-1]
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diff changeset
360 if not line1:
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diff changeset
361 break
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diff changeset
362 line2=inputfile.readline()[:-1]
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diff changeset
363 if not any(spe in line1 for spe in species):
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diff changeset
364 lines.append(line1)
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diff changeset
365 lines.append(line2)
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diff changeset
366 comp+=2
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diff changeset
367 l=len(lines[1])-1
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diff changeset
368
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diff changeset
369 for z in range(iterration):
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370 if z%(iterration/10)==0:
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diff changeset
371 print str(10*z/(iterration/10))+' %'
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diff changeset
372 seqa=[]
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diff changeset
373 seqb=[]
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diff changeset
374 for i in range(length):
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diff changeset
375 site=random.randrange(0,l,3)
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diff changeset
376 while viable(lines,site)==0:
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diff changeset
377 site=random.randrange(0,l,3)
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diff changeset
378 a='---'
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diff changeset
379 b='---'
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380 while ('-' in a) or ('-' in b):
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381 posa=2
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382 posb=2
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383 while posa==posb:
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384 posa=random.randrange(1,comp+1,2)
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385 posb=random.randrange(1,comp+1,2)
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386 a=lines[posa][site:site+3]
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387 b=lines[posb][site:site+3]
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388 seqa.append(a)
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389 seqb.append(b)
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390 seqa=(''.join(seqa)).lower()
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391 seqb=(''.join(seqb)).lower()
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392
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393 codonscounttemp, aacounttemp, aaclassifcounttemp, codonstemp, aatemp, aaclassiftemp, _, _, _, _, _, _, _=countings(seqa,seqb,code,classif,reversecode,reverseclassif)
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394 for f in codonscount:
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395 codonscount[f].append(codonscounttemp[f])
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396 for f in aacount:
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397 aacount[f].append(aacounttemp[f])
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398 for f in aaclassifcount:
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399 aaclassifcount[f].append(aaclassifcounttemp[f])
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400 for f in codons:
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401 for g in codons[f]:
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402 codons[f][g].append(codonstemp[f][g])
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403 for f in aa:
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404 for g in aa[f]:
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405 aa[f][g].append(aatemp[f][g])
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406 for f in aaclassif:
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407 for g in aaclassif[f]:
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408 aaclassif[f][g].append(aaclassiftemp[f][g]) #counts the occurences and mutation biases for each the bootstrapped sequence
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409
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410 print '100 %'
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411
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412 for f in codonscount:
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413 codonscount[f].sort()
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414 for f in aacount:
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415 aacount[f].sort()
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416 for f in aaclassifcount:
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417 aaclassifcount[f].sort()
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418 for f in codons:
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419 for g in codons[f]:
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420 codons[f][g].sort()
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421 for f in aa:
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422 for g in aa[f]:
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423 aa[f][g].sort()
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424 for f in aaclassif:
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425 for g in aaclassif[f]:
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426 aaclassif[f][g].sort()
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427
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428 return codonscount, aacount, aaclassifcount, codons, aa, aaclassif
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429
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430 ################
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431 ######RUN#######
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432 ################
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433
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434 import string, os, sys, re, random
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435 from math import pow
2
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436
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437 codons_counts = open("codons_counts.csv", "w")
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438 aa_counts = open("aa_counts.csv", "w")
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439 aatypes_counts = open("aatypes_counts.csv", "w")
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440 gc_counts = open("gc_counts.csv", "w")
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441
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442 # ou bien utiliser le reversecode plus bas
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443 column_index_codons = "Species,tat,tgt,tct,ttt,tgc,tgg,tac,ttc,tcg,tta,ttg,tcc,tca,gca,gta,gcc,gtc,gcg,gtg,caa,gtt,gct,acc,ggt,cga,cgc,gat,aag,cgg,act,ggg,gga,ggc,gag,aaa,gac,cgt,gaa,ctt,atg,aca,acg,atc,aac,ata,agg,cct,agc,aga,cat,aat,att,ctg,cta,ctc,cac,ccg,agt,cag,cca,ccc\n"
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444 column_index_aa = "Species,cys,asn,his,ile,ser,gln,lys,met,pro,thr,phe,ala,gly,val,leu,asp,arg,trp,glu,tyr\n"
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445 column_index_aatypes = "Species,aromatics,polar,unpolar,charged\n"
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446 column_index_gc = "Species,GC3,GC12,IVYWREL,EKQH,PAYRESDGM,purineload,CvP\n"
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447
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448 codons_counts.write(column_index_codons)
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449 aa_counts.write(column_index_aa)
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450 aatypes_counts.write(column_index_aatypes)
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451 gc_counts.write(column_index_gc)
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452
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453 aa_transitions = open("aa_transitions.csv", "w")
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454 aatypes_transitions = open("aatypes_transitions.csv", "w")
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455
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456 column_index_aa_transitions = "Species,cys>cys,asn>cys,his>cys,ile>cys,ser>cys,gln>cys,lys>cys,met>cys,pro>cys,thr>cys,phe>cys,ala>cys,gly>cys,val>cys,leu>cys,asp>cys,arg>cys,trp>cys,glu>cys,tyr>cys,cys>asn,asn>asn,his>asn,ile>asn,ser>asn,gln>asn,lys>asn,met>asn,pro>asn,thr>asn,phe>asn,ala>asn,gly>asn,val>asn,leu>asn,asp>asn,arg>asn,trp>asn,glu>asn,tyr>asn,cys>his,asn>his,his>his,ile>his,ser>his,gln>his,lys>his,met>his,pro>his,thr>his,phe>his,ala>his,gly>his,val>his,leu>his,asp>his,arg>his,trp>his,glu>his,tyr>his,cys>ile,asn>ile,his>ile,ile>ile,ser>ile,gln>ile,lys>ile,met>ile,pro>ile,thr>ile,phe>ile,ala>ile,gly>ile,val>ile,leu>ile,asp>ile,arg>ile,trp>ile,glu>ile,tyr>ile,cys>ser,asn>ser,his>ser,ile>ser,ser>ser,gln>ser,lys>ser,met>ser,pro>ser,thr>ser,phe>ser,ala>ser,gly>ser,val>ser,leu>ser,asp>ser,arg>ser,trp>ser,glu>ser,tyr>ser,cys>gln,asn>gln,his>gln,ile>gln,ser>gln,gln>gln,lys>gln,met>gln,pro>gln,thr>gln,phe>gln,ala>gln,gly>gln,val>gln,leu>gln,asp>gln,arg>gln,trp>gln,glu>gln,tyr>gln,cys>lys,asn>lys,his>lys,ile>lys,ser>lys,gln>lys,lys>lys,met>lys,pro>lys,thr>lys,phe>lys,ala>lys,gly>lys,val>lys,leu>lys,asp>lys,arg>lys,trp>lys,glu>lys,tyr>lys,cys>met,asn>met,his>met,ile>met,ser>met,gln>met,lys>met,met>met,pro>met,thr>met,phe>met,ala>met,gly>met,val>met,leu>met,asp>met,arg>met,trp>met,glu>met,tyr>met,cys>pro,asn>pro,his>pro,ile>pro,ser>pro,gln>pro,lys>pro,met>pro,pro>pro,thr>pro,phe>pro,ala>pro,gly>pro,val>pro,leu>pro,asp>pro,arg>pro,trp>pro,glu>pro,tyr>pro,cys>thr,asn>thr,his>thr,ile>thr,ser>thr,gln>thr,lys>thr,met>thr,pro>thr,thr>thr,phe>thr,ala>thr,gly>thr,val>thr,leu>thr,asp>thr,arg>thr,trp>thr,glu>thr,tyr>thr,cys>phe,asn>phe,his>phe,ile>phe,ser>phe,gln>phe,lys>phe,met>phe,pro>phe,thr>phe,phe>phe,ala>phe,gly>phe,val>phe,leu>phe,asp>phe,arg>phe,trp>phe,glu>phe,tyr>phe,cys>ala,asn>ala,his>ala,ile>ala,ser>ala,gln>ala,lys>ala,met>ala,pro>ala,thr>ala,phe>ala,ala>ala,gly>ala,val>ala,leu>ala,asp>ala,arg>ala,trp>ala,glu>ala,tyr>ala,cys>gly,asn>gly,his>gly,ile>gly,ser>gly,gln>gly,lys>gly,met>gly,pro>gly,thr>gly,phe>gly,ala>gly,gly>gly,val>gly,leu>gly,asp>gly,arg>gly,trp>gly,glu>gly,tyr>gly,cys>val,asn>val,his>val,ile>val,ser>val,gln>val,lys>val,met>val,pro>val,thr>val,phe>val,ala>val,gly>val,val>val,leu>val,asp>val,arg>val,trp>val,glu>val,tyr>val,cys>leu,asn>leu,his>leu,ile>leu,ser>leu,gln>leu,lys>leu,met>leu,pro>leu,thr>leu,phe>leu,ala>leu,gly>leu,val>leu,leu>leu,asp>leu,arg>leu,trp>leu,glu>leu,tyr>leu,cys>asp,asn>asp,his>asp,ile>asp,ser>asp,gln>asp,lys>asp,met>asp,pro>asp,thr>asp,phe>asp,ala>asp,gly>asp,val>asp,leu>asp,asp>asp,arg>asp,trp>asp,glu>asp,tyr>asp,cys>arg,asn>arg,his>arg,ile>arg,ser>arg,gln>arg,lys>arg,met>arg,pro>arg,thr>arg,phe>arg,ala>arg,gly>arg,val>arg,leu>arg,asp>arg,arg>arg,trp>arg,glu>arg,tyr>arg,cys>trp,asn>trp,his>trp,ile>trp,ser>trp,gln>trp,lys>trp,met>trp,pro>trp,thr>trp,phe>trp,ala>trp,gly>trp,val>trp,leu>trp,asp>trp,arg>trp,trp>trp,glu>trp,tyr>trp,cys>glu,asn>glu,his>glu,ile>glu,ser>glu,gln>glu,lys>glu,met>glu,pro>glu,thr>glu,phe>glu,ala>glu,gly>glu,val>glu,leu>glu,asp>glu,arg>glu,trp>glu,glu>glu,tyr>glu,cys>tyr,asn>tyr,his>tyr,ile>tyr,ser>tyr,gln>tyr,lys>tyr,met>tyr,pro>tyr,thr>tyr,phe>tyr,ala>tyr,gly>tyr,val>tyr,leu>tyr,asp>tyr,arg>tyr,trp>tyr,glu>tyr,tyr>tyr\n"
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
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diff changeset
457 column_index_aatypes_transitions = "Species,aromatics>aromatics,polar>aromatics,unpolar>aromatics,charged>aromatics,aromatics>polar,polar>polar,unpolar>polar,charged>polar,aromatics>unpolar,polar>unpolar,unpolar>unpolar,charged>unpolar,aromatics>charged,polar>charged,unpolar>charged,charged>charged\n"
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
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diff changeset
458
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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diff changeset
459 aa_transitions.write(column_index_aa_transitions)
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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diff changeset
460 aatypes_transitions.write(column_index_aatypes_transitions)
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
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diff changeset
461
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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diff changeset
462 PATH = sys.argv[1]
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
463 length=1000
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
464 iterration=100
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diff changeset
465 background=0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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466 speciesboot=['all']
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467 stringcounts=[' ']
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
468 stringbiases=[' ']
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diff changeset
469 towrite=1
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
470
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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471 code={'phe':['ttt','ttc'],'leu':['tta','ttg','ctt','ctc','cta','ctg'],'ile':['att','atc','ata'],'met':['atg'],'val':['gtt','gtc','gta','gtg'],'ser':['tct','tcc','tca','tcg','agt','agc'],'pro':['cct','cca','ccg','ccc'],'thr':['act','acc','aca','acg'],'ala':['gct','gcc','gca','gcg'],'tyr':['tat','tac'],'his':['cat','cac'],'gln':['caa','cag'],'asn':['aat','aac'],'lys':['aaa','aag'],'asp':['gat','gac'],'glu':['gaa','gag'],'cys':['tgt','tgc'],'trp':['tgg'],'arg':['cgt','cgc','cga','cgg','aga','agg'],'gly':['ggt','ggc','gga','ggg']}
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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472 classif={'unpolar':['gly','ala','val','leu','met','ile'],'polar':['ser','thr','cys','pro','asn','gln'],'charged':['lys','arg','his','asp','glu'],'aromatics':['phe','tyr','trp']}
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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diff changeset
473
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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474 reversecode={v:k for k in code for v in code[k]}
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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475 reverseclassif={v:k for k in classif for v in classif[k]}
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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476
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
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diff changeset
477 # --------------------------------------------------------------
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
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diff changeset
478
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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479 pairs=open("pairs.txt","r") #finds the pairs to analyze
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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480 pairlist=[]
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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diff changeset
481 while 1:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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482 line=pairs.readline()
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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483 if not line:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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diff changeset
484 #if not lastline.startswith('#'):
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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485 #pairlist[-1][1]=string.split(lastline,' ')[1]
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
486 break
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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487 #lastline=line
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488 if not line.startswith('#'):
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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489 if not line.startswith('background:'):
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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490 if background==0:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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491 pairlist.append([string.split(line,' ')[0],string.split(line,' ')[1][:-1]])
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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492 elif background==1:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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493 pairlist.append([string.split(line,' ')[0],string.split(line,' ')[1][:-1],length,iterration,plusminus,species])
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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494 background=0
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495 else:
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496 parameters=string.split(line[:-1],': ')[1]
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497 listparameters=string.split(parameters,' ')
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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498 length=int(listparameters[0])
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diff changeset
499 iterration=int(listparameters[1])
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500 plusminus=listparameters[2]
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501 species=listparameters[3:]
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502 background=1
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503
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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504 # --------------------------------------------------------------
0
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505
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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506 concat=open(sys.argv[1],"r")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
507
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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diff changeset
508 last_iter = 1
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
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diff changeset
509 for p in pairlist: #pairs analysis
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
510 concat.seek(0)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
511 while 1:
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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diff changeset
512 # Everything lowercase
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
513 line=concat.readline()
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
514 seq=concat.readline()
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
515 if p[0] in line:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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516 seq1=seq[:-1].lower()
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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517 elif p[1] in line:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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518 seq2=seq[:-1].lower()
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diff changeset
519 if not line:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
520 break
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
521
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
522 if len(p)>2: #bootstrap simulations if the background changed
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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diff changeset
523 # Only len(pairlist[0]) > 2
0
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diff changeset
524 length=p[2]
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diff changeset
525 iterration=p[3]
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diff changeset
526 plusminus=p[4]
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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diff changeset
527 species=p[5] # ex : 'all'
0
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diff changeset
528 applause='background: '+str(length)+' '+str(iterration)+' '+str(plusminus)+' '+' '.join(species)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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529 print applause
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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530 stringcounts.append(applause+'\n\n\n')
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
531 stringbiases.append(applause+'\n\n\n')
2
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abims-sbr
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diff changeset
532 # variables below are computed on the first iteration and then used for the rest of the loop
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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diff changeset
533 codonscountboot, aacountboot, aaclassifcountboot, codonsboot, aaboot, aaclassifboot=sampling(concat,length,iterration,plusminus,species,code,classif,reversecode,reverseclassif)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
534 print str(p[0])+' vs '+str(p[1])
2
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abims-sbr
parents: 0
diff changeset
535
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
536 # -----------------------------
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
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diff changeset
537 # Mise en memoire des calculs pour les comptages par sps + Ecriture fichiers de sortie
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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diff changeset
538 codonscount, aacount, aaclassifcount, codons, aa, aaclassif, GC3, GC12, IVYWREL, EKQH, PAYRESDGM, purineload, CvP=countings(seq1,seq2,code,classif,reversecode,reverseclassif)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
539 codonscountpvalue, aacountpvalue, aaclassifcountpvalue, codonspvalue, aapvalue, aaclassifpvalue=gettables(0,reversecode,code,classif)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
540
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
541
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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diff changeset
542 for f in codons: #tests the countings and saves the pvalues
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
543 for g in codons[f]:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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diff changeset
544 codonspvalue[f][g]=testpvalue(codonsboot[f][g],codons[f][g],iterration)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
545 for f in aa:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
546 for g in aa[f]:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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diff changeset
547 aapvalue[f][g]=testpvalue(aaboot[f][g],aa[f][g],iterration)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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548 for f in aaclassif:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
549 for g in aaclassif[f]:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
550 aaclassifpvalue[f][g]=testpvalue(aaclassifboot[f][g],aaclassif[f][g],iterration)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
551
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
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diff changeset
553 for substring in stringcounts: #to not write twice the same counting with the same background
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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diff changeset
554 if (("counting of %s" % p[0]) in substring) and (applause in substring):
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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diff changeset
555 towrite=0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
556
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
557 if towrite:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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diff changeset
558 for f in codonscount:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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diff changeset
559 codonscountpvalue[f]=testpvalue(codonscountboot[f],codonscount[f],iterration)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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diff changeset
560 for f in aacount:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
561 aacountpvalue[f]=testpvalue(aacountboot[f],aacount[f],iterration)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
562 for f in aaclassifcount:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
563 aaclassifcountpvalue[f]=testpvalue(aaclassifcountboot[f],aaclassifcount[f],iterration)
2
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abims-sbr
parents: 0
diff changeset
564
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
565 ## Writing countings into separated output files ##
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
566
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
567 codons_counts.write(p[0] + ",") # Species name
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
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diff changeset
568 #codons_counts.write(",") # next cell
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
569 for value in codonscount.values()[0:-1]:
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
570 codons_counts.write(str(value) + ",") # write codons_counts line for the species
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
571 codons_counts.write(str(codonscount.values()[-1]))
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
572 codons_counts.write("\n") # next line
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
573
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
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diff changeset
574 codons_counts.write(p[0] + "_pvalue,") # Same species, but line for computed pvalues
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
575 for value in codonscountpvalue.values()[0:-1]:
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
576 codons_counts.write(str(value) + ",") # write pvalues line for the species
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
577 codons_counts.write(str(codonscountpvalue.values()[-1]))
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
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diff changeset
578 codons_counts.write("\n")
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
579
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diff changeset
580 aa_counts.write(p[0] + ",") # Same method as above
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
581 for value in aacount.values()[0:-1]:
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
582 aa_counts.write(str(value) + ",")
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
583 aa_counts.write(str(aacount.values()[-1]))
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
584 aa_counts.write("\n")
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
585
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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parents: 0
diff changeset
586 aa_counts.write(p[0] + "_pvalue,")
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
587 for value in aacountpvalue.values()[0:-1]:
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
588 aa_counts.write(str(value) + ",")
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
589 aa_counts.write(str(aacountpvalue.values()[-1]))
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
590 aa_counts.write("\n")
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
591
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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diff changeset
592 aatypes_counts.write(p[0] + ",")
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
593 for value in aaclassifcount.values()[0:-1]:
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
594 aatypes_counts.write(str(value) + ",")
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
595 aatypes_counts.write(str(aaclassifcount.values()[-1]))
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
596 aatypes_counts.write("\n")
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abims-sbr
parents: 0
diff changeset
597
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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diff changeset
598 aatypes_counts.write(p[0] + "_pvalue,")
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
599 for value in aaclassifcountpvalue.values()[0:-1]:
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
600 aatypes_counts.write(str(value) + ",")
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
601 aatypes_counts.write(str(aaclassifcountpvalue.values()[-1]))
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
602 aatypes_counts.write("\n")
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
603
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
604 gc_counts.write(p[0])
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
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diff changeset
605 gc_counts.write(",")
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
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diff changeset
606 gc_counts.write(str(GC3)+","+str(GC12)+","+str(IVYWREL)+","+str(EKQH)+","+str(PAYRESDGM)+","+str(purineload)+","+str(CvP)+"\n")
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
607
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
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diff changeset
608 """ IMPROVMENT BELOW :
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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diff changeset
609 Countings was not done on the last species of the list. It is now compute when the loop reaches the last iteration, thanks to the countings()
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
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diff changeset
610 function : it is called with a switch between the arguments 'seq1' and seq2'.
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
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diff changeset
611 """
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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diff changeset
612
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abims-sbr
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diff changeset
613 if last_iter == len(pairlist):
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
614 codonscount2, aacount2, aaclassifcount2, codons2, aa2, aaclassif2, GC3_b, GC12_b, IVYWREL_b, EKQH_b, PAYRESDGM_b, purineload_b, CvP_b=countings(seq2,seq1,code,classif,reversecode,reverseclassif)
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
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diff changeset
615 codonscountpvalue2, aacountpvalue2, aaclassifcountpvalue2, codonspvalue2, aapvalue2, aaclassifpvalue2=gettables(0,reversecode,code,classif)
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abims-sbr
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diff changeset
616
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
617 for f in codons2: #tests the countings and saves the pvalues
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
618 for g in codons2[f]:
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
619 codonspvalue2[f][g]=testpvalue(codonsboot[f][g],codons[f][g],iterration)
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
620 for f in aa2:
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
621 for g in aa2[f]:
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
622 aapvalue2[f][g]=testpvalue(aaboot[f][g],aa[f][g],iterration)
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
623 for f in aaclassif2:
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
624 for g in aaclassif2[f]:
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
625 aaclassifpvalue2[f][g]=testpvalue(aaclassifboot[f][g],aaclassif[f][g],iterration)
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
626
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
627 for f in codonscount2:
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
628 codonscountpvalue2[f]=testpvalue(codonscountboot[f],codonscount[f],iterration)
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
629 for f in aacount2:
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
630 aacountpvalue2[f]=testpvalue(aacountboot[f],aacount[f],iterration)
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
631 for f in aaclassifcount2:
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
632 aaclassifcountpvalue2[f]=testpvalue(aaclassifcountboot[f],aaclassifcount[f],iterration)
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
633
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
634 # write last line of each countings file
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
635
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
636 codons_counts.write(p[1] + ",") # second species of the couple, the last one to be written in the file
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
637 for value in codonscount2.values()[0:-1]:
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
638 codons_counts.write(str(value) + ",")
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
639 codons_counts.write(str(codonscount2.values()[-1]))
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
640 codons_counts.write("\n")
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
641
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
642 codons_counts.write(p[1] + "_pvalue,") # Same species, but line for computed pvalues
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
643 for value in codonscountpvalue2.values()[0:-1]:
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
644 codons_counts.write(str(value) + ",") # write pvalues line for the species
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
645 codons_counts.write(str(codonscountpvalue2.values()[-1]))
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
646 codons_counts.write("\n")
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
647
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
648 aa_counts.write(p[1] + ",")
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
649 for value in aacount2.values()[0:-1]:
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
650 aa_counts.write(str(value) + ",")
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
651 aa_counts.write(str(aacount2.values()[-1]))
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
652 aa_counts.write("\n")
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
653
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
654 aa_counts.write(p[1] + "_pvalue,")
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
655 for value in aacountpvalue2.values()[0:-1]:
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
656 aa_counts.write(str(value) + ",") # write pvalues line for the species
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
657 aa_counts.write(str(aacountpvalue2.values()[-1]))
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
658 aa_counts.write("\n")
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
659
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
660 aatypes_counts.write(p[1] + ",")
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
661 for value in aaclassifcount2.values()[0:-1]:
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
662 aatypes_counts.write(str(value) + ",")
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
663 aatypes_counts.write(str(aaclassifcount2.values()[-1]))
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
664 aatypes_counts.write("\n")
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
665
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
666 aatypes_counts.write(p[1] + "_pvalue,")
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
667 for value in aaclassifcountpvalue2.values()[0:-1]:
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
668 aatypes_counts.write(str(value) + ",") # write pvalues line for the species
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
669 aatypes_counts.write(str(aaclassifcountpvalue2.values()[-1]))
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
670 aatypes_counts.write("\n")
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
671
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
672 gc_counts.write(p[1])
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
673 gc_counts.write(",")
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
674 gc_counts.write(str(GC3_b)+","+str(GC12_b)+","+str(IVYWREL_b)+","+str(EKQH_b)+","+str(PAYRESDGM_b)+","+str(purineload_b)+","+str(CvP_b))
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
675
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
676 # end writing
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
677
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
678 stringcounts=stringcounts[:-1]+[''.join([stringcounts[-1],("counting of %s\n\n" % p[0])+''.join(strcountings(codonscount, aacount, aaclassifcount,codonscountpvalue,aacountpvalue,aaclassifcountpvalue,GC3,GC12,IVYWREL,EKQH,PAYRESDGM,purineload,CvP))+'\n\n'])]
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
679 else:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
680 towrite=1
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
681 # -----------------------------
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
682
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
683 stringbiases.append("mutation biases from %s to %s\n\n" % (p[1], p[0]))
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
684 stringbiases=stringbiases+strbiases(codons, aa, aaclassif,codonspvalue,aapvalue,aaclassifpvalue,aa_transitions,aatypes_transitions,p)
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
685 stringbiases.append('\n\n')
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
686 print 'done'
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
687 last_iter +=1
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
688
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
689 concat.close()
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
690
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
691 # --------------------------------------------------------------
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
692
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
693 stringcounts=''.join(stringcounts)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
694 stringbiases=''.join(stringbiases)
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
695
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
696 # results=open(os.path.dirname(PATH)+"/"+string(os.path.split(PATH)[1],' ')[0]+'_results.txt',"w")
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
697 #results=open('./codoncounting_results.txt',"w")
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
698 results1=open('./counts.txt', "w")
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
699 results1.write("%s" % stringcounts)
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
700 results1.close()
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
701 results2=open('./biases.txt', "w")
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
702 results2.write("%s" % stringbiases)
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
703 results2.close()
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
704 #results.write("%s" % stringcounts)
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
705 #results.write("\n\n")
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
706 #results.write("%s" % stringbiases)
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
707 #results.close()
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
708
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
709 codons_counts.close()
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
710 aa_counts.close()
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
711 aatypes_counts.close()
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
712 gc_counts.close()
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
713 aa_transitions.close()
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 0
diff changeset
714 aatypes_transitions.close()