Mercurial > repos > abims-sbr > mutcount

annotate scripts/S02a_codon_counting.py @ 0:78dd6454f6f0 draft

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planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
author abims-sbr
date Tue, 02 May 2017 04:20:51 -0400
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children 988467f963f0
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78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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1 #!/usr/bin/python
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3 #python codoncounting.py alignement_file
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4 #Warning!! alignement_file should always be preceded by a path, at least ./
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5 #Warning!! pairs.txt should be located in the same folder as alignement_file
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7 #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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8 #counting is then compared to empirical p-values, obtained from bootstrapped sequences obtained from a subset of sequences
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9 #the script takes as input the DNA alignment (fasta format): python codoncounting.py file_path.fasta
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10 #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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12 #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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13 #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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14 #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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15 #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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16 #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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17 #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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18 #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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19 #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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20 #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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23 #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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24 #countings are performed on each generated random alignement, thousands of alignments allow to draw a gaussian distribution of the countings
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25 #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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26 #in background: length iterration plusminus listofspecies
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27 #-> 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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28 #-> iterration is the number of alignments that will be generated (effect on the resolution of the gaussian distribution)
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29 #-> 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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30 #-> 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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31 #full example: background 5000 10000 + melanogaster elegans sapiens
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32 #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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33 #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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36 #added: also counts GC3 and IVYWREL
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37 #added: also counts GC12, CvP bias and EK/QH
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38 #added: also counts purine load and PAYRE/SDGM
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41 def viable(seqs,pos):
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42 r=0
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43 compt=0
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44 for i in range(len(seqs)):
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45 if i%2==1:
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46 if not '-' in seqs[i][pos:pos+3]:
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47 compt+=1
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48 if compt>1:
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49 r=1
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50 return r
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52 def substrcountings(table,pvalues):
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54 string=[]
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55 names=[]
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56 numbers=[]
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57 stats=['pvalues']
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58 for f in table:
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59 names.append(' %s' % f)
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60 numbers.append(' %f' % table[f])
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61 stats.append(' %f' % pvalues[f])
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62 names.append('\n')
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63 numbers.append('\n')
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64 stats.append('\n')
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65 string=names+numbers+stats
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67 return string
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69 def substrbiases(table,pvalues):
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71 string=[]
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72 names=[]
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73 numbers=[]
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74 stats=['pvalues']
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75 for f in table:
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76 for g in table[f]:
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77 names.append(' %s to %s' % (g,f))
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78 numbers.append(' %f' % table[f][g])
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79 stats.append(' %f' % pvalues[f][g])
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80 names.append('\n')
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81 numbers.append('\n')
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82 stats.append('\n')
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83 string=names+numbers+stats
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85 return string
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88 def strcountings(codons, aa, classif,codonspvalues,aapvalues,classifpvalues,GC3,GC12,IVYWREL,EKQH,PAYRESDGM,purineload,CvP):
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90 subcodons=['occurence of codons\n']+substrcountings(codons,codonspvalues)
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91 subaa=subcodons+['\noccurence of amino_acids\n']+substrcountings(aa,aapvalues)
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92 subclassif=subaa+['\noccurence of amino_acid types\n']+substrcountings(classif,classifpvalues)
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93
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94 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))]
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95
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96 return string
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97
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98
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99 def strbiases(codons, aa, classif,codonspvalues,aapvalues,classifpvalues):
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100
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101 subcodons=['codons mutations biases\n']+substrbiases(codons,codonspvalues)
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102 subaa=subcodons+['\namino acids mutation biases\n']+substrbiases(aa,aapvalues)
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103 subclassif=subaa+['\ntypes of amino_acids mutation biasecodoncountingv22.pys\n']+substrbiases(classif,classifpvalues)
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104
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105 return subclassif
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106
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107
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108 def testpvalue(bootstrap,value,iterration): #computes where the observed value is located in the expected counting distribution
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109
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110 maxval=iterration-1
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111 minval=0
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112 testval=(maxval+minval)/2
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113 while maxval-minval > 1:
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114 if value > bootstrap[testval]:
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115 minval=testval
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116 testval=(maxval+minval)/2
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117 elif value < bootstrap[testval]:
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118 maxval=testval
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119 testval=(maxval+minval)/2
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120 else:
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121 break
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122 pvalue=(testval+1)/float(iterration+1)
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123
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124 return pvalue
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125
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126
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127 def gettables(content,reversecode,code,classif): #generates the tables contening all the countings
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128
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129 if content==[]:
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130 codonscount={k:[] for k in reversecode}
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131 aacount={k:[] for k in code}
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132 aaclassifcount={k:[] for k in classif}
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133
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134 codons={}
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135 for k in reversecode:
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136 codons[k]={}
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137 for q in reversecode:
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138 codons[k][q]=[]
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139 aa={}
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140 for k in code:
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141 aa[k]={}
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142 for q in code:
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143 aa[k][q]=[]
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144 aaclassif={}
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145 for k in classif:
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146 aaclassif[k]={}
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147 for q in classif:
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148 aaclassif[k][q]=[]
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149
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150 elif content==0:
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151 codonscount={k:0 for k in reversecode}
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152 aacount={k:0 for k in code}
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153 aaclassifcount={k:0 for k in classif}
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154
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155 codons={}
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156 for k in reversecode:
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157 codons[k]={}
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158 for q in reversecode:
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159 codons[k][q]=0
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160 aa={}
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161 for k in code:
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162 aa[k]={}
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163 for q in code:
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164 aa[k][q]=0
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165 aaclassif={}
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166 for k in classif:
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167 aaclassif[k]={}
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168 for q in classif:
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169 aaclassif[k][q]=0
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170
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171 return codonscount, aacount, aaclassifcount, codons, aa, aaclassif
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172
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173
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174 def countings(seq1,seq2,code,classif,reversecode,reverseclassif):
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175 #countings actually counts occurence and mutation bias of codons, amino acids and types of amino acids
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176
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177 codonscount, aacount, aaclassifcount, codons, aa, aaclassif=gettables(0,reversecode,code,classif)
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178 codonscount2, aacount2, aaclassifcount2, _, _, _=gettables(0,reversecode,code,classif)
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179
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180 G12=0
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181 C12=0
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182 G3=0
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183 C3=0
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184 A=0
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185 T=0
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186
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187 i=0
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188 compcodons=0
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189 while i<len(seq1)-1:
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190 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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diff changeset
191 compcodons+=1
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diff changeset
192
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diff changeset
193 if (seq1[i]=='g'):
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diff changeset
194 G12+=1
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195 if (seq1[i]=='c'):
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diff changeset
196 C12+=1
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abims-sbr
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diff changeset
197 if (seq1[i+1]=='g'):
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diff changeset
198 G12+=1
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abims-sbr
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diff changeset
199 if (seq1[i+1]=='c'):
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diff changeset
200 C12+=1
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abims-sbr
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diff changeset
201 if (seq1[i+2]=='g'):
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abims-sbr
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diff changeset
202 G3+=1
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abims-sbr
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diff changeset
203 if (seq1[i+2]=='c'):
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diff changeset
204 C3+=1
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abims-sbr
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diff changeset
205
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diff changeset
206 if (seq1[i]=='a'):
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diff changeset
207 A+=1
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diff changeset
208 if (seq1[i]=='t'):
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abims-sbr
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diff changeset
209 T+=1
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diff changeset
210 if (seq1[i+1]=='a'):
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abims-sbr
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diff changeset
211 A+=1
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diff changeset
212 if (seq1[i+1]=='t'):
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diff changeset
213 T+=1
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diff changeset
214 if (seq1[i+2]=='a'):
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diff changeset
215 A+=1
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diff changeset
216 if (seq1[i+2]=='t'):
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diff changeset
217 T+=1
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218
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diff changeset
219 codonscount[seq1[i:i+3]]+=1
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diff changeset
220 aacount[reversecode[seq1[i:i+3]]]+=1
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diff changeset
221 aaclassifcount[reverseclassif[reversecode[seq1[i:i+3]]]]+=1
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diff changeset
222 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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diff changeset
223 codons[seq1[i:i+3]][seq2[i:i+3]]+=1
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diff changeset
224 codonscount2[seq2[i:i+3]]+=1
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diff changeset
225 aacount2[reversecode[seq2[i:i+3]]]+=1
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diff changeset
226 aaclassifcount2[reverseclassif[reversecode[seq2[i:i+3]]]]+=1
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diff changeset
227 i+=3
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diff changeset
228
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diff changeset
229 IVYWREL=aacount['ile']+aacount['val']+aacount['tyr']+aacount['trp']+aacount['arg']+aacount['glu']+aacount['leu']
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diff changeset
230 EKQH=(aacount['glu']+aacount['lys'])/max([float(aacount['gln']+aacount['his']),1])
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diff changeset
231 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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diff changeset
232
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diff changeset
233 for i in codons:
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diff changeset
234 for j in codons[i]:
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diff changeset
235 if not reversecode[i]==reversecode[j]:
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diff changeset
236 aa[reversecode[i]][reversecode[j]]+=codons[i][j]
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diff changeset
237
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diff changeset
238 for i in aa:
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239 for j in aa[i]:
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240 if not reverseclassif[i]==reverseclassif[j]:
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diff changeset
241 aaclassif[reverseclassif[i]][reverseclassif[j]]+=aa[i][j]
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diff changeset
242
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diff changeset
243
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244 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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245 for g in codons[f]:
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diff changeset
246 codons[f][g]=codons[f][g]/float(max([codonscount2[g],1]))
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247 for f in aa:
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248 for g in aa[f]:
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249 aa[f][g]=aa[f][g]/float(max([aacount2[g],1]))
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250 for f in aaclassif:
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251 for g in aaclassif[f]:
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252 aaclassif[f][g]=aaclassif[f][g]/float(max([aaclassifcount2[g],1]))
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253 for f in codonscount: #occurences are normalized by the total number of non ambiguous codons in the sequence
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254 codonscount[f]=codonscount[f]/float(compcodons)
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255 for f in aacount:
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diff changeset
256 aacount[f]=aacount[f]/float(compcodons)
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257 for f in aaclassifcount:
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258 aaclassifcount[f]=aaclassifcount[f]/float(compcodons)
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diff changeset
259
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260 for f in codons:
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diff changeset
261 for g in codons[f]:
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262 if f==g:
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diff changeset
263 break
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264 if (codons[g][f]==0) and (codons[f][g])>0:
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diff changeset
265 codons[f][g]=1
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diff changeset
266 elif (codons[g][f]==0) and (codons[f][g])==0:
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diff changeset
267 codons[f][g]=0
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diff changeset
268 else:
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diff changeset
269 x=codons[f][g]/codons[g][f]
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diff changeset
270 codons[f][g]=-pow(2,1-x)+1
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diff changeset
271
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272 for f in aa:
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273 for g in aa[f]:
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274 if f==g:
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diff changeset
275 break
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276 if (aa[g][f]==0) and (aa[f][g])>0:
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diff changeset
277 aa[f][g]=1
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278 elif (aa[g][f]==0) and (aa[f][g])==0:
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diff changeset
279 aa[f][g]=0
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diff changeset
280 else:
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diff changeset
281 x=aa[f][g]/aa[g][f]
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diff changeset
282 aa[f][g]=-pow(2,1-x)+1
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diff changeset
283
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284 for f in aaclassif:
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285 for g in aaclassif[f]:
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286 if f==g:
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287 break
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288 if (aaclassif[g][f]==0) and (aaclassif[f][g])>0:
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289 aaclassif[f][g]=1
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290 elif (aaclassif[g][f]==0) and (aaclassif[f][g])==0:
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291 aaclassif[f][g]=0
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292 else:
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293 x=aaclassif[f][g]/aaclassif[g][f]
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294 aaclassif[f][g]=-pow(2,1-x)+1
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295
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296 GC3=(G3+C3)/float(compcodons)
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297 GC12=(G12+C12)/float(2*compcodons)
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298 purineload=(1000*(G12+G3+A-C12-C3-T))/float(3*compcodons)
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299 IVYWREL=IVYWREL/float(compcodons)
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300 CvP=aaclassifcount['charged']-aaclassifcount['polar']
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301
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302
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303 return codonscount, aacount, aaclassifcount, codons, aa, aaclassif, GC3, GC12, IVYWREL, EKQH, PAYRESDGM, purineload, CvP
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304
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305
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306 def sampling(inputfile,length,iterration,plusminus,species,code,classif,reversecode,reverseclassif):
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307 #sampling provides 'iterations' pairs of sequences of 'length' non ambiguous codons obtained from the dataset specified by 'species' and 'plusminus'
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308 #sort of bootstrap
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309
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310 codonscount, aacount, aaclassifcount, codons, aa, aaclassif=gettables([],reversecode,code,classif)
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311
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312 inputfile.seek(0) #generates the bootstrapped sequences
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313 lines=[]
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314 comp=-1
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315 if species==['all']:
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316 while 1:
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317 line=inputfile.readline()[:-1]
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318 if not line:
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319 break
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diff changeset
320 lines.append(line)
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321 comp+=1
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322 else:
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323 if plusminus=='+':
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324 while 1:
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325 line1=inputfile.readline()[:-1]
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326 if not line1:
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327 break
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328 line2=inputfile.readline()[:-1]
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329 if any(spe in line1 for spe in species):
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330 lines.append(line1)
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diff changeset
331 lines.append(line2)
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332 comp+=2
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333 elif plusminus=='-':
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334 while 1:
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335 line1=inputfile.readline()[:-1]
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336 if not line1:
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337 break
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338 line2=inputfile.readline()[:-1]
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339 if not any(spe in line1 for spe in species):
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340 lines.append(line1)
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341 lines.append(line2)
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342 comp+=2
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343 l=len(lines[1])-1
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344
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345 for z in range(iterration):
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346 if z%(iterration/10)==0:
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347 print str(10*z/(iterration/10))+' %'
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348 seqa=[]
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diff changeset
349 seqb=[]
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350 for i in range(length):
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351 site=random.randrange(0,l,3)
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352 while viable(lines,site)==0:
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353 site=random.randrange(0,l,3)
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diff changeset
354 a='---'
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355 b='---'
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356 while ('-' in a) or ('-' in b):
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diff changeset
357 posa=2
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358 posb=2
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359 while posa==posb:
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360 posa=random.randrange(1,comp+1,2)
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361 posb=random.randrange(1,comp+1,2)
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diff changeset
362 a=lines[posa][site:site+3]
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363 b=lines[posb][site:site+3]
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364 seqa.append(a)
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365 seqb.append(b)
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366 seqa=(''.join(seqa)).lower()
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367 seqb=(''.join(seqb)).lower()
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368
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diff changeset
369 codonscounttemp, aacounttemp, aaclassifcounttemp, codonstemp, aatemp, aaclassiftemp, _, _, _, _, _, _, _=countings(seqa,seqb,code,classif,reversecode,reverseclassif)
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370 for f in codonscount:
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371 codonscount[f].append(codonscounttemp[f])
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372 for f in aacount:
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373 aacount[f].append(aacounttemp[f])
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374 for f in aaclassifcount:
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diff changeset
375 aaclassifcount[f].append(aaclassifcounttemp[f])
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376 for f in codons:
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377 for g in codons[f]:
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diff changeset
378 codons[f][g].append(codonstemp[f][g])
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diff changeset
379 for f in aa:
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diff changeset
380 for g in aa[f]:
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381 aa[f][g].append(aatemp[f][g])
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382 for f in aaclassif:
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diff changeset
383 for g in aaclassif[f]:
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parents:
diff changeset
384 aaclassif[f][g].append(aaclassiftemp[f][g]) #counts the occurences and mutation biases for each the bootstrapped sequence
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abims-sbr
parents:
diff changeset
385
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diff changeset
386 print '100 %'
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abims-sbr
parents:
diff changeset
387
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
388 for f in codonscount:
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diff changeset
389 codonscount[f].sort()
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abims-sbr
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diff changeset
390 for f in aacount:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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diff changeset
391 aacount[f].sort()
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abims-sbr
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diff changeset
392 for f in aaclassifcount:
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abims-sbr
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diff changeset
393 aaclassifcount[f].sort()
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394 for f in codons:
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abims-sbr
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diff changeset
395 for g in codons[f]:
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diff changeset
396 codons[f][g].sort()
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abims-sbr
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diff changeset
397 for f in aa:
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abims-sbr
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diff changeset
398 for g in aa[f]:
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abims-sbr
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diff changeset
399 aa[f][g].sort()
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abims-sbr
parents:
diff changeset
400 for f in aaclassif:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
401 for g in aaclassif[f]:
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abims-sbr
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diff changeset
402 aaclassif[f][g].sort()
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abims-sbr
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diff changeset
403
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diff changeset
404 return codonscount, aacount, aaclassifcount, codons, aa, aaclassif
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abims-sbr
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diff changeset
405
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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diff changeset
406 ################
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abims-sbr
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diff changeset
407 ######RUN#######
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diff changeset
408 ################
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parents:
diff changeset
409
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diff changeset
410 import string, os, sys, re, random
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diff changeset
411 from math import pow
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412 PATH = sys.argv[1]
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diff changeset
413 length=1000
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diff changeset
414 iterration=100
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diff changeset
415 background=0
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diff changeset
416 speciesboot=['all']
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diff changeset
417 stringcounts=[' ']
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diff changeset
418 stringbiases=[' ']
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419 towrite=1
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diff changeset
420
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diff changeset
421 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']}
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diff changeset
422 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']}
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parents:
diff changeset
423
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diff changeset
424 reversecode={v:k for k in code for v in code[k]}
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diff changeset
425 reverseclassif={v:k for k in classif for v in classif[k]}
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abims-sbr
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diff changeset
426
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diff changeset
427 pairs=open("pairs.txt","r") #finds the pairs to analyze
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diff changeset
428 pairlist=[]
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abims-sbr
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diff changeset
429 while 1:
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diff changeset
430 line=pairs.readline()
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abims-sbr
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diff changeset
431 if not line:
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abims-sbr
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diff changeset
432 #if not lastline.startswith('#'):
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diff changeset
433 #pairlist[-1][1]=string.split(lastline,' ')[1]
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diff changeset
434 break
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diff changeset
435 #lastline=line
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abims-sbr
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diff changeset
436 if not line.startswith('#'):
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
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diff changeset
437 if not line.startswith('background:'):
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abims-sbr
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diff changeset
438 if background==0:
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diff changeset
439 pairlist.append([string.split(line,' ')[0],string.split(line,' ')[1][:-1]])
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abims-sbr
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diff changeset
440 elif background==1:
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diff changeset
441 pairlist.append([string.split(line,' ')[0],string.split(line,' ')[1][:-1],length,iterration,plusminus,species])
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diff changeset
442 background=0
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diff changeset
443 else:
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diff changeset
444 parameters=string.split(line[:-1],': ')[1]
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diff changeset
445 listparameters=string.split(parameters,' ')
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diff changeset
446 length=int(listparameters[0])
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diff changeset
447 iterration=int(listparameters[1])
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diff changeset
448 plusminus=listparameters[2]
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diff changeset
449 species=listparameters[3:]
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diff changeset
450 background=1
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diff changeset
451
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diff changeset
452
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diff changeset
453 concat=open(sys.argv[1],"r")
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diff changeset
454
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diff changeset
455 for p in pairlist: #pairs analysis
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diff changeset
456 concat.seek(0)
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diff changeset
457 while 1:
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diff changeset
458 line=concat.readline()
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diff changeset
459 seq=concat.readline()
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abims-sbr
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diff changeset
460 if p[0] in line:
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diff changeset
461 seq1=seq[:-1].lower()
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diff changeset
462 elif p[1] in line:
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abims-sbr
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diff changeset
463 seq2=seq[:-1].lower()
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diff changeset
464 if not line:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
465 break
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abims-sbr
parents:
diff changeset
466
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
467 if len(p)>2: #bootstrap simulations if the background changed
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diff changeset
468 length=p[2]
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diff changeset
469 iterration=p[3]
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diff changeset
470 plusminus=p[4]
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diff changeset
471 species=p[5]
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diff changeset
472 applause='background: '+str(length)+' '+str(iterration)+' '+str(plusminus)+' '+' '.join(species)
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abims-sbr
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diff changeset
473 print applause
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abims-sbr
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diff changeset
474 stringcounts.append(applause+'\n\n\n')
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parents:
diff changeset
475 stringbiases.append(applause+'\n\n\n')
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
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diff changeset
476 codonscountboot, aacountboot, aaclassifcountboot, codonsboot, aaboot, aaclassifboot=sampling(concat,length,iterration,plusminus,species,code,classif,reversecode,reverseclassif)
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diff changeset
477 print str(p[0])+' vs '+str(p[1])
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
478 codonscount, aacount, aaclassifcount, codons, aa, aaclassif, GC3, GC12, IVYWREL, EKQH, PAYRESDGM, purineload, CvP=countings(seq1,seq2,code,classif,reversecode,reverseclassif)
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479 codonscountpvalue, aacountpvalue, aaclassifcountpvalue, codonspvalue, aapvalue, aaclassifpvalue=gettables(0,reversecode,code,classif)
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480
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481
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482 for f in codons: #tests the countings and saves the pvalues
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483 for g in codons[f]:
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484 codonspvalue[f][g]=testpvalue(codonsboot[f][g],codons[f][g],iterration)
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485 for f in aa:
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486 for g in aa[f]:
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487 aapvalue[f][g]=testpvalue(aaboot[f][g],aa[f][g],iterration)
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488 for f in aaclassif:
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489 for g in aaclassif[f]:
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490 aaclassifpvalue[f][g]=testpvalue(aaclassifboot[f][g],aaclassif[f][g],iterration)
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491
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492
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493 for substring in stringcounts: #to not write twice the same counting with the same background
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494 if (("counting of %s" % p[0]) in substring) and (applause in substring):
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495 towrite=0
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496
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497 if towrite:
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498 for f in codonscount:
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499 codonscountpvalue[f]=testpvalue(codonscountboot[f],codonscount[f],iterration)
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500 for f in aacount:
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501 aacountpvalue[f]=testpvalue(aacountboot[f],aacount[f],iterration)
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502 for f in aaclassifcount:
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503 aaclassifcountpvalue[f]=testpvalue(aaclassifcountboot[f],aaclassifcount[f],iterration)
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504
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505 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'])]
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506 else:
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507 towrite=1
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508
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509 stringbiases.append("mutation biases from %s to %s\n\n" % (p[1], p[0]))
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510 stringbiases=stringbiases+strbiases(codons, aa, aaclassif,codonspvalue,aapvalue,aaclassifpvalue)
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511 stringbiases.append('\n\n')
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512 print 'done'
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513
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514 concat.close()
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515
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516 stringcounts=''.join(stringcounts)
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517 stringbiases=''.join(stringbiases)
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518 # results=open(os.path.dirname(PATH)+"/"+string(os.path.split(PATH)[1],' ')[0]+'_results.txt',"w")
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519 results=open('./codoncounting_results.txt',"w")
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520 results.write("%s" % stringcounts)
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521 results.write("\n\n")
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522 results.write("%s" % stringbiases)
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523 results.close()
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524
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525