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1 #!/bin/bash
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2
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3 #########################################
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4 ### SPECIFY THE NUMBER OF CPU ###
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5 #########################################
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4
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6 cpu=8
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0
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7
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8
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9
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10
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11
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12 #########################################
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13 ### Recover the arguments ###
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14 #########################################
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15 html=$1;shift
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16 len_file_path=$1;shift
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17 estimSign=$1;shift
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18 parameters=$1;shift
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19 working_dir=`pwd`
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20
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21
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22
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23 mkdir in
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24 cd in
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25
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26 names=$(sed 's/\s/_/g' <<< $*)
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27 names=$(sed 's/_\// \//g' <<< $names)
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28 names=$(sed 's/_annotated//g' <<< $names)
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29 names=$(sed 's/_filtered//g' <<< $names)
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30 names=$(sed 's/\.txt_/_/' <<< $names)
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31
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32 for name in ${names}
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33 do
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34 file=$(sed 's/=/ /' <<< $name);
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35 echo $file
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36 ln -s $file
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37 done
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38 cd ..
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39
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40 output_dir=${html%%.*}_files
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41
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42
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43 #########################################
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44 ### Calculates the statistics ###
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45 #########################################
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46
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47 perl $SCRIPT_PATH/mutspecStat.pl --outfile $output_dir \
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48 --temp "$working_dir/temp" \
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49 --pathRscript $SCRIPT_PATH \
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50 $parameters \
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51 $working_dir/in
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52
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53
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54 #########################################
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55 ### Estimate the number of signatures ###
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56 #########################################
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57 if [[ $estimSign > 0 ]]; then
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58 Rscript $SCRIPT_PATH/R/estimateSign_Galaxy.r --input $output_dir/Mutational_Analysis/Figures/Input_NMF/Input_NMF_Count.txt --stop $estimSign --cpu $cpu --output $output_dir/Mutational_Analysis/Figures/Estimate_Number_Signatures.png 2>&1
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59 fi
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60
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61
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62 #########################################
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63 ### Create css #
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64 #########################################
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65 css=$output_dir/Mutational_Analysis/style.css
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66 echo ".legend{position:relative}.legend .legend-hidden{display:none;position:absolute;background-color:#fff;border:3px solid #03F;padding:3px;color:#000;font-size:1em;border-radius:10px;margin-top:-40px}.legend:hover .legend-hidden{display:block}" > $css
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67
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68
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69
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70 # HMTL page for the result of the tool
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71 echo "<html>" >> $html
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72 echo "<body>" >> $html
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73
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74 if [ -d $output_dir/Mutational_Analysis/Figures ]; then
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75
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76 echo "<center> <h2>Mutational spectra report summary</h2> </center>" >> $html
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77
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78 echo "<br/> Download the full report in Excel" >> $html
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79
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80 ## One report with all the samples. Specify the full path
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81 if [[ -e "$output_dir/Mutational_Analysis/Report_Mutation_Spectra.xls" ]]
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82 then
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83 # Interpreted by Galaxy so don't need the full path
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84 echo "<br/><a href="Mutational_Analysis/Report_Mutation_Spectra.xls">Report_Mutation_Spectra.xls</a>" >> $html
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85 fi
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86 ## One report for each samples
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87 for file in $names
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88 do
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89 name=$(echo ${file}| cut -d"=" -f2)
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90 name=${name%.*}
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91
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92 # One report for each samples
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93 if [[ -e "$output_dir/Mutational_Analysis/Report_Mutation_Spectra-$name.xls" ]]
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94 then
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95 echo "<br/><a href="Mutational_Analysis/Report_Mutation_Spectra-$name.xls">Report_Mutation_Spectra-$name.xls</a>" >> $html
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96 fi
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97 done
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98 ## One report for each samples: Pool_Data
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99 if [[ $parameters =~ "--pooldata" ]]; then
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100 if [[ -e "$output_dir/Mutational_Analysis/Report_Mutation_Spectra-Pool_Data.xls" ]]; then
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101 echo "<br/><a href="Mutational_Analysis/Report_Mutation_Spectra-Pool_Data.xls">Report_Mutation_Spectra-Pool_Data.xls</a>" >> $html
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102 fi
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103 fi
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104
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105
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106 ## Input file for NMF
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107 if [[ -e "$output_dir/Mutational_Analysis/Figures/Input_NMF/Input_NMF_Count.txt" ]]
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108 then
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109 # Interpreted by Galaxy so don't need the full path
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110 echo "<br/><br/> Download the input file for the tool mutSpec-NMF" >> $html
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111 echo "<br/><a href="Mutational_Analysis/Figures/Input_NMF/Input_NMF_Count.txt">Input_NMF_Count.txt</a><br/>" >> $html
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112 fi
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113
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114 ## Computed statistics for estimating the number of signatures
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115 if [[ $estimSign > 0 ]]; then
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116 echo "<br/> Link to the computed statistics for estimating the number of signatures <br/>" >> $html
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117 if [[ -e "$output_dir/Mutational_Analysis/Figures/Estimate_Number_Signatures.png" ]]; then
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118 outEstimateSign="$output_dir/Mutational_Analysis/EstimatingSignatures.html"
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119 touch $outEstimateSign
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120 echo "<a href='Mutational_Analysis/EstimatingSignatures.html'>Estimating the number of signatures</a><br/>" >> $html
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121 echo "<br/> <center> <h2>Computed statistics for estimating the number of signatures</h2> </center> <br/>" >> $outEstimateSign
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122 echo "Several approaches have been proposed to choose the optimal number of signatures to extract with NMF. <br/>
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123 Brunet et al. 2004, proposed to take the first number of signature for which the cophenetic coefficient starts decreasing, <br/>
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4
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124 Hutchins et al. 2008, suggested to choose the first value where the RSS curve presents an inflection point. <br/>
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125 Frigyesi et al. 2008, considered the smallest value at which the decrease in the RSS is lower than the decrease of the RSS obtained from random data. <br/><br/>
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126 The estimation are based on Brunet’s algorithm computed from 50 runs for each value of signature to estimate. <br/> <br/>
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127 The original data are shuffled for comparing the quality measures obtained with our data (Data x) and from randomized data (Data y). The curves for the actual data are in solid line, those for the randomized data are in dashed line. <br/> <br/>" >> $outEstimateSign
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128 echo "<img src="Figures/Estimate_Number_Signatures.png width="1000""/><br/></td>" >> $outEstimateSign
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129 else
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130 echo "<br/>There is not enough mutations for estimating the number of signatures <br/>" >> $html
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131 echo "Read the tool standard output for more detail<br/>" >> $html
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132 fi
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133 fi
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134
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135
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136 ## HMTL Link to the samples
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137 echo "<br/> Link to individual samples <br/>" >> $html
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138 for file in $names
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139 do
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140 name=$(echo ${file}| cut -d"=" -f2)
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141 name=${name%.*}
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142 outfile="$output_dir/Mutational_Analysis/$name.html"
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143 touch $outfile # Create an empty file named $outfile
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144 echo "<a href='Mutational_Analysis/$name.html'>$name</a><br/>" >> $html
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145
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146 #-------------------------------------------------------------------------------------------------------------------------------------------------------------------------#
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147 # INDIVIDUAL SAMPLES #
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148 #-------------------------------------------------------------------------------------------------------------------------------------------------------------------------#
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149 echo "<br/> <center> <h2>Mutational Spectra report for $name</h2> </center> <br/>" >> $outfile
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150
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151 echo "<html>" >> $outfile
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152
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153 echo "<head>" >> $outfile
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154 echo "<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">" >> $outfile
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155 # Link to the css style file for having a legend when we pass the mouse on the figures
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156 echo "<link rel="stylesheet" href="style.css" />" >> $outfile
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157 echo "</head>" >> $outfile
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158
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159 echo "<body>" >> $outfile
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160
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161 echo "<table>" >> $outfile
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162 echo "<tr>" >> $outfile
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163 echo "<th><h3>Overall mutation distribution</h3></th>" >> $outfile
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164 echo "<th><h3>Impact on protein sequence</h3></th>" >> $outfile
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165 echo "</tr><tr>" >> $outfile
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166 echo "<td> <center> <a href="Figures/Overall_mutation_distribution/$name/$name-OverallMutationDistribution.txt">$name-OverallMutationDistribution.txt</a> </center> </td>" >> $outfile
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167 echo "<td> <center> <a href="Figures/Impact_protein_sequence/$name/$name-DistributionExoFunc.txt">$name-DistributionExoFunc.txt</a> </center> </td>" >> $outfile
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168 echo "</tr><tr>" >> $outfile
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169
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170 echo "<td>" >> $outfile
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171 echo "<span class="legend"><img src="Figures/Overall_mutation_distribution/$name/$name-OverallMutationDistribution.png width="280""/>" >> $outfile
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172 echo "<span class="legend-hidden">" >> $outfile
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173 echo "<center><B>Overall Mutation Distribution</center></B><br/>Proportion of all mutation types (total count are indicated in parenthesis). For indels the counts are based on annotation retrieved from the database ExonicFunc.refGene<br/>" >> $outfile
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174 echo "</td>" >> $outfile
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175 echo "<td>" >> $outfile
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176 echo "<span class="legend"><img src="Figures/Impact_protein_sequence/$name/$name-DistributionExoFunc.png width="400""/>" >> $outfile
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177 echo "<span class="legend-hidden">" >> $outfile
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178 echo "<center><B>Graph 1. Impact on protein sequence</center></B><br/>Impact of all mutations (SBS and Indel) on the protein sequence based on the ExonicFunc.refGene annotation<br/>" >> $outfile
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179 echo "</td>" >> $outfile
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180
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181 echo "</tr>" >> $outfile
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182 echo "</table>" >> $outfile
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183
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184 echo "<br/><br/>" >> $outfile
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185
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186
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187 echo "<table>" >> $outfile
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188 echo "<tr>" >> $outfile
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189 echo "<th><h3>SBS distribution</h3></th>" >> $outfile
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190 echo "<th><h3>Stranded distribution of SBS</h3></th>" >> $outfile
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191 echo "</tr><tr>" >> $outfile
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192 echo "<td> <center> <a href="Figures/SBS_distribution/$name/$name-SBS_distribution.txt">$name-SBS_distribution.txt</a> </center> </td>" >> $outfile
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193 echo "<td> <center> <a href="Figures/Stranded_Analysis/$name/$name-StrandBias.txt">$name-StrandBias.txt</a> </center> </td>" >> $outfile
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194 echo "</tr><tr>" >> $outfile
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195
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196 echo "<td>" >> $outfile
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197 echo "<span class="legend"><img src="Figures/SBS_distribution/$name/$name-SBS_distribution.png width="550""/>" >> $outfile
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198 echo "<span class="legend-hidden">" >> $outfile
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199 echo "<center><B>Graph 2. SBS distribution</center></B><br/>Proportion of each type of single base substitution (SBS)<br/>" >> $outfile
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200 echo "</td>" >> $outfile
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201 echo "<td>" >> $outfile
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202 echo "<span class="legend"><img src="Figures/Stranded_Analysis/$name/$name-StrandBias.png width="400""/>" >> $outfile
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203 echo "<span class="legend-hidden">" >> $outfile
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204 echo "<center><B>Graph 3. Stranded distribution of SBS</center></B><br/>Count of the six substitution types on the transcribed and non-transcribed strand<br/>" >> $outfile
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205 echo "</td>" >> $outfile
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206
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207 echo "</tr>" >> $outfile
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208 echo "</table>" >> $outfile
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209
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210
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211 echo "<br/><br/>" >> $outfile
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212
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213
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214 ######################################################
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215 # Trinucleotide sequence context of SBS on genomic #
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216 ######################################################
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217 echo "<table>" >> $outfile
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218 echo "<h3>Trinucleotide sequence context of SBS on the genomic sequence</h3>" >> $outfile
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219 echo "<tr>" >> $outfile
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220 echo "<td> <center> <a href="Figures/Trinucleotide_Sequence_Context/$name/$name-MutationSpectraPercent-Genomic.txt">$name-MutationSpectraPercent.txt</a> </center> </td>" >> $outfile
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221 echo "<td> <center> <a href="Figures/Trinucleotide_Sequence_Context/$name/$name-HeatmapPercent-Genomic.txt">$name-HeatmapPercent-Genomic.txt</a> </center> </td>" >> $outfile
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222 echo "</tr><tr>" >> $outfile
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223
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224 echo "<td>" >> $outfile
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225 echo "<span class="legend"><img src="Figures/Trinucleotide_Sequence_Context/$name/$name-MutationSpectraPercent-Genomic.png width="1000""/>" >> $outfile
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226 echo "<span class="legend-hidden">" >> $outfile
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227 echo "<center><B>Panel 1. Trinucleotide sequence context of SBS on the genomic sequence</center></B><br/>Proportion of the six substitution types with their trinucleotide sequence context (total number of mutation is shown in parenthesis)<br/>" >> $outfile
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228 echo "</td>" >> $outfile
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229 echo "<td>" >> $outfile
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230 echo "<span class="legend"><img src="Figures/Trinucleotide_Sequence_Context/$name/$name-HeatmapPercent-Genomic.png width="250""/>" >> $outfile
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231 echo "<span class="legend-hidden">" >> $outfile
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232 echo "<center><B>Panel 1. Trinucleotide sequence context of SBS on the genomic sequence</center></B><br/>Proportion of the six substitution types with their trinucleotide sequence context<br/>" >> $outfile
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233 echo "</td>" >> $outfile
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234
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235 echo "</tr>" >> $outfile
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236 echo "</table>" >> $outfile
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237
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238
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239 echo "<br/><br/>" >> $outfile
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240
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241
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242 ##############################################################
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243 # Trinucleotide sequence context of SBS on coding sequence #
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244 ##############################################################
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245 echo "<table>" >> $outfile
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246 echo "<h3>Stranded analysis of trinucleotide sequence context of SBS</h3>" >> $outfile
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247 echo "<tr>" >> $outfile
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248 echo "<td> <center> <a href="Figures/Stranded_Analysis/$name/$name-StrandedSignaturePercent.txt">$name-StrandedSignaturePercent.txt</a> </center> </td>" >> $outfile
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249 echo "</tr><tr>" >> $outfile
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250
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251 echo "<td>" >> $outfile
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252 echo "<span class="legend"><img src="Figures/Stranded_Analysis/$name/$name-StrandedSignaturePercent.png width="1300""/>" >> $outfile
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253 echo "<span class="legend-hidden">" >> $outfile
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254 echo "<center><B>Panel 2. Stranded analysis of trinucleotide sequence context of SBS</center></B><br/>Proportion of SBS with their trinucleotide context considering the non-transcribed and transcribed strand<br/>" >> $outfile
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255 echo "</td>" >> $outfile
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256 echo "</tr>" >> $outfile
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257 echo "</table>" >> $outfile
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258
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259 echo "<br/><br/>" >> $outfile
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260
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261
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262 #############################################
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263 # Sequence logo generated with Weblogo3 #
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264 #############################################
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265 echo "<table>" >> $outfile
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266 echo "<h3>Wider sequence context with Weblogo3</h3>" >> $outfile
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267 # Legende de la figure : Panel 3. Wider sequence context on genomic strand generated with Weblogo3
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268
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269 # C>A
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270 echo "<tr>" >> $outfile
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271 if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/$name/$name-CA-Probability.png" ]]; then
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272 echo "<td>WARNING: No sequence for C>A </br> </td>" >> $outfile
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273 else
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274 echo "<td><a href="Figures/WebLogo/$name/$name-CA.fa">$name-CA.fa</a><br/>" >> $outfile
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275 echo "<img src="Figures/WebLogo/$name/$name-CA-Probability.png"/><br/></td>" >> $outfile
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276 fi
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277 # C>G
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278 if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/$name/$name-CG-Probability.png" ]]; then
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279 echo "<td> WARNING: No sequence for C>G </br> </td>" >> $outfile
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280 else
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281 echo "<td><a href="Figures/WebLogo/$name/$name-CG.fa">$name-CG.fa</a><br/>" >> $outfile
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282 echo "<img src="Figures/WebLogo/$name/$name-CG-Probability.png"/><br/></td>" >> $outfile
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283 fi
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284 # C>T
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285 if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/$name/$name-CT-Probability.png" ]]; then
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286 echo "<td> WARNING: No sequence for C>T </br> </td>" >> $outfile
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287 else
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288 echo "<td><a href="Figures/WebLogo/$name/$name-CT.fa">$name-CT.fa</a><br/>" >> $outfile
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289 echo "<img src="Figures/WebLogo/$name/$name-CT-Probability.png"/><br/></td>" >> $outfile
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290 fi
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291 echo "</tr>" >> $outfile
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292
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293 # T>A
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294 echo "<tr>" >> $outfile
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295 if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/$name/$name-TA-Probability.png" ]]; then
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296 echo "<td>WARNING: No sequence for T>A </br> </td>" >> $outfile
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297 else
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298 echo "<td><a href="Figures/WebLogo/$name/$name-TA.fa">$name-TA.fa</a><br/>" >> $outfile
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299 echo "<img src="Figures/WebLogo/$name/$name-TA-Probability.png"/><br/></td>" >> $outfile
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300 fi
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301 # T>C
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302 if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/$name/$name-TC-Probability.png" ]]; then
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303 echo "<td>WARNING: No sequence for T>C </br> </td>" >> $outfile
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304 else
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305 echo "<td><a href="Figures/WebLogo/$name/$name-TC.fa">$name-TC.fa</a><br/>" >> $outfile
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306 echo "<img src="Figures/WebLogo/$name/$name-TC-Probability.png"/><br/></td>" >> $outfile
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307 fi
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308 # T>G
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309 if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/$name/$name-TG-Probability.png" ]]; then
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310 echo "<td>WARNING: No sequence for T>G </br> </td>" >> $outfile
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311 else
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312 echo "<td><a href="Figures/WebLogo/$name/$name-TG.fa">$name-TG.fa</a><br/>" >> $outfile
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313 echo "<img src="Figures/WebLogo/$name/$name-TG-Probability.png"/><br/></td>" >> $outfile
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314 fi
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315 echo "</tr>" >> $outfile
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316
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317 echo "</table>" >> $outfile
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318
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319 echo "</body></html>" >> $outfile
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320
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321 done
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322
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323 #-------------------------------------------------------------------------------------------------------------------------------------------------------------------------#
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324 # POOL DATA #
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325 #-------------------------------------------------------------------------------------------------------------------------------------------------------------------------#
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326 ## HMTL Link to Pool_Data
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327 if [[ $parameters =~ "--pooldata" ]]; then
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328 outfilePoolData="$output_dir/Mutational_Analysis/Pool_Data.html"
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329 touch $outfilePoolData # Create an empty file named $outfile
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330 echo "<a href='Mutational_Analysis/Pool_Data.html'>Pool_Data</a><br/>" >> $html
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331
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332
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333 echo "<br/> <center> <h2>Mutational Spectra report for Pool_Data</h2> </center> <br/>" >> $outfilePoolData
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334 echo "<html>" >> $outfilePoolData
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335
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336 echo "<head>" >> $outfilePoolData
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337 echo "<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">" >> $outfilePoolData
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338 # Link to the css style file for having a legend when we pass the mouse on the figures
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339 echo "<link rel="stylesheet" href="style.css" />" >> $outfilePoolData
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340 echo "</head>" >> $outfilePoolData
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341
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342 echo "<body>" >> $outfilePoolData
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343
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344 echo "<table>" >> $outfilePoolData
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345 echo "<tr>" >> $outfilePoolData
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346 echo "<th><h3>Overall mutation distribution</h3></th>" >> $outfilePoolData
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347 echo "<th><h3>Impact on protein sequence</h3></th>" >> $outfilePoolData
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348 echo "</tr><tr>" >> $outfilePoolData
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349 echo "<td> <center> <a href="Figures/Overall_mutation_distribution/Pool_Data/Pool_Data-OverallMutationDistribution.txt">Pool_Data-OverallMutationDistribution.txt</a> </center> </td>" >> $outfilePoolData
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350 echo "<td> <center> <a href="Figures/Impact_protein_sequence/Pool_Data/Pool_Data-DistributionExoFunc.txt">Pool_Data-DistributionExoFunc.txt</a> </center> </td>" >> $outfilePoolData
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351 echo "</tr><tr>" >> $outfilePoolData
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352
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353 echo "<td>" >> $outfilePoolData
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354 echo "<span class="legend"><img src="Figures/Overall_mutation_distribution/Pool_Data/Pool_Data-OverallMutationDistribution.png width="280""/>" >> $outfilePoolData
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355 echo "<span class="legend-hidden">" >> $outfilePoolData
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356 echo "<center><B>Overall Mutation Distribution</center></B><br/>Proportion of all mutation types (total count are indicated in parenthesis). For indels the counts are based on annotation retrieved from the database ExonicFunc.refGene<br/>" >> $outfilePoolData
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357 echo "</td>" >> $outfilePoolData
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358 echo "<td>" >> $outfilePoolData
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359 echo "<span class="legend"><img src="Figures/Impact_protein_sequence/Pool_Data/Pool_Data-DistributionExoFunc.png width="400""/>" >> $outfilePoolData
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360 echo "<span class="legend-hidden">" >> $outfilePoolData
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361 echo "<center><B>Graph 1. Impact on protein sequence</center></B><br/>Impact of all mutations (SBS and Indel) on the protein sequence based on the ExonicFunc.refGene annotation<br/>" >> $outfilePoolData
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362 echo "</td>" >> $outfilePoolData
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363
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364 echo "</tr>" >> $outfilePoolData
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365 echo "</table>" >> $outfilePoolData
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366
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367 echo "<br/><br/>" >> $outfilePoolData
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368
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369
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370 echo "<table>" >> $outfilePoolData
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371 echo "<tr>" >> $outfilePoolData
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372 echo "<th><h3>SBS distribution</h3></th>" >> $outfilePoolData
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373 echo "<th><h3>Stranded distribution of SBS</h3></th>" >> $outfilePoolData
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374 echo "</tr><tr>" >> $outfilePoolData
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375 echo "<td> <center> <a href="Figures/SBS_distribution/Pool_Data/Pool_Data-SBS_distribution.txt">Pool_Data-SBS_distribution.txt</a> </center> </td>" >> $outfilePoolData
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376 echo "<td> <center> <a href="Figures/Stranded_Analysis/Pool_Data/Pool_Data-StrandBias.txt">Pool_Data-StrandBias.txt</a> </center> </td>" >> $outfilePoolData
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377 echo "</tr><tr>" >> $outfilePoolData
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378
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379 echo "<td>" >> $outfilePoolData
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380 echo "<span class="legend"><img src="Figures/SBS_distribution/Pool_Data/Pool_Data-SBS_distribution.png width="550""/>" >> $outfilePoolData
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381 echo "<span class="legend-hidden">" >> $outfilePoolData
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382 echo "<center><B>Graph 2. SBS distribution</center></B><br/>Proportion of each type of single base substitution (SBS)<br/>" >> $outfilePoolData
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383 echo "</td>" >> $outfilePoolData
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384 echo "<td>" >> $outfilePoolData
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385 echo "<span class="legend"><img src="Figures/Stranded_Analysis/Pool_Data/Pool_Data-StrandBias.png width="400""/>" >> $outfilePoolData
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386 echo "<span class="legend-hidden">" >> $outfilePoolData
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387 echo "<center><B>Graph 3. Stranded distribution of SBS</center></B><br/>Count of the six substitution types on the transcribed and non-transcribed strand<br/>" >> $outfilePoolData
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388 echo "</td>" >> $outfilePoolData
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389
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390 echo "</tr>" >> $outfilePoolData
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391 echo "</table>" >> $outfilePoolData
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392
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393
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394 echo "<br/><br/>" >> $outfilePoolData
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395
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396
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397 ##########################################################
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398 # Trinucleotide sequence context of SBS on genomic: Pool #
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399 ##########################################################
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400 echo "<table>" >> $outfilePoolData
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401 echo "<h3>Trinucleotide sequence context of SBS on the genomic sequence</h3>" >> $outfilePoolData
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402 echo "<tr>" >> $outfilePoolData
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403 echo "<td> <center> <a href="Figures/Trinucleotide_Sequence_Context/Pool_Data/Pool_Data-MutationSpectraPercent-Genomic.txt">Pool_Data-MutationSpectraPercent.txt</a> </center> </td>" >> $outfilePoolData
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404 echo "<td> <center> <a href="Figures/Trinucleotide_Sequence_Context/Pool_Data/Pool_Data-HeatmapPercent-Genomic.txt">Pool_Data-HeatmapPercent-Genomic.txt</a> </center> </td>" >> $outfilePoolData
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405 echo "</tr><tr>" >> $outfilePoolData
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406
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407 echo "<td>" >> $outfilePoolData
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408 echo "<span class="legend"><img src="Figures/Trinucleotide_Sequence_Context/Pool_Data/Pool_Data-MutationSpectraPercent-Genomic.png width="1000""/>" >> $outfilePoolData
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409 echo "<span class="legend-hidden">" >> $outfilePoolData
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410 echo "<center><B>Panel 1. Trinucleotide sequence context of SBS on the genomic sequence</center></B><br/>Proportion of the six substitution types with their trinucleotide sequence context (total number of mutation is shown in parenthesis)<br/>" >> $outfilePoolData
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411 echo "</td>" >> $outfilePoolData
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412 echo "<td>" >> $outfilePoolData
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413 echo "<span class="legend"><img src="Figures/Trinucleotide_Sequence_Context/Pool_Data/Pool_Data-HeatmapPercent-Genomic.png width="250""/>" >> $outfilePoolData
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414 echo "<span class="legend-hidden">" >> $outfilePoolData
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415 echo "<center><B>Panel 1. Trinucleotide sequence context of SBS on the genomic sequence</center></B><br/>Proportion of the six substitution types with their trinucleotide sequence context<br/>" >> $outfilePoolData
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416 echo "</td>" >> $outfilePoolData
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417
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418 echo "</tr>" >> $outfilePoolData
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419 echo "</table>" >> $outfilePoolData
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420
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421
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422 echo "<br/><br/>" >> $outfilePoolData
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423
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424
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425 ##################################################################
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426 # Trinucleotide sequence context of SBS on coding sequence: Pool #
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427 ##################################################################
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428 echo "<table>" >> $outfilePoolData
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429 echo "<h3>Stranded analysis of trinucleotide sequence context of SBS</h3>" >> $outfilePoolData
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430 echo "<tr>" >> $outfilePoolData
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431 echo "<td> <center> <a href="Figures/Stranded_Analysis/Pool_Data/Pool_Data-StrandedSignaturePercent.txt">Pool_Data-StrandedSignaturePercent.txt</a> </center> </td>" >> $outfilePoolData
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432 echo "</tr><tr>" >> $outfilePoolData
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433
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434 echo "<td>" >> $outfilePoolData
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435 echo "<span class="legend"><img src="Figures/Stranded_Analysis/Pool_Data/Pool_Data-StrandedSignaturePercent.png width="1300""/>" >> $outfilePoolData
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436 echo "<span class="legend-hidden">" >> $outfilePoolData
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437 echo "<center><B>Panel 2. Stranded analysis of trinucleotide sequence context of SBS</center></B><br/>Proportion of SBS with their trinucleotide context considering the non-transcribed and transcribed strand<br/>" >> $outfilePoolData
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438 echo "</td>" >> $outfilePoolData
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439 echo "</tr>" >> $outfilePoolData
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440 echo "</table>" >> $outfilePoolData
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441
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442 echo "<br/><br/>" >> $outfilePoolData
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443
|
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444 #####################################################
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445 # Sequence logo generated with Weblogo3: Pool #
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446 #####################################################
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447 echo "<table>" >> $outfilePoolData
|
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448 echo "<h3>Sequence logo generated with Weblogo3</h3>" >> $outfilePoolData
|
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449 # C>A
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450 echo "<tr>" >> $outfilePoolData
|
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451 if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/Pool_Data/Pool_Data-CA-Probability.png" ]]; then
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452 echo "<td>WARNING: No sequence for C>A </br> </td>" >> $outfilePoolData
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453 else
|
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454 echo "<td><a href="Figures/WebLogo/Pool_Data/Pool_Data-CA.fa">Pool_Data-CA.fa</a><br/>" >> $outfilePoolData
|
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455 echo "<img src="Figures/WebLogo/Pool_Data/Pool_Data-CA-Probability.png"/><br/></td>" >> $outfilePoolData
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456 fi
|
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457 # C>G
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458 if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/Pool_Data/Pool_Data-CG-Probability.png" ]]; then
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459 echo "<td>WARNING: No sequence for C>G </br> </td>" >> $outfilePoolData
|
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460 else
|
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461 echo "<td><a href="Figures/WebLogo/Pool_Data/Pool_Data-CG.fa">Pool_Data-CG.fa</a><br/>" >> $outfilePoolData
|
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462 echo "<img src="Figures/WebLogo/Pool_Data/Pool_Data-CG-Probability.png"/><br/></td>" >> $outfilePoolData
|
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463 fi
|
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464 # C>T
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465 if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/Pool_Data/Pool_Data-CT-Probability.png" ]]; then
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466 echo "<td>WARNING: No sequence for C>T </br> </td>" >> $outfilePoolData
|
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467 else
|
|
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468 echo "<td><a href="Figures/WebLogo/Pool_Data/Pool_Data-CT.fa">Pool_Data-CT.fa</a><br/>" >> $outfilePoolData
|
|
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469 echo "<img src="Figures/WebLogo/Pool_Data/Pool_Data-CT-Probability.png"/><br/></td>" >> $outfilePoolData
|
|
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470 fi
|
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471 echo "</tr>" >> $outfilePoolData
|
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472
|
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473 # T>A
|
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474 echo "<tr>" >> $outfilePoolData
|
|
|
475 if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/Pool_Data/Pool_Data-TA-Probability.png" ]]; then
|
|
|
476 echo "<td>WARNING: No sequence for T>A </br> </td>" >> $outfilePoolData
|
|
|
477 else
|
|
|
478 echo "<td><a href="Figures/WebLogo/Pool_Data/Pool_Data-TA.fa">Pool_Data-TA.fa</a><br/>" >> $outfilePoolData
|
|
|
479 echo "<img src="Figures/WebLogo/Pool_Data/Pool_Data-TA-Probability.png"/><br/></td>" >> $outfilePoolData
|
|
|
480 fi
|
|
|
481 # T>C
|
|
|
482 if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/Pool_Data/Pool_Data-TC-Probability.png" ]]; then
|
|
|
483 echo "<td>WARNING: No sequence for T>C </br> </td>" >> $outfilePoolData
|
|
|
484 else
|
|
|
485 echo "<td><a href="Figures/WebLogo/Pool_Data/Pool_Data-TC.fa">Pool_Data-TC.fa</a><br/>" >> $outfilePoolData
|
|
|
486 echo "<img src="Figures/WebLogo/Pool_Data/Pool_Data-TC-Probability.png"/><br/></td>" >> $outfilePoolData
|
|
|
487 fi
|
|
|
488 # T>G
|
|
|
489 if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/Pool_Data/Pool_Data-TG-Probability.png" ]]; then
|
|
|
490 echo "<td>WARNING: No sequence for T>G </br> </td>" >> $outfilePoolData
|
|
|
491 else
|
|
|
492 echo "<td><a href="Figures/WebLogo/Pool_Data/Pool_Data-TG.fa">Pool_Data-TG.fa</a><br/>" >> $outfilePoolData
|
|
|
493 echo "<img src="Figures/WebLogo/Pool_Data/Pool_Data-TG-Probability.png"/><br/></td>" >> $outfilePoolData
|
|
|
494 fi
|
|
|
495 echo "</tr>" >> $outfilePoolData
|
|
|
496 echo "</table>" >> $outfilePoolData
|
|
|
497
|
|
|
498 echo "</body></html>" >> $outfilePoolData
|
|
|
499
|
|
|
500 fi # End if --poolData
|
|
|
501
|
|
|
502 fi # End if [ -d $output_dir/Mutational_Analysis/Figures ]
|
|
|
503
|
|
|
504 echo "</body></html>" >> $html
|
|
|
505
|
|
|
506 exit 0
|
|
|
507
|
