Mercurial > repos > iarc > mutspec
diff mutspecStat_wrapper.sh @ 7:eda59b985b1c draft default tip
Uploaded
| author | iarc |
|---|---|
| date | Mon, 13 Mar 2017 08:21:19 -0400 |
| parents | 46a10309dfe2 |
| children |
line wrap: on
line diff
--- a/mutspecStat_wrapper.sh Tue Jun 28 02:59:32 2016 -0400 +++ b/mutspecStat_wrapper.sh Mon Mar 13 08:21:19 2017 -0400 @@ -1,507 +1,527 @@ -#!/bin/bash - -######################################### -### SPECIFY THE NUMBER OF CPU ### -######################################### -cpu=1 - - - - - -######################################### -### Recover the arguments ### -######################################### -html=$1;shift -len_file_path=$1;shift -estimSign=$1;shift -parameters=$1;shift -working_dir=`pwd` - - - -mkdir in -cd in - -names=$(sed 's/\s/_/g' <<< $*) -names=$(sed 's/_\// \//g' <<< $names) -names=$(sed 's/_annotated//g' <<< $names) -names=$(sed 's/_filtered//g' <<< $names) -names=$(sed 's/\.txt_/_/' <<< $names) - -for name in ${names} -do - file=$(sed 's/=/ /' <<< $name); - echo $file - ln -s $file -done -cd .. - -output_dir=${html%%.*}_files - - -######################################### -### Calculates the statistics ### -######################################### - -perl $SCRIPT_PATH/mutspecStat.pl --outfile $output_dir \ - --temp "$working_dir/temp" \ - --pathRscript $SCRIPT_PATH \ - $parameters \ - $working_dir/in - - -######################################### -### Estimate the number of signatures ### -######################################### -if [[ $estimSign > 0 ]]; then - Rscript $SCRIPT_PATH/R/estimateSign_Galaxy.r --input $output_dir/Mutational_Analysis/Figures/Input_NMF/Input_NMF_Count.txt --stop $estimSign --cpu $cpu --output $output_dir/Mutational_Analysis/Figures/Estimate_Number_Signatures.png 2>&1 -fi - - -######################################### -### Create css # -######################################### -css=$output_dir/Mutational_Analysis/style.css -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 - - - -# HMTL page for the result of the tool -echo "<html>" >> $html -echo "<body>" >> $html - -if [ -d $output_dir/Mutational_Analysis/Figures ]; then - -echo "<center> <h2>Mutational spectra report summary</h2> </center>" >> $html - -echo "<br/> Download the full report in Excel" >> $html - -## One report with all the samples. Specify the full path -if [[ -e "$output_dir/Mutational_Analysis/Report_Mutation_Spectra.xls" ]] -then - # Interpreted by Galaxy so don't need the full path - echo "<br/><a href="Mutational_Analysis/Report_Mutation_Spectra.xls">Report_Mutation_Spectra.xls</a>" >> $html -fi -## One report for each samples -for file in $names -do - name=$(echo ${file}| cut -d"=" -f2) - name=${name%.*} - - # One report for each samples - if [[ -e "$output_dir/Mutational_Analysis/Report_Mutation_Spectra-$name.xls" ]] - then - echo "<br/><a href="Mutational_Analysis/Report_Mutation_Spectra-$name.xls">Report_Mutation_Spectra-$name.xls</a>" >> $html - fi -done -## One report for each samples: Pool_Data -if [[ $parameters =~ "--pooldata" ]]; then - if [[ -e "$output_dir/Mutational_Analysis/Report_Mutation_Spectra-Pool_Data.xls" ]]; then - echo "<br/><a href="Mutational_Analysis/Report_Mutation_Spectra-Pool_Data.xls">Report_Mutation_Spectra-Pool_Data.xls</a>" >> $html - fi -fi - - -## Input file for NMF -if [[ -e "$output_dir/Mutational_Analysis/Figures/Input_NMF/Input_NMF_Count.txt" ]] -then - # Interpreted by Galaxy so don't need the full path - echo "<br/><br/> Download the input file for the tool mutSpec-NMF" >> $html - echo "<br/><a href="Mutational_Analysis/Figures/Input_NMF/Input_NMF_Count.txt">Input_NMF_Count.txt</a><br/>" >> $html -fi - -## Computed statistics for estimating the number of signatures -if [[ $estimSign > 0 ]]; then - echo "<br/> Link to the computed statistics for estimating the number of signatures <br/>" >> $html - if [[ -e "$output_dir/Mutational_Analysis/Figures/Estimate_Number_Signatures.png" ]]; then - outEstimateSign="$output_dir/Mutational_Analysis/EstimatingSignatures.html" - touch $outEstimateSign - echo "<a href='Mutational_Analysis/EstimatingSignatures.html'>Estimating the number of signatures</a><br/>" >> $html - echo "<br/> <center> <h2>Computed statistics for estimating the number of signatures</h2> </center> <br/>" >> $outEstimateSign - echo "Several approaches have been proposed to choose the optimal number of signatures to extract with NMF. <br/> - Brunet et al. 2004, proposed to take the first number of signature for which the cophenetic coefficient starts decreasing, <br/> - Hutchins et al. 2008, suggested to choose the first value where the RSS curve presents an inflection point. <br/> - 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/> - The estimation are based on Brunet’s algorithm computed from 50 runs for each value of signature to estimate. <br/> <br/> - 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 - echo "<img src="Figures/Estimate_Number_Signatures.png width="1000""/><br/></td>" >> $outEstimateSign - else - echo "<br/>There is not enough mutations for estimating the number of signatures <br/>" >> $html - echo "Read the tool standard output for more detail<br/>" >> $html - fi -fi - - -## HMTL Link to the samples -echo "<br/> Link to individual samples <br/>" >> $html -for file in $names -do - name=$(echo ${file}| cut -d"=" -f2) - name=${name%.*} - outfile="$output_dir/Mutational_Analysis/$name.html" - touch $outfile # Create an empty file named $outfile - echo "<a href='Mutational_Analysis/$name.html'>$name</a><br/>" >> $html - -#-------------------------------------------------------------------------------------------------------------------------------------------------------------------------# -# INDIVIDUAL SAMPLES # -#-------------------------------------------------------------------------------------------------------------------------------------------------------------------------# -echo "<br/> <center> <h2>Mutational Spectra report for $name</h2> </center> <br/>" >> $outfile - -echo "<html>" >> $outfile - -echo "<head>" >> $outfile -echo "<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">" >> $outfile -# Link to the css style file for having a legend when we pass the mouse on the figures -echo "<link rel="stylesheet" href="style.css" />" >> $outfile -echo "</head>" >> $outfile - -echo "<body>" >> $outfile - -echo "<table>" >> $outfile -echo "<tr>" >> $outfile -echo "<th><h3>Overall mutation distribution</h3></th>" >> $outfile -echo "<th><h3>Impact on protein sequence</h3></th>" >> $outfile -echo "</tr><tr>" >> $outfile -echo "<td> <center> <a href="Figures/Overall_mutation_distribution/$name/$name-OverallMutationDistribution.txt">$name-OverallMutationDistribution.txt</a> </center> </td>" >> $outfile -echo "<td> <center> <a href="Figures/Impact_protein_sequence/$name/$name-DistributionExoFunc.txt">$name-DistributionExoFunc.txt</a> </center> </td>" >> $outfile -echo "</tr><tr>" >> $outfile - -echo "<td>" >> $outfile -echo "<span class="legend"><img src="Figures/Overall_mutation_distribution/$name/$name-OverallMutationDistribution.png width="280""/>" >> $outfile -echo "<span class="legend-hidden">" >> $outfile -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 -echo "</td>" >> $outfile -echo "<td>" >> $outfile -echo "<span class="legend"><img src="Figures/Impact_protein_sequence/$name/$name-DistributionExoFunc.png width="400""/>" >> $outfile -echo "<span class="legend-hidden">" >> $outfile -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 -echo "</td>" >> $outfile - -echo "</tr>" >> $outfile -echo "</table>" >> $outfile - -echo "<br/><br/>" >> $outfile - - -echo "<table>" >> $outfile -echo "<tr>" >> $outfile -echo "<th><h3>SBS distribution</h3></th>" >> $outfile -echo "<th><h3>Stranded distribution of SBS</h3></th>" >> $outfile -echo "</tr><tr>" >> $outfile -echo "<td> <center> <a href="Figures/SBS_distribution/$name/$name-SBS_distribution.txt">$name-SBS_distribution.txt</a> </center> </td>" >> $outfile -echo "<td> <center> <a href="Figures/Stranded_Analysis/$name/$name-StrandBias.txt">$name-StrandBias.txt</a> </center> </td>" >> $outfile -echo "</tr><tr>" >> $outfile - -echo "<td>" >> $outfile -echo "<span class="legend"><img src="Figures/SBS_distribution/$name/$name-SBS_distribution.png width="550""/>" >> $outfile -echo "<span class="legend-hidden">" >> $outfile -echo "<center><B>Graph 2. SBS distribution</center></B><br/>Proportion of each type of single base substitution (SBS)<br/>" >> $outfile -echo "</td>" >> $outfile -echo "<td>" >> $outfile -echo "<span class="legend"><img src="Figures/Stranded_Analysis/$name/$name-StrandBias.png width="400""/>" >> $outfile -echo "<span class="legend-hidden">" >> $outfile -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 -echo "</td>" >> $outfile - -echo "</tr>" >> $outfile -echo "</table>" >> $outfile - - -echo "<br/><br/>" >> $outfile - - -###################################################### -# Trinucleotide sequence context of SBS on genomic # -###################################################### -echo "<table>" >> $outfile -echo "<h3>Trinucleotide sequence context of SBS on the genomic sequence</h3>" >> $outfile -echo "<tr>" >> $outfile -echo "<td> <center> <a href="Figures/Trinucleotide_Sequence_Context/$name/$name-MutationSpectraPercent-Genomic.txt">$name-MutationSpectraPercent.txt</a> </center> </td>" >> $outfile -echo "<td> <center> <a href="Figures/Trinucleotide_Sequence_Context/$name/$name-HeatmapPercent-Genomic.txt">$name-HeatmapPercent-Genomic.txt</a> </center> </td>" >> $outfile -echo "</tr><tr>" >> $outfile - -echo "<td>" >> $outfile -echo "<span class="legend"><img src="Figures/Trinucleotide_Sequence_Context/$name/$name-MutationSpectraPercent-Genomic.png width="1000""/>" >> $outfile -echo "<span class="legend-hidden">" >> $outfile -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 -echo "</td>" >> $outfile -echo "<td>" >> $outfile -echo "<span class="legend"><img src="Figures/Trinucleotide_Sequence_Context/$name/$name-HeatmapPercent-Genomic.png width="250""/>" >> $outfile -echo "<span class="legend-hidden">" >> $outfile -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 -echo "</td>" >> $outfile - -echo "</tr>" >> $outfile -echo "</table>" >> $outfile - - -echo "<br/><br/>" >> $outfile - - -############################################################## -# Trinucleotide sequence context of SBS on coding sequence # -############################################################## -echo "<table>" >> $outfile -echo "<h3>Stranded analysis of trinucleotide sequence context of SBS</h3>" >> $outfile -echo "<tr>" >> $outfile -echo "<td> <center> <a href="Figures/Stranded_Analysis/$name/$name-StrandedSignaturePercent.txt">$name-StrandedSignaturePercent.txt</a> </center> </td>" >> $outfile -echo "</tr><tr>" >> $outfile - -echo "<td>" >> $outfile -echo "<span class="legend"><img src="Figures/Stranded_Analysis/$name/$name-StrandedSignaturePercent.png width="1300""/>" >> $outfile -echo "<span class="legend-hidden">" >> $outfile -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 -echo "</td>" >> $outfile -echo "</tr>" >> $outfile -echo "</table>" >> $outfile - -echo "<br/><br/>" >> $outfile - - -############################################# -# Sequence logo generated with Weblogo3 # -############################################# -echo "<table>" >> $outfile -echo "<h3>Wider sequence context with Weblogo3</h3>" >> $outfile -# Legende de la figure : Panel 3. Wider sequence context on genomic strand generated with Weblogo3 - -# C>A -echo "<tr>" >> $outfile -if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/$name/$name-CA-Probability.png" ]]; then - echo "<td>WARNING: No sequence for C>A </br> </td>" >> $outfile -else - echo "<td><a href="Figures/WebLogo/$name/$name-CA.fa">$name-CA.fa</a><br/>" >> $outfile - echo "<img src="Figures/WebLogo/$name/$name-CA-Probability.png"/><br/></td>" >> $outfile -fi -# C>G -if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/$name/$name-CG-Probability.png" ]]; then - echo "<td> WARNING: No sequence for C>G </br> </td>" >> $outfile -else - echo "<td><a href="Figures/WebLogo/$name/$name-CG.fa">$name-CG.fa</a><br/>" >> $outfile - echo "<img src="Figures/WebLogo/$name/$name-CG-Probability.png"/><br/></td>" >> $outfile -fi -# C>T -if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/$name/$name-CT-Probability.png" ]]; then - echo "<td> WARNING: No sequence for C>T </br> </td>" >> $outfile -else - echo "<td><a href="Figures/WebLogo/$name/$name-CT.fa">$name-CT.fa</a><br/>" >> $outfile - echo "<img src="Figures/WebLogo/$name/$name-CT-Probability.png"/><br/></td>" >> $outfile -fi -echo "</tr>" >> $outfile - -# T>A -echo "<tr>" >> $outfile -if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/$name/$name-TA-Probability.png" ]]; then - echo "<td>WARNING: No sequence for T>A </br> </td>" >> $outfile -else - echo "<td><a href="Figures/WebLogo/$name/$name-TA.fa">$name-TA.fa</a><br/>" >> $outfile - echo "<img src="Figures/WebLogo/$name/$name-TA-Probability.png"/><br/></td>" >> $outfile -fi -# T>C -if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/$name/$name-TC-Probability.png" ]]; then - echo "<td>WARNING: No sequence for T>C </br> </td>" >> $outfile -else - echo "<td><a href="Figures/WebLogo/$name/$name-TC.fa">$name-TC.fa</a><br/>" >> $outfile - echo "<img src="Figures/WebLogo/$name/$name-TC-Probability.png"/><br/></td>" >> $outfile -fi -# T>G -if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/$name/$name-TG-Probability.png" ]]; then - echo "<td>WARNING: No sequence for T>G </br> </td>" >> $outfile -else - echo "<td><a href="Figures/WebLogo/$name/$name-TG.fa">$name-TG.fa</a><br/>" >> $outfile - echo "<img src="Figures/WebLogo/$name/$name-TG-Probability.png"/><br/></td>" >> $outfile -fi -echo "</tr>" >> $outfile - -echo "</table>" >> $outfile - -echo "</body></html>" >> $outfile - -done - -#-------------------------------------------------------------------------------------------------------------------------------------------------------------------------# -# POOL DATA # -#-------------------------------------------------------------------------------------------------------------------------------------------------------------------------# -## HMTL Link to Pool_Data -if [[ $parameters =~ "--pooldata" ]]; then - outfilePoolData="$output_dir/Mutational_Analysis/Pool_Data.html" - touch $outfilePoolData # Create an empty file named $outfile - echo "<a href='Mutational_Analysis/Pool_Data.html'>Pool_Data</a><br/>" >> $html - - - echo "<br/> <center> <h2>Mutational Spectra report for Pool_Data</h2> </center> <br/>" >> $outfilePoolData - echo "<html>" >> $outfilePoolData - - echo "<head>" >> $outfilePoolData - echo "<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">" >> $outfilePoolData - # Link to the css style file for having a legend when we pass the mouse on the figures - echo "<link rel="stylesheet" href="style.css" />" >> $outfilePoolData - echo "</head>" >> $outfilePoolData - - echo "<body>" >> $outfilePoolData - - echo "<table>" >> $outfilePoolData - echo "<tr>" >> $outfilePoolData - echo "<th><h3>Overall mutation distribution</h3></th>" >> $outfilePoolData - echo "<th><h3>Impact on protein sequence</h3></th>" >> $outfilePoolData - echo "</tr><tr>" >> $outfilePoolData - echo "<td> <center> <a href="Figures/Overall_mutation_distribution/Pool_Data/Pool_Data-OverallMutationDistribution.txt">Pool_Data-OverallMutationDistribution.txt</a> </center> </td>" >> $outfilePoolData - echo "<td> <center> <a href="Figures/Impact_protein_sequence/Pool_Data/Pool_Data-DistributionExoFunc.txt">Pool_Data-DistributionExoFunc.txt</a> </center> </td>" >> $outfilePoolData - echo "</tr><tr>" >> $outfilePoolData - - echo "<td>" >> $outfilePoolData - echo "<span class="legend"><img src="Figures/Overall_mutation_distribution/Pool_Data/Pool_Data-OverallMutationDistribution.png width="280""/>" >> $outfilePoolData - echo "<span class="legend-hidden">" >> $outfilePoolData - 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 - echo "</td>" >> $outfilePoolData - echo "<td>" >> $outfilePoolData - echo "<span class="legend"><img src="Figures/Impact_protein_sequence/Pool_Data/Pool_Data-DistributionExoFunc.png width="400""/>" >> $outfilePoolData - echo "<span class="legend-hidden">" >> $outfilePoolData - 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 - echo "</td>" >> $outfilePoolData - - echo "</tr>" >> $outfilePoolData - echo "</table>" >> $outfilePoolData - - echo "<br/><br/>" >> $outfilePoolData - - - echo "<table>" >> $outfilePoolData - echo "<tr>" >> $outfilePoolData - echo "<th><h3>SBS distribution</h3></th>" >> $outfilePoolData - echo "<th><h3>Stranded distribution of SBS</h3></th>" >> $outfilePoolData - echo "</tr><tr>" >> $outfilePoolData - echo "<td> <center> <a href="Figures/SBS_distribution/Pool_Data/Pool_Data-SBS_distribution.txt">Pool_Data-SBS_distribution.txt</a> </center> </td>" >> $outfilePoolData - echo "<td> <center> <a href="Figures/Stranded_Analysis/Pool_Data/Pool_Data-StrandBias.txt">Pool_Data-StrandBias.txt</a> </center> </td>" >> $outfilePoolData - echo "</tr><tr>" >> $outfilePoolData - - echo "<td>" >> $outfilePoolData - echo "<span class="legend"><img src="Figures/SBS_distribution/Pool_Data/Pool_Data-SBS_distribution.png width="550""/>" >> $outfilePoolData - echo "<span class="legend-hidden">" >> $outfilePoolData - echo "<center><B>Graph 2. SBS distribution</center></B><br/>Proportion of each type of single base substitution (SBS)<br/>" >> $outfilePoolData - echo "</td>" >> $outfilePoolData - echo "<td>" >> $outfilePoolData - echo "<span class="legend"><img src="Figures/Stranded_Analysis/Pool_Data/Pool_Data-StrandBias.png width="400""/>" >> $outfilePoolData - echo "<span class="legend-hidden">" >> $outfilePoolData - 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 - echo "</td>" >> $outfilePoolData - - echo "</tr>" >> $outfilePoolData - echo "</table>" >> $outfilePoolData - - - echo "<br/><br/>" >> $outfilePoolData - - - ########################################################## - # Trinucleotide sequence context of SBS on genomic: Pool # - ########################################################## - echo "<table>" >> $outfilePoolData - echo "<h3>Trinucleotide sequence context of SBS on the genomic sequence</h3>" >> $outfilePoolData - echo "<tr>" >> $outfilePoolData - echo "<td> <center> <a href="Figures/Trinucleotide_Sequence_Context/Pool_Data/Pool_Data-MutationSpectraPercent-Genomic.txt">Pool_Data-MutationSpectraPercent.txt</a> </center> </td>" >> $outfilePoolData - 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 - echo "</tr><tr>" >> $outfilePoolData - - echo "<td>" >> $outfilePoolData - echo "<span class="legend"><img src="Figures/Trinucleotide_Sequence_Context/Pool_Data/Pool_Data-MutationSpectraPercent-Genomic.png width="1000""/>" >> $outfilePoolData - echo "<span class="legend-hidden">" >> $outfilePoolData - 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 - echo "</td>" >> $outfilePoolData - echo "<td>" >> $outfilePoolData - echo "<span class="legend"><img src="Figures/Trinucleotide_Sequence_Context/Pool_Data/Pool_Data-HeatmapPercent-Genomic.png width="250""/>" >> $outfilePoolData - echo "<span class="legend-hidden">" >> $outfilePoolData - 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 - echo "</td>" >> $outfilePoolData - - echo "</tr>" >> $outfilePoolData - echo "</table>" >> $outfilePoolData - - - echo "<br/><br/>" >> $outfilePoolData - - - ################################################################## - # Trinucleotide sequence context of SBS on coding sequence: Pool # - ################################################################## - echo "<table>" >> $outfilePoolData - echo "<h3>Stranded analysis of trinucleotide sequence context of SBS</h3>" >> $outfilePoolData - echo "<tr>" >> $outfilePoolData - echo "<td> <center> <a href="Figures/Stranded_Analysis/Pool_Data/Pool_Data-StrandedSignaturePercent.txt">Pool_Data-StrandedSignaturePercent.txt</a> </center> </td>" >> $outfilePoolData - echo "</tr><tr>" >> $outfilePoolData - - echo "<td>" >> $outfilePoolData - echo "<span class="legend"><img src="Figures/Stranded_Analysis/Pool_Data/Pool_Data-StrandedSignaturePercent.png width="1300""/>" >> $outfilePoolData - echo "<span class="legend-hidden">" >> $outfilePoolData - 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 - echo "</td>" >> $outfilePoolData - echo "</tr>" >> $outfilePoolData - echo "</table>" >> $outfilePoolData - - echo "<br/><br/>" >> $outfilePoolData - - ##################################################### - # Sequence logo generated with Weblogo3: Pool # - ##################################################### - echo "<table>" >> $outfilePoolData - echo "<h3>Sequence logo generated with Weblogo3</h3>" >> $outfilePoolData - # C>A - echo "<tr>" >> $outfilePoolData - if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/Pool_Data/Pool_Data-CA-Probability.png" ]]; then - echo "<td>WARNING: No sequence for C>A </br> </td>" >> $outfilePoolData - else - echo "<td><a href="Figures/WebLogo/Pool_Data/Pool_Data-CA.fa">Pool_Data-CA.fa</a><br/>" >> $outfilePoolData - echo "<img src="Figures/WebLogo/Pool_Data/Pool_Data-CA-Probability.png"/><br/></td>" >> $outfilePoolData - fi - # C>G - if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/Pool_Data/Pool_Data-CG-Probability.png" ]]; then - echo "<td>WARNING: No sequence for C>G </br> </td>" >> $outfilePoolData - else - echo "<td><a href="Figures/WebLogo/Pool_Data/Pool_Data-CG.fa">Pool_Data-CG.fa</a><br/>" >> $outfilePoolData - echo "<img src="Figures/WebLogo/Pool_Data/Pool_Data-CG-Probability.png"/><br/></td>" >> $outfilePoolData - fi - # C>T - if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/Pool_Data/Pool_Data-CT-Probability.png" ]]; then - echo "<td>WARNING: No sequence for C>T </br> </td>" >> $outfilePoolData - else - echo "<td><a href="Figures/WebLogo/Pool_Data/Pool_Data-CT.fa">Pool_Data-CT.fa</a><br/>" >> $outfilePoolData - echo "<img src="Figures/WebLogo/Pool_Data/Pool_Data-CT-Probability.png"/><br/></td>" >> $outfilePoolData - fi - echo "</tr>" >> $outfilePoolData - - # T>A - echo "<tr>" >> $outfilePoolData - if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/Pool_Data/Pool_Data-TA-Probability.png" ]]; then - echo "<td>WARNING: No sequence for T>A </br> </td>" >> $outfilePoolData - else - echo "<td><a href="Figures/WebLogo/Pool_Data/Pool_Data-TA.fa">Pool_Data-TA.fa</a><br/>" >> $outfilePoolData - echo "<img src="Figures/WebLogo/Pool_Data/Pool_Data-TA-Probability.png"/><br/></td>" >> $outfilePoolData - fi - # T>C - if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/Pool_Data/Pool_Data-TC-Probability.png" ]]; then - echo "<td>WARNING: No sequence for T>C </br> </td>" >> $outfilePoolData - else - echo "<td><a href="Figures/WebLogo/Pool_Data/Pool_Data-TC.fa">Pool_Data-TC.fa</a><br/>" >> $outfilePoolData - echo "<img src="Figures/WebLogo/Pool_Data/Pool_Data-TC-Probability.png"/><br/></td>" >> $outfilePoolData - fi - # T>G - if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/Pool_Data/Pool_Data-TG-Probability.png" ]]; then - echo "<td>WARNING: No sequence for T>G </br> </td>" >> $outfilePoolData - else - echo "<td><a href="Figures/WebLogo/Pool_Data/Pool_Data-TG.fa">Pool_Data-TG.fa</a><br/>" >> $outfilePoolData - echo "<img src="Figures/WebLogo/Pool_Data/Pool_Data-TG-Probability.png"/><br/></td>" >> $outfilePoolData - fi - echo "</tr>" >> $outfilePoolData - echo "</table>" >> $outfilePoolData - - echo "</body></html>" >> $outfilePoolData - -fi # End if --poolData - -fi # End if [ -d $output_dir/Mutational_Analysis/Figures ] - -echo "</body></html>" >> $html - -exit 0 - +#!/bin/bash + +######################################### +### SPECIFY THE NUMBER OF CPU ### +######################################### +cpu=8 + + + + + +######################################### +### Recover the arguments ### +######################################### +html=$1;shift +len_file_path=$1;shift +estimSign=$1;shift +parameters=$1;shift +working_dir=`pwd` + + + +mkdir in +cd in + +names=$(sed 's/\s/_/g' <<< $*) +names=$(sed 's/_\// \//g' <<< $names) +names=$(sed 's/_annotated//g' <<< $names) +names=$(sed 's/_filtered//g' <<< $names) +names=$(sed 's/\.txt_/_/' <<< $names) + +for name in ${names} +do + file=$(sed 's/=/ /' <<< $name); + echo $file + ln -s $file +done +cd .. + +output_dir=${html%%.*}_files + + +######################################### +### Calculates the statistics ### +######################################### + +perl $SCRIPT_PATH/mutspecStat.pl --outfile $output_dir \ + --temp "$working_dir/temp" \ + --pathRscript $SCRIPT_PATH \ + $parameters \ + $working_dir/in + + +######################################### +### Estimate the number of signatures ### +######################################### +if [[ $estimSign > 0 ]]; then + Rscript $SCRIPT_PATH/R/estimateSign_Galaxy.r --input $output_dir/Mutational_Analysis/Figures/Input_NMF/Input_NMF_Count.txt --stop $estimSign --cpu $cpu --output $output_dir/Mutational_Analysis/Figures/Estimate_Number_Signatures.png 2>&1 +fi + + +######################################### +### Create css # +######################################### +css=$output_dir/Mutational_Analysis/style.css +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 + + +######################################### +### Create an archive with all results # +######################################### +cd $output_dir +zip -r "$output_dir/Mutational_Analysis.zip" "Mutational_Analysis" + + + +# HMTL page for the result of the tool +echo "<html>" >> $html +echo "<body>" >> $html + +if [ -d $output_dir/Mutational_Analysis/Figures ]; then + +echo "<center> <h2>Mutational spectra report summary</h2> </center>" >> $html + +echo "<br/> Download the results" >> $html +echo "<br/><a href="Mutational_Analysis.zip">Mutational_Analysis.zip</a><br/>" >> $html + +echo "<br/> Download the full report in Excel" >> $html + +## One report with all the samples. Specify the full path +if [[ -e "$output_dir/Mutational_Analysis/Report_Mutation_Spectra.xls" ]] +then + # Interpreted by Galaxy so don't need the full path + echo "<br/><a href="Mutational_Analysis/Report_Mutation_Spectra.xls">Report_Mutation_Spectra.xls</a>" >> $html +fi +## One report for each samples +for file in $names +do + name=$(echo ${file}| cut -d"=" -f2) + name=${name%.*} + + # One report for each samples + if [[ -e "$output_dir/Mutational_Analysis/Report_Mutation_Spectra-$name.xls" ]] + then + echo "<br/><a href="Mutational_Analysis/Report_Mutation_Spectra-$name.xls">Report_Mutation_Spectra-$name.xls</a>" >> $html + fi +done +## One report for each samples: Pool_Data +if [[ $parameters =~ "--pooldata" ]]; then + if [[ -e "$output_dir/Mutational_Analysis/Report_Mutation_Spectra-Pool_Data.xls" ]]; then + echo "<br/><a href="Mutational_Analysis/Report_Mutation_Spectra-Pool_Data.xls">Report_Mutation_Spectra-Pool_Data.xls</a>" >> $html + fi +fi + + +## Input file for NMF +if [[ -e "$output_dir/Mutational_Analysis/Figures/Input_NMF/Input_NMF_Count.txt" ]] +then + # Interpreted by Galaxy so don't need the full path + echo "<br/><br/> Download the input file for the tool mutSpec-NMF" >> $html + echo "<br/><a href="Mutational_Analysis/Figures/Input_NMF/Input_NMF_Count.txt">Input_NMF_Count.txt</a><br/>" >> $html +fi + +## Computed statistics for estimating the number of signatures +if [[ $estimSign > 0 ]]; then + echo "<br/> Link to the computed statistics for estimating the number of signatures <br/>" >> $html + if [[ -e "$output_dir/Mutational_Analysis/Figures/Estimate_Number_Signatures.png" ]]; then + outEstimateSign="$output_dir/Mutational_Analysis/EstimatingSignatures.html" + touch $outEstimateSign + echo "<a href='Mutational_Analysis/EstimatingSignatures.html'>Estimating the number of signatures</a><br/>" >> $html + echo "<br/> <center> <h2>Computed statistics for estimating the number of signatures</h2> </center> <br/>" >> $outEstimateSign + echo "Several approaches have been proposed to choose the optimal number of signatures to extract with NMF. <br/> + Brunet et al. 2004, proposed to take the first number of signature for which the cophenetic coefficient starts decreasing, <br/> + Hutchins et al. 2008, suggested to choose the first value where the RSS curve presents an inflection point. <br/> + 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/> + The estimation are based on Brunet’s algorithm computed from 50 runs for each value of signature to estimate. <br/> <br/> + 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 + echo "<img src="Figures/Estimate_Number_Signatures.png width="1000""/><br/></td>" >> $outEstimateSign + else + echo "<br/>There is not enough mutations for estimating the number of signatures <br/>" >> $html + echo "Read the tool standard output for more detail<br/>" >> $html + fi +fi + + +## HMTL Link to the samples +echo "<br/> Link to individual samples <br/>" >> $html + + +## Consider only samples with at least one mutation +for file in `ls $output_dir/Mutational_Analysis/Figures/Impact_protein_sequence` +do + + name=$(echo ${file}| cut -d"=" -f2) + name=${name%.*} + + ## Pool Data is handle separately + if [ $name = "Pool_Data" ]; then + continue + fi + + outfile="$output_dir/Mutational_Analysis/$name.html" + touch $outfile # Create an empty file named $outfile + echo "<a href='Mutational_Analysis/$name.html'>$name</a><br/>" >> $html + +#-----------------------------------------------------------------------------------------------------------------------------------------------------# +# INDIVIDUAL SAMPLES # +#-----------------------------------------------------------------------------------------------------------------------------------------------------# +echo "<br/> <center> <h2>Mutational Spectra report for $name</h2> </center> <br/>" >> $outfile + +echo "<html>" >> $outfile + +echo "<head>" >> $outfile +echo "<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">" >> $outfile +# Link to the css style file for having a legend when we pass the mouse on the figures +echo "<link rel="stylesheet" href="style.css" />" >> $outfile +echo "</head>" >> $outfile + +echo "<body>" >> $outfile + +echo "<table>" >> $outfile +echo "<tr>" >> $outfile +echo "<th><h3>Overall mutation distribution</h3></th>" >> $outfile +echo "<th><h3>Impact on protein sequence</h3></th>" >> $outfile +echo "</tr><tr>" >> $outfile +echo "<td> <center> <a href="Figures/Overall_mutation_distribution/$name/$name-OverallMutationDistribution.txt">$name-OverallMutationDistribution.txt</a> </center> </td>" >> $outfile +echo "<td> <center> <a href="Figures/Impact_protein_sequence/$name/$name-DistributionExoFunc.txt">$name-DistributionExoFunc.txt</a> </center> </td>" >> $outfile +echo "</tr><tr>" >> $outfile + +echo "<td>" >> $outfile +echo "<span class="legend"><img src="Figures/Overall_mutation_distribution/$name/$name-OverallMutationDistribution.png width="280""/>" >> $outfile +echo "<span class="legend-hidden">" >> $outfile +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 +echo "</td>" >> $outfile +echo "<td>" >> $outfile +echo "<span class="legend"><img src="Figures/Impact_protein_sequence/$name/$name-DistributionExoFunc.png width="400""/>" >> $outfile +echo "<span class="legend-hidden">" >> $outfile +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 +echo "</td>" >> $outfile + +echo "</tr>" >> $outfile +echo "</table>" >> $outfile + +echo "<br/><br/>" >> $outfile + + +echo "<table>" >> $outfile +echo "<tr>" >> $outfile +echo "<th><h3>SBS distribution</h3></th>" >> $outfile +echo "<th><h3>Stranded distribution of SBS</h3></th>" >> $outfile +echo "</tr><tr>" >> $outfile +echo "<td> <center> <a href="Figures/SBS_distribution/$name/$name-SBS_distribution.txt">$name-SBS_distribution.txt</a> </center> </td>" >> $outfile +echo "<td> <center> <a href="Figures/Stranded_Analysis/$name/$name-StrandBias.txt">$name-StrandBias.txt</a> </center> </td>" >> $outfile +echo "</tr><tr>" >> $outfile + +echo "<td>" >> $outfile +echo "<span class="legend"><img src="Figures/SBS_distribution/$name/$name-SBS_distribution.png width="550""/>" >> $outfile +echo "<span class="legend-hidden">" >> $outfile +echo "<center><B>Graph 2. SBS distribution</center></B><br/>Proportion of each type of single base substitution (SBS)<br/>" >> $outfile +echo "</td>" >> $outfile +echo "<td>" >> $outfile +echo "<span class="legend"><img src="Figures/Stranded_Analysis/$name/$name-StrandBias.png width="400""/>" >> $outfile +echo "<span class="legend-hidden">" >> $outfile +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 +echo "</td>" >> $outfile + +echo "</tr>" >> $outfile +echo "</table>" >> $outfile + + +echo "<br/><br/>" >> $outfile + + +###################################################### +# Trinucleotide sequence context of SBS on genomic # +###################################################### +echo "<table>" >> $outfile +echo "<h3>Trinucleotide sequence context of SBS on the genomic sequence</h3>" >> $outfile +echo "<tr>" >> $outfile +echo "<td> <center> <a href="Figures/Trinucleotide_Sequence_Context/$name/$name-MutationSpectraPercent-Genomic.txt">$name-MutationSpectraPercent.txt</a> </center> </td>" >> $outfile +echo "<td> <center> <a href="Figures/Trinucleotide_Sequence_Context/$name/$name-HeatmapPercent-Genomic.txt">$name-HeatmapPercent-Genomic.txt</a> </center> </td>" >> $outfile +echo "</tr><tr>" >> $outfile + +echo "<td>" >> $outfile +echo "<span class="legend"><img src="Figures/Trinucleotide_Sequence_Context/$name/$name-MutationSpectraPercent-Genomic.png width="1000""/>" >> $outfile +echo "<span class="legend-hidden">" >> $outfile +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 +echo "</td>" >> $outfile +echo "<td>" >> $outfile +echo "<span class="legend"><img src="Figures/Trinucleotide_Sequence_Context/$name/$name-HeatmapPercent-Genomic.png width="250""/>" >> $outfile +echo "<span class="legend-hidden">" >> $outfile +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 +echo "</td>" >> $outfile + +echo "</tr>" >> $outfile +echo "</table>" >> $outfile + + +echo "<br/><br/>" >> $outfile + + +############################################################## +# Trinucleotide sequence context of SBS on coding sequence # +############################################################## +echo "<table>" >> $outfile +echo "<h3>Stranded analysis of trinucleotide sequence context of SBS</h3>" >> $outfile +echo "<tr>" >> $outfile +echo "<td> <center> <a href="Figures/Stranded_Analysis/$name/$name-StrandedSignaturePercent.txt">$name-StrandedSignaturePercent.txt</a> </center> </td>" >> $outfile +echo "</tr><tr>" >> $outfile + +echo "<td>" >> $outfile +echo "<span class="legend"><img src="Figures/Stranded_Analysis/$name/$name-StrandedSignaturePercent.png width="1300""/>" >> $outfile +echo "<span class="legend-hidden">" >> $outfile +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 +echo "</td>" >> $outfile +echo "</tr>" >> $outfile +echo "</table>" >> $outfile + +echo "<br/><br/>" >> $outfile + + +############################################# +# Sequence logo generated with Weblogo3 # +############################################# +echo "<table>" >> $outfile +echo "<h3>Wider sequence context with Weblogo3</h3>" >> $outfile +# Legende de la figure : Panel 3. Wider sequence context on genomic strand generated with Weblogo3 + +# C>A +echo "<tr>" >> $outfile +if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/$name/$name-CA-Probability.png" ]]; then + echo "<td>WARNING: No sequence for C>A </br> </td>" >> $outfile +else + echo "<td><a href="Figures/WebLogo/$name/$name-CA.fa">$name-CA.fa</a><br/>" >> $outfile + echo "<img src="Figures/WebLogo/$name/$name-CA-Probability.png width="600" "/><br/></td>" >> $outfile +fi +# C>G +if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/$name/$name-CG-Probability.png" ]]; then + echo "<td> WARNING: No sequence for C>G </br> </td>" >> $outfile +else + echo "<td><a href="Figures/WebLogo/$name/$name-CG.fa">$name-CG.fa</a><br/>" >> $outfile + echo "<img src="Figures/WebLogo/$name/$name-CG-Probability.png width="600" "/><br/></td>" >> $outfile +fi +# C>T +if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/$name/$name-CT-Probability.png" ]]; then + echo "<td> WARNING: No sequence for C>T </br> </td>" >> $outfile +else + echo "<td><a href="Figures/WebLogo/$name/$name-CT.fa">$name-CT.fa</a><br/>" >> $outfile + echo "<img src="Figures/WebLogo/$name/$name-CT-Probability.png width="600" "/><br/></td>" >> $outfile +fi +echo "</tr>" >> $outfile + +# T>A +echo "<tr>" >> $outfile +if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/$name/$name-TA-Probability.png" ]]; then + echo "<td>WARNING: No sequence for T>A </br> </td>" >> $outfile +else + echo "<td><a href="Figures/WebLogo/$name/$name-TA.fa">$name-TA.fa</a><br/>" >> $outfile + echo "<img src="Figures/WebLogo/$name/$name-TA-Probability.png width="600" "/><br/></td>" >> $outfile +fi +# T>C +if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/$name/$name-TC-Probability.png" ]]; then + echo "<td>WARNING: No sequence for T>C </br> </td>" >> $outfile +else + echo "<td><a href="Figures/WebLogo/$name/$name-TC.fa">$name-TC.fa</a><br/>" >> $outfile + echo "<img src="Figures/WebLogo/$name/$name-TC-Probability.png width="600" "/><br/></td>" >> $outfile +fi +# T>G +if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/$name/$name-TG-Probability.png" ]]; then + echo "<td>WARNING: No sequence for T>G </br> </td>" >> $outfile +else + echo "<td><a href="Figures/WebLogo/$name/$name-TG.fa">$name-TG.fa</a><br/>" >> $outfile + echo "<img src="Figures/WebLogo/$name/$name-TG-Probability.png width="600" "/><br/></td>" >> $outfile +fi +echo "</tr>" >> $outfile + +echo "</table>" >> $outfile + +echo "</body></html>" >> $outfile + +done + +#-----------------------------------------------------------------------------------------------------------------------------------------------------# +# POOL DATA # +#-----------------------------------------------------------------------------------------------------------------------------------------------------# +## HMTL Link to Pool_Data +if [[ $parameters =~ "--pooldata" ]]; then + outfilePoolData="$output_dir/Mutational_Analysis/Pool_Data.html" + touch $outfilePoolData # Create an empty file named $outfile + echo "<a href='Mutational_Analysis/Pool_Data.html'>Pool_Data</a><br/>" >> $html + + + echo "<br/> <center> <h2>Mutational Spectra report for Pool_Data</h2> </center> <br/>" >> $outfilePoolData + echo "<html>" >> $outfilePoolData + + echo "<head>" >> $outfilePoolData + echo "<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">" >> $outfilePoolData + # Link to the css style file for having a legend when we pass the mouse on the figures + echo "<link rel="stylesheet" href="style.css" />" >> $outfilePoolData + echo "</head>" >> $outfilePoolData + + echo "<body>" >> $outfilePoolData + + echo "<table>" >> $outfilePoolData + echo "<tr>" >> $outfilePoolData + echo "<th><h3>Overall mutation distribution</h3></th>" >> $outfilePoolData + echo "<th><h3>Impact on protein sequence</h3></th>" >> $outfilePoolData + echo "</tr><tr>" >> $outfilePoolData + echo "<td> <center> <a href="Figures/Overall_mutation_distribution/Pool_Data/Pool_Data-OverallMutationDistribution.txt">Pool_Data-OverallMutationDistribution.txt</a> </center> </td>" >> $outfilePoolData + echo "<td> <center> <a href="Figures/Impact_protein_sequence/Pool_Data/Pool_Data-DistributionExoFunc.txt">Pool_Data-DistributionExoFunc.txt</a> </center> </td>" >> $outfilePoolData + echo "</tr><tr>" >> $outfilePoolData + + echo "<td>" >> $outfilePoolData + echo "<span class="legend"><img src="Figures/Overall_mutation_distribution/Pool_Data/Pool_Data-OverallMutationDistribution.png width="280""/>" >> $outfilePoolData + echo "<span class="legend-hidden">" >> $outfilePoolData + 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 + echo "</td>" >> $outfilePoolData + echo "<td>" >> $outfilePoolData + echo "<span class="legend"><img src="Figures/Impact_protein_sequence/Pool_Data/Pool_Data-DistributionExoFunc.png width="400""/>" >> $outfilePoolData + echo "<span class="legend-hidden">" >> $outfilePoolData + 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 + echo "</td>" >> $outfilePoolData + + echo "</tr>" >> $outfilePoolData + echo "</table>" >> $outfilePoolData + + echo "<br/><br/>" >> $outfilePoolData + + + echo "<table>" >> $outfilePoolData + echo "<tr>" >> $outfilePoolData + echo "<th><h3>SBS distribution</h3></th>" >> $outfilePoolData + echo "<th><h3>Stranded distribution of SBS</h3></th>" >> $outfilePoolData + echo "</tr><tr>" >> $outfilePoolData + echo "<td> <center> <a href="Figures/SBS_distribution/Pool_Data/Pool_Data-SBS_distribution.txt">Pool_Data-SBS_distribution.txt</a> </center> </td>" >> $outfilePoolData + echo "<td> <center> <a href="Figures/Stranded_Analysis/Pool_Data/Pool_Data-StrandBias.txt">Pool_Data-StrandBias.txt</a> </center> </td>" >> $outfilePoolData + echo "</tr><tr>" >> $outfilePoolData + + echo "<td>" >> $outfilePoolData + echo "<span class="legend"><img src="Figures/SBS_distribution/Pool_Data/Pool_Data-SBS_distribution.png width="550""/>" >> $outfilePoolData + echo "<span class="legend-hidden">" >> $outfilePoolData + echo "<center><B>Graph 2. SBS distribution</center></B><br/>Proportion of each type of single base substitution (SBS)<br/>" >> $outfilePoolData + echo "</td>" >> $outfilePoolData + echo "<td>" >> $outfilePoolData + echo "<span class="legend"><img src="Figures/Stranded_Analysis/Pool_Data/Pool_Data-StrandBias.png width="400""/>" >> $outfilePoolData + echo "<span class="legend-hidden">" >> $outfilePoolData + 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 + echo "</td>" >> $outfilePoolData + + echo "</tr>" >> $outfilePoolData + echo "</table>" >> $outfilePoolData + + + echo "<br/><br/>" >> $outfilePoolData + + + ########################################################## + # Trinucleotide sequence context of SBS on genomic: Pool # + ########################################################## + echo "<table>" >> $outfilePoolData + echo "<h3>Trinucleotide sequence context of SBS on the genomic sequence</h3>" >> $outfilePoolData + echo "<tr>" >> $outfilePoolData + echo "<td> <center> <a href="Figures/Trinucleotide_Sequence_Context/Pool_Data/Pool_Data-MutationSpectraPercent-Genomic.txt">Pool_Data-MutationSpectraPercent.txt</a> </center> </td>" >> $outfilePoolData + 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 + echo "</tr><tr>" >> $outfilePoolData + + echo "<td>" >> $outfilePoolData + echo "<span class="legend"><img src="Figures/Trinucleotide_Sequence_Context/Pool_Data/Pool_Data-MutationSpectraPercent-Genomic.png width="1000""/>" >> $outfilePoolData + echo "<span class="legend-hidden">" >> $outfilePoolData + 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 + echo "</td>" >> $outfilePoolData + echo "<td>" >> $outfilePoolData + echo "<span class="legend"><img src="Figures/Trinucleotide_Sequence_Context/Pool_Data/Pool_Data-HeatmapPercent-Genomic.png width="250""/>" >> $outfilePoolData + echo "<span class="legend-hidden">" >> $outfilePoolData + 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 + echo "</td>" >> $outfilePoolData + + echo "</tr>" >> $outfilePoolData + echo "</table>" >> $outfilePoolData + + + echo "<br/><br/>" >> $outfilePoolData + + + ################################################################## + # Trinucleotide sequence context of SBS on coding sequence: Pool # + ################################################################## + echo "<table>" >> $outfilePoolData + echo "<h3>Stranded analysis of trinucleotide sequence context of SBS</h3>" >> $outfilePoolData + echo "<tr>" >> $outfilePoolData + echo "<td> <center> <a href="Figures/Stranded_Analysis/Pool_Data/Pool_Data-StrandedSignaturePercent.txt">Pool_Data-StrandedSignaturePercent.txt</a> </center> </td>" >> $outfilePoolData + echo "</tr><tr>" >> $outfilePoolData + + echo "<td>" >> $outfilePoolData + echo "<span class="legend"><img src="Figures/Stranded_Analysis/Pool_Data/Pool_Data-StrandedSignaturePercent.png width="1300""/>" >> $outfilePoolData + echo "<span class="legend-hidden">" >> $outfilePoolData + 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 + echo "</td>" >> $outfilePoolData + echo "</tr>" >> $outfilePoolData + echo "</table>" >> $outfilePoolData + + echo "<br/><br/>" >> $outfilePoolData + + ##################################################### + # Sequence logo generated with Weblogo3: Pool # + ##################################################### + echo "<table>" >> $outfilePoolData + echo "<h3>Sequence logo generated with Weblogo3</h3>" >> $outfilePoolData + # C>A + echo "<tr>" >> $outfilePoolData + if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/Pool_Data/Pool_Data-CA-Probability.png" ]]; then + echo "<td>WARNING: No sequence for C>A </br> </td>" >> $outfilePoolData + else + echo "<td><a href="Figures/WebLogo/Pool_Data/Pool_Data-CA.fa">Pool_Data-CA.fa</a><br/>" >> $outfilePoolData + echo "<img src="Figures/WebLogo/Pool_Data/Pool_Data-CA-Probability.png"/><br/></td>" >> $outfilePoolData + fi + # C>G + if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/Pool_Data/Pool_Data-CG-Probability.png" ]]; then + echo "<td>WARNING: No sequence for C>G </br> </td>" >> $outfilePoolData + else + echo "<td><a href="Figures/WebLogo/Pool_Data/Pool_Data-CG.fa">Pool_Data-CG.fa</a><br/>" >> $outfilePoolData + echo "<img src="Figures/WebLogo/Pool_Data/Pool_Data-CG-Probability.png"/><br/></td>" >> $outfilePoolData + fi + # C>T + if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/Pool_Data/Pool_Data-CT-Probability.png" ]]; then + echo "<td>WARNING: No sequence for C>T </br> </td>" >> $outfilePoolData + else + echo "<td><a href="Figures/WebLogo/Pool_Data/Pool_Data-CT.fa">Pool_Data-CT.fa</a><br/>" >> $outfilePoolData + echo "<img src="Figures/WebLogo/Pool_Data/Pool_Data-CT-Probability.png"/><br/></td>" >> $outfilePoolData + fi + echo "</tr>" >> $outfilePoolData + + # T>A + echo "<tr>" >> $outfilePoolData + if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/Pool_Data/Pool_Data-TA-Probability.png" ]]; then + echo "<td>WARNING: No sequence for T>A </br> </td>" >> $outfilePoolData + else + echo "<td><a href="Figures/WebLogo/Pool_Data/Pool_Data-TA.fa">Pool_Data-TA.fa</a><br/>" >> $outfilePoolData + echo "<img src="Figures/WebLogo/Pool_Data/Pool_Data-TA-Probability.png"/><br/></td>" >> $outfilePoolData + fi + # T>C + if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/Pool_Data/Pool_Data-TC-Probability.png" ]]; then + echo "<td>WARNING: No sequence for T>C </br> </td>" >> $outfilePoolData + else + echo "<td><a href="Figures/WebLogo/Pool_Data/Pool_Data-TC.fa">Pool_Data-TC.fa</a><br/>" >> $outfilePoolData + echo "<img src="Figures/WebLogo/Pool_Data/Pool_Data-TC-Probability.png"/><br/></td>" >> $outfilePoolData + fi + # T>G + if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/Pool_Data/Pool_Data-TG-Probability.png" ]]; then + echo "<td>WARNING: No sequence for T>G </br> </td>" >> $outfilePoolData + else + echo "<td><a href="Figures/WebLogo/Pool_Data/Pool_Data-TG.fa">Pool_Data-TG.fa</a><br/>" >> $outfilePoolData + echo "<img src="Figures/WebLogo/Pool_Data/Pool_Data-TG-Probability.png"/><br/></td>" >> $outfilePoolData + fi + echo "</tr>" >> $outfilePoolData + echo "</table>" >> $outfilePoolData + + echo "</body></html>" >> $outfilePoolData + +fi # End if --poolData + +fi # End if [ -d $output_dir/Mutational_Analysis/Figures ] + +echo "</body></html>" >> $html + +exit 0 +