Progress
| info | |||||||||||||||
| ----------------------------------- | |||||||||||||||
| Sample $count of patient $id is an archive file, using IMGT Loader | |||||||||||||||
| Sample $count of patient $id is not a zip file so assuming fasta/fastq, using igBLASTn | |||||||||||||||
| ----------------------------------- | |||||||||||||||
| merging | |||||||||||||||
| done | |||||||||||||||
| ----------------------------------- | |||||||||||||||
| plotting | |||||||||||||||
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diff -r e35b82f31ec7 -r 124b7fd92a3e report_clonality/naive_cdr3_char.htm
--- a/report_clonality/naive_cdr3_char.htm Thu Aug 08 07:40:36 2019 -0400
+++ b/report_clonality/naive_cdr3_char.htm Thu Feb 25 13:36:15 2021 +0000
@@ -1,101 +1,101 @@
-
-
-
-
-
-
-
-
-
-
-
-
" > $2 -echo "" >> $2
-echo "
" >> $2 -echo "Table showing the number and percentage of (unique) productive and unproductive sequences per donor and per replicate.
" >> $2 -echo "The definition of unique sequences is based on the clonal type definition filter setting chosen. " >> $2 -echo "Report on:" >> $outputFile
-
-mkdir $outputDir/circos
-cp -R $dir/circos/* $outputDir/circos/
-
-USECIRCOS="no"
-path_to_circos=$(which circos)
-if [ -x "$path_to_circos" ]; then
- USECIRCOS="yes"
-fi
-
-echo "Using Circos: $USECIRCOS"
-sed -i "s%DATA_DIR%$outputDir/circos%" $outputDir/circos/circos.conf
-for sample in $samples; do #output the samples to a file and create the circos plots with the R script output
- echo " $sample" >> $outputFile
-
- if [[ "$USECIRCOS" != "yes" ]]; then
- continue
- fi
-
- circos_file="$outputDir/${sample}_VJ_circos.txt"
- sed -i -- 's%/%:%g' $circos_file
- echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
- echo "Circos tools command:"
- echo "cat \"${circos_file}\" | parse-table -configfile $dir/circos/parse-table.conf 2>&1 | make-conf -dir $outputDir/circos/"
- cat "${circos_file}" | parse-table -configfile $dir/circos/parse-table.conf 2>&1 | make-conf -dir $outputDir/circos/
-
- echo "Circos command:"
- echo "circos -conf $outputDir/circos/circos.conf 2>&1"
- circos -conf $outputDir/circos/circos.conf 2>&1
- mv $outputDir/circos/circos.png $outputDir/circosVJ_${sample}.png
- mv $outputDir/circos/circos.svg $outputDir/circosVJ_${sample}.svg
-
-
- if [[ "$useD" == "true" ]] ; then
- circos_file="$outputDir/${sample}_VD_circos.txt"
- sed -i -- 's%/%:%g' $circos_file
- echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
- cat "${circos_file}" | parse-table -configfile $dir/circos/parse-table.conf 2>&1 | make-conf -dir $outputDir/circos/
- sed -i -- 's%/%:%g' $outputDir/circos/cells.txt
- circos -conf $outputDir/circos/circos.conf 2>&1
- mv $outputDir/circos/circos.png $outputDir/circosVD_${sample}.png
- mv $outputDir/circos/circos.svg $outputDir/circosVD_${sample}.svg
-
- circos_file="$outputDir/${sample}_DJ_circos.txt"
- sed -i -- 's%/%:%g' $circos_file
- echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
- cat "${circos_file}" | parse-table -configfile $dir/circos/parse-table.conf 2>&1 | make-conf -dir $outputDir/circos/
- sed -i -- 's%/%:%g' $outputDir/circos/cells.txt
- circos -conf $outputDir/circos/circos.conf 2>&1
- mv $outputDir/circos/circos.png $outputDir/circosDJ_${sample}.png
- mv $outputDir/circos/circos.svg $outputDir/circosDJ_${sample}.svg
- fi
-done
-echo " " >> $outputFile
-echo "" >> $outputFile
-echo "" >> $outputFile
-echo "" >> $outputFile
-echo "" >> $outputFile
-echo "" >> $outputFile
-
-echo "
" >> $outputFile
-
-
-#circos
-
-if [[ "$USECIRCOS" == "yes" ]]; then
-
- echo "" >> $outputFile
-fi
-#echo "" >> $outputFile
-
-hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)"
-echo "$hasReplicateColumn"
-#if its a 'new' merged file with replicate info
-if [[ "$hasReplicateColumn" == "Yes" && "${clonality_method}" != "none" ]] ; then
- if [[ "${clonality_method}" == "boyd" ]] ; then
- echo "
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+CDR3 characteristics tab
- -This tab gives information on the -different characteristics of the CDR3.
- -Graphs
- -length distribution of CDR3
- -Graph visualizing for each donor the -distribution of the CDR3 length in amino acids between all sequences.
- -Amino acid composition of CDR3
- -Bar graph visualizing for each donor how -frequent each amino acid is used in the CDR3 of all sequences. The red colour -in the background indicate positively charged amino acids, and the blue colour -in the background indicate negatively charged amino acids. The amino acids are -ordered from hydrophilic (left) to hydrophobic (right).
- -Table
- -Table showing for each donor the median -CDR3 length.
- -- -
+
+
+
+
+
+
diff -r e35b82f31ec7 -r 124b7fd92a3e report_clonality/naive_circos.htm
--- a/report_clonality/naive_circos.htm Thu Aug 08 07:40:36 2019 -0400
+++ b/report_clonality/naive_circos.htm Thu Feb 25 13:36:15 2021 +0000
@@ -1,59 +1,59 @@
-
-
-
-
-
-
-
-
-
-
-
-CDR3 characteristics tab
+ +This tab gives information on the +different characteristics of the CDR3.
+ +Graphs
+ +length distribution of CDR3
+ +Graph visualizing for each donor the +distribution of the CDR3 length in amino acids between all sequences.
+ +Amino acid composition of CDR3
+ +Bar graph visualizing for each donor how +frequent each amino acid is used in the CDR3 of all sequences. The red colour +in the background indicate positively charged amino acids, and the blue colour +in the background indicate negatively charged amino acids. The amino acids are +ordered from hydrophilic (left) to hydrophobic (right).
+ +Table
+ +Table showing for each donor the median +CDR3 length.
+ ++ +
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+Martin Krzywinski, Jacqueline Schein, İnan -Birol, Joseph Connors, Randy Gascoyne, Doug Horsman, Steven J. Jones and Marco -A. Marra (2009). Circos: An information aesthetic for comparative genomics. In Genome -Research 10.1101/gr.092759.109.
- -Circos plot showing the V-D, V-J, and D-J gen usage. -The thicker the line the more frequent this gene combination is used.
- -
+
+
+
+
+
+
diff -r e35b82f31ec7 -r 124b7fd92a3e report_clonality/naive_clonality.htm
--- a/report_clonality/naive_clonality.htm Thu Aug 08 07:40:36 2019 -0400
+++ b/report_clonality/naive_clonality.htm Thu Feb 25 13:36:15 2021 +0000
@@ -1,67 +1,67 @@
-
-
-
-
-
-
-
-
-
-
-
-Martin Krzywinski, Jacqueline Schein, İnan +Birol, Joseph Connors, Randy Gascoyne, Doug Horsman, Steven J. Jones and Marco +A. Marra (2009). Circos: An information aesthetic for comparative genomics. In Genome +Research 10.1101/gr.092759.109.
+ +Circos plot showing the V-D, V-J, and D-J gen usage. +The thicker the line the more frequent this gene combination is used.
+ +
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+For each donor a -subtab is provided containing information on the sequence overlap between -replicates of the different replicates of one donor. Dependent on the settings -of the Shared clonal types / clonality filter a clonality score is given. The clonality -score is calculated according to the formula described by Boyd -et al, PMID: 20161664.
- -For each -individual replicate the number of reads is reported. In addition, the number -of coincidences between the different replicates of the same donor are reported. -
- -- -
+
+
+
+
+
+
diff -r e35b82f31ec7 -r 124b7fd92a3e report_clonality/naive_compare.htm
--- a/report_clonality/naive_compare.htm Thu Aug 08 07:40:36 2019 -0400
+++ b/report_clonality/naive_compare.htm Thu Feb 25 13:36:15 2021 +0000
@@ -1,61 +1,61 @@
-
-
-
-
-
-
-
-
-
-
-
-For each donor a +subtab is provided containing information on the sequence overlap between +replicates of the different replicates of one donor. Dependent on the settings +of the Shared clonal types / clonality filter a clonality score is given. The clonality +score is calculated according to the formula described by Boyd +et al, PMID: 20161664.
+ +For each +individual replicate the number of reads is reported. In addition, the number +of coincidences between the different replicates of the same donor are reported. +
+ ++ +
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+The tab allows -you to compare the VD, VJ and DJ heatmaps of multiple donors to each other.
- -By ticking the include box of a donor, the three -heatmaps of this donor is visualized underneath eachother. By clicking the -include box of multiple replicates the heatmaps of these replicates are visualized -next to each other allowing easy comparison of heatmaps.
- -- -
+
+
+
+
+
+
diff -r e35b82f31ec7 -r 124b7fd92a3e report_clonality/naive_downloads.htm
--- a/report_clonality/naive_downloads.htm Thu Aug 08 07:40:36 2019 -0400
+++ b/report_clonality/naive_downloads.htm Thu Feb 25 13:36:15 2021 +0000
@@ -1,197 +1,197 @@
-
-
-
-
-
-
-
-
-
-
-
-The tab allows +you to compare the VD, VJ and DJ heatmaps of multiple donors to each other.
+ +By ticking the include box of a donor, the three +heatmaps of this donor is visualized underneath eachother. By clicking the +include box of multiple replicates the heatmaps of these replicates are visualized +next to each other allowing easy comparison of heatmaps.
+ ++ +
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+Downloads -tab
- -Description
- -The -filtered dataset: Allows you to download information on V D and J gene usage, -the junctions and the amino acid sequence of the sequences that passed the chosen -filter settings. Note: this file contains only 1 sequences of a replicate -sequence.
- -Gene -frequencies
- -The dataset used to generate the distribution -of V gene families graph: Downloads a table with information used to generate -the distribution of V gene families graph.
- -The dataset used to generate the -distribution of D gene families graph: Downloads a table with information used -to generate the distribution of D gene families graph.
- -The -dataset used to generate the relative frequency of V gene usage graph: -Downloads the data used to generate the relative frequency of V gene usage -graph. In addition information on the chromosomal order of the V genes can be -found.
- -The -dataset used to generate the relative frequency of D gene usage graph: -Downloads the data used to generate the relative frequency of D gene usage -graph. In addition information on the chromosomal order of the D genes can be -found.
- -The -dataset used to generate the relative frequency of J gene usage graph: Downloads -the data used to generate the relative frequency of J gene usage graph. In -addition information on the chromosomal order of the J genes can be found.
- -The dataset used to generate the relative frequency of the D -reading frame graph: Downloads -the data used to generate the relative frequency of the D reading frame.
- -CDR3 characteristics
- -The dataset used to generate the CDR3 -length frequency graph: Downloads a table with information used for the -length distribution of CDR3 plot.
- -The -dataset used to generate the Amino Acid Composition in the CDR3 graph: -Downloads the frequency of the different amino acids in the CDR3 of all -filtered sequences. This data set is used for the generation of the Amino Acid -Composition in the CDR3 graph. In addition the order of amino acids based on hydrophobicity -in included.
- -Heatmaps
- -The -data used to generate the VD heatmap for donor name: -Downloads the data set used for the generation of the VD heatmap. For each -uploaded donor a separate download is generated.
- -The -data used to generate the VJ heatmap for donor name: -Downloads the data set used for the generation of the VJ heatmap. For each -uploaded donor a separate download is generated.
- -The -data used to generate the DJ heatmap for sample name: -Downloads the data set used for the generation of the DJ heatmap. For each -uploaded donor a separate download is generated.
- -Circos
- -The -data used to generate the VD circus plots for donor name: -Downloads the data set used for the generation of the VD heatmap. For each -uploaded donor a separate download is generated.
- -The -data used to generate the VJ circus plots for donor name: -Downloads the data set used for the generation of the VJ heatmap. For each -uploaded donor a separate download is generated.
- -The -data used to generate the DJ circus plots for sample name: -Downloads the data set used for the generation of the DJ heatmap. For each -uploaded donor a separate download is generated.
- -Clonality
- -The -dataset used to calculate clonality score: Allows you to -download information on V D and J gene usage, the junctions and the amino acid -sequence of the sequences that passed the chosen filter settings. Note: this -file contains all the replicate sequences form the different input files.
- -Sequences -that are present in more than one replicate: Allows you to -download a table containing all the sequences that were present in more than -one replicate. It provides the concidence type, clonaltype, sequence name, -replicate number, and the nucleotide sequence
- -- -
+
+
+
+
+
+
diff -r e35b82f31ec7 -r 124b7fd92a3e report_clonality/naive_gene_freq.htm
--- a/report_clonality/naive_gene_freq.htm Thu Aug 08 07:40:36 2019 -0400
+++ b/report_clonality/naive_gene_freq.htm Thu Feb 25 13:36:15 2021 +0000
@@ -1,220 +1,220 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-Downloads +tab
+ +Description
+ +The +filtered dataset: Allows you to download information on V D and J gene usage, +the junctions and the amino acid sequence of the sequences that passed the chosen +filter settings. Note: this file contains only 1 sequences of a replicate +sequence.
+ +Gene +frequencies
+ +The dataset used to generate the distribution +of V gene families graph: Downloads a table with information used to generate +the distribution of V gene families graph.
+ +The dataset used to generate the +distribution of D gene families graph: Downloads a table with information used +to generate the distribution of D gene families graph.
+ +The +dataset used to generate the relative frequency of V gene usage graph: +Downloads the data used to generate the relative frequency of V gene usage +graph. In addition information on the chromosomal order of the V genes can be +found.
+ +The +dataset used to generate the relative frequency of D gene usage graph: +Downloads the data used to generate the relative frequency of D gene usage +graph. In addition information on the chromosomal order of the D genes can be +found.
+ +The +dataset used to generate the relative frequency of J gene usage graph: Downloads +the data used to generate the relative frequency of J gene usage graph. In +addition information on the chromosomal order of the J genes can be found.
+ +The dataset used to generate the relative frequency of the D +reading frame graph: Downloads +the data used to generate the relative frequency of the D reading frame.
+ +CDR3 characteristics
+ +The dataset used to generate the CDR3 +length frequency graph: Downloads a table with information used for the +length distribution of CDR3 plot.
+ +The +dataset used to generate the Amino Acid Composition in the CDR3 graph: +Downloads the frequency of the different amino acids in the CDR3 of all +filtered sequences. This data set is used for the generation of the Amino Acid +Composition in the CDR3 graph. In addition the order of amino acids based on hydrophobicity +in included.
+ +Heatmaps
+ +The +data used to generate the VD heatmap for donor name: +Downloads the data set used for the generation of the VD heatmap. For each +uploaded donor a separate download is generated.
+ +The +data used to generate the VJ heatmap for donor name: +Downloads the data set used for the generation of the VJ heatmap. For each +uploaded donor a separate download is generated.
+ +The +data used to generate the DJ heatmap for sample name: +Downloads the data set used for the generation of the DJ heatmap. For each +uploaded donor a separate download is generated.
+ +Circos
+ +The +data used to generate the VD circus plots for donor name: +Downloads the data set used for the generation of the VD heatmap. For each +uploaded donor a separate download is generated.
+ +The +data used to generate the VJ circus plots for donor name: +Downloads the data set used for the generation of the VJ heatmap. For each +uploaded donor a separate download is generated.
+ +The +data used to generate the DJ circus plots for sample name: +Downloads the data set used for the generation of the DJ heatmap. For each +uploaded donor a separate download is generated.
+ +Clonality
+ +The +dataset used to calculate clonality score: Allows you to +download information on V D and J gene usage, the junctions and the amino acid +sequence of the sequences that passed the chosen filter settings. Note: this +file contains all the replicate sequences form the different input files.
+ +Sequences +that are present in more than one replicate: Allows you to +download a table containing all the sequences that were present in more than +one replicate. It provides the concidence type, clonaltype, sequence name, +replicate number, and the nucleotide sequence
+ ++ +
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Gene frequencies tab
- -This tab gives
-information on the frequency of V, D and J gene usage.
Graphs
- -Distribution of
-V gene families
Bar graph showing the frequency of V gene family usage
-in all uploaded donors.
Relative
-frequency of V gene usage
Bar graph showing the frequency of V genes in all
-uploaded donors. The order of the V genes on the x-axis can be altered by
-altering the Order of V(D)J genes
-in graphs filter on the main page of the Immune repertoire pipeline.
Relative
-frequency of D gene usage
Bar graph showing the frequency of D genes in all uploaded donors. The
-order of the D genes on the x-axis can be altered by altering the Order of V(D)J genes in graphs filter on
-the main page of the Immune repertoire pipeline.
Relative
-frequency of J gene usage
Bar graph showing the frequency of J genes in all uploaded donors. The
-order of the J genes on the x-axis can be altered by altering the Order of V(D)J genes in graphs filter on
-the main page of the Immune repertoire pipeline.
D
-reading frame
Bar graph visualizing the frequency by which each D reading frame is -used in each donor.
- -
+
+
+
+
+
+
diff -r e35b82f31ec7 -r 124b7fd92a3e report_clonality/naive_heatmap.htm
--- a/report_clonality/naive_heatmap.htm Thu Aug 08 07:40:36 2019 -0400
+++ b/report_clonality/naive_heatmap.htm Thu Feb 25 13:36:15 2021 +0000
@@ -1,57 +1,57 @@
-
-
-
-
-
-
-
-
-
-
-
-Gene frequencies tab
+ +This tab gives
+information on the frequency of V, D and J gene usage.
Graphs
+ +Distribution of
+V gene families
Bar graph showing the frequency of V gene family usage
+in all uploaded donors.
Relative
+frequency of V gene usage
Bar graph showing the frequency of V genes in all
+uploaded donors. The order of the V genes on the x-axis can be altered by
+altering the Order of V(D)J genes
+in graphs filter on the main page of the Immune repertoire pipeline.
Relative
+frequency of D gene usage
Bar graph showing the frequency of D genes in all uploaded donors. The
+order of the D genes on the x-axis can be altered by altering the Order of V(D)J genes in graphs filter on
+the main page of the Immune repertoire pipeline.
Relative
+frequency of J gene usage
Bar graph showing the frequency of J genes in all uploaded donors. The
+order of the J genes on the x-axis can be altered by altering the Order of V(D)J genes in graphs filter on
+the main page of the Immune repertoire pipeline.
D
+reading frame
Bar graph visualizing the frequency by which each D reading frame is +used in each donor.
+ +
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+In this tab -heatmaps are provided showing the frequency of different combinations V and D, -D and J and V and J genes according together. For each donor a subtab with all -three heatmaps is provided.
- -- -
+
+
+
+
+
+
diff -r e35b82f31ec7 -r 124b7fd92a3e report_clonality/naive_junction.htm
--- a/report_clonality/naive_junction.htm Thu Aug 08 07:40:36 2019 -0400
+++ b/report_clonality/naive_junction.htm Thu Feb 25 13:36:15 2021 +0000
@@ -1,206 +1,206 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-In this tab +heatmaps are provided showing the frequency of different combinations V and D, +D and J and V and J genes according together. For each donor a subtab with all +three heatmaps is provided.
+ ++ +
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Junction -analysis tab
- -Tables:
- -The unique -rearrangements are separated in sequences that contain both a -V, D and J gene and sequences that contain only a V and J gene.
- -Productive mean
-tables
Reports -for each donor the number of productive sequences and the mean number of -deletions, N-nucleotides and P-nucleotides. -For explanation about the different deletions and N and P nucleotides see -figure above.
- -Unproductive
-mean table
Reports -for each donor the number of unproductive sequences and the mean number of -deletions, N-nucleotides and P-nucleotides. -For explanation about the different deletions and N and P nucleotides see -figure above.
- -Productive
-median table
Reports -for each donor the number of productive sequences and the median number of -deletions, N-nucleotides and P-nucleotides. -For explanation about the different deletions and N and P nucleotides see -figure above.
- -Unproductive
-median table
Reports -for each donor the number of unproductive sequences and the median number of -deletions, N-nucleotides and P-nucleotides. -For explanation about the different deletions and N and P nucleotides see -figure above.
- -- -
+
+
+
+
+
+
diff -r e35b82f31ec7 -r 124b7fd92a3e report_clonality/naive_overview.htm
--- a/report_clonality/naive_overview.htm Thu Aug 08 07:40:36 2019 -0400
+++ b/report_clonality/naive_overview.htm Thu Feb 25 13:36:15 2021 +0000
@@ -1,65 +1,65 @@
-
-
-
-
-
-
-
-
-
-
-
-Junction +analysis tab
+ +Tables:
+ +The unique +rearrangements are separated in sequences that contain both a +V, D and J gene and sequences that contain only a V and J gene.
+ +Productive mean
+tables
Reports +for each donor the number of productive sequences and the mean number of +deletions, N-nucleotides and P-nucleotides. +For explanation about the different deletions and N and P nucleotides see +figure above.
+ +Unproductive
+mean table
Reports +for each donor the number of unproductive sequences and the mean number of +deletions, N-nucleotides and P-nucleotides. +For explanation about the different deletions and N and P nucleotides see +figure above.
+ +Productive
+median table
Reports +for each donor the number of productive sequences and the median number of +deletions, N-nucleotides and P-nucleotides. +For explanation about the different deletions and N and P nucleotides see +figure above.
+ +Unproductive
+median table
Reports +for each donor the number of unproductive sequences and the median number of +deletions, N-nucleotides and P-nucleotides. +For explanation about the different deletions and N and P nucleotides see +figure above.
+ ++ +
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+Table showing the number and percentage of -(unique) productive and unproductive sequences per sample and per replicate.
- -- -
The definition -of unique sequences is based on the clonal type definition filter setting -chosen.
- -- -
+
+
+
+
+
+
diff -r e35b82f31ec7 -r 124b7fd92a3e report_clonality/pure-min.css
--- a/report_clonality/pure-min.css Thu Aug 08 07:40:36 2019 -0400
+++ b/report_clonality/pure-min.css Thu Feb 25 13:36:15 2021 +0000
@@ -1,11 +1,11 @@
-/*!
-Pure v0.6.0
-Copyright 2014 Yahoo! Inc. All rights reserved.
-Licensed under the BSD License.
-https://github.com/yahoo/pure/blob/master/LICENSE.md
-*/
-/*!
-normalize.css v^3.0 | MIT License | git.io/normalize
-Copyright (c) Nicolas Gallagher and Jonathan Neal
-*/
+/*!
+Pure v0.6.0
+Copyright 2014 Yahoo! Inc. All rights reserved.
+Licensed under the BSD License.
+https://github.com/yahoo/pure/blob/master/LICENSE.md
+*/
+/*!
+normalize.css v^3.0 | MIT License | git.io/normalize
+Copyright (c) Nicolas Gallagher and Jonathan Neal
+*/
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diff -r e35b82f31ec7 -r 124b7fd92a3e report_clonality/r_wrapper.sh
--- a/report_clonality/r_wrapper.sh Thu Aug 08 07:40:36 2019 -0400
+++ b/report_clonality/r_wrapper.sh Thu Feb 25 13:36:15 2021 +0000
@@ -1,391 +1,391 @@
-#!/bin/bash
-
-inputFile=$1
-outputDir=$3
-outputFile=$3/index.html #$2
-clonalType=$4
-species=$5
-locus=$6
-filterproductive=$7
-clonality_method=$8
-
-dir="$(cd "$(dirname "$0")" && pwd)"
-useD="false"
-if grep -q "$species.*${locus}D" "$dir/genes.txt" ; then
- echo "species D region in reference db"
- useD="true"
-fi
-echo "$species"
-if [[ "$species" == *"custom"* ]] ; then
- loci=(${locus//;/ })
- useD="true"
- echo "${loci[@]}"
- if [[ "${#loci[@]}" -eq "2" ]] ; then
- useD="false"
- fi
-fi
-mkdir $3
-cp $dir/genes.txt $outputDir
-Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType "$species" "$locus" $filterproductive ${clonality_method} 2>&1
-cp $dir/tabber.js $outputDir
-cp $dir/style.css $outputDir
-cp $dir/script.js $outputDir
-cp $dir/jquery-1.11.0.min.js $outputDir
-cp $dir/pure-min.css $outputDir
-cp $dir/IGH_junctie_analyse.png $outputDir
-samples=`cat $outputDir/samples.txt`
-
-echo "Table showing the number and percentage of +(unique) productive and unproductive sequences per sample and per replicate.
+ ++ +
The definition +of unique sequences is based on the clonal type definition filter setting +chosen.
+ ++ +
Click here for the results
Tip: Open it in a new tab (middle mouse button or right mouse button -> 'open in new tab' on the link above)" > $2 -echo "
| Donor/Replicate | All | Productive | Unique Productive | Unproductive | Unique Unproductive |
|---|---|---|---|---|---|
| $sample | " >> $2 - echo "$all | " >> $2 - if [[ "$productive" != "0" ]] ; then - echo "$productive (${perc_prod}%) | " >> $2 - echo "$productive_unique (${perc_prod_un}%) | " >> $2 - echo "$unproductive (${perc_unprod}%) | " >> $2 - echo "$unproductive_unique (${perc_unprod_un}%) | No productive sequences! | " >> $2 - fi -done < $outputDir/productive_counting.txt -echo "
" >> $2 -echo "Table showing the number and percentage of (unique) productive and unproductive sequences per donor and per replicate.
" >> $2 -echo "The definition of unique sequences is based on the clonal type definition filter setting chosen. " >> $2 -echo "
" >> $outputFile
-
-
-echo "
" >> $outputFile
-if [[ "$useD" == "true" ]] ; then
- echo "
" >> $outputFile
-fi
-echo "
" >> $outputFile
-if [[ "$useD" == "true" ]] ; then
- echo "
" >> $outputFile
-fi
-echo "
" >> $outputFile - -echo "
" >> $outputFile
-
-cat $dir/naive_gene_freq.htm >> $outputFile
-
-echo "
" >> $outputFile
-
-echo "" >> $outputFile
-if [[ "$useD" == "true" ]] ; then
- echo "" >> $outputFile
-fi
-echo "" >> $outputFile
-if [[ "$useD" == "true" ]] ; then
- echo "" >> $outputFile
-fi
-echo " " >> $outputFile - -echo "
" >> $outputFile
-
-cat $dir/naive_gene_freq.htm >> $outputFile
-
-echo "" >> $outputFile
-echo "
" >> $outputFile -echo "
" >> $outputFile
-
-
-echo "" >> $outputFile
-echo "
" >> $outputFile
-
-cat $dir/naive_cdr3_char.htm >> $outputFile
-
-echo "
" >> $outputFile
-
-#Heatmaps
-
-count=1
-echo "" >> $outputFile -echo "
" >> $outputFile
-
-
-echo "| Donor | Median CDR3 Length |
|---|---|
| $Sample | $median |
" >> $outputFile
-for sample in $samples; do
- echo "
" >> $outputFile
- count=$((count+1))
-done
-
-cat $dir/naive_heatmap.htm >> $outputFile
-
-echo "
 | " >> $outputFile
- fi
- echo " | " >> $outputFile
- if [[ "$useD" == "true" ]] ; then
- echo " | " >> $outputFile
- fi
- echo "
| ID | Include |
|---|---|
| $sample |
" >> $outputFile
-echo "
" >> $outputFile
-echo "
" >> $outputFile
-echo "
" >> $outputFile
-
-cat $dir/naive_compare.htm >> $outputFile
-
-echo "
" >> $outputFile
- for sample in $samples; do
- echo "
" >> $outputFile
- count=$((count+1))
- done
-
- cat $dir/naive_circos.htm >> $outputFile
-
- echo "
| V-D |  |
| V-J |  |
| D-J |  |
" >> $outputFile
- else
- echo "" >> $outputFile
-fi
-
-#hasJunctionData="$(if head -n 1 $inputFile | grep -qE '3V.REGION.trimmed.nt.nb'; then echo 'Yes'; else echo 'No'; fi)"
-
-#if [[ "$hasJunctionData" == "Yes" ]] ; then
-if [ -a "$outputDir/junctionAnalysisProd_mean_wD.txt" ] ; then
- echo "
" > $2 +echo "" >> $2
+echo "
" >> $2 +echo "Table showing the number and percentage of (unique) productive and unproductive sequences per donor and per replicate.
" >> $2 +echo "The definition of unique sequences is based on the clonal type definition filter setting chosen. " >> $2 +echo "Report on:" >> $outputFile
+
+mkdir $outputDir/circos
+cp -R $dir/circos/* $outputDir/circos/
+
+USECIRCOS="no"
+path_to_circos=$(which circos)
+if [ -x "$path_to_circos" ]; then
+ USECIRCOS="yes"
+fi
+
+echo "Using Circos: $USECIRCOS"
+sed -i "s%DATA_DIR%$outputDir/circos%" $outputDir/circos/circos.conf
+for sample in $samples; do #output the samples to a file and create the circos plots with the R script output
+ echo " $sample" >> $outputFile
+
+ if [[ "$USECIRCOS" != "yes" ]]; then
+ continue
+ fi
+
+ circos_file="$outputDir/${sample}_VJ_circos.txt"
+ sed -i -- 's%/%:%g' $circos_file
+ echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
+ echo "Circos tools command:"
+ echo "cat \"${circos_file}\" | parse-table -configfile $dir/circos/parse-table.conf 2>&1 | make-conf -dir $outputDir/circos/"
+ cat "${circos_file}" | parse-table -configfile $dir/circos/parse-table.conf 2>&1 | make-conf -dir $outputDir/circos/
+
+ echo "Circos command:"
+ echo "circos -conf $outputDir/circos/circos.conf 2>&1"
+ circos -conf $outputDir/circos/circos.conf 2>&1
+ mv $outputDir/circos/circos.png $outputDir/circosVJ_${sample}.png
+ mv $outputDir/circos/circos.svg $outputDir/circosVJ_${sample}.svg
+
+
+ if [[ "$useD" == "true" ]] ; then
+ circos_file="$outputDir/${sample}_VD_circos.txt"
+ sed -i -- 's%/%:%g' $circos_file
+ echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
+ cat "${circos_file}" | parse-table -configfile $dir/circos/parse-table.conf 2>&1 | make-conf -dir $outputDir/circos/
+ sed -i -- 's%/%:%g' $outputDir/circos/cells.txt
+ circos -conf $outputDir/circos/circos.conf 2>&1
+ mv $outputDir/circos/circos.png $outputDir/circosVD_${sample}.png
+ mv $outputDir/circos/circos.svg $outputDir/circosVD_${sample}.svg
+
+ circos_file="$outputDir/${sample}_DJ_circos.txt"
+ sed -i -- 's%/%:%g' $circos_file
+ echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
+ cat "${circos_file}" | parse-table -configfile $dir/circos/parse-table.conf 2>&1 | make-conf -dir $outputDir/circos/
+ sed -i -- 's%/%:%g' $outputDir/circos/cells.txt
+ circos -conf $outputDir/circos/circos.conf 2>&1
+ mv $outputDir/circos/circos.png $outputDir/circosDJ_${sample}.png
+ mv $outputDir/circos/circos.svg $outputDir/circosDJ_${sample}.svg
+ fi
+done
+echo " " >> $outputFile
+echo "" >> $outputFile
+echo "" >> $outputFile
+echo "" >> $outputFile
+echo "" >> $outputFile
+echo "" >> $outputFile
+
+echo "
" >> $outputFile
+
+
+#circos
+
+if [[ "$USECIRCOS" == "yes" ]]; then
+
+ echo "" >> $outputFile
+fi
+#echo "" >> $outputFile
+
+hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)"
+echo "$hasReplicateColumn"
+#if its a 'new' merged file with replicate info
+if [[ "$hasReplicateColumn" == "Yes" && "${clonality_method}" != "none" ]] ; then
+ if [[ "${clonality_method}" == "boyd" ]] ; then
+ echo "
" >> $outputFile
- fi
-
- for sample in $samples; do
- echo "${clonality_method}"
-
- echo "" >> $outputFile
-
- if [[ "${clonality_method}" == "boyd" ]] ; then
- clonalityScore="$(cat $outputDir/lymphclon_clonality_${sample}.txt)"
- echo "
" >> $outputFile
- done
-
- cat $dir/naive_clonality.htm >> $outputFile
-
- echo "
| Clonality Score: | $clonalityScore |
| Replicate ID | Number of Sequences |
| $replicate | $reads |
| Sum | $readsSum |
| Number of replicates containing the coincidence | Number of sequences shared between replicates |
| $type | $count |
| $type | $count |
" >> $outputFile
- echo "
" >> $outputFile
-
- echo "
" >> $outputFile
-
- echo "
" >> $outputFile
-
- echo "
" >> $outputFile
-
- echo "
" >> $outputFile
-
- # again for no-d
- echo "
" >> $outputFile
-
- echo "
" >> $outputFile
-
- echo "
" >> $outputFile
-
- echo "
" >> $outputFile
-
- cat $dir/naive_junction.htm >> $outputFile
-
- echo "
" >> $outputFile
-fi
-
-echo "" >> $outputFile
-
- echo "Unique rearrangements with a V, D and J gene assigned
| Donor | Number of sequences | V.DEL | P1 | N1 | P2 | DEL.D | D.DEL | P3 | N2 | P4 | DEL.J | Total.Del | Total.N | Total.P | CDR3.Length |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| $Sample | $unique | $VDEL | $P1 | $N1 | $P2 | $DELD | $DDEL | $P3 | $N2 | $P4 | $DELJ | $TotalDel | $TotalN | $TotalP | $median |
| Donor | Number of sequences | V.DEL | P1 | N1 | P2 | DEL.D | D.DEL | P3 | N2 | P4 | DEL.J | Total.Del | Total.N | Total.P | CDR3.Length |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| $Sample | $unique | $VDEL | $P1 | $N1 | $P2 | $DELD | $DDEL | $P3 | $N2 | $P4 | $DELJ | $TotalDel | $TotalN | $TotalP | - |
| Donor | Number of sequences | V.DEL | P1 | N1 | P2 | DEL.D | D.DEL | P3 | N2 | P4 | DEL.J | Total.Del | Total.N | Total.P | CDR3.Length |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| $Sample | $unique | $VDEL | $P1 | $N1 | $P2 | $DELD | $DDEL | $P3 | $N2 | $P4 | $DELJ | $TotalDel | $TotalN | $TotalP | $median |
| Donor | Number of sequences | V.DEL | P1 | N1 | P2 | DEL.D | D.DEL | P3 | N2 | P4 | DEL.J | Total.Del | Total.N | Total.P | CDR3.Length |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| $Sample | $unique | $VDEL | $P1 | $N1 | $P2 | $DELD | $DDEL | $P3 | $N2 | $P4 | $DELJ | $TotalDel | $TotalN | $TotalP | - |
Unique rearrangements with only a V and J gene assigned
| Donor | Number of sequences | V.DEL | P1 | N | P2 | DEL.J | Total.Del | Total.N | Total.P | CDR3.Length |
|---|---|---|---|---|---|---|---|---|---|---|
| $Sample | $unique | $VDEL | $P1 | $N1 | $P2 | $DELJ | $TotalDel | $TotalN | $TotalP | $median |
| Donor | Number of sequences | V.DEL | P1 | N | P2 | DEL.J | Total.Del | Total.N | Total.P | CDR3.Length |
|---|---|---|---|---|---|---|---|---|---|---|
| $Sample | $unique | $VDEL | $P1 | $N1 | $P2 | $DELJ | $TotalDel | $TotalN | $TotalP | - |
| Donor | Number of sequences | V.DEL | P1 | N | P2 | DEL.J | Total.Del | Total.N | Total.P | CDR3.Length |
|---|---|---|---|---|---|---|---|---|---|---|
| $Sample | $unique | $VDEL | $P1 | $N1 | $P2 | $DELJ | $TotalDel | $TotalN | $TotalP | $median |
| Donor | Number of sequences | V.DEL | P1 | N | P2 | DEL.J | Total.Del | Total.N | Total.P | CDR3.Length |
|---|---|---|---|---|---|---|---|---|---|---|
| $Sample | $unique | $VDEL | $P1 | $N1 | $P2 | $DELJ | $TotalDel | $TotalN | $TotalP | - |
" >> $outputFile
-echo "" >> $outputFile
-echo "
" >> $outputFile
-
-cat $dir/naive_downloads.htm >> $outputFile
-
-echo "
" >> $outputFile
+#!/bin/bash
+
+inputFile=$1
+outputDir=$3
+outputFile=$3/index.html #$2
+clonalType=$4
+species=$5
+locus=$6
+filterproductive=$7
+clonality_method=$8
+
+dir="$(cd "$(dirname "$0")" && pwd)"
+useD="false"
+if grep -q "$species.*${locus}D" "$dir/genes.txt" ; then
+ echo "species D region in reference db"
+ useD="true"
+fi
+echo "$species"
+if [[ "$species" == *"custom"* ]] ; then
+ loci=(${locus//;/ })
+ useD="true"
+ echo "${loci[@]}"
+ if [[ "${#loci[@]}" -eq "2" ]] ; then
+ useD="false"
+ fi
+fi
+mkdir $3
+cp $dir/genes.txt $outputDir
+Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType "$species" "$locus" $filterproductive ${clonality_method} 2>&1
+cp $dir/tabber.js $outputDir
+cp $dir/style.css $outputDir
+cp $dir/script.js $outputDir
+cp $dir/jquery-1.11.0.min.js $outputDir
+cp $dir/pure-min.css $outputDir
+cp $dir/IGH_junctie_analyse.png $outputDir
+samples=`cat $outputDir/samples.txt`
+
+echo "| Description | Link |
|---|---|
| The filtered dataset | Download |
| Gene frequencies | |
| The dataset used to generate the distribution of V gene families graph | Download |
| The dataset used to generate the distribution of D gene families graph | Download |
| The dataset used to generate the relative frequency of V gene usage graph | Download |
| The dataset used to generate the relative frequency of D gene usage graph | Download |
| The dataset used to generate the relative frequency of J gene usage graph | Download |
| The dataset used to generate the relative frequency of the D reading frame graph | Download |
| CDR3 Characteristics | |
| The dataset used to generate the CDR3 length frequency graph | Download |
| The dataset used to generate the Amino Acid Composition in the CDR3 graph | Download |
| Heatmaps | |
| The data used to generate the VD heatmap for $sample. | Download |
| The data used to generate the VJ heatmap for $sample. | Download |
| The data used to generate the DJ heatmap for $sample. | Download |
| Circos | |
| The data used to generate the VD Circos plots for $sample. | Download |
| The data used to generate the VJ Circos plots for $sample. | Download |
| The data used to generate the DJ Circos plots for $sample. | Download |
| A frequency count of V Gene + J Gene + CDR3 | Download |
| Clonality | |
| The dataset used to calculate clonality score (Unique based on clonaltype, $clonalType) | Download |
| Sequences that are present in more than one replicate | Download |
Click here for the results
Tip: Open it in a new tab (middle mouse button or right mouse button -> 'open in new tab' on the link above)" > $2 +echo "
| Donor/Replicate | All | Productive | Unique Productive | Unproductive | Unique Unproductive |
|---|---|---|---|---|---|
| $sample | " >> $2 + echo "$all | " >> $2 + if [[ "$productive" != "0" ]] ; then + echo "$productive (${perc_prod}%) | " >> $2 + echo "$productive_unique (${perc_prod_un}%) | " >> $2 + echo "$unproductive (${perc_unprod}%) | " >> $2 + echo "$unproductive_unique (${perc_unprod_un}%) | No productive sequences! | " >> $2 + fi +done < $outputDir/productive_counting.txt +echo "
" >> $2 +echo "Table showing the number and percentage of (unique) productive and unproductive sequences per donor and per replicate.
" >> $2 +echo "The definition of unique sequences is based on the clonal type definition filter setting chosen. " >> $2 +echo "
" >> $outputFile
+
+
+echo "" >> $outputFile
+if [[ "$useD" == "true" ]] ; then
+ echo "" >> $outputFile
+fi
+echo "" >> $outputFile
+if [[ "$useD" == "true" ]] ; then
+ echo "" >> $outputFile
+fi
+echo "
" >> $outputFile + +echo "" >> $outputFile
+
+cat $dir/naive_gene_freq.htm >> $outputFile
+
+echo "
" >> $outputFile
+
+echo "" >> $outputFile
+if [[ "$useD" == "true" ]] ; then
+ echo "" >> $outputFile
+fi
+echo "" >> $outputFile
+if [[ "$useD" == "true" ]] ; then
+ echo "" >> $outputFile
+fi
+echo " " >> $outputFile + +echo "
" >> $outputFile
+
+cat $dir/naive_gene_freq.htm >> $outputFile
+
+echo "" >> $outputFile
+echo "
" >> $outputFile +echo "" >> $outputFile
+
+
+echo "" >> $outputFile
+echo "
" >> $outputFile
+
+cat $dir/naive_cdr3_char.htm >> $outputFile
+
+echo "
" >> $outputFile
+
+#Heatmaps
+
+count=1
+echo "" >> $outputFile +echo "
" >> $outputFile
+
+
+echo "| Donor | Median CDR3 Length |
|---|---|
| $Sample | $median |
" >> $outputFile
+for sample in $samples; do
+ echo "
" >> $outputFile
+ count=$((count+1))
+done
+
+cat $dir/naive_heatmap.htm >> $outputFile
+
+echo "
| " >> $outputFile
+ fi
+ echo " | " >> $outputFile
+ if [[ "$useD" == "true" ]] ; then
+ echo " | " >> $outputFile
+ fi
+ echo "
| ID | Include |
|---|---|
| $sample |
" >> $outputFile
+echo "
" >> $outputFile
+echo "
" >> $outputFile
+echo "
" >> $outputFile
+
+cat $dir/naive_compare.htm >> $outputFile
+
+echo "
" >> $outputFile
+ for sample in $samples; do
+ echo "
" >> $outputFile
+ count=$((count+1))
+ done
+
+ cat $dir/naive_circos.htm >> $outputFile
+
+ echo "
| V-D | |
| V-J | |
| D-J | |
" >> $outputFile
+ else
+ echo "" >> $outputFile
+fi
+
+#hasJunctionData="$(if head -n 1 $inputFile | grep -qE '3V.REGION.trimmed.nt.nb'; then echo 'Yes'; else echo 'No'; fi)"
+
+#if [[ "$hasJunctionData" == "Yes" ]] ; then
+if [ -a "$outputDir/junctionAnalysisProd_mean_wD.txt" ] ; then
+ echo "nav';for(arg in argsObj){this[arg]=argsObj[arg];}
-this.REclassMain=new RegExp('\\b'+this.classMain+'\\b','gi');this.REclassMainLive=new RegExp('\\b'+this.classMainLive+'\\b','gi');this.REclassTab=new RegExp('\\b'+this.classTab+'\\b','gi');this.REclassTabDefault=new RegExp('\\b'+this.classTabDefault+'\\b','gi');this.REclassTabHide=new RegExp('\\b'+this.classTabHide+'\\b','gi');this.tabs=new Array();if(this.div){this.init(this.div);this.div=null;}}
-tabberObj.prototype.init=function(e)
-{var
-childNodes,i,i2,t,defaultTab=0,DOM_ul,DOM_li,DOM_a,aId,headingElement;if(!document.getElementsByTagName){return false;}
-if(e.id){this.id=e.id;}
-this.tabs.length=0;childNodes=e.childNodes;for(i=0;i/gi," ");t.headingText=t.headingText.replace(/<[^>]+>/g,"");}
-break;}}}
-if(!t.headingText){t.headingText=i+1;}
-DOM_li=document.createElement("li");t.li=DOM_li;DOM_a=document.createElement("a");DOM_a.appendChild(document.createTextNode(t.headingText));DOM_a.href="javascript:void(null);";DOM_a.title=t.headingText;DOM_a.onclick=this.navClick;DOM_a.tabber=this;DOM_a.tabberIndex=i;if(this.addLinkId&&this.linkIdFormat){aId=this.linkIdFormat;aId=aId.replace(//gi,this.id);aId=aId.replace(//gi,i);aId=aId.replace(//gi,i+1);aId=aId.replace(//gi,t.headingText.replace(/[^a-zA-Z0-9\-]/gi,''));DOM_a.id=aId;}
-DOM_li.appendChild(DOM_a);DOM_ul.appendChild(DOM_li);}
-e.insertBefore(DOM_ul,e.firstChild);e.className=e.className.replace(this.REclassMain,this.classMainLive);this.tabShow(defaultTab);if(typeof this.onLoad=='function'){this.onLoad({tabber:this});}
-return this;};tabberObj.prototype.navClick=function(event)
-{var
-rVal,a,self,tabberIndex,onClickArgs;a=this;if(!a.tabber){return false;}
-self=a.tabber;tabberIndex=a.tabberIndex;a.blur();if(typeof self.onClick=='function'){onClickArgs={'tabber':self,'index':tabberIndex,'event':event};if(!event){onClickArgs.event=window.event;}
-rVal=self.onClick(onClickArgs);if(rVal===false){return false;}}
-self.tabShow(tabberIndex);return false;};tabberObj.prototype.tabHideAll=function()
-{var i;for(i=0;inav';for(arg in argsObj){this[arg]=argsObj[arg];}
+this.REclassMain=new RegExp('\\b'+this.classMain+'\\b','gi');this.REclassMainLive=new RegExp('\\b'+this.classMainLive+'\\b','gi');this.REclassTab=new RegExp('\\b'+this.classTab+'\\b','gi');this.REclassTabDefault=new RegExp('\\b'+this.classTabDefault+'\\b','gi');this.REclassTabHide=new RegExp('\\b'+this.classTabHide+'\\b','gi');this.tabs=new Array();if(this.div){this.init(this.div);this.div=null;}}
+tabberObj.prototype.init=function(e)
+{var
+childNodes,i,i2,t,defaultTab=0,DOM_ul,DOM_li,DOM_a,aId,headingElement;if(!document.getElementsByTagName){return false;}
+if(e.id){this.id=e.id;}
+this.tabs.length=0;childNodes=e.childNodes;for(i=0;i/gi," ");t.headingText=t.headingText.replace(/<[^>]+>/g,"");}
+break;}}}
+if(!t.headingText){t.headingText=i+1;}
+DOM_li=document.createElement("li");t.li=DOM_li;DOM_a=document.createElement("a");DOM_a.appendChild(document.createTextNode(t.headingText));DOM_a.href="javascript:void(null);";DOM_a.title=t.headingText;DOM_a.onclick=this.navClick;DOM_a.tabber=this;DOM_a.tabberIndex=i;if(this.addLinkId&&this.linkIdFormat){aId=this.linkIdFormat;aId=aId.replace(//gi,this.id);aId=aId.replace(//gi,i);aId=aId.replace(//gi,i+1);aId=aId.replace(//gi,t.headingText.replace(/[^a-zA-Z0-9\-]/gi,''));DOM_a.id=aId;}
+DOM_li.appendChild(DOM_a);DOM_ul.appendChild(DOM_li);}
+e.insertBefore(DOM_ul,e.firstChild);e.className=e.className.replace(this.REclassMain,this.classMainLive);this.tabShow(defaultTab);if(typeof this.onLoad=='function'){this.onLoad({tabber:this});}
+return this;};tabberObj.prototype.navClick=function(event)
+{var
+rVal,a,self,tabberIndex,onClickArgs;a=this;if(!a.tabber){return false;}
+self=a.tabber;tabberIndex=a.tabberIndex;a.blur();if(typeof self.onClick=='function'){onClickArgs={'tabber':self,'index':tabberIndex,'event':event};if(!event){onClickArgs.event=window.event;}
+rVal=self.onClick(onClickArgs);if(rVal===false){return false;}}
+self.tabShow(tabberIndex);return false;};tabberObj.prototype.tabHideAll=function()
+{var i;for(i=0;i
" >> $outputFile
+ fi
+
+ for sample in $samples; do
+ echo "${clonality_method}"
+
+ echo "" >> $outputFile
+
+ if [[ "${clonality_method}" == "boyd" ]] ; then
+ clonalityScore="$(cat $outputDir/lymphclon_clonality_${sample}.txt)"
+ echo "
" >> $outputFile
+ done
+
+ cat $dir/naive_clonality.htm >> $outputFile
+
+ echo "
| Clonality Score: | $clonalityScore |
| Replicate ID | Number of Sequences |
| $replicate | $reads |
| Sum | $readsSum |
| Number of replicates containing the coincidence | Number of sequences shared between replicates |
| $type | $count |
| $type | $count |
" >> $outputFile
+ echo "" >> $outputFile
+
+ echo "
" >> $outputFile
+
+ echo "
" >> $outputFile
+
+ echo "
" >> $outputFile
+
+ echo "
" >> $outputFile
+
+ # again for no-d
+ echo "
" >> $outputFile
+
+ echo "
" >> $outputFile
+
+ echo "
" >> $outputFile
+
+ echo "
" >> $outputFile
+
+ cat $dir/naive_junction.htm >> $outputFile
+
+ echo "
" >> $outputFile
+fi
+
+echo "" >> $outputFile
+
+ echo "Unique rearrangements with a V, D and J gene assigned
| Donor | Number of sequences | V.DEL | P1 | N1 | P2 | DEL.D | D.DEL | P3 | N2 | P4 | DEL.J | Total.Del | Total.N | Total.P | CDR3.Length |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| $Sample | $unique | $VDEL | $P1 | $N1 | $P2 | $DELD | $DDEL | $P3 | $N2 | $P4 | $DELJ | $TotalDel | $TotalN | $TotalP | $median |
| Donor | Number of sequences | V.DEL | P1 | N1 | P2 | DEL.D | D.DEL | P3 | N2 | P4 | DEL.J | Total.Del | Total.N | Total.P | CDR3.Length |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| $Sample | $unique | $VDEL | $P1 | $N1 | $P2 | $DELD | $DDEL | $P3 | $N2 | $P4 | $DELJ | $TotalDel | $TotalN | $TotalP | - |
| Donor | Number of sequences | V.DEL | P1 | N1 | P2 | DEL.D | D.DEL | P3 | N2 | P4 | DEL.J | Total.Del | Total.N | Total.P | CDR3.Length |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| $Sample | $unique | $VDEL | $P1 | $N1 | $P2 | $DELD | $DDEL | $P3 | $N2 | $P4 | $DELJ | $TotalDel | $TotalN | $TotalP | $median |
| Donor | Number of sequences | V.DEL | P1 | N1 | P2 | DEL.D | D.DEL | P3 | N2 | P4 | DEL.J | Total.Del | Total.N | Total.P | CDR3.Length |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| $Sample | $unique | $VDEL | $P1 | $N1 | $P2 | $DELD | $DDEL | $P3 | $N2 | $P4 | $DELJ | $TotalDel | $TotalN | $TotalP | - |
Unique rearrangements with only a V and J gene assigned
| Donor | Number of sequences | V.DEL | P1 | N | P2 | DEL.J | Total.Del | Total.N | Total.P | CDR3.Length |
|---|---|---|---|---|---|---|---|---|---|---|
| $Sample | $unique | $VDEL | $P1 | $N1 | $P2 | $DELJ | $TotalDel | $TotalN | $TotalP | $median |
| Donor | Number of sequences | V.DEL | P1 | N | P2 | DEL.J | Total.Del | Total.N | Total.P | CDR3.Length |
|---|---|---|---|---|---|---|---|---|---|---|
| $Sample | $unique | $VDEL | $P1 | $N1 | $P2 | $DELJ | $TotalDel | $TotalN | $TotalP | - |
| Donor | Number of sequences | V.DEL | P1 | N | P2 | DEL.J | Total.Del | Total.N | Total.P | CDR3.Length |
|---|---|---|---|---|---|---|---|---|---|---|
| $Sample | $unique | $VDEL | $P1 | $N1 | $P2 | $DELJ | $TotalDel | $TotalN | $TotalP | $median |
| Donor | Number of sequences | V.DEL | P1 | N | P2 | DEL.J | Total.Del | Total.N | Total.P | CDR3.Length |
|---|---|---|---|---|---|---|---|---|---|---|
| $Sample | $unique | $VDEL | $P1 | $N1 | $P2 | $DELJ | $TotalDel | $TotalN | $TotalP | - |
" >> $outputFile
+echo "" >> $outputFile
+echo "
" >> $outputFile
+
+cat $dir/naive_downloads.htm >> $outputFile
+
+echo "
" >> $outputFile
diff -r e35b82f31ec7 -r 124b7fd92a3e report_clonality/script.js
--- a/report_clonality/script.js Thu Aug 08 07:40:36 2019 -0400
+++ b/report_clonality/script.js Thu Feb 25 13:36:15 2021 +0000
@@ -1,36 +1,36 @@
-function compareAdd(id){
- var img = document.createElement('img');
- img.setAttribute('src', 'HeatmapVD_' + id + '.png');
- var td = document.createElement('td');
- td.setAttribute('id', "comparison_vd_" + id);
- td.appendChild(img)
- $('#comparison_table_vd').append(td);
-
- img = document.createElement('img');
- img.setAttribute('src', 'HeatmapVJ_' + id + '.png');
- td = document.createElement('td');
- td.setAttribute('id', "comparison_vj_" + id);
- td.appendChild(img)
- $('#comparison_table_vj').append(td);
-
- img = document.createElement('img');
- img.setAttribute('src', 'HeatmapDJ_' + id + '.png');
- td = document.createElement('td');
- td.setAttribute('id', "comparison_dj_" + id);
- td.appendChild(img)
- $('#comparison_table_dj').append(td);
-
- $('#compare_checkbox_' + id).attr('onchange', "javascript:compareRemove('" + id + "')");
-}
-
-
-function compareRemove(id){
- $("#comparison_vd_" + id).remove()
- $("#comparison_vj_" + id).remove()
- $("#comparison_dj_" + id).remove()
- $("#compare_checkbox_" + id).attr('onchange', "javascript:compareAdd('" + id + "')");
-}
-
-$( document ).ready(function () {
- $('#junction_table').tablesorter();
-})
+function compareAdd(id){
+ var img = document.createElement('img');
+ img.setAttribute('src', 'HeatmapVD_' + id + '.png');
+ var td = document.createElement('td');
+ td.setAttribute('id', "comparison_vd_" + id);
+ td.appendChild(img)
+ $('#comparison_table_vd').append(td);
+
+ img = document.createElement('img');
+ img.setAttribute('src', 'HeatmapVJ_' + id + '.png');
+ td = document.createElement('td');
+ td.setAttribute('id', "comparison_vj_" + id);
+ td.appendChild(img)
+ $('#comparison_table_vj').append(td);
+
+ img = document.createElement('img');
+ img.setAttribute('src', 'HeatmapDJ_' + id + '.png');
+ td = document.createElement('td');
+ td.setAttribute('id', "comparison_dj_" + id);
+ td.appendChild(img)
+ $('#comparison_table_dj').append(td);
+
+ $('#compare_checkbox_' + id).attr('onchange', "javascript:compareRemove('" + id + "')");
+}
+
+
+function compareRemove(id){
+ $("#comparison_vd_" + id).remove()
+ $("#comparison_vj_" + id).remove()
+ $("#comparison_dj_" + id).remove()
+ $("#compare_checkbox_" + id).attr('onchange', "javascript:compareAdd('" + id + "')");
+}
+
+$( document ).ready(function () {
+ $('#junction_table').tablesorter();
+})
diff -r e35b82f31ec7 -r 124b7fd92a3e report_clonality/style.css
--- a/report_clonality/style.css Thu Aug 08 07:40:36 2019 -0400
+++ b/report_clonality/style.css Thu Feb 25 13:36:15 2021 +0000
@@ -1,109 +1,109 @@
-/* $Id: example.css,v 1.5 2006/03/27 02:44:36 pat Exp $ */
-
-/*--------------------------------------------------
- REQUIRED to hide the non-active tab content.
- But do not hide them in the print stylesheet!
- --------------------------------------------------*/
-.tabberlive .tabbertabhide {
- display:none;
-}
-
-/*--------------------------------------------------
- .tabber = before the tabber interface is set up
- .tabberlive = after the tabber interface is set up
- --------------------------------------------------*/
-.tabber {
-}
-.tabberlive {
- margin-top:1em;
-}
-
-/*--------------------------------------------------
- ul.tabbernav = the tab navigation list
- li.tabberactive = the active tab
- --------------------------------------------------*/
-ul.tabbernav
-{
- margin:0;
- padding: 3px 0;
- border-bottom: 1px solid #778;
- font: bold 12px Verdana, sans-serif;
-}
-
-ul.tabbernav li
-{
- list-style: none;
- margin: 0;
- display: inline;
-}
-
-ul.tabbernav li a
-{
- padding: 3px 0.5em;
- margin-left: 3px;
- border: 1px solid #778;
- border-bottom: none;
- background: #DDE;
- text-decoration: none;
-}
-
-ul.tabbernav li a:link { color: #448; }
-ul.tabbernav li a:visited { color: #667; }
-
-ul.tabbernav li a:hover
-{
- color: #000;
- background: #AAE;
- border-color: #227;
-}
-
-ul.tabbernav li.tabberactive a
-{
- background-color: #fff;
- border-bottom: 1px solid #fff;
-}
-
-ul.tabbernav li.tabberactive a:hover
-{
- color: #000;
- background: white;
- border-bottom: 1px solid white;
-}
-
-/*--------------------------------------------------
- .tabbertab = the tab content
- Add style only after the tabber interface is set up (.tabberlive)
- --------------------------------------------------*/
-.tabberlive .tabbertab {
- padding:5px;
- border:1px solid #aaa;
- border-top:0;
-
- /* If you don't want the tab size changing whenever a tab is changed
- you can set a fixed height */
-
- /* height:200px; */
-
- /* If you set a fix height set overflow to auto and you will get a
- scrollbar when necessary */
-
- /* overflow:auto; */
-}
-
-/* If desired, hide the heading since a heading is provided by the tab */
-.tabberlive .tabbertab h2 {
- display:none;
-}
-.tabberlive .tabbertab h3 {
- display:none;
-}
-
-/* Example of using an ID to set different styles for the tabs on the page */
-.tabberlive#tab1 {
-}
-.tabberlive#tab2 {
-}
-.tabberlive#tab2 .tabbertab {
- height:200px;
- overflow:auto;
-}
+/* $Id: example.css,v 1.5 2006/03/27 02:44:36 pat Exp $ */
+
+/*--------------------------------------------------
+ REQUIRED to hide the non-active tab content.
+ But do not hide them in the print stylesheet!
+ --------------------------------------------------*/
+.tabberlive .tabbertabhide {
+ display:none;
+}
+
+/*--------------------------------------------------
+ .tabber = before the tabber interface is set up
+ .tabberlive = after the tabber interface is set up
+ --------------------------------------------------*/
+.tabber {
+}
+.tabberlive {
+ margin-top:1em;
+}
+
+/*--------------------------------------------------
+ ul.tabbernav = the tab navigation list
+ li.tabberactive = the active tab
+ --------------------------------------------------*/
+ul.tabbernav
+{
+ margin:0;
+ padding: 3px 0;
+ border-bottom: 1px solid #778;
+ font: bold 12px Verdana, sans-serif;
+}
+
+ul.tabbernav li
+{
+ list-style: none;
+ margin: 0;
+ display: inline;
+}
+
+ul.tabbernav li a
+{
+ padding: 3px 0.5em;
+ margin-left: 3px;
+ border: 1px solid #778;
+ border-bottom: none;
+ background: #DDE;
+ text-decoration: none;
+}
+
+ul.tabbernav li a:link { color: #448; }
+ul.tabbernav li a:visited { color: #667; }
+
+ul.tabbernav li a:hover
+{
+ color: #000;
+ background: #AAE;
+ border-color: #227;
+}
+
+ul.tabbernav li.tabberactive a
+{
+ background-color: #fff;
+ border-bottom: 1px solid #fff;
+}
+
+ul.tabbernav li.tabberactive a:hover
+{
+ color: #000;
+ background: white;
+ border-bottom: 1px solid white;
+}
+
+/*--------------------------------------------------
+ .tabbertab = the tab content
+ Add style only after the tabber interface is set up (.tabberlive)
+ --------------------------------------------------*/
+.tabberlive .tabbertab {
+ padding:5px;
+ border:1px solid #aaa;
+ border-top:0;
+
+ /* If you don't want the tab size changing whenever a tab is changed
+ you can set a fixed height */
+
+ /* height:200px; */
+
+ /* If you set a fix height set overflow to auto and you will get a
+ scrollbar when necessary */
+
+ /* overflow:auto; */
+}
+
+/* If desired, hide the heading since a heading is provided by the tab */
+.tabberlive .tabbertab h2 {
+ display:none;
+}
+.tabberlive .tabbertab h3 {
+ display:none;
+}
+
+/* Example of using an ID to set different styles for the tabs on the page */
+.tabberlive#tab1 {
+}
+.tabberlive#tab2 {
+}
+.tabberlive#tab2 .tabbertab {
+ height:200px;
+ overflow:auto;
+}
diff -r e35b82f31ec7 -r 124b7fd92a3e report_clonality/tabber.js
--- a/report_clonality/tabber.js Thu Aug 08 07:40:36 2019 -0400
+++ b/report_clonality/tabber.js Thu Feb 25 13:36:15 2021 +0000
@@ -1,40 +1,40 @@
-/* Copyright (c) 2006 Patrick Fitzgerald */
-
-function tabberObj(argsObj)
-{var arg;this.div=null;this.classMain="tabber";this.classMainLive="tabberlive";this.classTab="tabbertab";this.classTabDefault="tabbertabdefault";this.classNav="tabbernav";this.classTabHide="tabbertabhide";this.classNavActive="tabberactive";this.titleElements=['h2','h3','h4','h5','h6'];this.titleElementsStripHTML=true;this.removeTitle=true;this.addLinkId=false;this.linkIdFormat='| Description | Link |
|---|---|
| The filtered dataset | Download |
| Gene frequencies | |
| The dataset used to generate the distribution of V gene families graph | Download |
| The dataset used to generate the distribution of D gene families graph | Download |
| The dataset used to generate the relative frequency of V gene usage graph | Download |
| The dataset used to generate the relative frequency of D gene usage graph | Download |
| The dataset used to generate the relative frequency of J gene usage graph | Download |
| The dataset used to generate the relative frequency of the D reading frame graph | Download |
| CDR3 Characteristics | |
| The dataset used to generate the CDR3 length frequency graph | Download |
| The dataset used to generate the Amino Acid Composition in the CDR3 graph | Download |
| Heatmaps | |
| The data used to generate the VD heatmap for $sample. | Download |
| The data used to generate the VJ heatmap for $sample. | Download |
| The data used to generate the DJ heatmap for $sample. | Download |
| Circos | |
| The data used to generate the VD Circos plots for $sample. | Download |
| The data used to generate the VJ Circos plots for $sample. | Download |
| The data used to generate the DJ Circos plots for $sample. | Download |
| A frequency count of V Gene + J Gene + CDR3 | Download |
| Clonality | |
| The dataset used to calculate clonality score (Unique based on clonaltype, $clonalType) | Download |
| Sequences that are present in more than one replicate | Download |