Mercurial > repos > davidvanzessen > shm_csr
annotate wrapper.sh @ 93:8fcf31272f6e draft
planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
| author | rhpvorderman |
|---|---|
| date | Mon, 06 Mar 2023 11:36:32 +0000 |
| parents | cf8ad181628f |
| children | 84e9e5c8c101 |
| rev | line source |
|---|---|
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1 #!/usr/bin/env bash |
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2 set -e -o pipefail |
| 81 | 3 dir="$(cd "$(dirname "$0")" && pwd)" |
| 4 input=$1 | |
| 5 method=$2 | |
| 6 log=$3 #becomes the main html page at the end | |
| 7 outdir=$4 | |
| 8 output="$outdir/index.html" #copied to $log location at the end | |
| 9 title="$5" | |
| 10 include_fr1=$6 | |
| 11 functionality=$7 | |
| 12 unique=$8 | |
| 13 naive_output=$9 | |
| 14 naive_output_ca=${10} | |
| 15 naive_output_cg=${11} | |
| 16 naive_output_cm=${12} | |
| 17 naive_output_ce=${13} | |
| 18 naive_output_all=${14} | |
| 19 filter_unique=${15} | |
| 20 filter_unique_count=${16} | |
| 21 class_filter=${17} | |
| 22 empty_region_filter=${18} | |
| 23 fast=${19} | |
| 24 | |
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25 BASENAME=$(basename $input) |
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26 # Cut off .txz or .tgz suffix |
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27 NEW_IMGT_PREFIX="new_IMGT_${BASENAME%.*}" |
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28 |
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29 #exec 5> debug_output.txt |
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30 #BASH_XTRACEFD="5" |
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31 ## Busybox date does not support '+%s.%N'. So use a custom program. Can be |
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32 ## Compiled with cc -Os show_time_as_float.c -o show_time_as_float |
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33 #PS4='$(${dir}/show_time_as_float) $LINENO: ' |
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34 #set -x |
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35 |
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36 mkdir -p $outdir |
| 81 | 37 |
| 38 tar -xzf $dir/style.tar.gz -C $outdir | |
| 39 | |
| 40 echo "---------------- read parameters ----------------" | |
| 41 echo "---------------- read parameters ----------------<br />" > $log | |
| 42 | |
| 43 echo "unpacking IMGT file" | |
| 44 | |
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45 type="`file -L $input`" |
| 81 | 46 if [[ "$type" == *"Zip archive"* ]] ; then |
| 47 echo "Zip archive" | |
| 48 echo "unzip $input -d $PWD/files/" | |
| 49 unzip $input -d $PWD/files/ | |
| 50 elif [[ "$type" == *"XZ compressed data"* ]] ; then | |
| 51 echo "ZX archive" | |
| 52 echo "tar -xJf $input -C $PWD/files/" | |
| 53 mkdir -p "$PWD/files/$title" | |
| 54 tar -xJf $input -C "$PWD/files/$title" | |
| 55 else | |
| 56 echo "Unrecognized format $type" | |
| 57 echo "Unrecognized format $type" > $log | |
| 58 exit 1 | |
| 59 fi | |
| 60 | |
| 61 cat "`find $PWD/files/ -name "1_*"`" > $PWD/summary.txt | |
| 62 cat "`find $PWD/files/ -name "2_*"`" > $PWD/gapped_nt.txt | |
| 63 cat "`find $PWD/files/ -name "3_*"`" > $PWD/sequences.txt | |
| 64 cat "`find $PWD/files/ -name "4_*"`" > $PWD/gapped_aa.txt | |
| 65 cat "`find $PWD/files/ -name "5_*"`" > $PWD/aa.txt | |
| 66 cat "`find $PWD/files/ -name "6_*"`" > $PWD/junction.txt | |
| 67 cat "`find $PWD/files/ -name "7_*"`" > $PWD/mutationanalysis.txt | |
| 68 cat "`find $PWD/files/ -name "8_*"`" > $PWD/mutationstats.txt | |
| 69 cat "`find $PWD/files/ -name "9_*"`" > $PWD/aa_change_stats.txt | |
| 70 cat "`find $PWD/files/ -name "10_*"`" > $PWD/hotspots.txt | |
| 71 | |
| 72 echo "---------------- unique id check ----------------" | |
| 73 | |
| 74 Rscript $dir/check_unique_id.r $PWD/summary.txt $PWD/gapped_nt.txt $PWD/sequences.txt $PWD/gapped_aa.txt $PWD/aa.txt $PWD/junction.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/aa_change_stats.txt $PWD/hotspots.txt | |
| 75 | |
| 76 if [[ ${#BLASTN_DIR} -ge 5 ]] ; then | |
| 77 echo "On server, using BLASTN_DIR env: ${BLASTN_DIR}" | |
| 78 else | |
| 79 BLASTN_DIR="/home/galaxy/Downloads/ncbi-blast-2.4.0+/bin" | |
| 80 echo "Dev Galaxy set BLASTN_DIR to: ${BLASTN_DIR}" | |
| 81 fi | |
| 82 | |
| 83 echo "---------------- class identification ----------------" | |
| 84 echo "---------------- class identification ----------------<br />" >> $log | |
| 85 | |
| 86 python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt | |
| 87 | |
| 88 echo "---------------- merge_and_filter.r ----------------" | |
| 89 echo "---------------- merge_and_filter.r ----------------<br />" >> $log | |
| 90 | |
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91 Rscript $dir/merge_and_filter.r \ |
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92 $PWD/summary.txt \ |
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93 $PWD/sequences.txt \ |
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94 $PWD/mutationanalysis.txt \ |
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95 $PWD/mutationstats.txt \ |
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96 $PWD/hotspots.txt \ |
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97 "$PWD/gapped_aa.txt" \ |
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98 $outdir/identified_genes.txt \ |
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99 $outdir/merged.txt \ |
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100 $outdir/before_unique_filter.txt \ |
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101 $outdir/unmatched.txt \ |
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102 $method \ |
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103 $functionality \ |
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104 $unique \ |
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105 ${filter_unique} \ |
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106 ${filter_unique_count} \ |
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107 ${class_filter} \ |
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108 ${empty_region_filter} |
| 81 | 109 |
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110 echo "---------------- creating new IMGT zips ----------------" |
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111 echo "---------------- creating new IMGT zips ----------------<br />" >> $log |
| 81 | 112 |
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113 python $dir/split_imgt_file.py --outdir $outdir $input $outdir/merged.txt \ |
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114 --prefix "${NEW_IMGT_PREFIX}" \ |
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115 - IGA IGA1 IGA2 IGG IGG1 IGG2 IGG3 IGG4 IGM IGE |
| 81 | 116 |
| 117 | |
| 118 echo "---------------- shm_csr.r ----------------" | |
| 119 echo "---------------- shm_csr.r ----------------<br />" >> $log | |
| 120 | |
| 121 classes="IGA,IGA1,IGA2,IGG,IGG1,IGG2,IGG3,IGG4,IGM,IGE,unmatched" | |
| 122 echo "R mutation analysis" | |
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123 Rscript $dir/shm_csr.r $outdir/merged.txt $classes $outdir ${empty_region_filter} |
| 81 | 124 |
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125 echo "---------- Split naive memory IGM ---------" |
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126 echo "---------- Split naive memory IGM ---------<br />" >> $log |
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127 |
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128 python $dir/igm_naive_mutations.py $outdir/scatter.txt $outdir/igm_naive_mutations.txt \ |
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129 $outdir/igm_naive_memory_mutations.txt |
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130 |
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131 python $dir/split_imgt_file.py --outdir $outdir $outdir/${NEW_IMGT_PREFIX}_IGM.txz \ |
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132 $outdir/igm_naive_mutations.txt \ |
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133 --prefix "${NEW_IMGT_PREFIX}_IGM_NAIVE" - |
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134 |
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135 python $dir/split_imgt_file.py --outdir $outdir $outdir/${NEW_IMGT_PREFIX}_IGM.txz \ |
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136 $outdir/igm_naive_memory_mutations.txt \ |
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137 --prefix "${NEW_IMGT_PREFIX}_IGM_NAIVE_MEMORY" - |
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138 |
| 81 | 139 echo "---------------- plot_pdfs.r ----------------" |
| 140 echo "---------------- plot_pdfs.r ----------------<br />" >> $log | |
| 141 | |
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142 echo "Rscript $dir/shm_csr.r $outdir/pdfplots.RData $outdir" |
| 81 | 143 |
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144 Rscript $dir/plot_pdf.r "$outdir/pdfplots.RData" "$outdir" |
| 81 | 145 |
| 146 echo "---------------- shm_csr.py ----------------" | |
| 147 echo "---------------- shm_csr.py ----------------<br />" >> $log | |
| 148 | |
| 149 python $dir/shm_csr.py --input $outdir/merged.txt --genes $classes --empty_region_filter "${empty_region_filter}" --output $outdir/hotspot_analysis.txt | |
| 150 | |
| 151 echo "---------------- aa_histogram.r ----------------" | |
| 152 echo "---------------- aa_histogram.r ----------------<br />" >> $log | |
| 153 | |
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154 Rscript $dir/aa_histogram.r \ |
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155 $outdir/aa_id_mutations.txt \ |
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156 $outdir/absent_aa_id.txt "IGA,IGG,IGM,IGE" \ |
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157 $outdir/ |
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158 |
| 81 | 159 if [ -e "$outdir/aa_histogram_.png" ]; then |
| 160 mv $outdir/aa_histogram_.png $outdir/aa_histogram.png | |
| 161 mv $outdir/aa_histogram_.pdf $outdir/aa_histogram.pdf | |
| 162 mv $outdir/aa_histogram_.txt $outdir/aa_histogram.txt | |
| 163 mv $outdir/aa_histogram_absent_.txt $outdir/aa_histogram_absent.txt | |
| 164 mv $outdir/aa_histogram_count_.txt $outdir/aa_histogram_count.txt | |
| 165 mv $outdir/aa_histogram_sum_.txt $outdir/aa_histogram_sum.txt | |
| 166 fi | |
| 167 | |
| 168 genes=(IGA IGA1 IGA2 IGG IGG1 IGG2 IGG3 IGG4 IGM IGE) | |
| 169 | |
| 170 funcs=(sum mean median) | |
| 171 funcs=(sum) | |
| 172 | |
| 173 echo "---------------- sequence_overview.r ----------------" | |
| 174 echo "---------------- sequence_overview.r ----------------<br />" >> $log | |
| 175 | |
| 176 mkdir $outdir/sequence_overview | |
| 177 | |
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178 python $dir/sequence_overview.py --before-unique $outdir/before_unique_filter.txt \ |
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179 --outdir $outdir/sequence_overview --empty-region-filter ${empty_region_filter} |
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180 Rscript $dir/nt_overview.r \ |
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181 $outdir/merged.txt \ |
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182 $outdir/sequence_overview \ |
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183 $classes \ |
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184 $outdir/hotspot_analysis_sum.txt \ |
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185 ${empty_region_filter} |
| 81 | 186 |
| 187 echo "<table border='1'>" > $outdir/base_overview.html | |
| 188 | |
| 189 while IFS=$'\t' read ID class seq A C G T | |
| 190 do | |
| 191 echo "<tr><td>$ID</td><td>$seq</td><td>$class</td><td>$A</td><td>$C</td><td>$G</td><td>$T</td></tr>" >> $outdir/base_overview.html | |
| 192 done < $outdir/sequence_overview/ntoverview.txt | |
| 193 | |
| 194 echo "<html><center><h1>$title</h1></center>" > $output | |
| 195 echo "<meta name='viewport' content='width=device-width, initial-scale=1'>" >> $output | |
| 196 echo "<script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $output | |
| 197 echo "<script type='text/javascript' src='tabber.js'></script>" >> $output | |
| 198 echo "<script type='text/javascript' src='script.js'></script>" >> $output | |
| 199 echo "<link rel='stylesheet' type='text/css' href='style.css'>" >> $output | |
| 200 echo "<link rel='stylesheet' type='text/css' href='pure-min.css'>" >> $output | |
| 201 | |
| 202 matched_count="`cat $outdir/merged.txt | grep -v 'unmatched' | tail -n +2 | wc -l`" | |
| 203 unmatched_count="`cat $outdir/unmatched.txt | tail -n +2 | wc -l`" | |
| 204 total_count=$((matched_count + unmatched_count)) | |
| 205 perc_count=$((unmatched_count / total_count * 100)) | |
| 206 perc_count=`bc -l <<< "scale=2; ${unmatched_count} / ${total_count} * 100"` | |
| 207 perc_count=`bc -l <<< "scale=2; (${unmatched_count} / ${total_count} * 100 ) / 1"` | |
| 208 | |
| 209 echo "<center><h2>Total: ${total_count}</h2></center>" >> $output | |
| 210 echo "<center><h2>Matched: ${matched_count} Unmatched: ${unmatched_count}</h2></center>" >> $output | |
| 211 echo "<center><h2>Percentage unmatched: ${perc_count}</h2></center>" >> $output | |
| 212 | |
| 213 echo "---------------- main tables ----------------" | |
| 214 echo "---------------- main tables ----------------<br />" >> $log | |
| 215 | |
| 216 echo "<div class='tabber'>" >> $output | |
| 217 echo "<div class='tabbertab' title='SHM Overview' style='width: 3000px;'>" >> $output | |
| 218 | |
| 219 for func in ${funcs[@]} | |
| 220 do | |
| 221 | |
| 222 echo "---------------- $func table ----------------" | |
| 223 echo "---------------- $func table ----------------<br />" >> $log | |
| 224 | |
| 225 cat $outdir/mutations_${func}.txt $outdir/shm_overview_tandem_row.txt $outdir/hotspot_analysis_${func}.txt > $outdir/data_${func}.txt | |
| 226 | |
| 227 echo "---------------- pattern_plots.r ----------------" | |
| 228 echo "---------------- pattern_plots.r ----------------<br />" >> $log | |
| 229 | |
|
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230 Rscript $dir/pattern_plots.r \ |
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231 $outdir/data_${func}.txt \ |
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232 $outdir/aid_motives \ |
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233 $outdir/relative_mutations \ |
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234 $outdir/absolute_mutations \ |
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235 $outdir/shm_overview.txt |
| 81 | 236 |
| 237 echo "<table class='pure-table pure-table-striped'>" >> $output | |
| 238 echo "<thead><tr><th>info</th>" >> $output | |
| 239 | |
|
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240 if [ "${class_filter}" != "101_101_all" ] ; then |
| 81 | 241 |
| 242 for gene in ${genes[@]} | |
| 243 do | |
| 244 tmp=`cat $outdir/${gene}_${func}_n.txt` | |
| 245 echo "<th><a href='matched_${gene}_${func}.txt'>${gene} (N = $tmp)</a></th>" >> $output | |
| 246 done | |
| 247 | |
| 248 tmp=`cat $outdir/all_${func}_n.txt` | |
| 249 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output | |
| 250 tmp=`cat $outdir/unmatched_${func}_n.txt` | |
| 251 echo "<th><a href='unmatched.txt'>unmatched (N = ${unmatched_count})</a></th><tr></thead>" >> $output | |
| 252 | |
| 253 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz | |
| 254 do | |
| 255 if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] || [ "$name" == "Tandems/Expected (ratio)" ] ; then #meh | |
| 256 echo "<tr><td>$name</td><td>${cax}/${cay} (${caz})</td><td>${ca1x}/${ca1y} (${ca1z})</td><td>${ca2x}/${ca2y} (${ca2z})</td><td>${cgx}/${cgy} (${cgz})</td><td>${cg1x}/${cg1y} (${cg1z})</td><td>${cg2x}/${cg2y} (${cg2z})</td><td>${cg3x}/${cg3y} (${cg3z})</td><td>${cg4x}/${cg4y} (${cg4z})</td><td>${cmx}/${cmy} (${cmz})</td><td>${cex}/${cey} (${cez})</td><td>${allx}/${ally} (${allz})</td><td>${unx}/${uny} (${unz})</td></tr>" >> $output | |
| 257 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then | |
| 258 echo "<tr><td>$name</td><td>${caz}%</td><td>${ca1z}%</td><td>${ca2z}%</td><td>${cgz}%</td><td>${cg1z}%</td><td>${cg2z}%</td><td>${cg3z}%</td><td>${cg4z}%</td><td>${cmz}%</td><td>${cez}%</td><td>${allz}%</td><td>${unz}%</td></tr>" >> $output | |
| 259 else | |
| 260 echo "<tr><td>$name</td><td>${cax}/${cay} (${caz}%)</td><td>${ca1x}/${ca1y} (${ca1z}%)</td><td>${ca2x}/${ca2y} (${ca2z}%)</td><td>${cgx}/${cgy} (${cgz}%)</td><td>${cg1x}/${cg1y} (${cg1z}%)</td><td>${cg2x}/${cg2y} (${cg2z}%)</td><td>${cg3x}/${cg3y} (${cg3z}%)</td><td>${cg4x}/${cg4y} (${cg4z}%)</td><td>${cmx}/${cmy} (${cmz}%)</td><td>${cex}/${cey} (${cez}%)</td><td>${allx}/${ally} (${allz}%)</td><td>${unx}/${uny} (${unz}%)</td></tr>" >> $output | |
| 261 fi | |
| 262 done < $outdir/data_${func}.txt | |
| 263 | |
| 264 else | |
| 265 tmp=`cat $outdir/all_${func}_n.txt` | |
| 266 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output | |
| 267 | |
| 268 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz | |
| 269 do | |
| 270 if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] ; then #meh | |
| 271 echo "<tr><td>$name</td><td>${allx}/${ally}</td></tr>" >> $output | |
| 272 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then | |
| 273 echo "<tr><td>$name</td><td>${allz}%</td></tr>" >> $output | |
| 274 else | |
| 275 echo "<tr><td>$name</td><td>${allx}/${ally} (${allz}%)</td></tr>" >> $output | |
| 276 fi | |
| 277 done < $outdir/data_${func}.txt | |
| 278 | |
| 279 fi | |
| 280 echo "</table>" >> $output | |
| 281 #echo "<a href='data_${func}.txt'>Download data</a>" >> $output | |
| 282 done | |
| 283 | |
| 284 echo "<a href='aid_motives.pdf'><img src='aid_motives.png' /></a><br />" >> $output | |
| 285 echo "<a href='relative_mutations.pdf'><img src='relative_mutations.png' /></a><br />" >> $output | |
| 286 echo "<a href='absolute_mutations.pdf'><img src='absolute_mutations.png' /></a><br />" >> $output | |
| 287 echo "<br />" >> $output | |
| 288 cat $dir/shm_overview.htm >> $output | |
| 289 echo "</div>" >> $output #SHM overview tab end | |
| 290 | |
| 291 echo "---------------- images ----------------" | |
| 292 echo "---------------- images ----------------<br />" >> $log | |
| 293 | |
| 294 echo "<div class='tabbertab' title='SHM Frequency' style='width: 3000px;'></a>" >> $output | |
| 295 | |
| 296 if [ -a $outdir/scatter.png ] | |
| 297 then | |
| 298 echo "<a href='scatter.pdf'><img src='scatter.png'/><br />" >> $output | |
| 299 fi | |
| 300 if [ -a $outdir/frequency_ranges.png ] | |
| 301 then | |
| 302 echo "<a href='frequency_ranges.pdf'><img src='frequency_ranges.png'/></a><br />" >> $output | |
| 303 fi | |
| 304 | |
| 305 echo "<br />" >> $output | |
| 306 cat $dir/shm_frequency.htm >> $output | |
| 307 | |
| 308 echo "</div>" >> $output #SHM frequency tab end | |
| 309 | |
| 310 echo "<div class='tabbertab' title='Transition tables' style='width: 3000px;'>" >> $output | |
| 311 | |
| 312 echo "<table border='0'>" >> $output | |
| 313 | |
| 314 for gene in ${genes[@]} | |
| 315 do | |
| 316 echo "<tr>" >> $output | |
| 317 echo "<td><h1>${gene}</h1></td>" >> $output | |
| 318 | |
| 319 if [ -e $outdir/transitions_heatmap_${gene}.png ] | |
| 320 then | |
| 321 echo "<td><a href='transitions_heatmap_${gene}.pdf'><img src='transitions_heatmap_${gene}.png' /></a></td>" >> $output | |
| 322 else | |
| 323 echo "<td></td>" >> $output | |
| 324 fi | |
| 325 | |
| 326 if [ -e $outdir/transitions_stacked_${gene}.png ] | |
| 327 then | |
| 328 echo "<td><a href='transitions_stacked_${gene}.pdf'><img src='transitions_stacked_${gene}.png' /></a></td>" >> $output | |
| 329 else | |
| 330 echo "<td></td>" >> $output | |
| 331 fi | |
| 332 | |
| 333 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output | |
| 334 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output | |
| 335 first="true" | |
| 336 while IFS=, read from a c g t | |
| 337 do | |
| 338 if [ "$first" == "true" ] ; then | |
| 339 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output | |
| 340 first="false" | |
| 341 else | |
| 342 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output | |
| 343 fi | |
| 344 done < $outdir/transitions_${gene}_sum.txt | |
| 345 echo "</table></td>" >> $output | |
| 346 | |
| 347 echo "</tr>" >> $output | |
| 348 done | |
| 349 | |
| 350 echo "<tr>" >> $output | |
| 351 echo "<td><h1>All</h1></td>" >> $output | |
| 352 echo "<td><a href='transitions_heatmap_all.pdf'><img src='transitions_heatmap_all.png' /></a></td>" >> $output | |
| 353 echo "<td><a href='transitions_stacked_all.pdf'><img src='transitions_stacked_all.png' /></a></td>" >> $output | |
| 354 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output | |
| 355 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output | |
| 356 first="true" | |
| 357 while IFS=, read from a c g t | |
| 358 do | |
| 359 if [ "$first" == "true" ] ; then | |
| 360 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output | |
| 361 first="false" | |
| 362 else | |
| 363 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output | |
| 364 fi | |
| 365 done < $outdir/transitions_all_sum.txt | |
| 366 echo "</table></td>" >> $output | |
| 367 | |
| 368 echo "</tr>" >> $output | |
| 369 | |
| 370 echo "</table>" >> $output | |
| 371 | |
| 372 echo "<br />" >> $output | |
| 373 cat $dir/shm_transition.htm >> $output | |
| 374 | |
| 375 echo "</div>" >> $output #transition tables tab end | |
| 376 | |
| 377 echo "<div class='tabbertab' title='Antigen Selection'>" >> $output | |
| 378 | |
| 379 if [ -e $outdir/aa_histogram.png ] | |
| 380 then | |
| 381 echo "<a href='aa_histogram.pdf'><img src='aa_histogram.png'/></a><br />" >> $output | |
| 382 fi | |
| 383 | |
| 384 if [ -e $outdir/aa_histogram_IGA.png ] | |
| 385 then | |
| 386 echo "<a href='aa_histogram_IGA.pdf'><img src='aa_histogram_IGA.png'/></a><br />" >> $output | |
| 387 fi | |
| 388 | |
| 389 if [ -e $outdir/aa_histogram_IGG.png ] | |
| 390 then | |
| 391 echo "<a href='aa_histogram_IGG.pdf'><img src='aa_histogram_IGG.png'/></a><br />" >> $output | |
| 392 fi | |
| 393 | |
| 394 if [ -e $outdir/aa_histogram_IGM.png ] | |
| 395 then | |
| 396 echo "<a href='aa_histogram_IGM.pdf'><img src='aa_histogram_IGM.png'/></a><br />" >> $output | |
| 397 fi | |
| 398 | |
| 399 if [ -e $outdir/aa_histogram_IGE.png ] | |
| 400 then | |
| 401 echo "<a href='aa_histogram_IGE.pdf'><img src='aa_histogram_IGE.png'/></a><br />" >> $output | |
| 402 fi | |
| 403 | |
|
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404 count_imgt_lines () { |
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405 tar -xJf $1 1_Summary.txt |
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406 # Use a pipe so wc -l does not display the filename |
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407 wc -l < 1_Summary.txt |
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408 rm 1_Summary.txt |
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409 } |
| 81 | 410 |
| 411 if [[ "$fast" == "no" ]] ; then | |
| 412 | |
| 413 | |
| 414 | |
| 415 echo "---------------- baseline ----------------" | |
| 416 echo "---------------- baseline ----------------<br />" >> $log | |
| 417 tmp="$PWD" | |
| 418 | |
|
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419 mkdir -p $outdir/baseline |
| 81 | 420 |
| 421 echo "<center><h1>BASELINe</h1>" >> $output | |
| 422 header_substring="Based on CDR1, FR2, CDR2, FR3 (27:27:38:55:65:104:-)" | |
| 423 | |
| 424 baseline_boundaries="27:27:38:55:65:104:-" | |
| 425 | |
| 426 if [[ "${empty_region_filter}" == "leader" ]] ; then | |
| 427 baseline_boundaries="1:26:38:55:65:104:-" | |
| 428 header_substring="Based on FR1, CDR1, FR2, CDR2, FR3 (1:26:38:55:65:104,-)" | |
| 429 fi | |
| 430 | |
| 431 echo "<p>${header_substring}</p></center>" >> $output | |
| 432 | |
| 433 mkdir $outdir/baseline/IGA_IGG_IGM | |
|
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434 if [[ "$(count_imgt_lines $outdir/${NEW_IMGT_PREFIX}.txz)" -gt "1" ]]; then |
| 81 | 435 cd $outdir/baseline/IGA_IGG_IGM |
|
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436 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/${NEW_IMGT_PREFIX}.txz "IGA_IGG_IGM_IGE" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt" |
| 81 | 437 else |
| 438 echo "No sequences" > "$outdir/baseline.txt" | |
| 439 fi | |
| 440 | |
| 441 mkdir $outdir/baseline/IGA | |
|
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442 if [[ "$(count_imgt_lines $outdir/${NEW_IMGT_PREFIX}_IGA.txz)" -gt "1" ]]; then |
| 81 | 443 cd $outdir/baseline/IGA |
|
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444 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/${NEW_IMGT_PREFIX}_IGA.txz "IGA" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGA.pdf" "Sequence.ID" "$outdir/baseline_IGA.txt" |
| 81 | 445 else |
| 446 echo "No IGA sequences" > "$outdir/baseline_IGA.txt" | |
| 447 fi | |
| 448 | |
| 449 mkdir $outdir/baseline/IGG | |
|
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450 if [[ "$(count_imgt_lines $outdir/${NEW_IMGT_PREFIX}_IGG.txz)" -gt "1" ]]; then |
| 81 | 451 cd $outdir/baseline/IGG |
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452 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/${NEW_IMGT_PREFIX}_IGG.txz "IGG" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGG.pdf" "Sequence.ID" "$outdir/baseline_IGG.txt" |
| 81 | 453 else |
| 454 echo "No IGG sequences" > "$outdir/baseline_IGG.txt" | |
| 455 fi | |
| 456 | |
| 457 mkdir $outdir/baseline/IGM | |
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458 if [[ "$(count_imgt_lines $outdir/${NEW_IMGT_PREFIX}_IGM.txz)" -gt "1" ]]; then |
| 81 | 459 cd $outdir/baseline/IGM |
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460 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/${NEW_IMGT_PREFIX}_IGM.txz "IGM" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGM.pdf" "Sequence.ID" "$outdir/baseline_IGM.txt" |
| 81 | 461 else |
| 462 echo "No IGM sequences" > "$outdir/baseline_IGM.txt" | |
| 463 fi | |
| 464 | |
| 465 mkdir $outdir/baseline/IGE | |
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466 if [[ "$(count_imgt_lines $outdir/${NEW_IMGT_PREFIX}_IGE.txz)" -gt "1" ]]; then |
| 81 | 467 cd $outdir/baseline/IGE |
|
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468 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/${NEW_IMGT_PREFIX}_IGE.txz "IGE" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGE.pdf" "Sequence.ID" "$outdir/baseline_IGE.txt" |
| 81 | 469 else |
| 470 echo "No IGE sequences" > "$outdir/baseline_IGE.txt" | |
| 471 fi | |
| 472 | |
| 473 cd $tmp | |
| 474 | |
| 475 echo "Cleaning up *.RData files" | |
| 476 find $outdir/baseline -name "*.RData" -type f -delete | |
| 477 | |
| 478 if [ -e $outdir/baseline.pdf ] | |
| 479 then | |
| 480 echo "<embed src='baseline.pdf' width='700px' height='1000px'>" >> $output | |
| 481 fi | |
| 482 | |
| 483 if [ -e $outdir/baseline_IGA.pdf ] | |
| 484 then | |
| 485 echo "<embed src='baseline_IGA.pdf' width='700px' height='1000px'>" >> $output | |
| 486 fi | |
| 487 | |
| 488 if [ -e $outdir/baseline_IGG.pdf ] | |
| 489 then | |
| 490 echo "<embed src='baseline_IGG.pdf' width='700px' height='1000px'>" >> $output | |
| 491 fi | |
| 492 | |
| 493 if [ -e $outdir/baseline_IGM.pdf ] | |
| 494 then | |
| 495 echo "<embed src='baseline_IGM.pdf' width='700px' height='1000px'>" >> $output | |
| 496 fi | |
| 497 | |
| 498 if [ -e $outdir/baseline_IGE.pdf ] | |
| 499 then | |
| 500 echo "<embed src='baseline_IGE.pdf' width='700px' height='1000px'>" >> $output | |
| 501 fi | |
| 502 fi | |
| 503 | |
| 504 echo "<br />" >> $output | |
| 505 cat $dir/shm_selection.htm >> $output | |
| 506 | |
| 507 echo "</div>" >> $output #antigen selection tab end | |
| 508 | |
| 509 echo "<div class='tabbertab' title='CSR'>" >> $output #CSR tab | |
| 510 | |
| 511 if [ -e $outdir/IGA.png ] | |
| 512 then | |
| 513 echo "<a href='IGA.pdf'><img src='IGA.png'/></a><br />" >> $output | |
| 514 fi | |
| 515 if [ -e $outdir/IGG.png ] | |
| 516 then | |
| 517 echo "<a href='IGG.pdf'><img src='IGG.png'/></a><br />" >> $output | |
| 518 fi | |
| 519 | |
| 520 echo "<br />" >> $output | |
| 521 cat $dir/shm_csr.htm >> $output | |
| 522 | |
| 523 echo "</div>" >> $output #CSR tab end | |
| 524 | |
| 525 if [[ "$fast" == "no" ]] ; then | |
| 526 | |
| 527 echo "---------------- change-o MakeDB ----------------" | |
| 528 | |
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529 mkdir -p $outdir/change_o |
| 81 | 530 |
| 531 tmp="$PWD" | |
| 532 | |
| 533 cd $outdir/change_o | |
| 534 | |
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535 bash $dir/change_o/makedb.sh $outdir/${NEW_IMGT_PREFIX}.txz false false false $outdir/change_o/change-o-db.txt |
| 81 | 536 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones.txt $outdir/change_o/change-o-defined_clones-summary.txt |
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537 Rscript $dir/change_o/select_first_in_clone.r \ |
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538 $outdir/change_o/change-o-db-defined_clones.txt \ |
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539 $outdir/change_o/change-o-db-defined_first_clones.txt |
| 81 | 540 |
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541 python $dir/split_imgt_file.py --outdir $outdir --prefix ${NEW_IMGT_PREFIX}_first_seq_of_clone \ |
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542 $outdir/${NEW_IMGT_PREFIX}.txz $outdir/change_o/change-o-db-defined_first_clones.txt \ |
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543 "-" |
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544 |
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545 Rscript $dir/merge.r \ |
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546 $outdir/change_o/change-o-db-defined_clones.txt \ |
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547 $outdir/merged.txt \ |
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548 "all" "Sequence.ID,best_match" "SEQUENCE_ID" "Sequence.ID" \ |
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549 $outdir/change_o/change-o-db-defined_clones.txt |
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550 echo "Rscript $dir/merge.r $outdir/change_o/change-o-db-defined_clones.txt $outdir/$outdir/merged.txt 'all' 'Sequence.ID,best_match' 'Sequence.ID' 'Sequence.ID' '\t' $outdir/change_o/change-o-db-defined_clones.txt" |
| 81 | 551 |
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552 if [[ "$(count_imgt_lines $outdir/${NEW_IMGT_PREFIX}_IGA.txz)" -gt "1" ]]; then |
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553 bash $dir/change_o/makedb.sh $outdir/${NEW_IMGT_PREFIX}_IGA.txz false false false $outdir/change_o/change-o-db-IGA.txt |
| 81 | 554 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGA.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGA.txt $outdir/change_o/change-o-defined_clones-summary-IGA.txt |
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555 Rscript $dir/change_o/select_first_in_clone.r \ |
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556 $outdir/change_o/change-o-db-defined_clones-IGA.txt \ |
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557 $outdir/change_o/change-o-db-defined_first_clones-IGA.txt |
| 81 | 558 |
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559 python $dir/split_imgt_file.py --outdir $outdir --prefix ${NEW_IMGT_PREFIX}_IGA_first_seq_of_clone \ |
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560 $outdir/${NEW_IMGT_PREFIX}.txz $outdir/change_o/change-o-db-defined_first_clones-IGA.txt \ |
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561 "-" |
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562 |
| 81 | 563 else |
| 564 echo "No IGA sequences" > "$outdir/change_o/change-o-db-defined_clones-IGA.txt" | |
| 565 echo "No IGA sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGA.txt" | |
| 566 fi | |
| 567 | |
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568 if [[ "$(count_imgt_lines $outdir/${NEW_IMGT_PREFIX}_IGG.txz)" -gt "1" ]]; then |
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569 bash $dir/change_o/makedb.sh $outdir/${NEW_IMGT_PREFIX}_IGG.txz false false false $outdir/change_o/change-o-db-IGG.txt |
| 81 | 570 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGG.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGG.txt $outdir/change_o/change-o-defined_clones-summary-IGG.txt |
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571 Rscript $dir/change_o/select_first_in_clone.r \ |
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572 $outdir/change_o/change-o-db-defined_clones-IGG.txt \ |
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573 $outdir/change_o/change-o-db-defined_first_clones-IGG.txt |
| 81 | 574 |
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575 python $dir/split_imgt_file.py --outdir $outdir --prefix ${NEW_IMGT_PREFIX}_IGG_first_seq_of_clone \ |
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576 $outdir/${NEW_IMGT_PREFIX}.txz $outdir/change_o/change-o-db-defined_first_clones-IGG.txt \ |
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577 "-" |
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578 |
| 81 | 579 else |
| 580 echo "No IGG sequences" > "$outdir/change_o/change-o-db-defined_clones-IGG.txt" | |
| 581 echo "No IGG sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGG.txt" | |
| 582 fi | |
| 583 | |
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584 if [[ "$(count_imgt_lines $outdir/${NEW_IMGT_PREFIX}_IGM.txz)" -gt "1" ]]; then |
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585 bash $dir/change_o/makedb.sh $outdir/${NEW_IMGT_PREFIX}_IGM.txz false false false $outdir/change_o/change-o-db-IGM.txt |
| 81 | 586 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGM.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGM.txt $outdir/change_o/change-o-defined_clones-summary-IGM.txt |
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587 Rscript $dir/change_o/select_first_in_clone.r \ |
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588 $outdir/change_o/change-o-db-defined_clones-IGM.txt \ |
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589 $outdir/change_o/change-o-db-defined_first_clones-IGM.txt |
| 81 | 590 |
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591 python $dir/split_imgt_file.py --outdir $outdir --prefix ${NEW_IMGT_PREFIX}_IGM_first_seq_of_clone \ |
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592 $outdir/${NEW_IMGT_PREFIX}.txz $outdir/change_o/change-o-db-defined_first_clones-IGM.txt \ |
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593 "-" |
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594 |
| 81 | 595 else |
| 596 echo "No IGM sequences" > "$outdir/change_o/change-o-db-defined_clones-IGM.txt" | |
| 597 echo "No IGM sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGM.txt" | |
| 598 fi | |
| 599 | |
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600 if [[ "$(count_imgt_lines $outdir/${NEW_IMGT_PREFIX}_IGE.txz)" -gt "1" ]]; then |
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601 bash $dir/change_o/makedb.sh $outdir/${NEW_IMGT_PREFIX}_IGE.txz false false false $outdir/change_o/change-o-db-IGE.txt |
| 81 | 602 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGE.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGE.txt $outdir/change_o/change-o-defined_clones-summary-IGE.txt |
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603 Rscript $dir/change_o/select_first_in_clone.r \ |
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604 $outdir/change_o/change-o-db-defined_clones-IGE.txt \ |
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605 $outdir/change_o/change-o-db-defined_first_clones-IGE.txt |
| 81 | 606 |
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607 python $dir/split_imgt_file.py --outdir $outdir --prefix ${NEW_IMGT_PREFIX}_IGE_first_seq_of_clone \ |
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608 $outdir/${NEW_IMGT_PREFIX}.txz $outdir/change_o/change-o-db-defined_first_clones-IGE.txt \ |
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609 "-" |
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610 |
| 81 | 611 else |
| 612 echo "No IGE sequences" > "$outdir/change_o/change-o-db-defined_clones-IGE.txt" | |
| 613 echo "No IGE sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGE.txt" | |
| 614 fi | |
| 615 | |
| 616 cd "$tmp" | |
| 617 | |
| 618 echo "<div class='tabbertab' title='Clonal Relation' style='width: 7000px;'>" >> $output #clonality tab | |
| 619 | |
| 620 function clonality_table { | |
| 621 local infile=$1 | |
| 622 local outfile=$2 | |
| 623 | |
| 624 echo "<table class='pure-table pure-table-striped'>" >> $outfile | |
| 625 echo "<thead><tr><th>Clone size</th><th>Nr of clones</th><th>Nr of sequences</th></tr></thead>" >> $outfile | |
| 626 | |
| 627 first='true' | |
| 628 | |
| 629 while read size clones seqs | |
| 630 do | |
| 631 if [[ "$first" == "true" ]]; then | |
| 632 first="false" | |
| 633 continue | |
| 634 fi | |
| 635 echo "<tr><td>$size</td><td>$clones</td><td>$seqs</td></tr>" >> $outfile | |
| 636 done < $infile | |
| 637 | |
| 638 echo "</table>" >> $outfile | |
| 639 } | |
| 640 echo "<div class='tabber'>" >> $output | |
| 641 | |
| 642 echo "<div class='tabbertab' title='All'>" >> $output | |
| 643 clonality_table $outdir/change_o/change-o-defined_clones-summary.txt $output | |
| 644 echo "</div>" >> $output | |
| 645 | |
| 646 echo "<div class='tabbertab' title='IGA'>" >> $output | |
| 647 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGA.txt $output | |
| 648 echo "</div>" >> $output | |
| 649 | |
| 650 echo "<div class='tabbertab' title='IGG'>" >> $output | |
| 651 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGG.txt $output | |
| 652 echo "</div>" >> $output | |
| 653 | |
| 654 echo "<div class='tabbertab' title='IGM'>" >> $output | |
| 655 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output | |
| 656 echo "</div>" >> $output | |
| 657 | |
| 658 echo "<div class='tabbertab' title='IGE'>" >> $output | |
| 659 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output | |
| 660 echo "</div>" >> $output | |
| 661 | |
| 662 echo "<div class='tabbertab' title='Overlap' style='width: 7000px;'>" >> $output | |
| 663 cat "$outdir/sequence_overview/index.html" | sed -e 's:</td>:</td>\n:g' | sed "s:href='\(.*\).html:href='sequence_overview/\1.html:g" >> $output # rewrite href to 'sequence_overview/..." | |
| 664 echo "</div>" >> $output | |
| 665 | |
| 666 echo "</div>" >> $output #clonality tabber end | |
| 667 | |
| 668 echo "<br />" >> $output | |
| 669 cat $dir/shm_clonality.htm >> $output | |
| 670 | |
| 671 echo "</div>" >> $output #clonality tab end | |
| 672 | |
| 673 fi | |
| 674 | |
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675 # Use python's zipfile utility to prevent needing another dependency in the |
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676 # container. |
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677 current_dir=$(pwd) |
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678 cd $outdir |
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679 python -m zipfile -c all_outputs.zip \ |
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680 merged.txt filtered.txt unmatched.txt shm_overview.txt motif_per_seq.txt \ |
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681 mutation_by_id.txt base_overview.html aid_motives.txt relative_mutations.txt \ |
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682 absolute_mutations.txt tandems_by_id.txt scatter.txt frequency_ranges_class.txt \ |
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683 frequency_ranges_subclasses.txt transitions_all_sum.txt transitions_IGA_sum.txt \ |
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684 transitions_IGA1_sum.txt transitions_IGA2_sum.txt transitions_IGG_sum.txt \ |
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685 transitions_IGG1_sum.txt transitions_IGG2_sum.txt transitions_IGG3_sum.txt \ |
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686 transitions_IGG4_sum.txt transitions_IGM_sum.txt transitions_IGE_sum.txt \ |
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687 aa_id_mutations.txt absent_aa_id.txt aa_histogram_sum.txt \ |
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688 aa_histogram_sum_IGA.txt aa_histogram_sum_IGG.txt aa_histogram_sum_IGM.txt \ |
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689 aa_histogram_sum_IGE.txt baseline.txt baseline_IGA.pdf baseline_IGA.txt \ |
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690 baseline_IGG.pdf baseline_IGG.txt baseline_IGM.pdf baseline_IGM.txt \ |
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691 baseline_IGE.pdf baseline_IGE.txt IGA_pie.txt IGG_pie.txt \ |
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692 sequence_overview/index.html change_o/change-o-db-defined_clones*.txt \ |
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693 *.txz |
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695 cd $current_dir |
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697 |
| 81 | 698 echo "<div class='tabbertab' title='Downloads'>" >> $output |
| 699 | |
| 700 echo "<table class='pure-table pure-table-striped'>" >> $output | |
| 701 echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output | |
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702 echo "<tr><td>All output files in a zip file</td><td><a href='all_outputs.zip' download='all_outputs.zip' >Download</a></td></tr>" >> $output |
| 81 | 703 echo "<tr><td>The complete dataset</td><td><a href='merged.txt' download='merged.txt' >Download</a></td></tr>" >> $output |
| 704 echo "<tr><td>The filtered dataset</td><td><a href='filtered.txt' download='filtered.txt' >Download</a></td></tr>" >> $output | |
| 705 echo "<tr><td>The alignment info on the unmatched sequences</td><td><a href='unmatched.txt' download='unmatched.txt' >Download</a></td></tr>" >> $output | |
| 706 | |
| 707 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Overview</td></tr>" >> $output | |
| 708 echo "<tr><td>The SHM Overview table as a dataset</td><td><a href='shm_overview.txt' download='shm_overview.txt' >Download</a></td></tr>" >> $output | |
| 709 echo "<tr><td>Motif data per sequence ID</td><td><a href='motif_per_seq.txt' download='motif_per_seq.txt' >Download</a></td></tr>" >> $output | |
| 710 echo "<tr><td>Mutation data per sequence ID</td><td><a href='mutation_by_id.txt' download='mutation_by_id.txt' >Download</a></td></tr>" >> $output | |
| 711 echo "<tr><td>Base count for every sequence</td><td><a href='base_overview.html'>View</a></td></tr>" >> $output | |
| 712 echo "<tr><td>The data used to generate the percentage of mutations in AID and pol eta motives plot</td><td><a href='aid_motives.txt' download='aid_motives.txt' >Download</a></td></tr>" >> $output | |
| 713 echo "<tr><td>The data used to generate the relative mutation patterns plot</td><td><a href='relative_mutations.txt' download='relative_mutations.txt' >Download</a></td></tr>" >> $output | |
| 714 echo "<tr><td>The data used to generate the absolute mutation patterns plot</td><td><a href='absolute_mutations.txt' download='absolute_mutations.txt' >Download</a></td></tr>" >> $output | |
| 715 echo "<tr><td>Data about tandem mutations by ID</td><td><a href='tandems_by_id.txt' download='tandems_by_id.txt' >Download</a></td></tr>" >> $output | |
| 716 | |
| 717 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Frequency</td></tr>" >> $output | |
| 718 echo "<tr><td>The data generate the frequency scatter plot</td><td><a href='scatter.txt' download='scatter.txt' >Download</a></td></tr>" >> $output | |
| 719 echo "<tr><td>The data used to generate the frequency by class plot</td><td><a href='frequency_ranges_classes.txt' download='frequency_ranges_classes.txt' >Download</a></td></tr>" >> $output | |
| 720 echo "<tr><td>The data for frequency by subclass</td><td><a href='frequency_ranges_subclasses.txt' download='frequency_ranges_subclasses.txt' >Download</a></td></tr>" >> $output | |
| 721 | |
| 722 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Transition Tables</td></tr>" >> $output | |
| 723 echo "<tr><td>The data for the 'all' transition plot</td><td><a href='transitions_all_sum.txt' download='transitions_all_sum.txt' >Download</a></td></tr>" >> $output | |
| 724 echo "<tr><td>The data for the 'IGA' transition plot</td><td><a href='transitions_IGA_sum.txt' download='transitions_IGA_sum.txt' >Download</a></td></tr>" >> $output | |
| 725 echo "<tr><td>The data for the 'IGA1' transition plot</td><td><a href='transitions_IGA1_sum.txt' download='transitions_IGA1_sum.txt' >Download</a></td></tr>" >> $output | |
| 726 echo "<tr><td>The data for the 'IGA2' transition plot</td><td><a href='transitions_IGA2_sum.txt' download='transitions_IGA2_sum.txt' >Download</a></td></tr>" >> $output | |
| 727 echo "<tr><td>The data for the 'IGG' transition plot</td><td><a href='transitions_IGG_sum.txt' download='transitions_IGG_sum.txt' >Download</a></td></tr>" >> $output | |
| 728 echo "<tr><td>The data for the 'IGG1' transition plot</td><td><a href='transitions_IGG1_sum.txt' download='transitions_IGG1_sum.txt' >Download</a></td></tr>" >> $output | |
| 729 echo "<tr><td>The data for the 'IGG2' transition plot</td><td><a href='transitions_IGG2_sum.txt' download='transitions_IGG2_sum.txt' >Download</a></td></tr>" >> $output | |
| 730 echo "<tr><td>The data for the 'IGG3' transition plot</td><td><a href='transitions_IGG3_sum.txt' download='transitions_IGG3_sum.txt' >Download</a></td></tr>" >> $output | |
| 731 echo "<tr><td>The data for the 'IGG4' transition plot</td><td><a href='transitions_IGG4_sum.txt' download='transitions_IGG4_sum.txt' >Download</a></td></tr>" >> $output | |
| 732 echo "<tr><td>The data for the 'IGM' transition plot</td><td><a href='transitions_IGM_sum.txt' download='transitions_IGM_sum.txt' >Download</a></td></tr>" >> $output | |
| 733 echo "<tr><td>The data for the 'IGE' transition plot</td><td><a href='transitions_IGE_sum.txt' download='transitions_IGE_sum.txt' >Download</a></td></tr>" >> $output | |
| 734 | |
| 735 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Antigen Selection</td></tr>" >> $output | |
| 736 echo "<tr><td>AA mutation data per sequence ID</td><td><a href='aa_id_mutations.txt' download='aa_id_mutations.txt' >Download</a></td></tr>" >> $output | |
| 737 echo "<tr><td>Presence of AA per sequence ID</td><td><a href='absent_aa_id.txt' download='absent_aa_id.txt' >Download</a></td></tr>" >> $output | |
| 738 | |
| 739 echo "<tr><td>The data used to generate the aa mutation frequency plot</td><td><a href='aa_histogram_sum.txt' download='aa_histogram_sum.txt' >Download</a></td></tr>" >> $output | |
| 740 echo "<tr><td>The data used to generate the aa mutation frequency plot for IGA</td><td><a href='aa_histogram_sum_IGA.txt' download='aa_histogram_sum_IGA.txt' >Download</a></td></tr>" >> $output | |
| 741 echo "<tr><td>The data used to generate the aa mutation frequency plot for IGG</td><td><a href='aa_histogram_sum_IGG.txt' download='aa_histogram_sum_IGG.txt' >Download</a></td></tr>" >> $output | |
| 742 echo "<tr><td>The data used to generate the aa mutation frequency plot for IGM</td><td><a href='aa_histogram_sum_IGM.txt' download='aa_histogram_sum_IGM.txt' >Download</a></td></tr>" >> $output | |
| 743 echo "<tr><td>The data used to generate the aa mutation frequency plot for IGE</td><td><a href='aa_histogram_sum_IGE.txt' download='aa_histogram_sum_IGE.txt' >Download</a></td></tr>" >> $output | |
| 744 | |
| 745 echo "<tr><td>Baseline PDF (<a href='http://selection.med.yale.edu/baseline/'>http://selection.med.yale.edu/baseline/</a>)</td><td><a href='baseline.pdf' download='baseline.pdf' >Download</a></td></tr>" >> $output | |
| 746 echo "<tr><td>Baseline data</td><td><a href='baseline.txt' download='baseline.txt' >Download</a></td></tr>" >> $output | |
| 747 echo "<tr><td>Baseline IGA PDF</td><td><a href='baseline_IGA.pdf' download='baseline_IGA.pdf' >Download</a></td></tr>" >> $output | |
| 748 echo "<tr><td>Baseline IGA data</td><td><a href='baseline_IGA.txt' download='baseline_IGA.txt' >Download</a></td></tr>" >> $output | |
| 749 echo "<tr><td>Baseline IGG PDF</td><td><a href='baseline_IGG.pdf' download='baseline_IGG.pdf' >Download</a></td></tr>" >> $output | |
| 750 echo "<tr><td>Baseline IGG data</td><td><a href='baseline_IGG.txt' download='baseline_IGG.txt' >Download</a></td></tr>" >> $output | |
| 751 echo "<tr><td>Baseline IGM PDF</td><td><a href='baseline_IGM.pdf' download='baseline_IGM.pdf' >Download</a></td></tr>" >> $output | |
| 752 echo "<tr><td>Baseline IGM data</td><td><a href='baseline_IGM.txt' download='baseline_IGM.txt' >Download</a></td></tr>" >> $output | |
| 753 echo "<tr><td>Baseline IGE PDF</td><td><a href='baseline_IGE.pdf' download='baseline_IGE.pdf' >Download</a></td></tr>" >> $output | |
| 754 echo "<tr><td>Baseline IGE data</td><td><a href='baseline_IGE.txt' download='baseline_IGE.txt' >Download</a></td></tr>" >> $output | |
| 755 | |
| 756 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>CSR</td></tr>" >> $output | |
| 757 echo "<tr><td>The data for the IGA subclass distribution plot</td><td><a href='IGA_pie.txt' download='IGA_pie.txt' >Download</a></td></tr>" >> $output | |
| 758 echo "<tr><td>The data for the IGG subclass distribution plot</td><td><a href='IGG_pie.txt' download='IGG_pie.txt' >Download</a></td></tr>" >> $output | |
| 759 | |
| 760 | |
| 761 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Clonal Relation</td></tr>" >> $output | |
| 762 echo "<tr><td>Sequence overlap between subclasses</td><td><a href='sequence_overview/index.html'>View</a></td></tr>" >> $output | |
| 763 echo "<tr><td>The Change-O DB file with defined clones and subclass annotation</td><td><a href='change_o/change-o-db-defined_clones.txt' download='change_o/change-o-db-defined_clones.txt' >Download</a></td></tr>" >> $output | |
| 764 echo "<tr><td>The Change-O DB defined clones summary file</td><td><a href='change_o/change-o-defined_clones-summary.txt' download='change_o/change-o-defined_clones-summary.txt' >Download</a></td></tr>" >> $output | |
|
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765 echo "<tr><td>An IMGT archive with just just the first sequence of a clone</td><td><a href='${NEW_IMGT_PREFIX}_first_seq_of_clone.txz' download='${NEW_IMGT_PREFIX}_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output |
| 81 | 766 |
| 767 echo "<tr><td>The Change-O DB file with defined clones of IGA</td><td><a href='change_o/change-o-db-defined_clones-IGA.txt' download='change_o/change-o-db-defined_clones-IGA.txt' >Download</a></td></tr>" >> $output | |
| 768 echo "<tr><td>The Change-O DB defined clones summary file of IGA</td><td><a href='change_o/change-o-defined_clones-summary-IGA.txt' download='change_o/change-o-defined_clones-summary-IGA.txt' >Download</a></td></tr>" >> $output | |
|
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769 echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGA)</td><td><a href='${NEW_IMGT_PREFIX}_IGA_first_seq_of_clone.txz' download='${NEW_IMGT_PREFIX}_IGA_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output |
| 81 | 770 |
| 771 echo "<tr><td>The Change-O DB file with defined clones of IGG</td><td><a href='change_o/change-o-db-defined_clones-IGG.txt' download='change_o/change-o-db-defined_clones-IGG.txt' >Download</a></td></tr>" >> $output | |
| 772 echo "<tr><td>The Change-O DB defined clones summary file of IGG</td><td><a href='change_o/change-o-defined_clones-summary-IGG.txt' download='change_o/change-o-defined_clones-summary-IGG.txt' >Download</a></td></tr>" >> $output | |
|
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773 echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGG)</td><td><a href='${NEW_IMGT_PREFIX}_IGG_first_seq_of_clone.txz' download='${NEW_IMGT_PREFIX}_IGG_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output |
| 81 | 774 |
| 775 echo "<tr><td>The Change-O DB file with defined clones of IGM</td><td><a href='change_o/change-o-db-defined_clones-IGM.txt' download='change_o/change-o-db-defined_clones-IGM.txt' >Download</a></td></tr>" >> $output | |
| 776 echo "<tr><td>The Change-O DB defined clones summary file of IGM</td><td><a href='change_o/change-o-defined_clones-summary-IGM.txt' download='change_o/change-o-defined_clones-summary-IGM.txt' >Download</a></td></tr>" >> $output | |
|
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777 echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGM)</td><td><a href='${NEW_IMGT_PREFIX}_IGM_first_seq_of_clone.txz' download='${NEW_IMGT_PREFIX}_IGM_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output |
| 81 | 778 |
| 779 echo "<tr><td>The Change-O DB file with defined clones of IGE</td><td><a href='change_o/change-o-db-defined_clones-IGE.txt' download='change_o/change-o-db-defined_clones-IGE.txt' >Download</a></td></tr>" >> $output | |
| 780 echo "<tr><td>The Change-O DB defined clones summary file of IGE</td><td><a href='change_o/change-o-defined_clones-summary-IGE.txt' download='change_o/change-o-defined_clones-summary-IGE.txt' >Download</a></td></tr>" >> $output | |
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781 echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGE)</td><td><a href='${NEW_IMGT_PREFIX}_IGE_first_seq_of_clone.txz' download='${NEW_IMGT_PREFIX}_IGE_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output |
| 81 | 782 |
| 783 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Filtered IMGT output files</td></tr>" >> $output | |
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784 echo "<tr><td>An IMGT archive with just the matched and filtered sequences</td><td><a href='${NEW_IMGT_PREFIX}.txz' download='${NEW_IMGT_PREFIX}.txz' >Download</a></td></tr>" >> $output |
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785 echo "<tr><td>An IMGT archive with just the matched and filtered IGA sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGA.txz' download='${NEW_IMGT_PREFIX}_IGA.txz' >Download</a></td></tr>" >> $output |
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786 echo "<tr><td>An IMGT archive with just the matched and filtered IGA1 sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGA1.txz' download='${NEW_IMGT_PREFIX}_IGA1.txz' >Download</a></td></tr>" >> $output |
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787 echo "<tr><td>An IMGT archive with just the matched and filtered IGA2 sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGA2.txz' download='${NEW_IMGT_PREFIX}_IGA2.txz' >Download</a></td></tr>" >> $output |
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788 echo "<tr><td>An IMGT archive with just the matched and filtered IGG sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGG.txz' download='${NEW_IMGT_PREFIX}_IGG.txz' >Download</a></td></tr>" >> $output |
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789 echo "<tr><td>An IMGT archive with just the matched and filtered IGG1 sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGG1.txz' download='${NEW_IMGT_PREFIX}_IGG1.txz' >Download</a></td></tr>" >> $output |
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790 echo "<tr><td>An IMGT archive with just the matched and filtered IGG2 sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGG2.txz' download='${NEW_IMGT_PREFIX}_IGG2.txz' >Download</a></td></tr>" >> $output |
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791 echo "<tr><td>An IMGT archive with just the matched and filtered IGG3 sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGG3.txz' download='${NEW_IMGT_PREFIX}_IGG3.txz' >Download</a></td></tr>" >> $output |
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792 echo "<tr><td>An IMGT archive with just the matched and filtered IGG4 sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGG4.txz' download='${NEW_IMGT_PREFIX}_IGG4.txz' >Download</a></td></tr>" >> $output |
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793 echo "<tr><td>An IMGT archive with just the matched and filtered IGM sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGM.txz' download='${NEW_IMGT_PREFIX}_IGM.txz' >Download</a></td></tr>" >> $output |
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794 echo "<tr><td>An IMGT archive with just the matched and filtered IGE sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGE.txz' download='${NEW_IMGT_PREFIX}_IGE.txz' >Download</a></td></tr>" >> $output |
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795 echo "<tr><td>An IMGT archive with just the matched and filtered naive IGM sequences (mutations below 2%)</td><td><a href='${NEW_IMGT_PREFIX}_IGM_NAIVE.txz' download='${NEW_IMGT_PREFIX}_IGM_NAIVE.txz' >Download</a></td></tr>" >> $output |
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796 echo "<tr><td>An IMGT archive with just the matched and filtered naive memory IGM sequences (mutations 2% or higher)</td><td><a href='${NEW_IMGT_PREFIX}_IGM_NAIVE_MEMORY.txz' download='${NEW_IMGT_PREFIX}_IGM_NAIVE_MEMORY.txz' >Download</a></td></tr>" >> $output |
| 81 | 797 echo "</table>" >> $output |
| 798 | |
| 799 echo "<br />" >> $output | |
| 800 cat $dir/shm_downloads.htm >> $output | |
| 801 | |
| 802 echo "</div>" >> $output #downloads tab end | |
| 803 | |
| 804 echo "</div>" >> $output #tabs end | |
| 805 | |
| 806 echo "</html>" >> $output | |
| 807 | |
| 808 | |
| 809 echo "---------------- naive_output.r ----------------" | |
| 810 echo "---------------- naive_output.r ----------------<br />" >> $log | |
| 811 | |
| 812 if [[ "$naive_output" == "yes" ]] | |
| 813 then | |
| 814 echo "output naive output" | |
|
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815 if [[ "${class_filter}" == "101_101_all" ]] |
| 81 | 816 then |
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817 echo "copy ${NEW_IMGT_PREFIX}.txz to ${naive_output_all}" |
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818 cp $outdir/${NEW_IMGT_PREFIX}.txz ${naive_output_all} |
| 81 | 819 else |
| 820 echo "copy for classes" | |
|
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821 cp $outdir/${NEW_IMGT_PREFIX}_IGA.txz ${naive_output_ca} |
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822 cp $outdir/${NEW_IMGT_PREFIX}_IGG.txz ${naive_output_cg} |
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823 cp $outdir/${NEW_IMGT_PREFIX}_IGM.txz ${naive_output_cm} |
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824 cp $outdir/${NEW_IMGT_PREFIX}_IGE.txz ${naive_output_ce} |
| 81 | 825 fi |
| 826 fi | |
| 827 | |
| 828 echo "</table>" >> $outdir/base_overview.html | |
| 829 | |
| 830 mv $log $outdir/log.html | |
| 831 | |
| 832 echo "<html><center><h1><a href='index.html'>Click here for the results</a></h1>Tip: Open it in a new tab (middle mouse button or right mouse button -> 'open in new tab' on the link above)<br />" > $log | |
| 833 echo "<table border = 1>" >> $log | |
| 834 echo "<thead><tr><th>Info</th><th>Sequences</th><th>Percentage</th></tr></thead>" >> $log | |
| 835 tIFS="$TMP" | |
| 836 IFS=$'\t' | |
| 837 while read step seq perc | |
| 838 do | |
| 839 echo "<tr>" >> $log | |
| 840 echo "<td>$step</td>" >> $log | |
| 841 echo "<td>$seq</td>" >> $log | |
| 842 echo "<td>${perc}%</td>" >> $log | |
| 843 echo "</tr>" >> $log | |
| 844 done < $outdir/filtering_steps.txt | |
| 845 echo "</table>" >> $log | |
| 846 echo "<br />" >> $log | |
| 847 cat $dir/shm_first.htm >> $log | |
| 848 echo "</center></html>" >> $log | |
| 849 | |
| 850 IFS="$tIFS" | |
| 851 | |
|
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852 echo "---------------- remove_files----------------" |
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853 echo "---------------- remove_files----------------<br />" >> $log |
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854 |
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855 rm -r -v -f $outdir/baseline |
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856 rm -r -v -f $PWD/files |
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857 rm -v $PWD/aa.txt |
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858 rm -v $PWD/aa_change_stats.txt |
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859 rm -v $PWD/gapped_aa.txt |
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860 rm -v $PWD/gapped_nt.txt |
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861 rm -v $PWD/hotspots.txt |
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862 rm -v $PWD/junction.txt |
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863 rm -v $PWD/mutationanalysis.txt |
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864 rm -v $PWD/mutationstats.txt |
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865 rm -v $PWD/sequences.txt |
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866 rm -v $PWD/summary.txt |
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867 rm -v $PWD/Rplots.pdf |
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868 |
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869 filename="$dir/remove_files.txt" |
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870 |
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871 while read file; do |
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872 rm -v -f $outdir/$file |
|
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873 done < "$filename" |
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874 |
| 81 | 875 echo "---------------- Done! ----------------" |
| 876 echo "---------------- Done! ----------------<br />" >> $outdir/log.html | |
| 877 | |
| 878 | |
| 879 | |
| 880 | |
| 881 | |
| 882 |