0
+ − 1 #!/bin/bash
+ − 2 #set -e
+ − 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
34
+ − 9 title="$5"
0
+ − 10 include_fr1=$6
+ − 11 functionality=$7
+ − 12 unique=$8
28
+ − 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=${15}
49
+ − 20 filter_unique_count=${16}
+ − 21 class_filter=${17}
+ − 22 empty_region_filter=${18}
+ − 23 fast=${19}
+ − 24
0
+ − 25 mkdir $outdir
+ − 26
+ − 27 tar -xzf $dir/style.tar.gz -C $outdir
+ − 28
+ − 29 echo "---------------- read parameters ----------------"
+ − 30 echo "---------------- read parameters ----------------<br />" > $log
+ − 31
+ − 32 echo "unpacking IMGT file"
+ − 33
+ − 34 type="`file $input`"
+ − 35 if [[ "$type" == *"Zip archive"* ]] ; then
+ − 36 echo "Zip archive"
+ − 37 echo "unzip $input -d $PWD/files/"
+ − 38 unzip $input -d $PWD/files/
+ − 39 elif [[ "$type" == *"XZ compressed data"* ]] ; then
+ − 40 echo "ZX archive"
+ − 41 echo "tar -xJf $input -C $PWD/files/"
34
+ − 42 mkdir -p "$PWD/files/$title"
+ − 43 tar -xJf $input -C "$PWD/files/$title"
0
+ − 44 fi
+ − 45
35
+ − 46 cat "`find $PWD/files/ -name "1_*"`" > $PWD/summary.txt
+ − 47 cat "`find $PWD/files/ -name "3_*"`" > $PWD/sequences.txt
40
+ − 48 cat "`find $PWD/files/ -name "4_*"`" > $PWD/gapped_aa.txt
35
+ − 49 cat "`find $PWD/files/ -name "5_*"`" > $PWD/aa.txt
+ − 50 cat "`find $PWD/files/ -name "6_*"`" > $PWD/junction.txt
+ − 51 cat "`find $PWD/files/ -name "7_*"`" > $PWD/mutationanalysis.txt
+ − 52 cat "`find $PWD/files/ -name "8_*"`" > $PWD/mutationstats.txt
+ − 53 cat "`find $PWD/files/ -name "10_*"`" > $PWD/hotspots.txt
0
+ − 54
+ − 55 if [[ ${#BLASTN_DIR} -ge 5 ]] ; then
+ − 56 echo "On server, using BLASTN_DIR env: ${BLASTN_DIR}"
+ − 57 else
+ − 58 BLASTN_DIR="/home/galaxy/Downloads/ncbi-blast-2.4.0+/bin"
+ − 59 echo "Dev Galaxy set BLASTN_DIR to: ${BLASTN_DIR}"
+ − 60 fi
+ − 61
+ − 62 echo "---------------- class identification ----------------"
+ − 63 echo "---------------- class identification ----------------<br />" >> $log
+ − 64
+ − 65 python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt
+ − 66
+ − 67 echo "---------------- merge_and_filter.r ----------------"
+ − 68 echo "---------------- merge_and_filter.r ----------------<br />" >> $log
+ − 69
49
+ − 70 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt "$PWD/gapped_aa.txt" $outdir/identified_genes.txt $outdir/merged.txt $outdir/before_unique_filter.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${filter_unique_count} ${class_filter} ${empty_region_filter} 2>&1
0
+ − 71
5
+ − 72 if [[ "$fast" == "no" ]] ; then
0
+ − 73
5
+ − 74 echo "---------------- creating new IMGT zips ----------------"
+ − 75 echo "---------------- creating new IMGT zips ----------------<br />" >> $log
+ − 76
+ − 77 mkdir $outdir/new_IMGT
0
+ − 78
36
+ − 79 cat "`find $PWD/files/ -name "1_*"`" > "$outdir/new_IMGT/1_Summary.txt"
+ − 80 cat "`find $PWD/files/ -name "2_*"`" > "$outdir/new_IMGT/2_IMGT-gapped-nt-sequences.txt"
+ − 81 cat "`find $PWD/files/ -name "3_*"`" > "$outdir/new_IMGT/3_Nt-sequences.txt"
+ − 82 cat "`find $PWD/files/ -name "4_*"`" > "$outdir/new_IMGT/4_IMGT-gapped-AA-sequences.txt"
+ − 83 cat "`find $PWD/files/ -name "5_*"`" > "$outdir/new_IMGT/5_AA-sequences.txt"
+ − 84 cat "`find $PWD/files/ -name "6_*"`" > "$outdir/new_IMGT/6_Junction.txt"
+ − 85 cat "`find $PWD/files/ -name "7_*"`" > "$outdir/new_IMGT/7_V-REGION-mutation-and-AA-change-table.txt"
+ − 86 cat "`find $PWD/files/ -name "8_*"`" > "$outdir/new_IMGT/8_V-REGION-nt-mutation-statistics.txt"
+ − 87 cat "`find $PWD/files/ -name "9_*"`" > "$outdir/new_IMGT/9_V-REGION-AA-change-statistics.txt"
+ − 88 cat "`find $PWD/files/ -name "10_*"`" > "$outdir/new_IMGT/10_V-REGION-mutation-hotspots.txt"
0
+ − 89
5
+ − 90 mkdir $outdir/new_IMGT_IGA
+ − 91 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA
0
+ − 92
5
+ − 93 mkdir $outdir/new_IMGT_IGA1
+ − 94 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA1
0
+ − 95
5
+ − 96 mkdir $outdir/new_IMGT_IGA2
+ − 97 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA2
0
+ − 98
5
+ − 99 mkdir $outdir/new_IMGT_IGG
+ − 100 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG
0
+ − 101
5
+ − 102 mkdir $outdir/new_IMGT_IGG1
+ − 103 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG1
0
+ − 104
5
+ − 105 mkdir $outdir/new_IMGT_IGG2
+ − 106 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG2
0
+ − 107
5
+ − 108 mkdir $outdir/new_IMGT_IGG3
+ − 109 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG3
0
+ − 110
5
+ − 111 mkdir $outdir/new_IMGT_IGG4
+ − 112 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG4
+ − 113
+ − 114 mkdir $outdir/new_IMGT_IGM
+ − 115 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGM
0
+ − 116
5
+ − 117 mkdir $outdir/new_IMGT_IGE
+ − 118 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGE
0
+ − 119
5
+ − 120 Rscript $dir/new_imgt.r $outdir/new_IMGT/ $outdir/merged.txt "-" 2>&1
+ − 121
+ − 122 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA/ $outdir/merged.txt "IGA" 2>&1
+ − 123 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA1/ $outdir/merged.txt "IGA1" 2>&1
+ − 124 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA2/ $outdir/merged.txt "IGA2" 2>&1
0
+ − 125
5
+ − 126 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG/ $outdir/merged.txt "IGG" 2>&1
+ − 127 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG1/ $outdir/merged.txt "IGG1" 2>&1
+ − 128 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG2/ $outdir/merged.txt "IGG2" 2>&1
+ − 129 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG3/ $outdir/merged.txt "IGG3" 2>&1
+ − 130 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG4/ $outdir/merged.txt "IGG4" 2>&1
0
+ − 131
5
+ − 132 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGM/ $outdir/merged.txt "IGM" 2>&1
0
+ − 133
5
+ − 134 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGE/ $outdir/merged.txt "IGE" 2>&1
0
+ − 135
+ − 136
5
+ − 137 tmp="$PWD"
+ − 138 cd $outdir/new_IMGT/ #tar weirdness...
+ − 139 tar -cJf ../new_IMGT.txz *
0
+ − 140
5
+ − 141 cd $outdir/new_IMGT_IGA/
+ − 142 tar -cJf ../new_IMGT_IGA.txz *
0
+ − 143
5
+ − 144 cd $outdir/new_IMGT_IGA1/
+ − 145 tar -cJf ../new_IMGT_IGA1.txz *
0
+ − 146
5
+ − 147 cd $outdir/new_IMGT_IGA2/
+ − 148 tar -cJf ../new_IMGT_IGA2.txz *
0
+ − 149
5
+ − 150 cd $outdir/new_IMGT_IGG/
+ − 151 tar -cJf ../new_IMGT_IGG.txz *
0
+ − 152
5
+ − 153 cd $outdir/new_IMGT_IGG1/
+ − 154 tar -cJf ../new_IMGT_IGG1.txz *
0
+ − 155
5
+ − 156 cd $outdir/new_IMGT_IGG2/
+ − 157 tar -cJf ../new_IMGT_IGG2.txz *
+ − 158
+ − 159 cd $outdir/new_IMGT_IGG3/
+ − 160 tar -cJf ../new_IMGT_IGG3.txz *
0
+ − 161
5
+ − 162 cd $outdir/new_IMGT_IGG4/
+ − 163 tar -cJf ../new_IMGT_IGG4.txz *
+ − 164
+ − 165 cd $outdir/new_IMGT_IGM/
+ − 166 tar -cJf ../new_IMGT_IGM.txz *
0
+ − 167
5
+ − 168 cd $outdir/new_IMGT_IGE/
+ − 169 tar -cJf ../new_IMGT_IGE.txz *
0
+ − 170
5
+ − 171 cd $tmp
+ − 172 fi
0
+ − 173
+ − 174 echo "---------------- shm_csr.r ----------------"
+ − 175 echo "---------------- shm_csr.r ----------------<br />" >> $log
+ − 176
5
+ − 177 classes="IGA,IGA1,IGA2,IGG,IGG1,IGG2,IGG3,IGG4,IGM,IGE,unmatched"
0
+ − 178 echo "R mutation analysis"
1
+ − 179 Rscript $dir/shm_csr.r $outdir/merged.txt $classes $outdir ${empty_region_filter} 2>&1
0
+ − 180
43
+ − 181 echo "---------------- plot_pdfs.r ----------------"
+ − 182 echo "---------------- plot_pdfs.r ----------------<br />" >> $log
+ − 183
+ − 184 echo "Rscript $dir/shm_csr.r $outdir/pdfplots.RData $outdir 2>&1"
+ − 185
+ − 186 Rscript $dir/plot_pdf.r "$outdir/pdfplots.RData" "$outdir" 2>&1
+ − 187
0
+ − 188 echo "---------------- shm_csr.py ----------------"
+ − 189 echo "---------------- shm_csr.py ----------------<br />" >> $log
+ − 190
1
+ − 191 python $dir/shm_csr.py --input $outdir/merged.txt --genes $classes --empty_region_filter "${empty_region_filter}" --output $outdir/hotspot_analysis.txt
0
+ − 192
+ − 193 echo "---------------- aa_histogram.r ----------------"
+ − 194 echo "---------------- aa_histogram.r ----------------<br />" >> $log
+ − 195
5
+ − 196 Rscript $dir/aa_histogram.r $outdir/aa_id_mutations.txt $outdir/absent_aa_id.txt "IGA,IGG,IGM,IGE" $outdir/ 2>&1
0
+ − 197 if [ -e "$outdir/aa_histogram_.png" ]; then
+ − 198 mv $outdir/aa_histogram_.png $outdir/aa_histogram.png
42
+ − 199 mv $outdir/aa_histogram_.pdf $outdir/aa_histogram.pdf
0
+ − 200 mv $outdir/aa_histogram_.txt $outdir/aa_histogram.txt
29
+ − 201 mv $outdir/aa_histogram_absent_.txt $outdir/aa_histogram_absent.txt
+ − 202 mv $outdir/aa_histogram_count_.txt $outdir/aa_histogram_count.txt
+ − 203 mv $outdir/aa_histogram_sum_.txt $outdir/aa_histogram_sum.txt
0
+ − 204 fi
+ − 205
5
+ − 206 genes=(IGA IGA1 IGA2 IGG IGG1 IGG2 IGG3 IGG4 IGM IGE)
0
+ − 207
+ − 208 funcs=(sum mean median)
+ − 209 funcs=(sum)
+ − 210
+ − 211 echo "---------------- sequence_overview.r ----------------"
+ − 212 echo "---------------- sequence_overview.r ----------------<br />" >> $log
+ − 213
+ − 214 mkdir $outdir/sequence_overview
+ − 215
7
+ − 216 Rscript $dir/sequence_overview.r $outdir/before_unique_filter.txt $outdir/merged.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt ${empty_region_filter} 2>&1
0
+ − 217
+ − 218 echo "<table border='1'>" > $outdir/base_overview.html
+ − 219
+ − 220 while IFS=$'\t' read ID class seq A C G T
+ − 221 do
+ − 222 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
+ − 223 done < $outdir/sequence_overview/ntoverview.txt
+ − 224
+ − 225 echo "<html><center><h1>$title</h1></center>" > $output
+ − 226 echo "<meta name='viewport' content='width=device-width, initial-scale=1'>" >> $output
+ − 227 echo "<script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $output
+ − 228 echo "<script type='text/javascript' src='tabber.js'></script>" >> $output
+ − 229 echo "<script type='text/javascript' src='script.js'></script>" >> $output
+ − 230 echo "<link rel='stylesheet' type='text/css' href='style.css'>" >> $output
+ − 231 echo "<link rel='stylesheet' type='text/css' href='pure-min.css'>" >> $output
+ − 232
+ − 233 matched_count="`cat $outdir/merged.txt | grep -v 'unmatched' | tail -n +2 | wc -l`"
+ − 234 unmatched_count="`cat $outdir/unmatched.txt | tail -n +2 | wc -l`"
+ − 235 total_count=$((matched_count + unmatched_count))
+ − 236 perc_count=$((unmatched_count / total_count * 100))
+ − 237 perc_count=`bc -l <<< "scale=2; ${unmatched_count} / ${total_count} * 100"`
+ − 238 perc_count=`bc -l <<< "scale=2; (${unmatched_count} / ${total_count} * 100 ) / 1"`
+ − 239
+ − 240 echo "<center><h2>Total: ${total_count}</h2></center>" >> $output
+ − 241 echo "<center><h2>Matched: ${matched_count} Unmatched: ${unmatched_count}</h2></center>" >> $output
+ − 242 echo "<center><h2>Percentage unmatched: ${perc_count}</h2></center>" >> $output
+ − 243
+ − 244 echo "---------------- main tables ----------------"
+ − 245 echo "---------------- main tables ----------------<br />" >> $log
+ − 246
+ − 247 echo "<div class='tabber'>" >> $output
23
+ − 248 echo "<div class='tabbertab' title='SHM Overview' style='width: 3000px;'>" >> $output
0
+ − 249
+ − 250 for func in ${funcs[@]}
+ − 251 do
+ − 252
+ − 253 echo "---------------- $func table ----------------"
+ − 254 echo "---------------- $func table ----------------<br />" >> $log
+ − 255
47
+ − 256 cat $outdir/mutations_${func}.txt $outdir/shm_overview_tandem_row.txt $outdir/hotspot_analysis_${func}.txt > $outdir/data_${func}.txt
0
+ − 257
+ − 258 echo "---------------- pattern_plots.r ----------------"
+ − 259 echo "---------------- pattern_plots.r ----------------<br />" >> $log
+ − 260
43
+ − 261 Rscript $dir/pattern_plots.r $outdir/data_${func}.txt $outdir/aid_motives $outdir/relative_mutations $outdir/absolute_mutations $outdir/shm_overview.txt 2>&1
0
+ − 262
+ − 263 echo "<table class='pure-table pure-table-striped'>" >> $output
+ − 264 echo "<thead><tr><th>info</th>" >> $output
+ − 265
+ − 266 if [ "${class_filter}" != "101_101" ] ; then
+ − 267
+ − 268 for gene in ${genes[@]}
+ − 269 do
+ − 270 tmp=`cat $outdir/${gene}_${func}_n.txt`
+ − 271 echo "<th><a href='matched_${gene}_${func}.txt'>${gene} (N = $tmp)</a></th>" >> $output
+ − 272 done
+ − 273
+ − 274 tmp=`cat $outdir/all_${func}_n.txt`
+ − 275 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
+ − 276 tmp=`cat $outdir/unmatched_${func}_n.txt`
+ − 277 echo "<th><a href='unmatched.txt'>unmatched (N = ${unmatched_count})</a></th><tr></thead>" >> $output
+ − 278
5
+ − 279 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
0
+ − 280 do
47
+ − 281 if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] || [ "$name" == "Tandems/Expected (ratio)" ] ; then #meh
5
+ − 282 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>" >> $output
0
+ − 283 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
5
+ − 284 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>" >> $output
0
+ − 285 else
5
+ − 286 echo "<tr><td>$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
0
+ − 287 fi
+ − 288 done < $outdir/data_${func}.txt
+ − 289
+ − 290 else
3
+ − 291 tmp=`cat $outdir/all_${func}_n.txt`
0
+ − 292 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
+ − 293
5
+ − 294 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
0
+ − 295 do
+ − 296 if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] ; then #meh
3
+ − 297 echo "<tr><td>$name</td><td>${allx}/${ally}</td></tr>" >> $output
0
+ − 298 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
3
+ − 299 echo "<tr><td>$name</td><td>${allz}%</td></tr>" >> $output
0
+ − 300 else
3
+ − 301 echo "<tr><td>$name</td><td>${allx}/${ally} (${allz}%)</td></tr>" >> $output
0
+ − 302 fi
+ − 303 done < $outdir/data_${func}.txt
+ − 304
+ − 305 fi
+ − 306 echo "</table>" >> $output
+ − 307 #echo "<a href='data_${func}.txt'>Download data</a>" >> $output
+ − 308 done
+ − 309
42
+ − 310 echo "<a href='aid_motives.pdf'><img src='aid_motives.png' /></a><br />" >> $output
+ − 311 echo "<a href='relative_mutations.pdf'><img src='relative_mutations.png' /></a><br />" >> $output
43
+ − 312 echo "<a href='absolute_mutations.pdf'><img src='absolute_mutations.png' /></a><br />" >> $output
39
+ − 313 echo "<br />" >> $output
+ − 314 cat $dir/shm_overview.htm >> $output
0
+ − 315 echo "</div>" >> $output #SHM overview tab end
+ − 316
+ − 317 echo "---------------- images ----------------"
+ − 318 echo "---------------- images ----------------<br />" >> $log
+ − 319
42
+ − 320 echo "<div class='tabbertab' title='SHM Frequency' style='width: 3000px;'></a>" >> $output
0
+ − 321
+ − 322 if [ -a $outdir/scatter.png ]
+ − 323 then
42
+ − 324 echo "<a href='scatter.pdf'><img src='scatter.png'/><br />" >> $output
0
+ − 325 fi
+ − 326 if [ -a $outdir/frequency_ranges.png ]
+ − 327 then
42
+ − 328 echo "<a href='frequency_ranges.pdf'><img src='frequency_ranges.png'/></a><br />" >> $output
0
+ − 329 fi
+ − 330
39
+ − 331 echo "<br />" >> $output
+ − 332 cat $dir/shm_frequency.htm >> $output
+ − 333
0
+ − 334 echo "</div>" >> $output #SHM frequency tab end
+ − 335
23
+ − 336 echo "<div class='tabbertab' title='Transition tables' style='width: 3000px;'>" >> $output
0
+ − 337
+ − 338 echo "<table border='0'>" >> $output
+ − 339
+ − 340 for gene in ${genes[@]}
+ − 341 do
+ − 342 echo "<tr>" >> $output
+ − 343 echo "<td><h1>${gene}</h1></td>" >> $output
23
+ − 344
+ − 345 if [ -e $outdir/transitions_heatmap_${gene}.png ]
+ − 346 then
42
+ − 347 echo "<td><a href='transitions_heatmap_${gene}.pdf'><img src='transitions_heatmap_${gene}.png' /></a></td>" >> $output
23
+ − 348 else
+ − 349 echo "<td></td>" >> $output
+ − 350 fi
+ − 351
+ − 352 if [ -e $outdir/transitions_stacked_${gene}.png ]
+ − 353 then
42
+ − 354 echo "<td><a href='transitions_stacked_${gene}.pdf'><img src='transitions_stacked_${gene}.png' /></a></td>" >> $output
23
+ − 355 else
+ − 356 echo "<td></td>" >> $output
+ − 357 fi
+ − 358
0
+ − 359 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
+ − 360 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
+ − 361 first="true"
+ − 362 while IFS=, read from a c g t
+ − 363 do
+ − 364 if [ "$first" == "true" ] ; then
+ − 365 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
+ − 366 first="false"
+ − 367 else
+ − 368 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
+ − 369 fi
+ − 370 done < $outdir/transitions_${gene}_sum.txt
+ − 371 echo "</table></td>" >> $output
+ − 372
+ − 373 echo "</tr>" >> $output
+ − 374 done
+ − 375
+ − 376 echo "<tr>" >> $output
+ − 377 echo "<td><h1>All</h1></td>" >> $output
42
+ − 378 echo "<td><a href='transitions_heatmap_all.pdf'><img src='transitions_heatmap_all.png' /></a></td>" >> $output
+ − 379 echo "<td><a href='transitions_stacked_all.pdf'><img src='transitions_stacked_all.png' /></a></td>" >> $output
0
+ − 380 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
+ − 381 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
+ − 382 first="true"
+ − 383 while IFS=, read from a c g t
+ − 384 do
+ − 385 if [ "$first" == "true" ] ; then
+ − 386 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
+ − 387 first="false"
+ − 388 else
+ − 389 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
+ − 390 fi
+ − 391 done < $outdir/transitions_all_sum.txt
+ − 392 echo "</table></td>" >> $output
+ − 393
+ − 394 echo "</tr>" >> $output
+ − 395
+ − 396 echo "</table>" >> $output
+ − 397
39
+ − 398 echo "<br />" >> $output
+ − 399 cat $dir/shm_transition.htm >> $output
+ − 400
0
+ − 401 echo "</div>" >> $output #transition tables tab end
+ − 402
+ − 403 echo "<div class='tabbertab' title='Antigen Selection'>" >> $output
+ − 404
23
+ − 405 if [ -e $outdir/aa_histogram.png ]
0
+ − 406 then
42
+ − 407 echo "<a href='aa_histogram.pdf'><img src='aa_histogram.png'/></a><br />" >> $output
23
+ − 408 fi
+ − 409
+ − 410 if [ -e $outdir/aa_histogram_IGA.png ]
+ − 411 then
42
+ − 412 echo "<a href='aa_histogram_IGA.pdf'><img src='aa_histogram_IGA.png'/></a><br />" >> $output
23
+ − 413 fi
+ − 414
+ − 415 if [ -e $outdir/aa_histogram_IGG.png ]
+ − 416 then
42
+ − 417 echo "<a href='aa_histogram_IGG.pdf'><img src='aa_histogram_IGG.png'/></a><br />" >> $output
23
+ − 418 fi
+ − 419
+ − 420 if [ -e $outdir/aa_histogram_IGM.png ]
+ − 421 then
42
+ − 422 echo "<a href='aa_histogram_IGM.pdf'><img src='aa_histogram_IGM.png'/></a><br />" >> $output
23
+ − 423 fi
+ − 424
+ − 425 if [ -e $outdir/aa_histogram_IGE.png ]
+ − 426 then
42
+ − 427 echo "<a href='aa_histogram_IGE.pdf'><img src='aa_histogram_IGE.png'/></a><br />" >> $output
0
+ − 428 fi
+ − 429
23
+ − 430
33
+ − 431
+ − 432 if [[ "$fast" == "no" ]] ; then
+ − 433
41
+ − 434
+ − 435
33
+ − 436 echo "---------------- baseline ----------------"
+ − 437 echo "---------------- baseline ----------------<br />" >> $log
+ − 438 tmp="$PWD"
+ − 439
+ − 440 mkdir $outdir/baseline
37
+ − 441
41
+ − 442 echo "<center><h1>BASELINe</h1>" >> $output
+ − 443 header_substring="Based on CDR1, FR2, CDR2, FR3 (27:27:38:55:65:104:-)"
+ − 444
37
+ − 445 baseline_boundaries="27:27:38:55:65:104:-"
+ − 446
+ − 447 if [[ "${empty_region_filter}" == "leader" ]] ; then
+ − 448 baseline_boundaries="1:26:38:55:65:104:-"
41
+ − 449 header_substring="Based on FR1, CDR1, FR2, CDR2, FR3 (1:26:38:55:65:104,-)"
37
+ − 450 fi
41
+ − 451
+ − 452 echo "<p>${header_substring}</p></center>" >> $output
23
+ − 453
33
+ − 454 mkdir $outdir/baseline/IGA_IGG_IGM
+ − 455 if [[ $(wc -l < $outdir/new_IMGT/1_Summary.txt) -gt "1" ]]; then
+ − 456 cd $outdir/baseline/IGA_IGG_IGM
41
+ − 457 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT.txz "IGA_IGG_IGM_IGE" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt"
33
+ − 458 else
+ − 459 echo "No sequences" > "$outdir/baseline.txt"
+ − 460 fi
+ − 461
+ − 462 mkdir $outdir/baseline/IGA
+ − 463 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
+ − 464 cd $outdir/baseline/IGA
37
+ − 465 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT_IGA.txz "IGA" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGA.pdf" "Sequence.ID" "$outdir/baseline_IGA.txt"
33
+ − 466 else
+ − 467 echo "No IGA sequences" > "$outdir/baseline_IGA.txt"
+ − 468 fi
+ − 469
+ − 470 mkdir $outdir/baseline/IGG
+ − 471 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
+ − 472 cd $outdir/baseline/IGG
37
+ − 473 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT_IGG.txz "IGG" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGG.pdf" "Sequence.ID" "$outdir/baseline_IGG.txt"
33
+ − 474 else
+ − 475 echo "No IGG sequences" > "$outdir/baseline_IGG.txt"
+ − 476 fi
23
+ − 477
33
+ − 478 mkdir $outdir/baseline/IGM
+ − 479 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
+ − 480 cd $outdir/baseline/IGM
37
+ − 481 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT_IGM.txz "IGM" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGM.pdf" "Sequence.ID" "$outdir/baseline_IGM.txt"
33
+ − 482 else
+ − 483 echo "No IGM sequences" > "$outdir/baseline_IGM.txt"
+ − 484 fi
+ − 485
+ − 486 mkdir $outdir/baseline/IGE
+ − 487 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
+ − 488 cd $outdir/baseline/IGE
37
+ − 489 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT_IGE.txz "IGE" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGE.pdf" "Sequence.ID" "$outdir/baseline_IGE.txt"
33
+ − 490 else
+ − 491 echo "No IGE sequences" > "$outdir/baseline_IGE.txt"
+ − 492 fi
+ − 493
+ − 494 cd $tmp
23
+ − 495
33
+ − 496 echo "Cleaning up *.RData files"
+ − 497 find $outdir/baseline -name "*.RData" -type f -delete
+ − 498
+ − 499 if [ -e $outdir/baseline.pdf ]
+ − 500 then
+ − 501 echo "<embed src='baseline.pdf' width='700px' height='1000px'>" >> $output
+ − 502 fi
+ − 503
+ − 504 if [ -e $outdir/baseline_IGA.pdf ]
+ − 505 then
+ − 506 echo "<embed src='baseline_IGA.pdf' width='700px' height='1000px'>" >> $output
+ − 507 fi
23
+ − 508
33
+ − 509 if [ -e $outdir/baseline_IGG.pdf ]
+ − 510 then
+ − 511 echo "<embed src='baseline_IGG.pdf' width='700px' height='1000px'>" >> $output
+ − 512 fi
+ − 513
+ − 514 if [ -e $outdir/baseline_IGM.pdf ]
+ − 515 then
+ − 516 echo "<embed src='baseline_IGM.pdf' width='700px' height='1000px'>" >> $output
+ − 517 fi
+ − 518
+ − 519 if [ -e $outdir/baseline_IGE.pdf ]
+ − 520 then
+ − 521 echo "<embed src='baseline_IGE.pdf' width='700px' height='1000px'>" >> $output
+ − 522 fi
23
+ − 523 fi
0
+ − 524
39
+ − 525 echo "<br />" >> $output
+ − 526 cat $dir/shm_selection.htm >> $output
+ − 527
0
+ − 528 echo "</div>" >> $output #antigen selection tab end
+ − 529
+ − 530 echo "<div class='tabbertab' title='CSR'>" >> $output #CSR tab
+ − 531
23
+ − 532 if [ -e $outdir/IGA.png ]
0
+ − 533 then
42
+ − 534 echo "<a href='IGA.pdf'><img src='IGA.png'/></a><br />" >> $output
0
+ − 535 fi
23
+ − 536 if [ -e $outdir/IGG.png ]
0
+ − 537 then
42
+ − 538 echo "<a href='IGG.pdf'><img src='IGG.png'/></a><br />" >> $output
0
+ − 539 fi
+ − 540
39
+ − 541 echo "<br />" >> $output
+ − 542 cat $dir/shm_csr.htm >> $output
+ − 543
0
+ − 544 echo "</div>" >> $output #CSR tab end
+ − 545
5
+ − 546 if [[ "$fast" == "no" ]] ; then
+ − 547
+ − 548 echo "---------------- change-o MakeDB ----------------"
0
+ − 549
5
+ − 550 mkdir $outdir/change_o
0
+ − 551
5
+ − 552 tmp="$PWD"
0
+ − 553
5
+ − 554 cd $outdir/change_o
0
+ − 555
5
+ − 556 bash $dir/change_o/makedb.sh $outdir/new_IMGT.txz false false false $outdir/change_o/change-o-db.txt
+ − 557 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
0
+ − 558
5
+ − 559 Rscript $dir/merge.r $outdir/change_o/change-o-db-defined_clones.txt $outdir/merged.txt "all" "Sequence.ID,best_match" "SEQUENCE_ID" "Sequence.ID" $outdir/change_o/change-o-db-defined_clones.txt 2>&1
0
+ − 560
5
+ − 561 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 2>&1"
0
+ − 562
5
+ − 563 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
+ − 564 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGA.txz false false false $outdir/change_o/change-o-db-IGA.txt
+ − 565 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 $outdir/change_o/change-o-defined_clones-summary-IGA.txt
+ − 566 else
+ − 567 echo "No IGA sequences" > "$outdir/change_o/change-o-db-defined_clones-IGA.txt"
+ − 568 echo "No IGA sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGA.txt"
+ − 569 fi
0
+ − 570
5
+ − 571 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
+ − 572 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGG.txz false false false $outdir/change_o/change-o-db-IGG.txt
+ − 573 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 $outdir/change_o/change-o-defined_clones-summary-IGG.txt
+ − 574 else
+ − 575 echo "No IGG sequences" > "$outdir/change_o/change-o-db-defined_clones-IGG.txt"
+ − 576 echo "No IGG sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGG.txt"
+ − 577 fi
0
+ − 578
5
+ − 579 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
+ − 580 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGM.txz false false false $outdir/change_o/change-o-db-IGM.txt
+ − 581 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 $outdir/change_o/change-o-defined_clones-summary-IGM.txt
+ − 582 else
+ − 583 echo "No IGM sequences" > "$outdir/change_o/change-o-db-defined_clones-IGM.txt"
+ − 584 echo "No IGM sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGM.txt"
+ − 585 fi
0
+ − 586
6
+ − 587 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
+ − 588 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGE.txz false false false $outdir/change_o/change-o-db-IGE.txt
+ − 589 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 $outdir/change_o/change-o-defined_clones-summary-IGE.txt
+ − 590 else
+ − 591 echo "No IGE sequences" > "$outdir/change_o/change-o-db-defined_clones-IGE.txt"
+ − 592 echo "No IGE sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGE.txt"
+ − 593 fi
+ − 594
5
+ − 595 PWD="$tmp"
0
+ − 596
39
+ − 597 echo "<div class='tabbertab' title='Clonal Relation' style='width: 7000px;'>" >> $output #clonality tab
0
+ − 598
16
+ − 599 function clonality_table {
+ − 600 local infile=$1
+ − 601 local outfile=$2
+ − 602
+ − 603 echo "<table class='pure-table pure-table-striped'>" >> $outfile
+ − 604 echo "<thead><tr><th>Clone size</th><th>Nr of clones</th><th>Nr of sequences</th></tr></thead>" >> $outfile
+ − 605
+ − 606 first='true'
+ − 607
+ − 608 while read size clones seqs
+ − 609 do
+ − 610 if [[ "$first" == "true" ]]; then
+ − 611 first="false"
+ − 612 continue
+ − 613 fi
+ − 614 echo "<tr><td>$size</td><td>$clones</td><td>$seqs</td></tr>" >> $outfile
+ − 615 done < $infile
+ − 616
+ − 617 echo "</table>" >> $outfile
+ − 618 }
+ − 619 echo "<div class='tabber'>" >> $output
0
+ − 620
16
+ − 621 echo "<div class='tabbertab' title='All'>" >> $output
+ − 622 clonality_table $outdir/change_o/change-o-defined_clones-summary.txt $output
+ − 623 echo "</div>" >> $output
0
+ − 624
16
+ − 625 echo "<div class='tabbertab' title='IGA'>" >> $output
+ − 626 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGA.txt $output
+ − 627 echo "</div>" >> $output
0
+ − 628
16
+ − 629 echo "<div class='tabbertab' title='IGG'>" >> $output
+ − 630 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGG.txt $output
+ − 631 echo "</div>" >> $output
0
+ − 632
16
+ − 633 echo "<div class='tabbertab' title='IGM'>" >> $output
+ − 634 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
+ − 635 echo "</div>" >> $output
6
+ − 636
16
+ − 637 echo "<div class='tabbertab' title='IGE'>" >> $output
+ − 638 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
+ − 639 echo "</div>" >> $output
0
+ − 640
39
+ − 641 echo "<div class='tabbertab' title='Overlap' style='width: 7000px;'>" >> $output
+ − 642 cat "$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/..."
16
+ − 643 echo "</div>" >> $output
39
+ − 644
16
+ − 645 echo "</div>" >> $output #clonality tabber end
39
+ − 646
+ − 647 echo "<br />" >> $output
+ − 648 cat $dir/shm_clonality.htm >> $output
+ − 649
16
+ − 650 echo "</div>" >> $output #clonality tab end
0
+ − 651
5
+ − 652 fi
+ − 653
0
+ − 654 echo "<div class='tabbertab' title='Downloads'>" >> $output
+ − 655
+ − 656 echo "<table class='pure-table pure-table-striped'>" >> $output
+ − 657 echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output
+ − 658 echo "<tr><td>The complete dataset</td><td><a href='merged.txt' download='merged.txt' >Download</a></td></tr>" >> $output
+ − 659 echo "<tr><td>The filtered dataset</td><td><a href='filtered.txt' download='filtered.txt' >Download</a></td></tr>" >> $output
+ − 660 echo "<tr><td>The alignment info on the unmatched sequences</td><td><a href='unmatched.txt' download='unmatched.txt' >Download</a></td></tr>" >> $output
+ − 661
2
+ − 662 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Overview</td></tr>" >> $output
23
+ − 663 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
2
+ − 664 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
+ − 665 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
+ − 666 echo "<tr><td>Base count for every sequence</td><td><a href='base_overview.html'>View</a></td></tr>" >> $output
39
+ − 667 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
+ − 668 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
43
+ − 669 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
47
+ − 670 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
2
+ − 671
+ − 672 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Frequency</td></tr>" >> $output
0
+ − 673 echo "<tr><td>The data generate the frequency scatter plot</td><td><a href='scatter.txt' download='scatter.txt' >Download</a></td></tr>" >> $output
+ − 674 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
+ − 675 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
+ − 676
2
+ − 677 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Transition Tables</td></tr>" >> $output
23
+ − 678 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
45
+ − 679 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
23
+ − 680 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
30
+ − 681 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
23
+ − 682 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
+ − 683 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
+ − 684 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
+ − 685 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
+ − 686 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
+ − 687 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
+ − 688 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
0
+ − 689
2
+ − 690 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Antigen Selection</td></tr>" >> $output
0
+ − 691 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
39
+ − 692 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
0
+ − 693
29
+ − 694 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
+ − 695 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
+ − 696 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
+ − 697 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
+ − 698 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
+ − 699
0
+ − 700 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
+ − 701 echo "<tr><td>Baseline data</td><td><a href='baseline.txt' download='baseline.txt' >Download</a></td></tr>" >> $output
+ − 702 echo "<tr><td>Baseline IGA PDF</td><td><a href='baseline_IGA.pdf' download='baseline_IGA.pdf' >Download</a></td></tr>" >> $output
+ − 703 echo "<tr><td>Baseline IGA data</td><td><a href='baseline_IGA.txt' download='baseline_IGA.txt' >Download</a></td></tr>" >> $output
+ − 704 echo "<tr><td>Baseline IGG PDF</td><td><a href='baseline_IGG.pdf' download='baseline_IGG.pdf' >Download</a></td></tr>" >> $output
+ − 705 echo "<tr><td>Baseline IGG data</td><td><a href='baseline_IGG.txt' download='baseline_IGG.txt' >Download</a></td></tr>" >> $output
+ − 706 echo "<tr><td>Baseline IGM PDF</td><td><a href='baseline_IGM.pdf' download='baseline_IGM.pdf' >Download</a></td></tr>" >> $output
+ − 707 echo "<tr><td>Baseline IGM data</td><td><a href='baseline_IGM.txt' download='baseline_IGM.txt' >Download</a></td></tr>" >> $output
31
+ − 708 echo "<tr><td>Baseline IGE PDF</td><td><a href='baseline_IGE.pdf' download='baseline_IGE.pdf' >Download</a></td></tr>" >> $output
6
+ − 709 echo "<tr><td>Baseline IGE data</td><td><a href='baseline_IGE.txt' download='baseline_IGE.txt' >Download</a></td></tr>" >> $output
0
+ − 710
2
+ − 711 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>CSR</td></tr>" >> $output
39
+ − 712 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
+ − 713 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
2
+ − 714
39
+ − 715 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Clonal Relation</td></tr>" >> $output
2
+ − 716 echo "<tr><td>Sequence overlap between subclasses</td><td><a href='sequence_overview/index.html'>View</a></td></tr>" >> $output
+ − 717 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
+ − 718 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
+ − 719 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
+ − 720 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
+ − 721 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
+ − 722 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
+ − 723 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
+ − 724 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
6
+ − 725 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
+ − 726 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
2
+ − 727
+ − 728 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Filtered IMGT output files</td></tr>" >> $output
0
+ − 729 echo "<tr><td>An IMGT archive with just the matched and filtered sequences</td><td><a href='new_IMGT.txz' download='new_IMGT.txz' >Download</a></td></tr>" >> $output
+ − 730 echo "<tr><td>An IMGT archive with just the matched and filtered IGA sequences</td><td><a href='new_IMGT_IGA.txz' download='new_IMGT_IGA.txz' >Download</a></td></tr>" >> $output
+ − 731 echo "<tr><td>An IMGT archive with just the matched and filtered IGA1 sequences</td><td><a href='new_IMGT_IGA1.txz' download='new_IMGT_IGA1.txz' >Download</a></td></tr>" >> $output
+ − 732 echo "<tr><td>An IMGT archive with just the matched and filtered IGA2 sequences</td><td><a href='new_IMGT_IGA2.txz' download='new_IMGT_IGA2.txz' >Download</a></td></tr>" >> $output
+ − 733 echo "<tr><td>An IMGT archive with just the matched and filtered IGG sequences</td><td><a href='new_IMGT_IGG.txz' download='new_IMGT_IGG.txz' >Download</a></td></tr>" >> $output
+ − 734 echo "<tr><td>An IMGT archive with just the matched and filtered IGG1 sequences</td><td><a href='new_IMGT_IGG1.txz' download='new_IMGT_IGG1.txz' >Download</a></td></tr>" >> $output
+ − 735 echo "<tr><td>An IMGT archive with just the matched and filtered IGG2 sequences</td><td><a href='new_IMGT_IGG2.txz' download='new_IMGT_IGG2.txz' >Download</a></td></tr>" >> $output
+ − 736 echo "<tr><td>An IMGT archive with just the matched and filtered IGG3 sequences</td><td><a href='new_IMGT_IGG3.txz' download='new_IMGT_IGG3.txz' >Download</a></td></tr>" >> $output
+ − 737 echo "<tr><td>An IMGT archive with just the matched and filtered IGG4 sequences</td><td><a href='new_IMGT_IGG4.txz' download='new_IMGT_IGG4.txz' >Download</a></td></tr>" >> $output
+ − 738 echo "<tr><td>An IMGT archive with just the matched and filtered IGM sequences</td><td><a href='new_IMGT_IGM.txz' download='new_IMGT_IGM.txz' >Download</a></td></tr>" >> $output
31
+ − 739 echo "<tr><td>An IMGT archive with just the matched and filtered IGE sequences</td><td><a href='new_IMGT_IGE.txz' download='new_IMGT_IGE.txz' >Download</a></td></tr>" >> $output
0
+ − 740
+ − 741 echo "</table>" >> $output
+ − 742
39
+ − 743 echo "<br />" >> $output
+ − 744 cat $dir/shm_downloads.htm >> $output
+ − 745
0
+ − 746 echo "</div>" >> $output #downloads tab end
+ − 747
+ − 748 echo "</div>" >> $output #tabs end
+ − 749
+ − 750 echo "</html>" >> $output
+ − 751
5
+ − 752
0
+ − 753 echo "---------------- naive_output.r ----------------"
+ − 754 echo "---------------- naive_output.r ----------------<br />" >> $log
+ − 755
5
+ − 756 if [[ "$naive_output" == "yes" ]]
0
+ − 757 then
28
+ − 758 echo "output naive output"
18
+ − 759 if [[ "${class_filter}" == "101_101" ]]
+ − 760 then
28
+ − 761 echo "copy new_IMGT.txz to ${naive_output_all}"
21
+ − 762 cp $outdir/new_IMGT.txz ${naive_output_all}
18
+ − 763 else
28
+ − 764 echo "copy for classes"
18
+ − 765 cp $outdir/new_IMGT_IGA.txz ${naive_output_ca}
+ − 766 cp $outdir/new_IMGT_IGG.txz ${naive_output_cg}
+ − 767 cp $outdir/new_IMGT_IGM.txz ${naive_output_cm}
+ − 768 cp $outdir/new_IMGT_IGE.txz ${naive_output_ce}
+ − 769 fi
0
+ − 770 fi
+ − 771
+ − 772 echo "</table>" >> $outdir/base_overview.html
+ − 773
+ − 774 mv $log $outdir/log.html
+ − 775
+ − 776 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
+ − 777 echo "<table border = 1>" >> $log
+ − 778 echo "<thead><tr><th>Info</th><th>Sequences</th><th>Percentage</th></tr></thead>" >> $log
+ − 779 tIFS="$TMP"
+ − 780 IFS=$'\t'
+ − 781 while read step seq perc
+ − 782 do
+ − 783 echo "<tr>" >> $log
+ − 784 echo "<td>$step</td>" >> $log
+ − 785 echo "<td>$seq</td>" >> $log
+ − 786 echo "<td>${perc}%</td>" >> $log
+ − 787 echo "</tr>" >> $log
+ − 788 done < $outdir/filtering_steps.txt
39
+ − 789 echo "</table>" >> $log
+ − 790 echo "<br />" >> $log
+ − 791 cat $dir/shm_first.htm >> $log
+ − 792 echo "</center></html>" >> $log
0
+ − 793
+ − 794 IFS="$tIFS"
+ − 795
+ − 796
+ − 797 echo "---------------- Done! ----------------"
+ − 798 echo "---------------- Done! ----------------<br />" >> $outdir/log.html
+ − 799
+ − 800
+ − 801
+ − 802
+ − 803
+ − 804
+ − 805
+ − 806
+ − 807
+ − 808
+ − 809
+ − 810
+ − 811
+ − 812
+ − 813
+ − 814
+ − 815
+ − 816
+ − 817
+ − 818
+ − 819
