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comparison wrapper.sh @ 114:e7b550d52eb7 draft

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Uploaded
author davidvanzessen
date Tue, 09 Aug 2016 07:20:41 -0400
parents ade5cf6fd2dc
children 4984c2a06c43
comparison
equal deleted inserted replaced
113:b84477f57318 114:e7b550d52eb7
13 naive_output_ca=$9 13 naive_output_ca=$9
14 naive_output_cg=${10} 14 naive_output_cg=${10}
15 naive_output_cm=${11} 15 naive_output_cm=${11}
16 filter_unique=${12} 16 filter_unique=${12}
17 class_filter=${13} 17 class_filter=${13}
18 empty_region_filter=${14}
18 mkdir $outdir 19 mkdir $outdir
19 20
20 tar -xzf $dir/style.tar.gz -C $outdir 21 tar -xzf $dir/style.tar.gz -C $outdir
21 22
22 echo "---------------- read parameters ----------------" 23 echo "---------------- read parameters ----------------"
78 fi 79 fi
79 80
80 echo "---------------- merge_and_filter.r ----------------" 81 echo "---------------- merge_and_filter.r ----------------"
81 echo "---------------- merge_and_filter.r ----------------<br />" >> $log 82 echo "---------------- merge_and_filter.r ----------------<br />" >> $log
82 83
83 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $outdir/identified_genes.txt $outdir/merged.txt $outdir/before_unique_filter.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${class_filter} 2>&1 84 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $outdir/identified_genes.txt $outdir/merged.txt $outdir/before_unique_filter.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${class_filter} ${empty_region_filter} 2>&1
84 85
85 echo "---------------- creating new IMGT zip ----------------" 86 echo "---------------- creating new IMGT zip ----------------"
86 echo "---------------- creating new IMGT zip ----------------<br />" >> $log 87 echo "---------------- creating new IMGT zip ----------------<br />" >> $log
87 88
88 mkdir $outdir/new_IMGT 89 mkdir $outdir/new_IMGT
105 cp $outdir/new_IMGT/* $outdir/new_IMGT_cg 106 cp $outdir/new_IMGT/* $outdir/new_IMGT_cg
106 107
107 mkdir $outdir/new_IMGT_cm 108 mkdir $outdir/new_IMGT_cm
108 cp $outdir/new_IMGT/* $outdir/new_IMGT_cm 109 cp $outdir/new_IMGT/* $outdir/new_IMGT_cm
109 110
110 Rscript $dir/tmp/igat.r $outdir/new_IMGT/ $outdir/merged.txt "-" 2>&1 111 Rscript $dir/new_imgt.r $outdir/new_IMGT/ $outdir/merged.txt "-" 2>&1
111 Rscript $dir/tmp/igat.r $outdir/new_IMGT_ca/ $outdir/merged.txt "ca" 2>&1 112 Rscript $dir/new_imgt.r $outdir/new_IMGT_ca/ $outdir/merged.txt "ca" 2>&1
112 Rscript $dir/tmp/igat.r $outdir/new_IMGT_cg/ $outdir/merged.txt "cg" 2>&1 113 Rscript $dir/new_imgt.r $outdir/new_IMGT_cg/ $outdir/merged.txt "cg" 2>&1
113 Rscript $dir/tmp/igat.r $outdir/new_IMGT_cm/ $outdir/merged.txt "cm" 2>&1 114 Rscript $dir/new_imgt.r $outdir/new_IMGT_cm/ $outdir/merged.txt "cm" 2>&1
114 115
115 116
116 tmp="$PWD" 117 tmp="$PWD"
117 cd $outdir/new_IMGT/ #tar weirdness... 118 cd $outdir/new_IMGT/ #tar weirdness...
118 tar -cJf ../new_IMGT.txz * 119 tar -cJf ../new_IMGT.txz *
119 cp $dir/tmp/IgAT.xlsm $outdir/new_IMGT/IgAT.xlsm
120 zip -r ../IgAT.zip *
121 120
122 cd $outdir/new_IMGT_ca/ 121 cd $outdir/new_IMGT_ca/
123 tar -cJf ../new_IMGT_ca.txz * 122 tar -cJf ../new_IMGT_ca.txz *
124 cp $dir/tmp/IgAT.xlsm $outdir/new_IMGT_ca/IgAT.xlsm
125 zip -r ../IgAT_ca.zip *
126 123
127 cd $outdir/new_IMGT_cg/ 124 cd $outdir/new_IMGT_cg/
128 tar -cJf ../new_IMGT_cg.txz * 125 tar -cJf ../new_IMGT_cg.txz *
129 cp $dir/tmp/IgAT.xlsm $outdir/new_IMGT_cg/IgAT.xlsm
130 zip -r ../IgAT_cg.zip *
131 126
132 cd $outdir/new_IMGT_cm/ 127 cd $outdir/new_IMGT_cm/
133 tar -cJf ../new_IMGT_cm.txz * 128 tar -cJf ../new_IMGT_cm.txz *
134 cp $dir/tmp/IgAT.xlsm $outdir/new_IMGT_cm/IgAT.xlsm
135 zip -r ../IgAT_cm.zip *
136 129
137 cd $tmp 130 cd $tmp
138 131
139 echo "---------------- mutation_analysis.r ----------------" 132 echo "---------------- mutation_analysis.r ----------------"
140 echo "---------------- mutation_analysis.r ----------------<br />" >> $log 133 echo "---------------- mutation_analysis.r ----------------<br />" >> $log
217 do 210 do
218 tmp=`cat $outdir/${gene}_${func}_n.txt` 211 tmp=`cat $outdir/${gene}_${func}_n.txt`
219 echo "<th><a href='matched_${gene}_${func}.txt'>${gene} (N = $tmp)</a></th>" >> $output 212 echo "<th><a href='matched_${gene}_${func}.txt'>${gene} (N = $tmp)</a></th>" >> $output
220 done 213 done
221 214
215 tmp=`cat $outdir/all_${func}_n.txt`
216 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
222 tmp=`cat $outdir/unmatched_${func}_n.txt` 217 tmp=`cat $outdir/unmatched_${func}_n.txt`
223 echo "<th><a href='unmatched.txt'>unmatched (N = ${unmatched_count})</a></th>" >> $output 218 echo "<th><a href='unmatched.txt'>unmatched (N = ${unmatched_count})</a></th>" >> $output
224 tmp=`cat $outdir/all_${func}_n.txt`
225 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
226 219
227 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz unx uny unz allx ally allz 220 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz unx uny unz allx ally allz
228 do 221 do
229 if [ "$name" == "FR S/R (ratio)" ] || [ "$name" == "CDR S/R (ratio)" ] ; then #meh 222 if [ "$name" == "FR S/R (ratio)" ] || [ "$name" == "CDR S/R (ratio)" ] ; then #meh
230 echo "<tr><td>$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} (${cmz})</td><td>${allx}/${ally} (${allz})</td></tr>" >> $output 223 echo "<tr><td>$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} (${cmz})</td><td>${allx}/${ally} (${allz})</td></tr>" >> $output
231 else 224 else
232 echo "<tr><td>$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} (${cmz}%)</td><td>${unx}/${uny} (${unz}%)</td><td>${allx}/${ally} (${allz}%)</td></tr>" >> $output 225 echo "<tr><td>$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} (${cmz}%)</td><td>${allx}/${ally} (${allz}%)</td><td>${unx}/${uny} (${unz}%)</td></tr>" >> $output
233 fi 226 fi
234 done < $outdir/data_${func}.txt 227 done < $outdir/data_${func}.txt
235 echo "</table>" >> $output 228 echo "</table>" >> $output
236 #echo "<a href='data_${func}.txt'>Download data</a>" >> $output 229 #echo "<a href='data_${func}.txt'>Download data</a>" >> $output
237 done 230 done
257 250
258 echo "</div>" >> $output #SHM frequency tab end 251 echo "</div>" >> $output #SHM frequency tab end
259 252
260 echo "<div class='tabbertab' title='Transition tables'>" >> $output 253 echo "<div class='tabbertab' title='Transition tables'>" >> $output
261 254
255 echo "<table border='0'>" >> $output
256
262 for gene in ${genes[@]} 257 for gene in ${genes[@]}
263 do 258 do
264 echo "<table border='1'><caption>$gene transition table</caption>" >> $output 259 echo "<tr>" >> $output
260 echo "<td><h1>${gene}</h1></td>" >> $output
261 echo "<td><img src='transitions_heatmap_${gene}.png' /></td>" >> $output
262 echo "<td><img src='transitions_stacked_${gene}.png' /></td>" >> $output
263 echo "<td><table border='1'>" >> $output
265 while IFS=, read from a c g t 264 while IFS=, read from a c g t
266 do 265 do
267 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output 266 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
268 done < $outdir/transitions_${gene}_sum.txt 267 done < $outdir/transitions_${gene}_sum.txt
269 echo "</table>" >> $output 268 echo "</table></td>" >> $output
269
270 echo "</tr>" >> $output
270 done 271 done
271 272
272 echo "<table border='1'><caption>All transition table</caption>" >> $output 273 echo "<tr>" >> $output
274 echo "<td><h1>All</h1></td>" >> $output
275 echo "<td><img src='transitions_heatmap_all.png' /></td>" >> $output
276 echo "<td><img src='transitions_stacked_all.png' /></td>" >> $output
277 echo "<td><table border='1'>" >> $output
273 while IFS=, read from a c g t 278 while IFS=, read from a c g t
274 do 279 do
275 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output 280 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
276 done < $outdir/transitions_all_sum.txt 281 done < $outdir/transitions_all_sum.txt
282 echo "</table></td>" >> $output
283
284 echo "</tr>" >> $output
285
277 echo "</table>" >> $output 286 echo "</table>" >> $output
278 287
279 echo "</div>" >> $output #transition tables tab end 288 echo "</div>" >> $output #transition tables tab end
280 289
281 echo "<div class='tabbertab' title='Antigen Selection'>" >> $output 290 echo "<div class='tabbertab' title='Antigen Selection'>" >> $output
313 322
314 echo "</div>" >> $output #CSR tab end 323 echo "</div>" >> $output #CSR tab end
315 324
316 echo "<div class='tabbertab' title='Downloads'>" >> $output 325 echo "<div class='tabbertab' title='Downloads'>" >> $output
317 326
318 echo "<a href='unmatched.txt'>unmatched</a><br />" >> $output 327 echo "<table border='1' width='700px'>" >> $output
319 echo "<a href='motif_per_seq.txt'>motif per sequence</a><br />" >> $output 328 echo "<tr><td>The complete dataset</td><td><a href='merged.txt'>Download</a></td></tr>" >> $output
320 echo "<a href='merged.txt'>all data</a><br />" >> $output 329 echo "<tr><td>The alignment info on the unmatched sequences</td><td><a href='unmatched.txt'>Download</a></td></tr>" >> $output
321 echo "<a href='mutation_by_id.txt'>mutations by id</a><br />" >> $output 330 echo "<tr><td>Motif data per sequence ID</td><td><a href='motif_per_seq.txt'>Download</a></td></tr>" >> $output
322 echo "<a href='aa_id_mutations.txt'>AA mutations location by id</a><br />" >> $output 331 echo "<tr><td>Mutation data per sequence ID</td><td><a href='mutation_by_id.txt'>Download</a></td></tr>" >> $output
323 echo "<a href='absent_aa_id.txt'>Absant AA locations by id</a><br />" >> $output 332 echo "<tr><td>AA mutation data per sequence ID</td><td><a href='aa_id_mutations.txt'>Download</a></td></tr>" >> $output
324 echo "<a href='sequence_overview/index.html'>Sequence Overview</a><br />" >> $output 333 echo "<tr><td>Absent AA location data per sequence ID</td><td><a href='absent_aa_id.txt'>Download</a></td></tr>" >> $output
325 echo "<a href='base_overview.html'>Base overview</a><br />" >> $output 334 echo "<tr><td>CDR1+FR2+CDR2+FR3+CDR3 sequences that show up more than once</td><td><a href='sequence_overview/index.html'>Download</a></td></tr>" >> $output
326 echo "<a href='baseline.pdf'>Baseline PDF</a><br />" >> $output 335 echo "<tr><td>Base count for every sequence</td><td><a href='base_overview.html'>Download</a></td></tr>" >> $output
327 echo "<a href='baseline.txt'>Baseline Table</a><br />" >> $output 336 echo "<tr><td>Baseline PDF (<href a='http://selection.med.yale.edu/baseline/'>http://selection.med.yale.edu/baseline/</a>)</td><td><a href='baseline.pdf'>Download</a></td></tr>" >> $output
328 echo "<a href='baseline_ca.pdf'>Baseline ca PDF</a><br />" >> $output 337 echo "<tr><td>Baseline data</td><td><a href='baseline.txt'>Download</a></td></tr>" >> $output
329 echo "<a href='baseline_ca.txt'>Baseline ca Table</a><br />" >> $output 338 echo "<tr><td>Baseline ca PDF</td><td><a href='baseline_ca.pdf'>Download</a></td></tr>" >> $output
330 echo "<a href='baseline_cg.pdf'>Baseline cg PDF</a><br />" >> $output 339 echo "<tr><td>Baseline ca data</td><td><a href='baseline_ca.txt'>Download</a></td></tr>" >> $output
331 echo "<a href='baseline_cg.txt'>Baseline cg Table</a><br />" >> $output 340 echo "<tr><td>Baseline cg PDF</td><td><a href='baseline_cg.pdf'>Download</a></td></tr>" >> $output
332 echo "<a href='baseline_cm.pdf'>Baseline cm PDF</a><br />" >> $output 341 echo "<tr><td>Baseline cg data</td><td><a href='baseline_cg.txt'>Download</a></td></tr>" >> $output
333 echo "<a href='baseline_cm.txt'>Baseline cm Table</a><br />" >> $output 342 echo "<tr><td>Baseline cm PDF</td><td><a href='baseline_cm.pdf'>Download</a></td></tr>" >> $output
334 echo "<a href='IgAT.zip'>IgAT zip</a><br />" >> $output 343 echo "<tr><td>Baseline cm data</td><td><a href='baseline_cm.txt'>Download</a></td></tr>" >> $output
335 echo "<a href='IgAT_ca.zip'>IgAT ca zip</a><br />" >> $output 344 #echo "<tr><td></td><td><a href='IgAT.zip'>IgAT zip</a></td></tr>" >> $output
336 echo "<a href='IgAT_cg.zip'>IgAT cg zip</a><br />" >> $output 345 #echo "<tr><td></td><td><a href='IgAT_ca.zip'>IgAT ca zip</a></td></tr>" >> $output
337 echo "<a href='IgAT_cm.zip'>IgAT cm zip</a><br />" >> $output 346 #echo "<tr><td></td><td><a href='IgAT_cg.zip'>IgAT cg zip</a></td></tr>" >> $output
338 echo "<a href='new_IMGT.txz'>Filtered IMGT zip</a><br />" >> $output 347 #echo "<tr><td></td><td><a href='IgAT_cm.zip'>IgAT cm zip</a></td></tr>" >> $output
339 echo "<a href='new_IMGT_ca.txz'>Filtered ca IMGT zip</a><br />" >> $output 348 echo "<tr><td>An IMGT archive with just the matched and filtered sequences</td><td><a href='new_IMGT.txz'>Download</a></td></tr>" >> $output
340 echo "<a href='new_IMGT_cg.txz'>Filtered cg IMGT zip</a><br />" >> $output 349 echo "<tr><td>An IMGT archive with just the matched and filtered ca sequences</td><td><a href='new_IMGT_ca.txz'>Download</a></td></tr>" >> $output
341 echo "<a href='new_IMGT_cm.txz'>Filtered cm IMGT zip</a><br />" >> $output 350 echo "<tr><td>An IMGT archive with just the matched and filtered cg sequences</td><td><a href='new_IMGT_cg.txz'>Download</a></td></tr>" >> $output
351 echo "<tr><td>An IMGT archive with just the matched and filtered cm sequences</td><td><a href='new_IMGT_cm.txz'>Download</a></td></tr>" >> $output
352 echo "</table>" >> $output
342 353
343 echo "</div>" >> $output #downloads tab end 354 echo "</div>" >> $output #downloads tab end
344 355
345 echo "</div>" >> $output #tabs end 356 echo "</div>" >> $output #tabs end
346 357
354 365
355 366
356 mkdir $outdir/baseline/ca_cg_cm 367 mkdir $outdir/baseline/ca_cg_cm
357 if [[ $(wc -l < $outdir/new_IMGT/1_Summary.txt) -gt "1" ]]; then 368 if [[ $(wc -l < $outdir/new_IMGT/1_Summary.txt) -gt "1" ]]; then
358 cd $outdir/baseline/ca_cg_cm 369 cd $outdir/baseline/ca_cg_cm
359 bash $dir/tmp/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT.txz "ca_cg_cm" "$dir/tmp/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt" 370 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT.txz "ca_cg_cm" "$dir/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt"
360 else 371 else
361 echo "No sequences" > "$outdir/baseline.txt" 372 echo "No sequences" > "$outdir/baseline.txt"
362 fi 373 fi
363 374
364 mkdir $outdir/baseline/ca 375 mkdir $outdir/baseline/ca
365 if [[ $(wc -l < $outdir/new_IMGT_ca/1_Summary.txt) -gt "1" ]]; then 376 if [[ $(wc -l < $outdir/new_IMGT_ca/1_Summary.txt) -gt "1" ]]; then
366 cd $outdir/baseline/ca 377 cd $outdir/baseline/ca
367 bash $dir/tmp/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_ca.txz "ca" "$dir/tmp/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_ca.pdf" "Sequence.ID" "$outdir/baseline_ca.txt" 378 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_ca.txz "ca" "$dir/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_ca.pdf" "Sequence.ID" "$outdir/baseline_ca.txt"
368 else 379 else
369 echo "No ca sequences" > "$outdir/baseline_ca.txt" 380 echo "No ca sequences" > "$outdir/baseline_ca.txt"
370 fi 381 fi
371 382
372 mkdir $outdir/baseline/cg 383 mkdir $outdir/baseline/cg
373 if [[ $(wc -l < $outdir/new_IMGT_cg/1_Summary.txt) -gt "1" ]]; then 384 if [[ $(wc -l < $outdir/new_IMGT_cg/1_Summary.txt) -gt "1" ]]; then
374 cd $outdir/baseline/cg 385 cd $outdir/baseline/cg
375 bash $dir/tmp/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_cg.txz "cg" "$dir/tmp/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_cg.pdf" "Sequence.ID" "$outdir/baseline_cg.txt" 386 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_cg.txz "cg" "$dir/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_cg.pdf" "Sequence.ID" "$outdir/baseline_cg.txt"
376 else 387 else
377 echo "No cg sequences" > "$outdir/baseline_cg.txt" 388 echo "No cg sequences" > "$outdir/baseline_cg.txt"
378 fi 389 fi
379 390
380 mkdir $outdir/baseline/cm 391 mkdir $outdir/baseline/cm
381 if [[ $(wc -l < $outdir/new_IMGT_cm/1_Summary.txt) -gt "1" ]]; then 392 if [[ $(wc -l < $outdir/new_IMGT_cm/1_Summary.txt) -gt "1" ]]; then
382 cd $outdir/baseline/cm 393 cd $outdir/baseline/cm
383 bash $dir/tmp/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_cm.txz "cm" "$dir/tmp/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_cm.pdf" "Sequence.ID" "$outdir/baseline_cm.txt" 394 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_cm.txz "cm" "$dir/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_cm.pdf" "Sequence.ID" "$outdir/baseline_cm.txt"
384 else 395 else
385 echo "No cm sequences" > "$outdir/baseline_cm.txt" 396 echo "No cm sequences" > "$outdir/baseline_cm.txt"
386 fi 397 fi
387 398
388 cd $tmp 399 cd $tmp
390 echo "---------------- naive_output.r ----------------" 401 echo "---------------- naive_output.r ----------------"
391 echo "---------------- naive_output.r ----------------<br />" >> $log 402 echo "---------------- naive_output.r ----------------<br />" >> $log
392 403
393 if [[ "$naive_output" != "None" ]] 404 if [[ "$naive_output" != "None" ]]
394 then 405 then
395 echo "---------------- imgt_loader.r ----------------" 406 #echo "---------------- imgt_loader.r ----------------"
396 echo "---------------- imgt_loader.r ----------------<br />" >> $log 407 #echo "---------------- imgt_loader.r ----------------<br />" >> $log
397 #python $dir/imgt_loader.py --summ $PWD/summary.txt --aa $PWD/aa.txt --junction $PWD/junction.txt --output $naive_output 408 #python $dir/imgt_loader.py --summ $PWD/summary.txt --aa $PWD/aa.txt --junction $PWD/junction.txt --output $naive_output
398 Rscript --verbose $dir/imgt_loader.r $PWD/summary.txt $PWD/aa.txt $PWD/junction.txt $outdir/loader_output.txt 2>&1 409 #Rscript --verbose $dir/imgt_loader.r $PWD/summary.txt $PWD/aa.txt $PWD/junction.txt $outdir/loader_output.txt 2>&1
399 410
400 echo "---------------- naive_output.r ----------------" 411 #echo "---------------- naive_output.r ----------------"
401 echo "---------------- naive_output.r ----------------<br />" >> $log 412 #echo "---------------- naive_output.r ----------------<br />" >> $log
402 Rscript $dir/naive_output.r $outdir/loader_output.txt $outdir/merged.txt ${naive_output_ca} ${naive_output_cg} ${naive_output_cm} $outdir/ntoverview.txt $outdir/ntsum.txt 2>&1 413 #Rscript $dir/naive_output.r $outdir/loader_output.txt $outdir/merged.txt ${naive_output_ca} ${naive_output_cg} ${naive_output_cm} $outdir/ntoverview.txt $outdir/ntsum.txt 2>&1
414
415 cp $outdir/new_IMGT_ca.txz ${naive_output_ca}
416 cp $outdir/new_IMGT_cg.txz ${naive_output_cg}
417 cp $outdir/new_IMGT_cm.txz ${naive_output_cm}
403 fi 418 fi
404 419
405 echo "</table>" >> $outdir/base_overview.html 420 echo "</table>" >> $outdir/base_overview.html
406 421
407 mv $log $outdir/log.html 422 mv $log $outdir/log.html