Mercurial > repos > davidvanzessen > mutation_analysis

comparison wrapper.sh @ 126:ffd5462da9d1 draft

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Uploaded
author davidvanzessen
date Mon, 29 Aug 2016 04:20:30 -0400
parents e87dcca14bd6
children afb0937ec0dc
comparison
equal deleted inserted replaced
125:e87dcca14bd6 126:ffd5462da9d1
347 echo "<embed src='baseline_cg.pdf' width='700px' height='1000px'>" >> $output 347 echo "<embed src='baseline_cg.pdf' width='700px' height='1000px'>" >> $output
348 echo "<embed src='baseline_cm.pdf' width='700px' height='1000px'>" >> $output 348 echo "<embed src='baseline_cm.pdf' width='700px' height='1000px'>" >> $output
349 349
350 echo "</div>" >> $output #antigen selection tab end 350 echo "</div>" >> $output #antigen selection tab end
351 351
352 echo "<div class='tabbertab' title='CSR'>" >> $output 352 echo "<div class='tabbertab' title='CSR'>" >> $output #CSR tab
353 353
354 if [ -a $outdir/ca.png ] 354 if [ -a $outdir/ca.png ]
355 then 355 then
356 echo "<img src='ca.png'/><br />" >> $output 356 echo "<img src='ca.png'/><br />" >> $output
357 echo "<a href='ca.txt'>download data</a><br />" >> $output 357 echo "<a href='ca.txt'>download data</a><br />" >> $output
361 echo "<img src='cg.png'/><br />" >> $output 361 echo "<img src='cg.png'/><br />" >> $output
362 echo "<a href='cg.txt'>download data</a><br />" >> $output 362 echo "<a href='cg.txt'>download data</a><br />" >> $output
363 fi 363 fi
364 364
365 echo "</div>" >> $output #CSR tab end 365 echo "</div>" >> $output #CSR tab end
366
367 echo "---------------- change-o MakeDB ----------------"
368
369 mkdir $outdir/change_o
370
371 tmp="$PWD"
372
373 cd $outdir/change_o
374
375 bash $dir/change_o/makedb.sh $input false false false $outdir/change_o/change-o-db.txt
376 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
377
378 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
379
380 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"
381
382 if [[ $(wc -l < $outdir/new_IMGT_ca/1_Summary.txt) -gt "1" ]]; then
383 bash $dir/change_o/makedb.sh $outdir/new_IMGT_ca.txz false false false $outdir/change_o/change-o-db-ca.txt
384 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-ca.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-ca.txt $outdir/change_o/change-o-defined_clones-summary-ca.txt
385 else
386 echo "No ca sequences" > "$outdir/change_o/change-o-db-defined_clones-ca.txt"
387 echo "No ca sequences" > "$outdir/change_o/change-o-defined_clones-summary-ca.txt"
388 fi
389
390 if [[ $(wc -l < $outdir/new_IMGT_cg/1_Summary.txt) -gt "1" ]]; then
391 bash $dir/change_o/makedb.sh $outdir/new_IMGT_cg.txz false false false $outdir/change_o/change-o-db-cg.txt
392 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-cg.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-cg.txt $outdir/change_o/change-o-defined_clones-summary-cg.txt
393 else
394 echo "No cg sequences" > "$outdir/change_o/change-o-db-defined_clones-cg.txt"
395 echo "No cg sequences" > "$outdir/change_o/change-o-defined_clones-summary-cg.txt"
396 fi
397
398 if [[ $(wc -l < $outdir/new_IMGT_cm/1_Summary.txt) -gt "1" ]]; then
399 bash $dir/change_o/makedb.sh $outdir/new_IMGT_cm.txz false false false $outdir/change_o/change-o-db-cm.txt
400 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-cm.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-cm.txt $outdir/change_o/change-o-defined_clones-summary-cm.txt
401 else
402 echo "No cm sequences" > "$outdir/change_o/change-o-db-defined_clones-cm.txt"
403 echo "No cm sequences" > "$outdir/change_o/change-o-defined_clones-summary-cm.txt"
404 fi
405
406 PWD="$tmp"
407
408 echo "<div class='tabbertab' title='Clonality'>" >> $output #clonality tab
409
410 function clonality_table {
411 local infile=$1
412 local outfile=$2
413
414 echo "<table class='pure-table pure-table-striped'>" >> $outfile
415 echo "<thead><tr><th>Clone size</th><th>Nr of clones</th><th>Nr of sequences</th></tr></thead>" >> $outfile
416
417 first='true'
418
419 while read size clones seqs
420 do
421 if [[ "$first" == "true" ]]; then
422 first="false"
423 continue
424 fi
425 echo "<tr><td>$size</td><td>$clones</td><td>$seqs</td></tr>" >> $outfile
426 done < $infile
427
428 echo "</table>" >> $outfile
429 }
430 echo "<div class='tabber'>" >> $output
431
432 echo "<div class='tabbertab' title='All'>" >> $output
433 clonality_table $outdir/change_o/change-o-defined_clones-summary.txt $output
434 echo "</div>" >> $output
435
436 echo "<div class='tabbertab' title='Ca'>" >> $output
437 clonality_table $outdir/change_o/change-o-defined_clones-summary-ca.txt $output
438 echo "</div>" >> $output
439
440 echo "<div class='tabbertab' title='Cg'>" >> $output
441 clonality_table $outdir/change_o/change-o-defined_clones-summary-cg.txt $output
442 echo "</div>" >> $output
443
444 echo "<div class='tabbertab' title='Cm'>" >> $output
445 clonality_table $outdir/change_o/change-o-defined_clones-summary-cm.txt $output
446 echo "</div>" >> $output
447
448 echo "</div>" >> $output #clonality tabber end
449
450 echo "</div>" >> $output #clonality tab end
366 451
367 echo "<div class='tabbertab' title='Downloads'>" >> $output 452 echo "<div class='tabbertab' title='Downloads'>" >> $output
368 453
369 echo "<table class='pure-table pure-table-striped'>" >> $output 454 echo "<table class='pure-table pure-table-striped'>" >> $output
370 echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output 455 echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output
470 cp $outdir/new_IMGT_cg.txz ${naive_output_cg} 555 cp $outdir/new_IMGT_cg.txz ${naive_output_cg}
471 cp $outdir/new_IMGT_cm.txz ${naive_output_cm} 556 cp $outdir/new_IMGT_cm.txz ${naive_output_cm}
472 fi 557 fi
473 558
474 echo "</table>" >> $outdir/base_overview.html 559 echo "</table>" >> $outdir/base_overview.html
475
476 echo "---------------- change-o MakeDB ----------------"
477
478 mkdir $outdir/change_o
479
480 tmp="$PWD"
481
482 cd $outdir/change_o
483
484 bash $dir/change_o/makedb.sh $input false false false $outdir/change_o/change-o-db.txt
485 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
486
487 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
488
489 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"
490
491 if [[ $(wc -l < $outdir/new_IMGT_ca/1_Summary.txt) -gt "1" ]]; then
492 bash $dir/change_o/makedb.sh $outdir/new_IMGT_ca.txz false false false $outdir/change_o/change-o-db-ca.txt
493 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-ca.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-ca.txt $outdir/change_o/change-o-defined_clones-summary-ca.txt
494 else
495 echo "No ca sequences" > "$outdir/change_o/change-o-db-defined_clones-ca.txt"
496 echo "No ca sequences" > "$outdir/change_o/change-o-defined_clones-summary-ca.txt"
497 fi
498
499 if [[ $(wc -l < $outdir/new_IMGT_cg/1_Summary.txt) -gt "1" ]]; then
500 bash $dir/change_o/makedb.sh $outdir/new_IMGT_cg.txz false false false $outdir/change_o/change-o-db-cg.txt
501 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-cg.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-cg.txt $outdir/change_o/change-o-defined_clones-summary-cg.txt
502 else
503 echo "No cg sequences" > "$outdir/change_o/change-o-db-defined_clones-cg.txt"
504 echo "No cg sequences" > "$outdir/change_o/change-o-defined_clones-summary-cg.txt"
505 fi
506
507 if [[ $(wc -l < $outdir/new_IMGT_cm/1_Summary.txt) -gt "1" ]]; then
508 bash $dir/change_o/makedb.sh $outdir/new_IMGT_cm.txz false false false $outdir/change_o/change-o-db-cm.txt
509 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-cm.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-cm.txt $outdir/change_o/change-o-defined_clones-summary-cm.txt
510 else
511 echo "No cm sequences" > "$outdir/change_o/change-o-db-defined_clones-cm.txt"
512 echo "No cm sequences" > "$outdir/change_o/change-o-defined_clones-summary-cm.txt"
513 fi
514
515 PWD="$tmp"
516 560
517 mv $log $outdir/log.html 561 mv $log $outdir/log.html
518 562
519 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 563 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
520 echo "<table border = 1>" >> $log 564 echo "<table border = 1>" >> $log