Mercurial > repos > davidvanzessen > shm_csr

comparison wrapper.sh @ 16:4e596473c25c draft

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Uploaded
author davidvanzessen
date Wed, 23 Nov 2016 09:05:40 -0500
parents 59765d2c8890
children 949a30f04d9b
comparison
equal deleted inserted replaced
15:61d0a6318711 16:4e596473c25c
445 echo "No IGE sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGE.txt" 445 echo "No IGE sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGE.txt"
446 fi 446 fi
447 447
448 PWD="$tmp" 448 PWD="$tmp"
449 449
450 echo "<div class='tabbertab' title='Clonality'>" >> $output #clonality tab 450 echo "<div class='tabbertab' title='Clonality'>" >> $output #clonality tab
451 451
452 function clonality_table { 452 function clonality_table {
453 local infile=$1 453 local infile=$1
454 local outfile=$2 454 local outfile=$2
455 455
456 echo "<table class='pure-table pure-table-striped'>" >> $outfile 456 echo "<table class='pure-table pure-table-striped'>" >> $outfile
457 echo "<thead><tr><th>Clone size</th><th>Nr of clones</th><th>Nr of sequences</th></tr></thead>" >> $outfile 457 echo "<thead><tr><th>Clone size</th><th>Nr of clones</th><th>Nr of sequences</th></tr></thead>" >> $outfile
458 458
459 first='true' 459 first='true'
460 460
461 while read size clones seqs 461 while read size clones seqs
462 do 462 do
463 if [[ "$first" == "true" ]]; then 463 if [[ "$first" == "true" ]]; then
464 first="false" 464 first="false"
465 continue 465 continue
466 fi 466 fi
467 echo "<tr><td>$size</td><td>$clones</td><td>$seqs</td></tr>" >> $outfile 467 echo "<tr><td>$size</td><td>$clones</td><td>$seqs</td></tr>" >> $outfile
468 done < $infile 468 done < $infile
469 469
470 echo "</table>" >> $outfile 470 echo "</table>" >> $outfile
471 } 471 }
472 echo "<div class='tabber'>" >> $output 472 echo "<div class='tabber'>" >> $output
473 473
474 echo "<div class='tabbertab' title='All'>" >> $output 474 echo "<div class='tabbertab' title='All'>" >> $output
475 clonality_table $outdir/change_o/change-o-defined_clones-summary.txt $output 475 clonality_table $outdir/change_o/change-o-defined_clones-summary.txt $output
476 echo "</div>" >> $output 476 echo "</div>" >> $output
477 477
478 echo "<div class='tabbertab' title='IGA'>" >> $output 478 echo "<div class='tabbertab' title='IGA'>" >> $output
479 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGA.txt $output 479 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGA.txt $output
480 echo "</div>" >> $output 480 echo "</div>" >> $output
481 481
482 echo "<div class='tabbertab' title='IGG'>" >> $output 482 echo "<div class='tabbertab' title='IGG'>" >> $output
483 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGG.txt $output 483 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGG.txt $output
484 echo "</div>" >> $output 484 echo "</div>" >> $output
485 485
486 echo "<div class='tabbertab' title='IGM'>" >> $output 486 echo "<div class='tabbertab' title='IGM'>" >> $output
487 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output 487 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
488 echo "</div>" >> $output 488 echo "</div>" >> $output
489 489
490 echo "<div class='tabbertab' title='IGE'>" >> $output 490 echo "<div class='tabbertab' title='IGE'>" >> $output
491 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output 491 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
492 echo "</div>" >> $output 492 echo "</div>" >> $output
493 493
494 echo "<div class='tabbertab' title='Overview'>" >> $output 494 echo "<div class='tabbertab' title='Overview'>" >> $output
495 cat "$outdir/sequence_overview/index.html" >> $output 495 cat "$outdir/sequence_overview/index.html" >> $output
496 echo "</div>" >> $output 496 echo "</div>" >> $output
497 497
498 498
499 echo "</div>" >> $output #clonality tabber end 499 echo "</div>" >> $output #clonality tabber end
500 500
501 echo "</div>" >> $output #clonality tab end 501 echo "</div>" >> $output #clonality tab end
502 502
503 fi 503 fi
504 504
505 echo "<div class='tabbertab' title='Downloads'>" >> $output 505 echo "<div class='tabbertab' title='Downloads'>" >> $output
506 506