Mercurial > repos > davidvanzessen > shm_csr
comparison wrapper.sh @ 16:4e596473c25c draft
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 |