Mercurial > repos > davidvanzessen > shm_csr

comparison wrapper.sh @ 41:b8ac74723ab0 draft

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Uploaded
author davidvanzessen
date Tue, 14 Mar 2017 09:30:16 -0400
parents ca2512e1e3ab
children 1cf60ae234b4
comparison
equal deleted inserted replaced
40:ca2512e1e3ab 41:b8ac74723ab0
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421 421
422 if [[ "$fast" == "no" ]] ; then 422 if [[ "$fast" == "no" ]] ; then
423 423
424
425
424 echo "---------------- baseline ----------------" 426 echo "---------------- baseline ----------------"
425 echo "---------------- baseline ----------------<br />" >> $log 427 echo "---------------- baseline ----------------<br />" >> $log
426 tmp="$PWD" 428 tmp="$PWD"
427 429
428 mkdir $outdir/baseline 430 mkdir $outdir/baseline
429 431
432 echo "<center><h1>BASELINe</h1>" >> $output
433 header_substring="Based on CDR1, FR2, CDR2, FR3 (27:27:38:55:65:104:-)"
434
430 baseline_boundaries="27:27:38:55:65:104:-" 435 baseline_boundaries="27:27:38:55:65:104:-"
431 436
432 if [[ "${empty_region_filter}" == "leader" ]] ; then 437 if [[ "${empty_region_filter}" == "leader" ]] ; then
433 baseline_boundaries="1:26:38:55:65:104:-" 438 baseline_boundaries="1:26:38:55:65:104:-"
434 fi 439 header_substring="Based on FR1, CDR1, FR2, CDR2, FR3 (1:26:38:55:65:104,-)"
440 fi
441
442 echo "<p>${header_substring}</p></center>" >> $output
435 443
436 mkdir $outdir/baseline/IGA_IGG_IGM 444 mkdir $outdir/baseline/IGA_IGG_IGM
437 if [[ $(wc -l < $outdir/new_IMGT/1_Summary.txt) -gt "1" ]]; then 445 if [[ $(wc -l < $outdir/new_IMGT/1_Summary.txt) -gt "1" ]]; then
438 cd $outdir/baseline/IGA_IGG_IGM 446 cd $outdir/baseline/IGA_IGG_IGM
439 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" 447 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"
440 else 448 else
441 echo "No sequences" > "$outdir/baseline.txt" 449 echo "No sequences" > "$outdir/baseline.txt"
442 fi 450 fi
443 451
444 mkdir $outdir/baseline/IGA 452 mkdir $outdir/baseline/IGA