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comparison wrapper.sh @ 37:767dd9327009 draft

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Uploaded
author davidvanzessen
date Fri, 16 Dec 2016 10:17:16 -0500
parents 43d182135230
children a24f8c93583a
comparison
equal deleted inserted replaced
36:43d182135230 37:767dd9327009
416 echo "---------------- baseline ----------------" 416 echo "---------------- baseline ----------------"
417 echo "---------------- baseline ----------------<br />" >> $log 417 echo "---------------- baseline ----------------<br />" >> $log
418 tmp="$PWD" 418 tmp="$PWD"
419 419
420 mkdir $outdir/baseline 420 mkdir $outdir/baseline
421 421
422 baseline_boundaries="27:27:38:55:65:104:-"
423
424 if [[ "${empty_region_filter}" == "leader" ]] ; then
425 baseline_boundaries="1:26:38:55:65:104:-"
426 fi
422 427
423 mkdir $outdir/baseline/IGA_IGG_IGM 428 mkdir $outdir/baseline/IGA_IGG_IGM
424 if [[ $(wc -l < $outdir/new_IMGT/1_Summary.txt) -gt "1" ]]; then 429 if [[ $(wc -l < $outdir/new_IMGT/1_Summary.txt) -gt "1" ]]; then
425 cd $outdir/baseline/IGA_IGG_IGM 430 cd $outdir/baseline/IGA_IGG_IGM
426 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT.txz "IGA_IGG_IGM" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt" 431 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT.txz "IGA_IGG_IGM" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt"
427 else 432 else
428 echo "No sequences" > "$outdir/baseline.txt" 433 echo "No sequences" > "$outdir/baseline.txt"
429 fi 434 fi
430 435
431 mkdir $outdir/baseline/IGA 436 mkdir $outdir/baseline/IGA
432 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then 437 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
433 cd $outdir/baseline/IGA 438 cd $outdir/baseline/IGA
434 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGA.txz "IGA" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGA.pdf" "Sequence.ID" "$outdir/baseline_IGA.txt" 439 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT_IGA.txz "IGA" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGA.pdf" "Sequence.ID" "$outdir/baseline_IGA.txt"
435 else 440 else
436 echo "No IGA sequences" > "$outdir/baseline_IGA.txt" 441 echo "No IGA sequences" > "$outdir/baseline_IGA.txt"
437 fi 442 fi
438 443
439 mkdir $outdir/baseline/IGG 444 mkdir $outdir/baseline/IGG
440 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then 445 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
441 cd $outdir/baseline/IGG 446 cd $outdir/baseline/IGG
442 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGG.txz "IGG" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGG.pdf" "Sequence.ID" "$outdir/baseline_IGG.txt" 447 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT_IGG.txz "IGG" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGG.pdf" "Sequence.ID" "$outdir/baseline_IGG.txt"
443 else 448 else
444 echo "No IGG sequences" > "$outdir/baseline_IGG.txt" 449 echo "No IGG sequences" > "$outdir/baseline_IGG.txt"
445 fi 450 fi
446 451
447 mkdir $outdir/baseline/IGM 452 mkdir $outdir/baseline/IGM
448 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then 453 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
449 cd $outdir/baseline/IGM 454 cd $outdir/baseline/IGM
450 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGM.txz "IGM" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGM.pdf" "Sequence.ID" "$outdir/baseline_IGM.txt" 455 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT_IGM.txz "IGM" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGM.pdf" "Sequence.ID" "$outdir/baseline_IGM.txt"
451 else 456 else
452 echo "No IGM sequences" > "$outdir/baseline_IGM.txt" 457 echo "No IGM sequences" > "$outdir/baseline_IGM.txt"
453 fi 458 fi
454 459
455 mkdir $outdir/baseline/IGE 460 mkdir $outdir/baseline/IGE
456 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then 461 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
457 cd $outdir/baseline/IGE 462 cd $outdir/baseline/IGE
458 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGE.txz "IGE" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGE.pdf" "Sequence.ID" "$outdir/baseline_IGE.txt" 463 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT_IGE.txz "IGE" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGE.pdf" "Sequence.ID" "$outdir/baseline_IGE.txt"
459 else 464 else
460 echo "No IGE sequences" > "$outdir/baseline_IGE.txt" 465 echo "No IGE sequences" > "$outdir/baseline_IGE.txt"
461 fi 466 fi
462 467
463 cd $tmp 468 cd $tmp