Mercurial > repos > davidvanzessen > shm_csr
comparison wrapper.sh @ 32:4c5ba6b5d10d draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Thu, 15 Dec 2016 09:21:54 -0500 |
| parents | fe44a905aee9 |
| children | 22fabe161cf3 |
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| 31:fe44a905aee9 | 32:4c5ba6b5d10d |
|---|---|
| 661 | 661 |
| 662 | 662 |
| 663 mkdir $outdir/baseline/IGA_IGG_IGM | 663 mkdir $outdir/baseline/IGA_IGG_IGM |
| 664 if [[ $(wc -l < $outdir/new_IMGT/1_Summary.txt) -gt "1" ]]; then | 664 if [[ $(wc -l < $outdir/new_IMGT/1_Summary.txt) -gt "1" ]]; then |
| 665 cd $outdir/baseline/IGA_IGG_IGM | 665 cd $outdir/baseline/IGA_IGG_IGM |
| 666 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/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt" | 666 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" |
| 667 else | 667 else |
| 668 echo "No sequences" > "$outdir/baseline.txt" | 668 echo "No sequences" > "$outdir/baseline.txt" |
| 669 fi | 669 fi |
| 670 | 670 |
| 671 mkdir $outdir/baseline/IGA | 671 mkdir $outdir/baseline/IGA |
| 672 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then | 672 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then |
| 673 cd $outdir/baseline/IGA | 673 cd $outdir/baseline/IGA |
| 674 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/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_IGA.pdf" "Sequence.ID" "$outdir/baseline_IGA.txt" | 674 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" |
| 675 else | 675 else |
| 676 echo "No IGA sequences" > "$outdir/baseline_IGA.txt" | 676 echo "No IGA sequences" > "$outdir/baseline_IGA.txt" |
| 677 fi | 677 fi |
| 678 | 678 |
| 679 mkdir $outdir/baseline/IGG | 679 mkdir $outdir/baseline/IGG |
| 680 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then | 680 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then |
| 681 cd $outdir/baseline/IGG | 681 cd $outdir/baseline/IGG |
| 682 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGG.txz "cg" "$dir/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_IGG.pdf" "Sequence.ID" "$outdir/baseline_IGG.txt" | 682 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGG.txz "cg" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGG.pdf" "Sequence.ID" "$outdir/baseline_IGG.txt" |
| 683 else | 683 else |
| 684 echo "No IGG sequences" > "$outdir/baseline_IGG.txt" | 684 echo "No IGG sequences" > "$outdir/baseline_IGG.txt" |
| 685 fi | 685 fi |
| 686 | 686 |
| 687 mkdir $outdir/baseline/IGM | 687 mkdir $outdir/baseline/IGM |
| 688 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then | 688 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then |
| 689 cd $outdir/baseline/IGM | 689 cd $outdir/baseline/IGM |
| 690 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/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_IGM.pdf" "Sequence.ID" "$outdir/baseline_IGM.txt" | 690 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" |
| 691 else | 691 else |
| 692 echo "No IGM sequences" > "$outdir/baseline_IGM.txt" | 692 echo "No IGM sequences" > "$outdir/baseline_IGM.txt" |
| 693 fi | 693 fi |
| 694 | 694 |
| 695 mkdir $outdir/baseline/IGE | 695 mkdir $outdir/baseline/IGE |
| 696 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then | 696 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then |
| 697 cd $outdir/baseline/IGE | 697 cd $outdir/baseline/IGE |
| 698 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/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_IGE.pdf" "Sequence.ID" "$outdir/baseline_IGE.txt" | 698 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" |
| 699 else | 699 else |
| 700 echo "No IGE sequences" > "$outdir/baseline_IGE.txt" | 700 echo "No IGE sequences" > "$outdir/baseline_IGE.txt" |
| 701 fi | 701 fi |
| 702 | 702 |
| 703 cd $tmp | 703 cd $tmp |