Mercurial > repos > davidvanzessen > shm_csr

comparison wrapper.sh @ 32:4c5ba6b5d10d draft

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author davidvanzessen
date Thu, 15 Dec 2016 09:21:54 -0500
parents fe44a905aee9
children 22fabe161cf3
comparison
equal deleted inserted replaced
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