Mercurial > repos > davidvanzessen > shm_csr
diff wrapper.sh @ 37:767dd9327009 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Fri, 16 Dec 2016 10:17:16 -0500 |
| parents | 43d182135230 |
| children | a24f8c93583a |
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--- a/wrapper.sh Fri Dec 16 10:03:43 2016 -0500 +++ b/wrapper.sh Fri Dec 16 10:17:16 2016 -0500 @@ -418,12 +418,17 @@ tmp="$PWD" mkdir $outdir/baseline - + + baseline_boundaries="27:27:38:55:65:104:-" + + if [[ "${empty_region_filter}" == "leader" ]] ; then + baseline_boundaries="1:26:38:55:65:104:-" + fi mkdir $outdir/baseline/IGA_IGG_IGM if [[ $(wc -l < $outdir/new_IMGT/1_Summary.txt) -gt "1" ]]; then cd $outdir/baseline/IGA_IGG_IGM - 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" + 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" else echo "No sequences" > "$outdir/baseline.txt" fi @@ -431,7 +436,7 @@ mkdir $outdir/baseline/IGA if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then cd $outdir/baseline/IGA - 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" + 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" else echo "No IGA sequences" > "$outdir/baseline_IGA.txt" fi @@ -439,7 +444,7 @@ mkdir $outdir/baseline/IGG if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then cd $outdir/baseline/IGG - 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" + 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" else echo "No IGG sequences" > "$outdir/baseline_IGG.txt" fi @@ -447,7 +452,7 @@ mkdir $outdir/baseline/IGM if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then cd $outdir/baseline/IGM - 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" + 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" else echo "No IGM sequences" > "$outdir/baseline_IGM.txt" fi @@ -455,7 +460,7 @@ mkdir $outdir/baseline/IGE if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then cd $outdir/baseline/IGE - 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" + 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" else echo "No IGE sequences" > "$outdir/baseline_IGE.txt" fi