| Previous changeset 36:43d182135230 (2016-12-16) Next changeset 38:05c62efdc393 (2016-12-20) |
|
Commit message:
Uploaded |
|
modified:
wrapper.sh |
| b |
| diff -r 43d182135230 -r 767dd9327009 wrapper.sh --- 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 |