| Previous changeset 32:4c5ba6b5d10d (2016-12-15) Next changeset 34:96c1276ceefe (2016-12-16) |
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Commit message:
Uploaded |
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modified:
sequence_overview.r wrapper.sh |
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| diff -r 4c5ba6b5d10d -r 22fabe161cf3 sequence_overview.r --- a/sequence_overview.r Thu Dec 15 09:21:54 2016 -0500 +++ b/sequence_overview.r Thu Dec 15 09:44:17 2016 -0500 |
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| @@ -245,9 +245,6 @@ in.cg.all = (cg1.n > 0 & cg2.n > 0 & cg3.n > 0 & cg4.n > 0) - - - #rw = c(as.character(dat[i,"seq_conc"]), functionality, ca1.html, ca2.html, cg1.html, cg2.html, cg3.html, cg4.html, cm.html, un.html) rw = c(as.character(dat[i,"seq_conc"]), functionality, ca1.html, ca2.html, cg1.html, cg2.html, cg3.html, cg4.html, cm.html, ce.html, un.html) rw = c(rw, ca.n, cg.n, cm.n, ce.n, in.classes, in.ca.cg, in.ca.cg.cm, in.ca.cg.ce, in.ca.cg.cm.ce, in.ca1.ca2, in.cg1.cg2, in.cg1.cg3, in.cg1.cg4, in.cg2.cg3, in.cg2.cg4, in.cg3.cg4, in.cg1.cg2.cg3, in.cg2.cg3.cg4, in.cg1.cg2.cg4, in.cg1.cg3.cg4, in.cg.all) |
| b |
| diff -r 4c5ba6b5d10d -r 22fabe161cf3 wrapper.sh --- a/wrapper.sh Thu Dec 15 09:21:54 2016 -0500 +++ b/wrapper.sh Thu Dec 15 09:44:17 2016 -0500 |
| [ |
| @@ -410,29 +410,85 @@ fi -if [ -e $outdir/baseline.pdf ] -then - echo "<embed src='baseline.pdf' width='700px' height='1000px'>" >> $output -fi + +if [[ "$fast" == "no" ]] ; then + + echo "---------------- baseline ----------------" + echo "---------------- baseline ----------------<br />" >> $log + tmp="$PWD" + + mkdir $outdir/baseline + -if [ -e $outdir/baseline_IGA.pdf ] -then - echo "<embed src='baseline_IGA.pdf' width='700px' height='1000px'>" >> $output -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" + else + echo "No sequences" > "$outdir/baseline.txt" + fi + + 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" + else + echo "No IGA sequences" > "$outdir/baseline_IGA.txt" + fi + + 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:-" $outdir/new_IMGT_IGG.txz "cg" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGG.pdf" "Sequence.ID" "$outdir/baseline_IGG.txt" + else + echo "No IGG sequences" > "$outdir/baseline_IGG.txt" + fi -if [ -e $outdir/baseline_IGG.pdf ] -then - echo "<embed src='baseline_IGG.pdf' width='700px' height='1000px'>" >> $output -fi + 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" + else + echo "No IGM sequences" > "$outdir/baseline_IGM.txt" + fi + + 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" + else + echo "No IGE sequences" > "$outdir/baseline_IGE.txt" + fi + + cd $tmp -if [ -e $outdir/baseline_IGM.pdf ] -then - echo "<embed src='baseline_IGM.pdf' width='700px' height='1000px'>" >> $output -fi + echo "Cleaning up *.RData files" + find $outdir/baseline -name "*.RData" -type f -delete + + if [ -e $outdir/baseline.pdf ] + then + echo "<embed src='baseline.pdf' width='700px' height='1000px'>" >> $output + fi + + if [ -e $outdir/baseline_IGA.pdf ] + then + echo "<embed src='baseline_IGA.pdf' width='700px' height='1000px'>" >> $output + fi -if [ -e $outdir/baseline_IGE.pdf ] -then - echo "<embed src='baseline_IGE.pdf' width='700px' height='1000px'>" >> $output + if [ -e $outdir/baseline_IGG.pdf ] + then + echo "<embed src='baseline_IGG.pdf' width='700px' height='1000px'>" >> $output + fi + + if [ -e $outdir/baseline_IGM.pdf ] + then + echo "<embed src='baseline_IGM.pdf' width='700px' height='1000px'>" >> $output + fi + + if [ -e $outdir/baseline_IGE.pdf ] + then + echo "<embed src='baseline_IGE.pdf' width='700px' height='1000px'>" >> $output + fi fi echo "</div>" >> $output #antigen selection tab end @@ -651,62 +707,6 @@ echo "</html>" >> $output -if [[ "$fast" == "no" ]] ; then - - echo "---------------- baseline ----------------" - echo "---------------- baseline ----------------<br />" >> $log - tmp="$PWD" - - mkdir $outdir/baseline - - - 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" - else - echo "No sequences" > "$outdir/baseline.txt" - fi - - 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" - else - echo "No IGA sequences" > "$outdir/baseline_IGA.txt" - fi - - 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:-" $outdir/new_IMGT_IGG.txz "cg" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGG.pdf" "Sequence.ID" "$outdir/baseline_IGG.txt" - else - echo "No IGG sequences" > "$outdir/baseline_IGG.txt" - fi - - 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" - else - echo "No IGM sequences" > "$outdir/baseline_IGM.txt" - fi - - 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" - else - echo "No IGE sequences" > "$outdir/baseline_IGE.txt" - fi - - cd $tmp - - echo "Cleaning up *.RData files" - find $outdir/baseline -name "*.RData" -type f -delete - -fi - echo "---------------- naive_output.r ----------------" echo "---------------- naive_output.r ----------------<br />" >> $log |