Mercurial > repos > davidvanzessen > shm_csr
diff wrapper.sh @ 93:8fcf31272f6e draft
planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
| author | rhpvorderman |
|---|---|
| date | Mon, 06 Mar 2023 11:36:32 +0000 |
| parents | cf8ad181628f |
| children | 84e9e5c8c101 |
line wrap: on
line diff
--- a/wrapper.sh Mon Dec 12 12:32:44 2022 +0000 +++ b/wrapper.sh Mon Mar 06 11:36:32 2023 +0000 @@ -22,12 +22,15 @@ empty_region_filter=${18} fast=${19} +BASENAME=$(basename $input) +# Cut off .txz or .tgz suffix +NEW_IMGT_PREFIX="new_IMGT_${BASENAME%.*}" + #exec 5> debug_output.txt #BASH_XTRACEFD="5" -## Busybox date does not support '+%s.%N'. So use the slower python instead. -## Using -S python does not do 'import site' which shortens the command -## to 10 milliseconds. -#PS4='$(python -Sc "import time; print(time.time())") $LINENO: ' +## Busybox date does not support '+%s.%N'. So use a custom program. Can be +## Compiled with cc -Os show_time_as_float.c -o show_time_as_float +#PS4='$(${dir}/show_time_as_float) $LINENO: ' #set -x mkdir -p $outdir @@ -39,7 +42,7 @@ echo "unpacking IMGT file" -type="`file $input`" +type="`file -L $input`" if [[ "$type" == *"Zip archive"* ]] ; then echo "Zip archive" echo "unzip $input -d $PWD/files/" @@ -85,13 +88,30 @@ echo "---------------- merge_and_filter.r ----------------" echo "---------------- merge_and_filter.r ----------------<br />" >> $log -Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt "$PWD/gapped_aa.txt" $outdir/identified_genes.txt $outdir/merged.txt $outdir/before_unique_filter.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${filter_unique_count} ${class_filter} ${empty_region_filter} 2>&1 +Rscript $dir/merge_and_filter.r \ + $PWD/summary.txt \ + $PWD/sequences.txt \ + $PWD/mutationanalysis.txt \ + $PWD/mutationstats.txt \ + $PWD/hotspots.txt \ + "$PWD/gapped_aa.txt" \ + $outdir/identified_genes.txt \ + $outdir/merged.txt \ + $outdir/before_unique_filter.txt \ + $outdir/unmatched.txt \ + $method \ + $functionality \ + $unique \ + ${filter_unique} \ + ${filter_unique_count} \ + ${class_filter} \ + ${empty_region_filter} echo "---------------- creating new IMGT zips ----------------" echo "---------------- creating new IMGT zips ----------------<br />" >> $log python $dir/split_imgt_file.py --outdir $outdir $input $outdir/merged.txt \ - --prefix new_IMGT \ + --prefix "${NEW_IMGT_PREFIX}" \ - IGA IGA1 IGA2 IGG IGG1 IGG2 IGG3 IGG4 IGM IGE @@ -100,7 +120,7 @@ classes="IGA,IGA1,IGA2,IGG,IGG1,IGG2,IGG3,IGG4,IGM,IGE,unmatched" echo "R mutation analysis" -Rscript $dir/shm_csr.r $outdir/merged.txt $classes $outdir ${empty_region_filter} 2>&1 +Rscript $dir/shm_csr.r $outdir/merged.txt $classes $outdir ${empty_region_filter} echo "---------- Split naive memory IGM ---------" echo "---------- Split naive memory IGM ---------<br />" >> $log @@ -108,20 +128,20 @@ python $dir/igm_naive_mutations.py $outdir/scatter.txt $outdir/igm_naive_mutations.txt \ $outdir/igm_naive_memory_mutations.txt -python $dir/split_imgt_file.py --outdir $outdir $outdir/new_IMGT_IGM.txz \ +python $dir/split_imgt_file.py --outdir $outdir $outdir/${NEW_IMGT_PREFIX}_IGM.txz \ $outdir/igm_naive_mutations.txt \ - --prefix new_IMGT_IGM_NAIVE - + --prefix "${NEW_IMGT_PREFIX}_IGM_NAIVE" - -python $dir/split_imgt_file.py --outdir $outdir $outdir/new_IMGT_IGM.txz \ +python $dir/split_imgt_file.py --outdir $outdir $outdir/${NEW_IMGT_PREFIX}_IGM.txz \ $outdir/igm_naive_memory_mutations.txt \ - --prefix new_IMGT_IGM_NAIVE_MEMORY - + --prefix "${NEW_IMGT_PREFIX}_IGM_NAIVE_MEMORY" - echo "---------------- plot_pdfs.r ----------------" echo "---------------- plot_pdfs.r ----------------<br />" >> $log -echo "Rscript $dir/shm_csr.r $outdir/pdfplots.RData $outdir 2>&1" +echo "Rscript $dir/shm_csr.r $outdir/pdfplots.RData $outdir" -Rscript $dir/plot_pdf.r "$outdir/pdfplots.RData" "$outdir" 2>&1 +Rscript $dir/plot_pdf.r "$outdir/pdfplots.RData" "$outdir" echo "---------------- shm_csr.py ----------------" echo "---------------- shm_csr.py ----------------<br />" >> $log @@ -131,7 +151,11 @@ echo "---------------- aa_histogram.r ----------------" echo "---------------- aa_histogram.r ----------------<br />" >> $log -Rscript $dir/aa_histogram.r $outdir/aa_id_mutations.txt $outdir/absent_aa_id.txt "IGA,IGG,IGM,IGE" $outdir/ 2>&1 +Rscript $dir/aa_histogram.r \ + $outdir/aa_id_mutations.txt \ + $outdir/absent_aa_id.txt "IGA,IGG,IGM,IGE" \ + $outdir/ + if [ -e "$outdir/aa_histogram_.png" ]; then mv $outdir/aa_histogram_.png $outdir/aa_histogram.png mv $outdir/aa_histogram_.pdf $outdir/aa_histogram.pdf @@ -153,7 +177,12 @@ python $dir/sequence_overview.py --before-unique $outdir/before_unique_filter.txt \ --outdir $outdir/sequence_overview --empty-region-filter ${empty_region_filter} -Rscript $dir/nt_overview.r $outdir/merged.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt ${empty_region_filter} 2>&1 +Rscript $dir/nt_overview.r \ + $outdir/merged.txt \ + $outdir/sequence_overview \ + $classes \ + $outdir/hotspot_analysis_sum.txt \ + ${empty_region_filter} echo "<table border='1'>" > $outdir/base_overview.html @@ -198,12 +227,17 @@ echo "---------------- pattern_plots.r ----------------" echo "---------------- pattern_plots.r ----------------<br />" >> $log - Rscript $dir/pattern_plots.r $outdir/data_${func}.txt $outdir/aid_motives $outdir/relative_mutations $outdir/absolute_mutations $outdir/shm_overview.txt 2>&1 + Rscript $dir/pattern_plots.r \ + $outdir/data_${func}.txt \ + $outdir/aid_motives \ + $outdir/relative_mutations \ + $outdir/absolute_mutations \ + $outdir/shm_overview.txt echo "<table class='pure-table pure-table-striped'>" >> $output echo "<thead><tr><th>info</th>" >> $output - if [ "${class_filter}" != "101_101" ] ; then + if [ "${class_filter}" != "101_101_all" ] ; then for gene in ${genes[@]} do @@ -397,41 +431,41 @@ echo "<p>${header_substring}</p></center>" >> $output mkdir $outdir/baseline/IGA_IGG_IGM - if [[ "$(count_imgt_lines $outdir/new_IMGT.txz)" -gt "1" ]]; then + if [[ "$(count_imgt_lines $outdir/${NEW_IMGT_PREFIX}.txz)" -gt "1" ]]; then cd $outdir/baseline/IGA_IGG_IGM - bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT.txz "IGA_IGG_IGM_IGE" "$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_PREFIX}.txz "IGA_IGG_IGM_IGE" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt" else echo "No sequences" > "$outdir/baseline.txt" fi mkdir $outdir/baseline/IGA - if [[ "$(count_imgt_lines $outdir/new_IMGT_IGA.txz)" -gt "1" ]]; then + if [[ "$(count_imgt_lines $outdir/${NEW_IMGT_PREFIX}_IGA.txz)" -gt "1" ]]; then cd $outdir/baseline/IGA - 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" + bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/${NEW_IMGT_PREFIX}_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 $outdir/baseline/IGG - if [[ "$(count_imgt_lines $outdir/new_IMGT_IGG.txz)" -gt "1" ]]; then + if [[ "$(count_imgt_lines $outdir/${NEW_IMGT_PREFIX}_IGG.txz)" -gt "1" ]]; then cd $outdir/baseline/IGG - 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" + bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/${NEW_IMGT_PREFIX}_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 mkdir $outdir/baseline/IGM - if [[ "$(count_imgt_lines $outdir/new_IMGT_IGM.txz)" -gt "1" ]]; then + if [[ "$(count_imgt_lines $outdir/${NEW_IMGT_PREFIX}_IGM.txz)" -gt "1" ]]; then cd $outdir/baseline/IGM - 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" + bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/${NEW_IMGT_PREFIX}_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 $outdir/baseline/IGE - if [[ "$(count_imgt_lines $outdir/new_IMGT_IGE.txz)" -gt "1" ]]; then + if [[ "$(count_imgt_lines $outdir/${NEW_IMGT_PREFIX}_IGE.txz)" -gt "1" ]]; then cd $outdir/baseline/IGE - 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" + bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/${NEW_IMGT_PREFIX}_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 @@ -498,24 +532,32 @@ cd $outdir/change_o - bash $dir/change_o/makedb.sh $outdir/new_IMGT.txz false false false $outdir/change_o/change-o-db.txt + bash $dir/change_o/makedb.sh $outdir/${NEW_IMGT_PREFIX}.txz false false false $outdir/change_o/change-o-db.txt bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones.txt $outdir/change_o/change-o-defined_clones-summary.txt - Rscript $dir/change_o/select_first_in_clone.r $outdir/change_o/change-o-db-defined_clones.txt $outdir/change_o/change-o-db-defined_first_clones.txt 2>&1 + Rscript $dir/change_o/select_first_in_clone.r \ + $outdir/change_o/change-o-db-defined_clones.txt \ + $outdir/change_o/change-o-db-defined_first_clones.txt - python $dir/split_imgt_file.py --outdir $outdir --prefix new_IMGT_first_seq_of_clone \ - $outdir/new_IMGT.txz $outdir/change_o/change-o-db-defined_first_clones.txt \ + python $dir/split_imgt_file.py --outdir $outdir --prefix ${NEW_IMGT_PREFIX}_first_seq_of_clone \ + $outdir/${NEW_IMGT_PREFIX}.txz $outdir/change_o/change-o-db-defined_first_clones.txt \ "-" - Rscript $dir/merge.r $outdir/change_o/change-o-db-defined_clones.txt $outdir/merged.txt "all" "Sequence.ID,best_match" "SEQUENCE_ID" "Sequence.ID" $outdir/change_o/change-o-db-defined_clones.txt 2>&1 - echo "Rscript $dir/merge.r $outdir/change_o/change-o-db-defined_clones.txt $outdir/$outdir/merged.txt 'all' 'Sequence.ID,best_match' 'Sequence.ID' 'Sequence.ID' '\t' $outdir/change_o/change-o-db-defined_clones.txt 2>&1" + Rscript $dir/merge.r \ + $outdir/change_o/change-o-db-defined_clones.txt \ + $outdir/merged.txt \ + "all" "Sequence.ID,best_match" "SEQUENCE_ID" "Sequence.ID" \ + $outdir/change_o/change-o-db-defined_clones.txt + echo "Rscript $dir/merge.r $outdir/change_o/change-o-db-defined_clones.txt $outdir/$outdir/merged.txt 'all' 'Sequence.ID,best_match' 'Sequence.ID' 'Sequence.ID' '\t' $outdir/change_o/change-o-db-defined_clones.txt" - if [[ "$(count_imgt_lines $outdir/new_IMGT_IGA.txz)" -gt "1" ]]; then - bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGA.txz false false false $outdir/change_o/change-o-db-IGA.txt + if [[ "$(count_imgt_lines $outdir/${NEW_IMGT_PREFIX}_IGA.txz)" -gt "1" ]]; then + bash $dir/change_o/makedb.sh $outdir/${NEW_IMGT_PREFIX}_IGA.txz false false false $outdir/change_o/change-o-db-IGA.txt bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGA.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGA.txt $outdir/change_o/change-o-defined_clones-summary-IGA.txt - Rscript $dir/change_o/select_first_in_clone.r $outdir/change_o/change-o-db-defined_clones-IGA.txt $outdir/change_o/change-o-db-defined_first_clones-IGA.txt 2>&1 + Rscript $dir/change_o/select_first_in_clone.r \ + $outdir/change_o/change-o-db-defined_clones-IGA.txt \ + $outdir/change_o/change-o-db-defined_first_clones-IGA.txt - python $dir/split_imgt_file.py --outdir $outdir --prefix new_IMGT_IGA_first_seq_of_clone \ - $outdir/new_IMGT.txz $outdir/change_o/change-o-db-defined_first_clones-IGA.txt \ + python $dir/split_imgt_file.py --outdir $outdir --prefix ${NEW_IMGT_PREFIX}_IGA_first_seq_of_clone \ + $outdir/${NEW_IMGT_PREFIX}.txz $outdir/change_o/change-o-db-defined_first_clones-IGA.txt \ "-" else @@ -523,13 +565,15 @@ echo "No IGA sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGA.txt" fi - if [[ "$(count_imgt_lines $outdir/new_IMGT_IGG.txz)" -gt "1" ]]; then - bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGG.txz false false false $outdir/change_o/change-o-db-IGG.txt + if [[ "$(count_imgt_lines $outdir/${NEW_IMGT_PREFIX}_IGG.txz)" -gt "1" ]]; then + bash $dir/change_o/makedb.sh $outdir/${NEW_IMGT_PREFIX}_IGG.txz false false false $outdir/change_o/change-o-db-IGG.txt bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGG.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGG.txt $outdir/change_o/change-o-defined_clones-summary-IGG.txt - Rscript $dir/change_o/select_first_in_clone.r $outdir/change_o/change-o-db-defined_clones-IGG.txt $outdir/change_o/change-o-db-defined_first_clones-IGG.txt 2>&1 + Rscript $dir/change_o/select_first_in_clone.r \ + $outdir/change_o/change-o-db-defined_clones-IGG.txt \ + $outdir/change_o/change-o-db-defined_first_clones-IGG.txt - python $dir/split_imgt_file.py --outdir $outdir --prefix new_IMGT_IGG_first_seq_of_clone \ - $outdir/new_IMGT.txz $outdir/change_o/change-o-db-defined_first_clones-IGG.txt \ + python $dir/split_imgt_file.py --outdir $outdir --prefix ${NEW_IMGT_PREFIX}_IGG_first_seq_of_clone \ + $outdir/${NEW_IMGT_PREFIX}.txz $outdir/change_o/change-o-db-defined_first_clones-IGG.txt \ "-" else @@ -537,13 +581,15 @@ echo "No IGG sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGG.txt" fi - if [[ "$(count_imgt_lines $outdir/new_IMGT_IGM.txz)" -gt "1" ]]; then - bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGM.txz false false false $outdir/change_o/change-o-db-IGM.txt + if [[ "$(count_imgt_lines $outdir/${NEW_IMGT_PREFIX}_IGM.txz)" -gt "1" ]]; then + bash $dir/change_o/makedb.sh $outdir/${NEW_IMGT_PREFIX}_IGM.txz false false false $outdir/change_o/change-o-db-IGM.txt bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGM.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGM.txt $outdir/change_o/change-o-defined_clones-summary-IGM.txt - Rscript $dir/change_o/select_first_in_clone.r $outdir/change_o/change-o-db-defined_clones-IGM.txt $outdir/change_o/change-o-db-defined_first_clones-IGM.txt 2>&1 + Rscript $dir/change_o/select_first_in_clone.r \ + $outdir/change_o/change-o-db-defined_clones-IGM.txt \ + $outdir/change_o/change-o-db-defined_first_clones-IGM.txt - python $dir/split_imgt_file.py --outdir $outdir --prefix new_IMGT_IGM_first_seq_of_clone \ - $outdir/new_IMGT.txz $outdir/change_o/change-o-db-defined_first_clones-IGM.txt \ + python $dir/split_imgt_file.py --outdir $outdir --prefix ${NEW_IMGT_PREFIX}_IGM_first_seq_of_clone \ + $outdir/${NEW_IMGT_PREFIX}.txz $outdir/change_o/change-o-db-defined_first_clones-IGM.txt \ "-" else @@ -551,13 +597,15 @@ echo "No IGM sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGM.txt" fi - if [[ "$(count_imgt_lines $outdir/new_IMGT_IGE.txz)" -gt "1" ]]; then - bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGE.txz false false false $outdir/change_o/change-o-db-IGE.txt + if [[ "$(count_imgt_lines $outdir/${NEW_IMGT_PREFIX}_IGE.txz)" -gt "1" ]]; then + bash $dir/change_o/makedb.sh $outdir/${NEW_IMGT_PREFIX}_IGE.txz false false false $outdir/change_o/change-o-db-IGE.txt bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGE.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGE.txt $outdir/change_o/change-o-defined_clones-summary-IGE.txt - Rscript $dir/change_o/select_first_in_clone.r $outdir/change_o/change-o-db-defined_clones-IGE.txt $outdir/change_o/change-o-db-defined_first_clones-IGE.txt 2>&1 + Rscript $dir/change_o/select_first_in_clone.r \ + $outdir/change_o/change-o-db-defined_clones-IGE.txt \ + $outdir/change_o/change-o-db-defined_first_clones-IGE.txt - python $dir/split_imgt_file.py --outdir $outdir --prefix new_IMGT_IGE_first_seq_of_clone \ - $outdir/new_IMGT.txz $outdir/change_o/change-o-db-defined_first_clones-IGE.txt \ + python $dir/split_imgt_file.py --outdir $outdir --prefix ${NEW_IMGT_PREFIX}_IGE_first_seq_of_clone \ + $outdir/${NEW_IMGT_PREFIX}.txz $outdir/change_o/change-o-db-defined_first_clones-IGE.txt \ "-" else @@ -714,38 +762,38 @@ echo "<tr><td>Sequence overlap between subclasses</td><td><a href='sequence_overview/index.html'>View</a></td></tr>" >> $output echo "<tr><td>The Change-O DB file with defined clones and subclass annotation</td><td><a href='change_o/change-o-db-defined_clones.txt' download='change_o/change-o-db-defined_clones.txt' >Download</a></td></tr>" >> $output echo "<tr><td>The Change-O DB defined clones summary file</td><td><a href='change_o/change-o-defined_clones-summary.txt' download='change_o/change-o-defined_clones-summary.txt' >Download</a></td></tr>" >> $output -echo "<tr><td>An IMGT archive with just just the first sequence of a clone</td><td><a href='new_IMGT_first_seq_of_clone.txz' download='new_IMGT_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output +echo "<tr><td>An IMGT archive with just just the first sequence of a clone</td><td><a href='${NEW_IMGT_PREFIX}_first_seq_of_clone.txz' download='${NEW_IMGT_PREFIX}_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output echo "<tr><td>The Change-O DB file with defined clones of IGA</td><td><a href='change_o/change-o-db-defined_clones-IGA.txt' download='change_o/change-o-db-defined_clones-IGA.txt' >Download</a></td></tr>" >> $output echo "<tr><td>The Change-O DB defined clones summary file of IGA</td><td><a href='change_o/change-o-defined_clones-summary-IGA.txt' download='change_o/change-o-defined_clones-summary-IGA.txt' >Download</a></td></tr>" >> $output -echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGA)</td><td><a href='new_IMGT_IGA_first_seq_of_clone.txz' download='new_IMGT_IGA_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output +echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGA)</td><td><a href='${NEW_IMGT_PREFIX}_IGA_first_seq_of_clone.txz' download='${NEW_IMGT_PREFIX}_IGA_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output echo "<tr><td>The Change-O DB file with defined clones of IGG</td><td><a href='change_o/change-o-db-defined_clones-IGG.txt' download='change_o/change-o-db-defined_clones-IGG.txt' >Download</a></td></tr>" >> $output echo "<tr><td>The Change-O DB defined clones summary file of IGG</td><td><a href='change_o/change-o-defined_clones-summary-IGG.txt' download='change_o/change-o-defined_clones-summary-IGG.txt' >Download</a></td></tr>" >> $output -echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGG)</td><td><a href='new_IMGT_IGG_first_seq_of_clone.txz' download='new_IMGT_IGG_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output +echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGG)</td><td><a href='${NEW_IMGT_PREFIX}_IGG_first_seq_of_clone.txz' download='${NEW_IMGT_PREFIX}_IGG_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output echo "<tr><td>The Change-O DB file with defined clones of IGM</td><td><a href='change_o/change-o-db-defined_clones-IGM.txt' download='change_o/change-o-db-defined_clones-IGM.txt' >Download</a></td></tr>" >> $output echo "<tr><td>The Change-O DB defined clones summary file of IGM</td><td><a href='change_o/change-o-defined_clones-summary-IGM.txt' download='change_o/change-o-defined_clones-summary-IGM.txt' >Download</a></td></tr>" >> $output -echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGM)</td><td><a href='new_IMGT_IGM_first_seq_of_clone.txz' download='new_IMGT_IGM_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output +echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGM)</td><td><a href='${NEW_IMGT_PREFIX}_IGM_first_seq_of_clone.txz' download='${NEW_IMGT_PREFIX}_IGM_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output echo "<tr><td>The Change-O DB file with defined clones of IGE</td><td><a href='change_o/change-o-db-defined_clones-IGE.txt' download='change_o/change-o-db-defined_clones-IGE.txt' >Download</a></td></tr>" >> $output echo "<tr><td>The Change-O DB defined clones summary file of IGE</td><td><a href='change_o/change-o-defined_clones-summary-IGE.txt' download='change_o/change-o-defined_clones-summary-IGE.txt' >Download</a></td></tr>" >> $output -echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGE)</td><td><a href='new_IMGT_IGE_first_seq_of_clone.txz' download='new_IMGT_IGE_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output +echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGE)</td><td><a href='${NEW_IMGT_PREFIX}_IGE_first_seq_of_clone.txz' download='${NEW_IMGT_PREFIX}_IGE_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Filtered IMGT output files</td></tr>" >> $output -echo "<tr><td>An IMGT archive with just the matched and filtered sequences</td><td><a href='new_IMGT.txz' download='new_IMGT.txz' >Download</a></td></tr>" >> $output -echo "<tr><td>An IMGT archive with just the matched and filtered IGA sequences</td><td><a href='new_IMGT_IGA.txz' download='new_IMGT_IGA.txz' >Download</a></td></tr>" >> $output -echo "<tr><td>An IMGT archive with just the matched and filtered IGA1 sequences</td><td><a href='new_IMGT_IGA1.txz' download='new_IMGT_IGA1.txz' >Download</a></td></tr>" >> $output -echo "<tr><td>An IMGT archive with just the matched and filtered IGA2 sequences</td><td><a href='new_IMGT_IGA2.txz' download='new_IMGT_IGA2.txz' >Download</a></td></tr>" >> $output -echo "<tr><td>An IMGT archive with just the matched and filtered IGG sequences</td><td><a href='new_IMGT_IGG.txz' download='new_IMGT_IGG.txz' >Download</a></td></tr>" >> $output -echo "<tr><td>An IMGT archive with just the matched and filtered IGG1 sequences</td><td><a href='new_IMGT_IGG1.txz' download='new_IMGT_IGG1.txz' >Download</a></td></tr>" >> $output -echo "<tr><td>An IMGT archive with just the matched and filtered IGG2 sequences</td><td><a href='new_IMGT_IGG2.txz' download='new_IMGT_IGG2.txz' >Download</a></td></tr>" >> $output -echo "<tr><td>An IMGT archive with just the matched and filtered IGG3 sequences</td><td><a href='new_IMGT_IGG3.txz' download='new_IMGT_IGG3.txz' >Download</a></td></tr>" >> $output -echo "<tr><td>An IMGT archive with just the matched and filtered IGG4 sequences</td><td><a href='new_IMGT_IGG4.txz' download='new_IMGT_IGG4.txz' >Download</a></td></tr>" >> $output -echo "<tr><td>An IMGT archive with just the matched and filtered IGM sequences</td><td><a href='new_IMGT_IGM.txz' download='new_IMGT_IGM.txz' >Download</a></td></tr>" >> $output -echo "<tr><td>An IMGT archive with just the matched and filtered IGE sequences</td><td><a href='new_IMGT_IGE.txz' download='new_IMGT_IGE.txz' >Download</a></td></tr>" >> $output -echo "<tr><td>An IMGT archive with just the matched and filtered naive IGM sequences (mutations below 2%)</td><td><a href='new_IMGT_IGM_NAIVE.txz' download='new_IMGT_IGM_NAIVE.txz' >Download</a></td></tr>" >> $output -echo "<tr><td>An IMGT archive with just the matched and filtered naive memory IGM sequences (mutations 2% or higher)</td><td><a href='new_IMGT_IGM_NAIVE_MEMORY.txz' download='new_IMGT_IGM_NAIVE_MEMORY.txz' >Download</a></td></tr>" >> $output +echo "<tr><td>An IMGT archive with just the matched and filtered sequences</td><td><a href='${NEW_IMGT_PREFIX}.txz' download='${NEW_IMGT_PREFIX}.txz' >Download</a></td></tr>" >> $output +echo "<tr><td>An IMGT archive with just the matched and filtered IGA sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGA.txz' download='${NEW_IMGT_PREFIX}_IGA.txz' >Download</a></td></tr>" >> $output +echo "<tr><td>An IMGT archive with just the matched and filtered IGA1 sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGA1.txz' download='${NEW_IMGT_PREFIX}_IGA1.txz' >Download</a></td></tr>" >> $output +echo "<tr><td>An IMGT archive with just the matched and filtered IGA2 sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGA2.txz' download='${NEW_IMGT_PREFIX}_IGA2.txz' >Download</a></td></tr>" >> $output +echo "<tr><td>An IMGT archive with just the matched and filtered IGG sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGG.txz' download='${NEW_IMGT_PREFIX}_IGG.txz' >Download</a></td></tr>" >> $output +echo "<tr><td>An IMGT archive with just the matched and filtered IGG1 sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGG1.txz' download='${NEW_IMGT_PREFIX}_IGG1.txz' >Download</a></td></tr>" >> $output +echo "<tr><td>An IMGT archive with just the matched and filtered IGG2 sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGG2.txz' download='${NEW_IMGT_PREFIX}_IGG2.txz' >Download</a></td></tr>" >> $output +echo "<tr><td>An IMGT archive with just the matched and filtered IGG3 sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGG3.txz' download='${NEW_IMGT_PREFIX}_IGG3.txz' >Download</a></td></tr>" >> $output +echo "<tr><td>An IMGT archive with just the matched and filtered IGG4 sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGG4.txz' download='${NEW_IMGT_PREFIX}_IGG4.txz' >Download</a></td></tr>" >> $output +echo "<tr><td>An IMGT archive with just the matched and filtered IGM sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGM.txz' download='${NEW_IMGT_PREFIX}_IGM.txz' >Download</a></td></tr>" >> $output +echo "<tr><td>An IMGT archive with just the matched and filtered IGE sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGE.txz' download='${NEW_IMGT_PREFIX}_IGE.txz' >Download</a></td></tr>" >> $output +echo "<tr><td>An IMGT archive with just the matched and filtered naive IGM sequences (mutations below 2%)</td><td><a href='${NEW_IMGT_PREFIX}_IGM_NAIVE.txz' download='${NEW_IMGT_PREFIX}_IGM_NAIVE.txz' >Download</a></td></tr>" >> $output +echo "<tr><td>An IMGT archive with just the matched and filtered naive memory IGM sequences (mutations 2% or higher)</td><td><a href='${NEW_IMGT_PREFIX}_IGM_NAIVE_MEMORY.txz' download='${NEW_IMGT_PREFIX}_IGM_NAIVE_MEMORY.txz' >Download</a></td></tr>" >> $output echo "</table>" >> $output echo "<br />" >> $output @@ -764,16 +812,16 @@ if [[ "$naive_output" == "yes" ]] then echo "output naive output" - if [[ "${class_filter}" == "101_101" ]] + if [[ "${class_filter}" == "101_101_all" ]] then - echo "copy new_IMGT.txz to ${naive_output_all}" - cp $outdir/new_IMGT.txz ${naive_output_all} + echo "copy ${NEW_IMGT_PREFIX}.txz to ${naive_output_all}" + cp $outdir/${NEW_IMGT_PREFIX}.txz ${naive_output_all} else echo "copy for classes" - cp $outdir/new_IMGT_IGA.txz ${naive_output_ca} - cp $outdir/new_IMGT_IGG.txz ${naive_output_cg} - cp $outdir/new_IMGT_IGM.txz ${naive_output_cm} - cp $outdir/new_IMGT_IGE.txz ${naive_output_ce} + cp $outdir/${NEW_IMGT_PREFIX}_IGA.txz ${naive_output_ca} + cp $outdir/${NEW_IMGT_PREFIX}_IGG.txz ${naive_output_cg} + cp $outdir/${NEW_IMGT_PREFIX}_IGM.txz ${naive_output_cm} + cp $outdir/${NEW_IMGT_PREFIX}_IGE.txz ${naive_output_ce} fi fi