Mercurial > repos > davidvanzessen > imgt_concatenate
changeset 2:d77d4700fd0a draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Tue, 27 Dec 2016 10:11:21 -0500 |
| parents | b360a373835f |
| children | 9ace06c6f6d8 |
| files | imgt_concatenate.sh imgt_concatenate.xml |
| diffstat | 2 files changed, 28 insertions(+), 12 deletions(-) [+] |
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--- a/imgt_concatenate.sh Thu Nov 24 10:27:14 2016 -0500 +++ b/imgt_concatenate.sh Tue Dec 27 10:11:21 2016 -0500 @@ -33,16 +33,30 @@ outdir=$2 start_line=$3 #line # to start at, 2 to skip header id=$4 - cat `find $indir/ -name "1_*"` | tail -n+${start_line} | awk -v id=$id '{ if($1 !~ /^header/) {$2=$2id; } print}' >> "$outdir/1_Summary.txt" - cat `find $indir/ -name "2_*"` | tail -n+${start_line} | awk -v id=$id '{ if($1 !~ /^header/) {$2=$2id; } print}' >> "$outdir/2_IMGT-gapped-nt-sequences.txt" - cat `find $indir/ -name "3_*"` | tail -n+${start_line} | awk -v id=$id '{ if($1 !~ /^header/) {$2=$2id; } print}' >> "$outdir/3_Nt-sequences.txt" - cat `find $indir/ -name "4_*"` | tail -n+${start_line} | awk -v id=$id '{ if($1 !~ /^header/) {$2=$2id; } print}' >> "$outdir/4_IMGT-gapped-AA-sequences.txt" - cat `find $indir/ -name "5_*"` | tail -n+${start_line} | awk -v id=$id '{ if($1 !~ /^header/) {$2=$2id; } print}' >> "$outdir/5_AA-sequences.txt" - cat `find $indir/ -name "6_*"` | tail -n+${start_line} | awk -v id=$id '{ if($1 !~ /^header/) {$2=$2id; } print}' >> "$outdir/6_Junction.txt" - cat `find $indir/ -name "7_*"` | tail -n+${start_line} | awk -v id=$id '{ if($1 !~ /^header/) {$2=$2id; } print}' >> "$outdir/7_V-REGION-mutation-and-AA-change-table.txt" - cat `find $indir/ -name "8_*"` | tail -n+${start_line} | awk -v id=$id '{ if($1 !~ /^header/) {$2=$2id; } print}' >> "$outdir/8_V-REGION-nt-mutation-statistics.txt" - cat `find $indir/ -name "9_*"` | tail -n+${start_line} | awk -v id=$id '{ if($1 !~ /^header/) {$2=$2id; } print}' >> "$outdir/9_V-REGION-AA-change-statistics.txt" - cat `find $indir/ -name "10_*"` | tail -n+${start_line} | awk -v id=$id '{ if($1 !~ /^header/) {$2=$2id; } print}' >> "$outdir/10_V-REGION-mutation-hotspots.txt" + if [[ "${start_line}" == "1" ]] ; then + cat `find $indir/ -name "1_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>1) {$2=$2id; } print}' >> "$outdir/1_Summary.txt" + cat `find $indir/ -name "2_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>1) {$2=$2id; } print}' >> "$outdir/2_IMGT-gapped-nt-sequences.txt" + cat `find $indir/ -name "3_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>1) {$2=$2id; } print}' >> "$outdir/3_Nt-sequences.txt" + cat `find $indir/ -name "4_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>1) {$2=$2id; } print}' >> "$outdir/4_IMGT-gapped-AA-sequences.txt" + cat `find $indir/ -name "5_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>1) {$2=$2id; } print}' >> "$outdir/5_AA-sequences.txt" + cat `find $indir/ -name "6_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>1) {$2=$2id; } print}' >> "$outdir/6_Junction.txt" + cat `find $indir/ -name "7_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>1) {$2=$2id; } print}' >> "$outdir/7_V-REGION-mutation-and-AA-change-table.txt" + cat `find $indir/ -name "8_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>1) {$2=$2id; } print}' >> "$outdir/8_V-REGION-nt-mutation-statistics.txt" + cat `find $indir/ -name "9_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>1) {$2=$2id; } print}' >> "$outdir/9_V-REGION-AA-change-statistics.txt" + cat `find $indir/ -name "10_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>1) {$2=$2id; } print}' >> "$outdir/10_V-REGION-mutation-hotspots.txt" + else + cat `find $indir/ -name "1_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>0) {$2=$2id; } print}' >> "$outdir/1_Summary.txt" + cat `find $indir/ -name "2_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>0) {$2=$2id; } print}' >> "$outdir/2_IMGT-gapped-nt-sequences.txt" + cat `find $indir/ -name "3_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>0) {$2=$2id; } print}' >> "$outdir/3_Nt-sequences.txt" + cat `find $indir/ -name "4_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>0) {$2=$2id; } print}' >> "$outdir/4_IMGT-gapped-AA-sequences.txt" + cat `find $indir/ -name "5_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>0) {$2=$2id; } print}' >> "$outdir/5_AA-sequences.txt" + cat `find $indir/ -name "6_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>0) {$2=$2id; } print}' >> "$outdir/6_Junction.txt" + cat `find $indir/ -name "7_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>0) {$2=$2id; } print}' >> "$outdir/7_V-REGION-mutation-and-AA-change-table.txt" + cat `find $indir/ -name "8_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>0) {$2=$2id; } print}' >> "$outdir/8_V-REGION-nt-mutation-statistics.txt" + cat `find $indir/ -name "9_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>0) {$2=$2id; } print}' >> "$outdir/9_V-REGION-AA-change-statistics.txt" + cat `find $indir/ -name "10_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>0) {$2=$2id; } print}' >> "$outdir/10_V-REGION-mutation-hotspots.txt" + fi + } echo "Unpacking IMGT file 1.." @@ -68,6 +82,8 @@ i=$((i+2)) done +echo "`head $workdir/output/1_Summary.txt`" + echo "Creating new IMGT zip" cd "$workdir/output"
--- a/imgt_concatenate.xml Thu Nov 24 10:27:14 2016 -0500 +++ b/imgt_concatenate.xml Tue Dec 27 10:11:21 2016 -0500 @@ -22,7 +22,7 @@ </param> <when value='true'> <repeat name="files" title="Sample" min="2" default="2"> - <param name="file" format="peptideshaker_archive" type="data" label="IMGT zip file" /> + <param name="file" type="data" label="IMGT zip file" /> <param name="id" type="text" label="ID for dataset" size="25"> <validator type="regex" message="Fill in an ID">.+</validator> </param> @@ -30,7 +30,7 @@ </when> <when value='false'> <repeat name="files" title="Sample" min="2" default="2"> - <param name="file" format="peptideshaker_archive" type="data" label="IMGT zip file" /> + <param name="file" type="data" label="IMGT zip file" /> </repeat> </when> </conditional>