shm_csr: wrapper.sh annotate

annotate wrapper.sh @ 0:64d74ba01a7c draft

"planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"

author	rhpvorderman
date	Wed, 27 Oct 2021 12:34:47 +0000
parents
children	72d68e2e1fd3

rev	line source
0 64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	1 #!/usr/bin/env bash
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	2 set -e -o pipefail
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	3 dir="$(cd "$(dirname "$0")" && pwd)"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	4 input=$1
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	5 method=$2
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	6 log=$3 #becomes the main html page at the end
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	7 outdir=$4
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	8 output="$outdir/index.html" #copied to $log location at the end
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	9 title="$5"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	10 include_fr1=$6
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	11 functionality=$7
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	12 unique=$8
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	13 naive_output=$9
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	14 naive_output_ca=${10}
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	15 naive_output_cg=${11}
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	16 naive_output_cm=${12}
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	17 naive_output_ce=${13}
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	18 naive_output_all=${14}
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	19 filter_unique=${15}
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	20 filter_unique_count=${16}
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	21 class_filter=${17}
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	22 empty_region_filter=${18}
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	23 fast=${19}
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	24
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	25 #exec 5> debug_output.txt
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	26 #BASH_XTRACEFD="5"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	27 #PS4='$(date +%s.%N) $LINENO: '
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	28 #set -x
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	29
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	30 mkdir -p $outdir
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	31
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	32 tar -xzf $dir/style.tar.gz -C $outdir
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	33
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	34 echo "---------------- read parameters ----------------"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	35 echo "---------------- read parameters ----------------<br />" > $log
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	36
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	37 echo "unpacking IMGT file"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	38
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	39 type="`file $input`"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	40 if [[ "$type" == "Zip archive" ]] ; then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	41 echo "Zip archive"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	42 echo "unzip $input -d $PWD/files/"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	43 unzip $input -d $PWD/files/
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	44 elif [[ "$type" == "XZ compressed data" ]] ; then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	45 echo "ZX archive"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	46 echo "tar -xJf $input -C $PWD/files/"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	47 mkdir -p "$PWD/files/$title"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	48 tar -xJf $input -C "$PWD/files/$title"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	49 else
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	50 echo "Unrecognized format $type"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	51 echo "Unrecognized format $type" > $log
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	52 exit 1
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	53 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	54
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	55 cat "`find $PWD/files/ -name "1_*"`" > $PWD/summary.txt
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	56 cat "`find $PWD/files/ -name "2_*"`" > $PWD/gapped_nt.txt
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	57 cat "`find $PWD/files/ -name "3_*"`" > $PWD/sequences.txt
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	58 cat "`find $PWD/files/ -name "4_*"`" > $PWD/gapped_aa.txt
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	59 cat "`find $PWD/files/ -name "5_*"`" > $PWD/aa.txt
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	60 cat "`find $PWD/files/ -name "6_*"`" > $PWD/junction.txt
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	61 cat "`find $PWD/files/ -name "7_*"`" > $PWD/mutationanalysis.txt
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	62 cat "`find $PWD/files/ -name "8_*"`" > $PWD/mutationstats.txt
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	63 cat "`find $PWD/files/ -name "9_*"`" > $PWD/aa_change_stats.txt
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	64 cat "`find $PWD/files/ -name "10_*"`" > $PWD/hotspots.txt
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	65
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	66 echo "---------------- unique id check ----------------"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	67
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	68 Rscript $dir/check_unique_id.r $PWD/summary.txt $PWD/gapped_nt.txt $PWD/sequences.txt $PWD/gapped_aa.txt $PWD/aa.txt $PWD/junction.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/aa_change_stats.txt $PWD/hotspots.txt
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	69
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	70 if [[ ${#BLASTN_DIR} -ge 5 ]] ; then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	71 echo "On server, using BLASTN_DIR env: ${BLASTN_DIR}"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	72 else
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	73 BLASTN_DIR="/home/galaxy/Downloads/ncbi-blast-2.4.0+/bin"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	74 echo "Dev Galaxy set BLASTN_DIR to: ${BLASTN_DIR}"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	75 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	76
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	77 echo "---------------- class identification ----------------"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	78 echo "---------------- class identification ----------------<br />" >> $log
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	79
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	80 python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	81
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	82 echo "---------------- merge_and_filter.r ----------------"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	83 echo "---------------- merge_and_filter.r ----------------<br />" >> $log
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	84
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	85 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} ${empty_region_filter} 2>&1
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	86
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	87 if [[ "${naive_output}" == "yes" ]] \|\| [[ "$fast" == "no" ]] ; then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	88
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	89 echo "---------------- creating new IMGT zips ----------------"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	90 echo "---------------- creating new IMGT zips ----------------<br />" >> $log
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	91
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	92 mkdir $outdir/new_IMGT
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	93
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	94 cp $PWD/summary.txt "$outdir/new_IMGT/1_Summary.txt"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	95 cp $PWD/gapped_nt.txt "$outdir/new_IMGT/2_IMGT-gapped-nt-sequences.txt"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	96 cp $PWD/sequences.txt "$outdir/new_IMGT/3_Nt-sequences.txt"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	97 cp $PWD/gapped_aa.txt "$outdir/new_IMGT/4_IMGT-gapped-AA-sequences.txt"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	98 cp $PWD/aa.txt "$outdir/new_IMGT/5_AA-sequences.txt"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	99 cp $PWD/junction.txt "$outdir/new_IMGT/6_Junction.txt"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	100 cp $PWD/mutationanalysis.txt "$outdir/new_IMGT/7_V-REGION-mutation-and-AA-change-table.txt"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	101 cp $PWD/mutationstats.txt "$outdir/new_IMGT/8_V-REGION-nt-mutation-statistics.txt"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	102 cp $PWD/aa_change_stats.txt "$outdir/new_IMGT/9_V-REGION-AA-change-statistics.txt"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	103 cp $PWD/hotspots.txt "$outdir/new_IMGT/10_V-REGION-mutation-hotspots.txt"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	104
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	105 mkdir $outdir/new_IMGT_IGA
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	106 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	107
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	108 mkdir $outdir/new_IMGT_IGA1
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	109 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA1
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	110
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	111 mkdir $outdir/new_IMGT_IGA2
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	112 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA2
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	113
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	114 mkdir $outdir/new_IMGT_IGG
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	115 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	116
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	117 mkdir $outdir/new_IMGT_IGG1
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	118 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG1
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	119
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	120 mkdir $outdir/new_IMGT_IGG2
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	121 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG2
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	122
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	123 mkdir $outdir/new_IMGT_IGG3
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	124 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG3
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	125
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	126 mkdir $outdir/new_IMGT_IGG4
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	127 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG4
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	128
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	129 mkdir $outdir/new_IMGT_IGM
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	130 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGM
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	131
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	132 mkdir $outdir/new_IMGT_IGE
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	133 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGE
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	134
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	135 Rscript $dir/new_imgt.r $outdir/new_IMGT/ $outdir/merged.txt "-" 2>&1
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	136
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	137 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA/ $outdir/merged.txt "IGA" 2>&1
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	138 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA1/ $outdir/merged.txt "IGA1" 2>&1
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	139 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA2/ $outdir/merged.txt "IGA2" 2>&1
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	140
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	141 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG/ $outdir/merged.txt "IGG" 2>&1
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	142 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG1/ $outdir/merged.txt "IGG1" 2>&1
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	143 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG2/ $outdir/merged.txt "IGG2" 2>&1
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	144 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG3/ $outdir/merged.txt "IGG3" 2>&1
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	145 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG4/ $outdir/merged.txt "IGG4" 2>&1
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	146
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	147 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGM/ $outdir/merged.txt "IGM" 2>&1
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	148
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	149 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGE/ $outdir/merged.txt "IGE" 2>&1
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	150
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	151
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	152 tmp="$PWD"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	153 cd $outdir/new_IMGT/ #tar weirdness...
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	154 tar -cJf ../new_IMGT.txz *
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	155
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	156 cd $outdir/new_IMGT_IGA/
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	157 tar -cJf ../new_IMGT_IGA.txz *
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	158
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	159 cd $outdir/new_IMGT_IGA1/
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	160 tar -cJf ../new_IMGT_IGA1.txz *
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	161
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	162 cd $outdir/new_IMGT_IGA2/
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	163 tar -cJf ../new_IMGT_IGA2.txz *
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	164
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	165 cd $outdir/new_IMGT_IGG/
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	166 tar -cJf ../new_IMGT_IGG.txz *
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	167
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	168 cd $outdir/new_IMGT_IGG1/
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	169 tar -cJf ../new_IMGT_IGG1.txz *
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	170
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	171 cd $outdir/new_IMGT_IGG2/
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	172 tar -cJf ../new_IMGT_IGG2.txz *
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	173
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	174 cd $outdir/new_IMGT_IGG3/
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	175 tar -cJf ../new_IMGT_IGG3.txz *
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	176
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	177 cd $outdir/new_IMGT_IGG4/
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	178 tar -cJf ../new_IMGT_IGG4.txz *
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	179
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	180 cd $outdir/new_IMGT_IGM/
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	181 tar -cJf ../new_IMGT_IGM.txz *
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	182
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	183 cd $outdir/new_IMGT_IGE/
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	184 tar -cJf ../new_IMGT_IGE.txz *
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	185
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	186 cd $tmp
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	187 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	188
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	189 echo "---------------- shm_csr.r ----------------"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	190 echo "---------------- shm_csr.r ----------------<br />" >> $log
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	191
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	192 classes="IGA,IGA1,IGA2,IGG,IGG1,IGG2,IGG3,IGG4,IGM,IGE,unmatched"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	193 echo "R mutation analysis"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	194 Rscript $dir/shm_csr.r $outdir/merged.txt $classes $outdir ${empty_region_filter} 2>&1
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	195
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	196 echo "---------------- plot_pdfs.r ----------------"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	197 echo "---------------- plot_pdfs.r ----------------<br />" >> $log
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	198
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	199 echo "Rscript $dir/shm_csr.r $outdir/pdfplots.RData $outdir 2>&1"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	200
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	201 Rscript $dir/plot_pdf.r "$outdir/pdfplots.RData" "$outdir" 2>&1
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	202
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	203 echo "---------------- shm_csr.py ----------------"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	204 echo "---------------- shm_csr.py ----------------<br />" >> $log
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	205
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	206 python $dir/shm_csr.py --input $outdir/merged.txt --genes $classes --empty_region_filter "${empty_region_filter}" --output $outdir/hotspot_analysis.txt
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	207
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	208 echo "---------------- aa_histogram.r ----------------"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	209 echo "---------------- aa_histogram.r ----------------<br />" >> $log
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	210
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	211 Rscript $dir/aa_histogram.r $outdir/aa_id_mutations.txt $outdir/absent_aa_id.txt "IGA,IGG,IGM,IGE" $outdir/ 2>&1
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	212 if [ -e "$outdir/aa_histogram_.png" ]; then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	213 mv $outdir/aa_histogram_.png $outdir/aa_histogram.png
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	214 mv $outdir/aa_histogram_.pdf $outdir/aa_histogram.pdf
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	215 mv $outdir/aa_histogram_.txt $outdir/aa_histogram.txt
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	216 mv $outdir/aa_histogram_absent_.txt $outdir/aa_histogram_absent.txt
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	217 mv $outdir/aa_histogram_count_.txt $outdir/aa_histogram_count.txt
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	218 mv $outdir/aa_histogram_sum_.txt $outdir/aa_histogram_sum.txt
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	219 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	220
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	221 genes=(IGA IGA1 IGA2 IGG IGG1 IGG2 IGG3 IGG4 IGM IGE)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	222
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	223 funcs=(sum mean median)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	224 funcs=(sum)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	225
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	226 echo "---------------- sequence_overview.r ----------------"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	227 echo "---------------- sequence_overview.r ----------------<br />" >> $log
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	228
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	229 mkdir $outdir/sequence_overview
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	230
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	231 Rscript $dir/sequence_overview.r $outdir/before_unique_filter.txt $outdir/merged.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt ${empty_region_filter} 2>&1
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	232
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	233 echo "<table border='1'>" > $outdir/base_overview.html
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	234
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	235 while IFS=$'\t' read ID class seq A C G T
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	236 do
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	237 echo "<tr><td>$ID</td><td>$seq</td><td>$class</td><td>$A</td><td>$C</td><td>$G</td><td>$T</td></tr>" >> $outdir/base_overview.html
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	238 done < $outdir/sequence_overview/ntoverview.txt
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	239
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	240 echo "<html><center><h1>$title</h1></center>" > $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	241 echo "<meta name='viewport' content='width=device-width, initial-scale=1'>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	242 echo "<script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	243 echo "<script type='text/javascript' src='tabber.js'></script>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	244 echo "<script type='text/javascript' src='script.js'></script>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	245 echo "<link rel='stylesheet' type='text/css' href='style.css'>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	246 echo "<link rel='stylesheet' type='text/css' href='pure-min.css'>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	247
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	248 matched_count="`cat $outdir/merged.txt \| grep -v 'unmatched' \| tail -n +2 \| wc -l`"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	249 unmatched_count="`cat $outdir/unmatched.txt \| tail -n +2 \| wc -l`"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	250 total_count=$((matched_count + unmatched_count))
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	251 perc_count=$((unmatched_count / total_count * 100))
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	252 perc_count=`bc -l <<< "scale=2; ${unmatched_count} / ${total_count} * 100"`
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	253 perc_count=`bc -l <<< "scale=2; (${unmatched_count} / ${total_count} * 100 ) / 1"`
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	254
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	255 echo "<center><h2>Total: ${total_count}</h2></center>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	256 echo "<center><h2>Matched: ${matched_count} Unmatched: ${unmatched_count}</h2></center>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	257 echo "<center><h2>Percentage unmatched: ${perc_count}</h2></center>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	258
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	259 echo "---------------- main tables ----------------"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	260 echo "---------------- main tables ----------------<br />" >> $log
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	261
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	262 echo "<div class='tabber'>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	263 echo "<div class='tabbertab' title='SHM Overview' style='width: 3000px;'>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	264
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	265 for func in ${funcs[@]}
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	266 do
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	267
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	268 echo "---------------- $func table ----------------"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	269 echo "---------------- $func table ----------------<br />" >> $log
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	270
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	271 cat $outdir/mutations_${func}.txt $outdir/shm_overview_tandem_row.txt $outdir/hotspot_analysis_${func}.txt > $outdir/data_${func}.txt
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	272
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	273 echo "---------------- pattern_plots.r ----------------"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	274 echo "---------------- pattern_plots.r ----------------<br />" >> $log
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	275
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	276 Rscript $dir/pattern_plots.r $outdir/data_${func}.txt $outdir/aid_motives $outdir/relative_mutations $outdir/absolute_mutations $outdir/shm_overview.txt 2>&1
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	277
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	278 echo "<table class='pure-table pure-table-striped'>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	279 echo "<thead><tr><th>info</th>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	280
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	281 if [ "${class_filter}" != "101_101" ] ; then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	282
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	283 for gene in ${genes[@]}
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	284 do
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	285 tmp=`cat $outdir/${gene}_${func}_n.txt`
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	286 echo "<th><a href='matched_${gene}_${func}.txt'>${gene} (N = $tmp)</a></th>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	287 done
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	288
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	289 tmp=`cat $outdir/all_${func}_n.txt`
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	290 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	291 tmp=`cat $outdir/unmatched_${func}_n.txt`
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	292 echo "<th><a href='unmatched.txt'>unmatched (N = ${unmatched_count})</a></th><tr></thead>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	293
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	294 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	295 do
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	296 if [ "$name" == "FR R/S (ratio)" ] \|\| [ "$name" == "CDR R/S (ratio)" ] \|\| [ "$name" == "Tandems/Expected (ratio)" ] ; then #meh
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	297 echo "<tr><td>$name</td><td>${cax}/${cay} (${caz})</td><td>${ca1x}/${ca1y} (${ca1z})</td><td>${ca2x}/${ca2y} (${ca2z})</td><td>${cgx}/${cgy} (${cgz})</td><td>${cg1x}/${cg1y} (${cg1z})</td><td>${cg2x}/${cg2y} (${cg2z})</td><td>${cg3x}/${cg3y} (${cg3z})</td><td>${cg4x}/${cg4y} (${cg4z})</td><td>${cmx}/${cmy} (${cmz})</td><td>${cex}/${cey} (${cez})</td><td>${allx}/${ally} (${allz})</td><td>${unx}/${uny} (${unz})</td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	298 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	299 echo "<tr><td>$name</td><td>${caz}%</td><td>${ca1z}%</td><td>${ca2z}%</td><td>${cgz}%</td><td>${cg1z}%</td><td>${cg2z}%</td><td>${cg3z}%</td><td>${cg4z}%</td><td>${cmz}%</td><td>${cez}%</td><td>${allz}%</td><td>${unz}%</td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	300 else
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	301 echo "<tr><td>$name</td><td>${cax}/${cay} (${caz}%)</td><td>${ca1x}/${ca1y} (${ca1z}%)</td><td>${ca2x}/${ca2y} (${ca2z}%)</td><td>${cgx}/${cgy} (${cgz}%)</td><td>${cg1x}/${cg1y} (${cg1z}%)</td><td>${cg2x}/${cg2y} (${cg2z}%)</td><td>${cg3x}/${cg3y} (${cg3z}%)</td><td>${cg4x}/${cg4y} (${cg4z}%)</td><td>${cmx}/${cmy} (${cmz}%)</td><td>${cex}/${cey} (${cez}%)</td><td>${allx}/${ally} (${allz}%)</td><td>${unx}/${uny} (${unz}%)</td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	302 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	303 done < $outdir/data_${func}.txt
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	304
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	305 else
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	306 tmp=`cat $outdir/all_${func}_n.txt`
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	307 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	308
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	309 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	310 do
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	311 if [ "$name" == "FR R/S (ratio)" ] \|\| [ "$name" == "CDR R/S (ratio)" ] ; then #meh
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	312 echo "<tr><td>$name</td><td>${allx}/${ally}</td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	313 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	314 echo "<tr><td>$name</td><td>${allz}%</td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	315 else
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	316 echo "<tr><td>$name</td><td>${allx}/${ally} (${allz}%)</td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	317 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	318 done < $outdir/data_${func}.txt
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	319
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	320 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	321 echo "</table>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	322 #echo "<a href='data_${func}.txt'>Download data</a>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	323 done
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	324
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	325 echo "<a href='aid_motives.pdf'><img src='aid_motives.png' /></a><br />" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	326 echo "<a href='relative_mutations.pdf'><img src='relative_mutations.png' /></a><br />" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	327 echo "<a href='absolute_mutations.pdf'><img src='absolute_mutations.png' /></a><br />" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	328 echo "<br />" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	329 cat $dir/shm_overview.htm >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	330 echo "</div>" >> $output #SHM overview tab end
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	331
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	332 echo "---------------- images ----------------"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	333 echo "---------------- images ----------------<br />" >> $log
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	334
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	335 echo "<div class='tabbertab' title='SHM Frequency' style='width: 3000px;'></a>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	336
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	337 if [ -a $outdir/scatter.png ]
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	338 then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	339 echo "<a href='scatter.pdf'><img src='scatter.png'/><br />" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	340 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	341 if [ -a $outdir/frequency_ranges.png ]
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	342 then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	343 echo "<a href='frequency_ranges.pdf'><img src='frequency_ranges.png'/></a><br />" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	344 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	345
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	346 echo "<br />" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	347 cat $dir/shm_frequency.htm >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	348
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	349 echo "</div>" >> $output #SHM frequency tab end
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	350
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	351 echo "<div class='tabbertab' title='Transition tables' style='width: 3000px;'>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	352
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	353 echo "<table border='0'>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	354
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	355 for gene in ${genes[@]}
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	356 do
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	357 echo "<tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	358 echo "<td><h1>${gene}</h1></td>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	359
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	360 if [ -e $outdir/transitions_heatmap_${gene}.png ]
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	361 then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	362 echo "<td><a href='transitions_heatmap_${gene}.pdf'><img src='transitions_heatmap_${gene}.png' /></a></td>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	363 else
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	364 echo "<td></td>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	365 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	366
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	367 if [ -e $outdir/transitions_stacked_${gene}.png ]
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	368 then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	369 echo "<td><a href='transitions_stacked_${gene}.pdf'><img src='transitions_stacked_${gene}.png' /></a></td>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	370 else
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	371 echo "<td></td>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	372 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	373
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	374 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	375 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	376 first="true"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	377 while IFS=, read from a c g t
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	378 do
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	379 if [ "$first" == "true" ] ; then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	380 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	381 first="false"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	382 else
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	383 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	384 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	385 done < $outdir/transitions_${gene}_sum.txt
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	386 echo "</table></td>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	387
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	388 echo "</tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	389 done
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	390
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	391 echo "<tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	392 echo "<td><h1>All</h1></td>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	393 echo "<td><a href='transitions_heatmap_all.pdf'><img src='transitions_heatmap_all.png' /></a></td>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	394 echo "<td><a href='transitions_stacked_all.pdf'><img src='transitions_stacked_all.png' /></a></td>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	395 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	396 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	397 first="true"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	398 while IFS=, read from a c g t
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	399 do
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	400 if [ "$first" == "true" ] ; then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	401 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	402 first="false"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	403 else
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	404 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	405 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	406 done < $outdir/transitions_all_sum.txt
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	407 echo "</table></td>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	408
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	409 echo "</tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	410
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	411 echo "</table>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	412
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	413 echo "<br />" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	414 cat $dir/shm_transition.htm >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	415
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	416 echo "</div>" >> $output #transition tables tab end
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	417
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	418 echo "<div class='tabbertab' title='Antigen Selection'>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	419
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	420 if [ -e $outdir/aa_histogram.png ]
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	421 then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	422 echo "<a href='aa_histogram.pdf'><img src='aa_histogram.png'/></a><br />" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	423 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	424
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	425 if [ -e $outdir/aa_histogram_IGA.png ]
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	426 then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	427 echo "<a href='aa_histogram_IGA.pdf'><img src='aa_histogram_IGA.png'/></a><br />" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	428 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	429
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	430 if [ -e $outdir/aa_histogram_IGG.png ]
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	431 then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	432 echo "<a href='aa_histogram_IGG.pdf'><img src='aa_histogram_IGG.png'/></a><br />" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	433 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	434
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	435 if [ -e $outdir/aa_histogram_IGM.png ]
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	436 then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	437 echo "<a href='aa_histogram_IGM.pdf'><img src='aa_histogram_IGM.png'/></a><br />" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	438 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	439
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	440 if [ -e $outdir/aa_histogram_IGE.png ]
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	441 then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	442 echo "<a href='aa_histogram_IGE.pdf'><img src='aa_histogram_IGE.png'/></a><br />" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	443 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	444
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	445
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	446
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	447 if [[ "$fast" == "no" ]] ; then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	448
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	449
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	450
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	451 echo "---------------- baseline ----------------"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	452 echo "---------------- baseline ----------------<br />" >> $log
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	453 tmp="$PWD"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	454
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	455 mkdir -p $outdir/baseline
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	456
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	457 echo "<center><h1>BASELINe</h1>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	458 header_substring="Based on CDR1, FR2, CDR2, FR3 (27:27:38:55:65:104:-)"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	459
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	460 baseline_boundaries="27:27:38:55:65:104:-"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	461
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	462 if [[ "${empty_region_filter}" == "leader" ]] ; then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	463 baseline_boundaries="1:26:38:55:65:104:-"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	464 header_substring="Based on FR1, CDR1, FR2, CDR2, FR3 (1:26:38:55:65:104,-)"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	465 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	466
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	467 echo "<p>${header_substring}</p></center>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	468
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	469 mkdir $outdir/baseline/IGA_IGG_IGM
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	470 if [[ $(wc -l < $outdir/new_IMGT/1_Summary.txt) -gt "1" ]]; then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	471 cd $outdir/baseline/IGA_IGG_IGM
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	472 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"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	473 else
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	474 echo "No sequences" > "$outdir/baseline.txt"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	475 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	476
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	477 mkdir $outdir/baseline/IGA
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	478 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	479 cd $outdir/baseline/IGA
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	480 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"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	481 else
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	482 echo "No IGA sequences" > "$outdir/baseline_IGA.txt"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	483 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	484
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	485 mkdir $outdir/baseline/IGG
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	486 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	487 cd $outdir/baseline/IGG
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	488 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"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	489 else
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	490 echo "No IGG sequences" > "$outdir/baseline_IGG.txt"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	491 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	492
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	493 mkdir $outdir/baseline/IGM
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	494 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	495 cd $outdir/baseline/IGM
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	496 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"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	497 else
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	498 echo "No IGM sequences" > "$outdir/baseline_IGM.txt"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	499 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	500
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	501 mkdir $outdir/baseline/IGE
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	502 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	503 cd $outdir/baseline/IGE
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	504 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"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	505 else
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	506 echo "No IGE sequences" > "$outdir/baseline_IGE.txt"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	507 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	508
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	509 cd $tmp
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	510
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	511 echo "Cleaning up *.RData files"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	512 find $outdir/baseline -name "*.RData" -type f -delete
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	513
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	514 if [ -e $outdir/baseline.pdf ]
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	515 then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	516 echo "<embed src='baseline.pdf' width='700px' height='1000px'>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	517 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	518
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	519 if [ -e $outdir/baseline_IGA.pdf ]
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	520 then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	521 echo "<embed src='baseline_IGA.pdf' width='700px' height='1000px'>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	522 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	523
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	524 if [ -e $outdir/baseline_IGG.pdf ]
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	525 then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	526 echo "<embed src='baseline_IGG.pdf' width='700px' height='1000px'>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	527 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	528
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	529 if [ -e $outdir/baseline_IGM.pdf ]
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	530 then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	531 echo "<embed src='baseline_IGM.pdf' width='700px' height='1000px'>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	532 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	533
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	534 if [ -e $outdir/baseline_IGE.pdf ]
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	535 then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	536 echo "<embed src='baseline_IGE.pdf' width='700px' height='1000px'>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	537 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	538 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	539
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	540 echo "<br />" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	541 cat $dir/shm_selection.htm >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	542
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	543 echo "</div>" >> $output #antigen selection tab end
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	544
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	545 echo "<div class='tabbertab' title='CSR'>" >> $output #CSR tab
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	546
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	547 if [ -e $outdir/IGA.png ]
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	548 then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	549 echo "<a href='IGA.pdf'><img src='IGA.png'/></a><br />" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	550 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	551 if [ -e $outdir/IGG.png ]
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	552 then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	553 echo "<a href='IGG.pdf'><img src='IGG.png'/></a><br />" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	554 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	555
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	556 echo "<br />" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	557 cat $dir/shm_csr.htm >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	558
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	559 echo "</div>" >> $output #CSR tab end
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	560
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	561 if [[ "$fast" == "no" ]] ; then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	562
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	563 echo "---------------- change-o MakeDB ----------------"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	564
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	565 mkdir -p $outdir/change_o
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	566
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	567 tmp="$PWD"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	568
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	569 cd $outdir/change_o
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	570
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	571 bash $dir/change_o/makedb.sh $outdir/new_IMGT.txz false false false $outdir/change_o/change-o-db.txt
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	572 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
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	573 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
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	574
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	575 mkdir $outdir/new_IMGT_changeo
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	576 cp $outdir/new_IMGT/* $outdir/new_IMGT_changeo
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	577
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	578 Rscript $dir/new_imgt.r $outdir/new_IMGT_changeo $outdir/change_o/change-o-db-defined_first_clones.txt "-" 2>&1
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	579
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	580 cd $outdir/new_IMGT_changeo
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	581 tar -cJf ../new_IMGT_first_seq_of_clone.txz *
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	582 cd $outdir/change_o
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	583
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	584 rm -rf $outdir/new_IMGT_changeo
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	585
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	586 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
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	587 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"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	588
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	589 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	590 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGA.txz false false false $outdir/change_o/change-o-db-IGA.txt
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	591 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
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	592 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
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	593
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	594 mkdir $outdir/new_IMGT_IGA_changeo
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	595 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA_changeo
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	596
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	597 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA_changeo $outdir/change_o/change-o-db-defined_first_clones-IGA.txt "-" 2>&1
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	598
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	599 cd $outdir/new_IMGT_IGA_changeo
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	600 tar -cJf ../new_IMGT_IGA_first_seq_of_clone.txz *
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	601
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	602 rm -rf $outdir/new_IMGT_IGA_changeo
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	603
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	604 cd $outdir/change_o
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	605 else
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	606 echo "No IGA sequences" > "$outdir/change_o/change-o-db-defined_clones-IGA.txt"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	607 echo "No IGA sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGA.txt"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	608 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	609
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	610 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	611 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGG.txz false false false $outdir/change_o/change-o-db-IGG.txt
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	612 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
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	613 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
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	614
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	615 mkdir $outdir/new_IMGT_IGG_changeo
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	616 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG_changeo
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	617
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	618 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG_changeo $outdir/change_o/change-o-db-defined_first_clones-IGG.txt "-" 2>&1
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	619
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	620 cd $outdir/new_IMGT_IGG_changeo
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	621 tar -cJf ../new_IMGT_IGG_first_seq_of_clone.txz *
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	622 rm -rf $outdir/new_IMGT_IGG_changeo
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	623
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	624 cd $outdir/change_o
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	625 else
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	626 echo "No IGG sequences" > "$outdir/change_o/change-o-db-defined_clones-IGG.txt"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	627 echo "No IGG sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGG.txt"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	628 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	629
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	630 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	631 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGM.txz false false false $outdir/change_o/change-o-db-IGM.txt
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	632 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
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	633 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
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	634
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	635 mkdir $outdir/new_IMGT_IGM_changeo
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	636 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGM_changeo
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	637
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	638 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGM_changeo $outdir/change_o/change-o-db-defined_first_clones-IGM.txt "-" 2>&1
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	639
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	640 cd $outdir/new_IMGT_IGM_changeo
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	641 tar -cJf ../new_IMGT_IGM_first_seq_of_clone.txz *
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	642
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	643 rm -rf $outdir/new_IMGT_IGM_changeo
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	644
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	645 cd $outdir/change_o
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	646 else
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	647 echo "No IGM sequences" > "$outdir/change_o/change-o-db-defined_clones-IGM.txt"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	648 echo "No IGM sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGM.txt"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	649 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	650
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	651 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	652 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGE.txz false false false $outdir/change_o/change-o-db-IGE.txt
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	653 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
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	654 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
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	655
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	656 mkdir $outdir/new_IMGT_IGE_changeo
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	657 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGE_changeo
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	658
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	659 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGE_changeo $outdir/change_o/change-o-db-defined_first_clones-IGE.txt "-" 2>&1
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	660
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	661 cd $outdir/new_IMGT_IGE_changeo
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	662 tar -cJf ../new_IMGT_IGE_first_seq_of_clone.txz *
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	663
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	664 rm -rf $outdir/new_IMGT_IGE_changeo
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	665
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	666 cd $outdir/change_o
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	667 else
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	668 echo "No IGE sequences" > "$outdir/change_o/change-o-db-defined_clones-IGE.txt"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	669 echo "No IGE sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGE.txt"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	670 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	671
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	672 cd "$tmp"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	673
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	674 rm -rf $outdir/new_IMGT
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	675 rm -rf $outdir/new_IMGT_IGA/
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	676 rm -rf $outdir/new_IMGT_IGA1/
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	677 rm -rf $outdir/new_IMGT_IGA2/
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	678 rm -rf $outdir/new_IMGT_IGG/
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	679 rm -rf $outdir/new_IMGT_IGG1/
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	680 rm -rf $outdir/new_IMGT_IGG2/
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	681 rm -rf $outdir/new_IMGT_IGG3/
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	682 rm -rf $outdir/new_IMGT_IGG4/
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	683 rm -rf $outdir/new_IMGT_IGM/
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	684 rm -rf $outdir/new_IMGT_IGE/
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	685
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	686 echo "<div class='tabbertab' title='Clonal Relation' style='width: 7000px;'>" >> $output #clonality tab
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	687
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	688 function clonality_table {
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	689 local infile=$1
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	690 local outfile=$2
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	691
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	692 echo "<table class='pure-table pure-table-striped'>" >> $outfile
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	693 echo "<thead><tr><th>Clone size</th><th>Nr of clones</th><th>Nr of sequences</th></tr></thead>" >> $outfile
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	694
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	695 first='true'
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	696
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	697 while read size clones seqs
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	698 do
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	699 if [[ "$first" == "true" ]]; then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	700 first="false"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	701 continue
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	702 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	703 echo "<tr><td>$size</td><td>$clones</td><td>$seqs</td></tr>" >> $outfile
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	704 done < $infile
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	705
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	706 echo "</table>" >> $outfile
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	707 }
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	708 echo "<div class='tabber'>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	709
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	710 echo "<div class='tabbertab' title='All'>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	711 clonality_table $outdir/change_o/change-o-defined_clones-summary.txt $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	712 echo "</div>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	713
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	714 echo "<div class='tabbertab' title='IGA'>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	715 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGA.txt $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	716 echo "</div>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	717
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	718 echo "<div class='tabbertab' title='IGG'>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	719 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGG.txt $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	720 echo "</div>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	721
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	722 echo "<div class='tabbertab' title='IGM'>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	723 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	724 echo "</div>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	725
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	726 echo "<div class='tabbertab' title='IGE'>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	727 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	728 echo "</div>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	729
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	730 echo "<div class='tabbertab' title='Overlap' style='width: 7000px;'>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	731 cat "$outdir/sequence_overview/index.html" \| sed -e 's:</td>:</td>\n:g' \| sed "s:href='$.*$.html:href='sequence_overview/\1.html:g" >> $output # rewrite href to 'sequence_overview/..."
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	732 echo "</div>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	733
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	734 echo "</div>" >> $output #clonality tabber end
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	735
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	736 echo "<br />" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	737 cat $dir/shm_clonality.htm >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	738
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	739 echo "</div>" >> $output #clonality tab end
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	740
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	741 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	742
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	743 echo "<div class='tabbertab' title='Downloads'>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	744
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	745 echo "<table class='pure-table pure-table-striped'>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	746 echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	747 echo "<tr><td>The complete dataset</td><td><a href='merged.txt' download='merged.txt' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	748 echo "<tr><td>The filtered dataset</td><td><a href='filtered.txt' download='filtered.txt' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	749 echo "<tr><td>The alignment info on the unmatched sequences</td><td><a href='unmatched.txt' download='unmatched.txt' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	750
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	751 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Overview</td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	752 echo "<tr><td>The SHM Overview table as a dataset</td><td><a href='shm_overview.txt' download='shm_overview.txt' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	753 echo "<tr><td>Motif data per sequence ID</td><td><a href='motif_per_seq.txt' download='motif_per_seq.txt' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	754 echo "<tr><td>Mutation data per sequence ID</td><td><a href='mutation_by_id.txt' download='mutation_by_id.txt' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	755 echo "<tr><td>Base count for every sequence</td><td><a href='base_overview.html'>View</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	756 echo "<tr><td>The data used to generate the percentage of mutations in AID and pol eta motives plot</td><td><a href='aid_motives.txt' download='aid_motives.txt' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	757 echo "<tr><td>The data used to generate the relative mutation patterns plot</td><td><a href='relative_mutations.txt' download='relative_mutations.txt' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	758 echo "<tr><td>The data used to generate the absolute mutation patterns plot</td><td><a href='absolute_mutations.txt' download='absolute_mutations.txt' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	759 echo "<tr><td>Data about tandem mutations by ID</td><td><a href='tandems_by_id.txt' download='tandems_by_id.txt' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	760
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	761 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Frequency</td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	762 echo "<tr><td>The data generate the frequency scatter plot</td><td><a href='scatter.txt' download='scatter.txt' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	763 echo "<tr><td>The data used to generate the frequency by class plot</td><td><a href='frequency_ranges_classes.txt' download='frequency_ranges_classes.txt' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	764 echo "<tr><td>The data for frequency by subclass</td><td><a href='frequency_ranges_subclasses.txt' download='frequency_ranges_subclasses.txt' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	765
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	766 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Transition Tables</td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	767 echo "<tr><td>The data for the 'all' transition plot</td><td><a href='transitions_all_sum.txt' download='transitions_all_sum.txt' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	768 echo "<tr><td>The data for the 'IGA' transition plot</td><td><a href='transitions_IGA_sum.txt' download='transitions_IGA_sum.txt' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	769 echo "<tr><td>The data for the 'IGA1' transition plot</td><td><a href='transitions_IGA1_sum.txt' download='transitions_IGA1_sum.txt' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	770 echo "<tr><td>The data for the 'IGA2' transition plot</td><td><a href='transitions_IGA2_sum.txt' download='transitions_IGA2_sum.txt' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	771 echo "<tr><td>The data for the 'IGG' transition plot</td><td><a href='transitions_IGG_sum.txt' download='transitions_IGG_sum.txt' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	772 echo "<tr><td>The data for the 'IGG1' transition plot</td><td><a href='transitions_IGG1_sum.txt' download='transitions_IGG1_sum.txt' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	773 echo "<tr><td>The data for the 'IGG2' transition plot</td><td><a href='transitions_IGG2_sum.txt' download='transitions_IGG2_sum.txt' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	774 echo "<tr><td>The data for the 'IGG3' transition plot</td><td><a href='transitions_IGG3_sum.txt' download='transitions_IGG3_sum.txt' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	775 echo "<tr><td>The data for the 'IGG4' transition plot</td><td><a href='transitions_IGG4_sum.txt' download='transitions_IGG4_sum.txt' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	776 echo "<tr><td>The data for the 'IGM' transition plot</td><td><a href='transitions_IGM_sum.txt' download='transitions_IGM_sum.txt' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	777 echo "<tr><td>The data for the 'IGE' transition plot</td><td><a href='transitions_IGE_sum.txt' download='transitions_IGE_sum.txt' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	778
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	779 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Antigen Selection</td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	780 echo "<tr><td>AA mutation data per sequence ID</td><td><a href='aa_id_mutations.txt' download='aa_id_mutations.txt' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	781 echo "<tr><td>Presence of AA per sequence ID</td><td><a href='absent_aa_id.txt' download='absent_aa_id.txt' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	782
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	783 echo "<tr><td>The data used to generate the aa mutation frequency plot</td><td><a href='aa_histogram_sum.txt' download='aa_histogram_sum.txt' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	784 echo "<tr><td>The data used to generate the aa mutation frequency plot for IGA</td><td><a href='aa_histogram_sum_IGA.txt' download='aa_histogram_sum_IGA.txt' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	785 echo "<tr><td>The data used to generate the aa mutation frequency plot for IGG</td><td><a href='aa_histogram_sum_IGG.txt' download='aa_histogram_sum_IGG.txt' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	786 echo "<tr><td>The data used to generate the aa mutation frequency plot for IGM</td><td><a href='aa_histogram_sum_IGM.txt' download='aa_histogram_sum_IGM.txt' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	787 echo "<tr><td>The data used to generate the aa mutation frequency plot for IGE</td><td><a href='aa_histogram_sum_IGE.txt' download='aa_histogram_sum_IGE.txt' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	788
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	789 echo "<tr><td>Baseline PDF (<a href='http://selection.med.yale.edu/baseline/'>http://selection.med.yale.edu/baseline/</a>)</td><td><a href='baseline.pdf' download='baseline.pdf' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	790 echo "<tr><td>Baseline data</td><td><a href='baseline.txt' download='baseline.txt' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	791 echo "<tr><td>Baseline IGA PDF</td><td><a href='baseline_IGA.pdf' download='baseline_IGA.pdf' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	792 echo "<tr><td>Baseline IGA data</td><td><a href='baseline_IGA.txt' download='baseline_IGA.txt' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	793 echo "<tr><td>Baseline IGG PDF</td><td><a href='baseline_IGG.pdf' download='baseline_IGG.pdf' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	794 echo "<tr><td>Baseline IGG data</td><td><a href='baseline_IGG.txt' download='baseline_IGG.txt' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	795 echo "<tr><td>Baseline IGM PDF</td><td><a href='baseline_IGM.pdf' download='baseline_IGM.pdf' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	796 echo "<tr><td>Baseline IGM data</td><td><a href='baseline_IGM.txt' download='baseline_IGM.txt' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	797 echo "<tr><td>Baseline IGE PDF</td><td><a href='baseline_IGE.pdf' download='baseline_IGE.pdf' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	798 echo "<tr><td>Baseline IGE data</td><td><a href='baseline_IGE.txt' download='baseline_IGE.txt' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	799
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	800 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>CSR</td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	801 echo "<tr><td>The data for the IGA subclass distribution plot</td><td><a href='IGA_pie.txt' download='IGA_pie.txt' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	802 echo "<tr><td>The data for the IGG subclass distribution plot</td><td><a href='IGG_pie.txt' download='IGG_pie.txt' >Download</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	803
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	804
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	805 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Clonal Relation</td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	806 echo "<tr><td>Sequence overlap between subclasses</td><td><a href='sequence_overview/index.html'>View</a></td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	807 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
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	808 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
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	809 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
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	810
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	811 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
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	812 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
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	813 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
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	814
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	815 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
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	816 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
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	817 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
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	818
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	819 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
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	820 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
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	821 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
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	822
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	823 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
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	824 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
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	825 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
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	826
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	827 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Filtered IMGT output files</td></tr>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	828 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
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	829 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
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	830 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
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	831 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
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	832 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
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	833 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
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	834 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
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	835 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
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	836 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
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	837 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
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	838 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
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	839
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	840 echo "</table>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	841
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	842 echo "<br />" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	843 cat $dir/shm_downloads.htm >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	844
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	845 echo "</div>" >> $output #downloads tab end
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	846
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	847 echo "</div>" >> $output #tabs end
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	848
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	849 echo "</html>" >> $output
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	850
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	851
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	852 echo "---------------- naive_output.r ----------------"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	853 echo "---------------- naive_output.r ----------------<br />" >> $log
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	854
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	855 if [[ "$naive_output" == "yes" ]]
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	856 then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	857 echo "output naive output"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	858 if [[ "${class_filter}" == "101_101" ]]
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	859 then
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	860 echo "copy new_IMGT.txz to ${naive_output_all}"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	861 cp $outdir/new_IMGT.txz ${naive_output_all}
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	862 else
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	863 echo "copy for classes"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	864 cp $outdir/new_IMGT_IGA.txz ${naive_output_ca}
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	865 cp $outdir/new_IMGT_IGG.txz ${naive_output_cg}
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	866 cp $outdir/new_IMGT_IGM.txz ${naive_output_cm}
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	867 cp $outdir/new_IMGT_IGE.txz ${naive_output_ce}
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	868 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	869 fi
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	870
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	871 echo "</table>" >> $outdir/base_overview.html
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	872
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	873 mv $log $outdir/log.html
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	874
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	875 echo "<html><center><h1><a href='index.html'>Click here for the results</a></h1>Tip: Open it in a new tab (middle mouse button or right mouse button -> 'open in new tab' on the link above)<br />" > $log
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	876 echo "<table border = 1>" >> $log
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	877 echo "<thead><tr><th>Info</th><th>Sequences</th><th>Percentage</th></tr></thead>" >> $log
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	878 tIFS="$TMP"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	879 IFS=$'\t'
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	880 while read step seq perc
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	881 do
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	882 echo "<tr>" >> $log
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	883 echo "<td>$step</td>" >> $log
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	884 echo "<td>$seq</td>" >> $log
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	885 echo "<td>${perc}%</td>" >> $log
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	886 echo "</tr>" >> $log
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	887 done < $outdir/filtering_steps.txt
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	888 echo "</table>" >> $log
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	889 echo "<br />" >> $log
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	890 cat $dir/shm_first.htm >> $log
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	891 echo "</center></html>" >> $log
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	892
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	893 IFS="$tIFS"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	894
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	895 echo "---------------- remove_files----------------"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	896 echo "---------------- remove_files----------------<br />" >> $log
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	897
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	898 rm -r -v results/baseline
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	899 rm -r -v files
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	900 filename='remove_files.txt'
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	901
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	902 while read file; do
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	903 rm -v $file
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	904 done < "$filename"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	905
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	906
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	907 echo "---------------- Done! ----------------"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	908 echo "---------------- Done! ----------------<br />" >> $outdir/log.html
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	909
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	910
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	911
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	912
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	913
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4" rhpvorderman parents: diff changeset	914

Mercurial > repos > rhpvorderman > shm_csr

annotate wrapper.sh @ 0:64d74ba01a7c draft