shm_csr: wrapper.sh annotate

annotate wrapper.sh @ 98:d714f5ea83d7 draft default tip

planemo upload commit 1a01065a084a817382872154f779b94090a35ebf

author	rhpvorderman
date	Wed, 10 Jan 2024 12:32:47 +0000
parents	385dea3c6cb5
children

rev	line source
83 729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57" rhpvorderman parents: 81 diff changeset	1 #!/usr/bin/env bash
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57" rhpvorderman parents: 81 diff changeset	2 set -e -o pipefail
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	3 dir="$(cd "$(dirname "$0")" && pwd)"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	4 input=$1
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	5 method=$2
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	6 log=$3 #becomes the main html page at the end
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	7 outdir=$4
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	8 output="$outdir/index.html" #copied to $log location at the end
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	9 title="$5"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	10 include_fr1=$6
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	11 functionality=$7
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	12 unique=$8
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	13 naive_output=$9
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	14 naive_output_ca=${10}
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	15 naive_output_cg=${11}
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	16 naive_output_cm=${12}
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	17 naive_output_ce=${13}
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	18 naive_output_all=${14}
94 84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140" rhpvorderman parents: 93 diff changeset	19 naive_output_igm_naive=${15}
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140" rhpvorderman parents: 93 diff changeset	20 naive_output_igm_naive_memory=${16}
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140" rhpvorderman parents: 93 diff changeset	21 filter_unique=${17}
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140" rhpvorderman parents: 93 diff changeset	22 filter_unique_count=${18}
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140" rhpvorderman parents: 93 diff changeset	23 class_filter=${19}
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140" rhpvorderman parents: 93 diff changeset	24 empty_region_filter=${20}
98 d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf rhpvorderman parents: 96 diff changeset	25 run_changeo=${21}
d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf rhpvorderman parents: 96 diff changeset	26 run_baseline=${22}
96 385dea3c6cb5 planemo upload commit 423a48569c69301fdbf893ac3a649128404dfff5 rhpvorderman parents: 95 diff changeset	27 BASENAME=$(basename "$title")
95 d63eff357515 planemo upload commit d96a736dcd6da34137f79861fbc6369716c332f1 rhpvorderman parents: 94 diff changeset	28 # Cut off .txz or .tgz suffix and also replace spaces with underscores.
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	29 NEW_IMGT_PREFIX="new_IMGT_${BASENAME%.*}"
95 d63eff357515 planemo upload commit d96a736dcd6da34137f79861fbc6369716c332f1 rhpvorderman parents: 94 diff changeset	30 NEW_IMGT_PREFIX=${NEW_IMGT_PREFIX// /_}
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	31
83 729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57" rhpvorderman parents: 81 diff changeset	32 #exec 5> debug_output.txt
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57" rhpvorderman parents: 81 diff changeset	33 #BASH_XTRACEFD="5"
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	34 ## Busybox date does not support '+%s.%N'. So use a custom program. Can be
96 385dea3c6cb5 planemo upload commit 423a48569c69301fdbf893ac3a649128404dfff5 rhpvorderman parents: 95 diff changeset	35 ## Compiled with cc -static -Os show_time_as_float.c -o show_time_as_float
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	36 #PS4='$(${dir}/show_time_as_float) $LINENO: '
83 729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57" rhpvorderman parents: 81 diff changeset	37 #set -x
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57" rhpvorderman parents: 81 diff changeset	38
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57" rhpvorderman parents: 81 diff changeset	39 mkdir -p $outdir
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	40
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	41 tar -xzf $dir/style.tar.gz -C $outdir
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	42
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	43 echo "---------------- read parameters ----------------"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	44 echo "---------------- read parameters ----------------<br />" > $log
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	45
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	46 echo "unpacking IMGT file"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	47
95 d63eff357515 planemo upload commit d96a736dcd6da34137f79861fbc6369716c332f1 rhpvorderman parents: 94 diff changeset	48 type="$(file -L "$input")"
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	49 if [[ "$type" == "Zip archive" ]] ; then
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	50 echo "Zip archive"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	51 echo "unzip $input -d $PWD/files/"
95 d63eff357515 planemo upload commit d96a736dcd6da34137f79861fbc6369716c332f1 rhpvorderman parents: 94 diff changeset	52 unzip "$input" -d $PWD/files/
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	53 elif [[ "$type" == "XZ compressed data" ]] ; then
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	54 echo "ZX archive"
95 d63eff357515 planemo upload commit d96a736dcd6da34137f79861fbc6369716c332f1 rhpvorderman parents: 94 diff changeset	55 echo "tar -xJf "$input" -C $PWD/files/"
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	56 mkdir -p "$PWD/files/$title"
95 d63eff357515 planemo upload commit d96a736dcd6da34137f79861fbc6369716c332f1 rhpvorderman parents: 94 diff changeset	57 tar -xJf "$input" -C "$PWD/files/$title"
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	58 else
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	59 echo "Unrecognized format $type"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	60 echo "Unrecognized format $type" > $log
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	61 exit 1
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	62 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	63
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	64 cat "`find $PWD/files/ -name "1_*"`" > $PWD/summary.txt
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	65 cat "`find $PWD/files/ -name "2_*"`" > $PWD/gapped_nt.txt
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	66 cat "`find $PWD/files/ -name "3_*"`" > $PWD/sequences.txt
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	67 cat "`find $PWD/files/ -name "4_*"`" > $PWD/gapped_aa.txt
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	68 cat "`find $PWD/files/ -name "5_*"`" > $PWD/aa.txt
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	69 cat "`find $PWD/files/ -name "6_*"`" > $PWD/junction.txt
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	70 cat "`find $PWD/files/ -name "7_*"`" > $PWD/mutationanalysis.txt
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	71 cat "`find $PWD/files/ -name "8_*"`" > $PWD/mutationstats.txt
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	72 cat "`find $PWD/files/ -name "9_*"`" > $PWD/aa_change_stats.txt
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	73 cat "`find $PWD/files/ -name "10_*"`" > $PWD/hotspots.txt
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	74
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	75 echo "---------------- unique id check ----------------"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	76
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	77 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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	78
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	79 if [[ ${#BLASTN_DIR} -ge 5 ]] ; then
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	80 echo "On server, using BLASTN_DIR env: ${BLASTN_DIR}"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	81 else
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	82 BLASTN_DIR="/home/galaxy/Downloads/ncbi-blast-2.4.0+/bin"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	83 echo "Dev Galaxy set BLASTN_DIR to: ${BLASTN_DIR}"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	84 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	85
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	86 echo "---------------- class identification ----------------"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	87 echo "---------------- class identification ----------------<br />" >> $log
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	88
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	89 python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	90
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	91 echo "---------------- merge_and_filter.r ----------------"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	92 echo "---------------- merge_and_filter.r ----------------<br />" >> $log
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	93
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	94 Rscript $dir/merge_and_filter.r \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	95 $PWD/summary.txt \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	96 $PWD/sequences.txt \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	97 $PWD/mutationanalysis.txt \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	98 $PWD/mutationstats.txt \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	99 $PWD/hotspots.txt \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	100 "$PWD/gapped_aa.txt" \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	101 $outdir/identified_genes.txt \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	102 $outdir/merged.txt \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	103 $outdir/before_unique_filter.txt \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	104 $outdir/unmatched.txt \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	105 $method \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	106 $functionality \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	107 $unique \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	108 ${filter_unique} \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	109 ${filter_unique_count} \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	110 ${class_filter} \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	111 ${empty_region_filter}
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	112
92 cf8ad181628f planemo upload commit 36be3b053802693392f935e6619ba3f2b1704e3c rhpvorderman parents: 91 diff changeset	113 echo "---------------- creating new IMGT zips ----------------"
cf8ad181628f planemo upload commit 36be3b053802693392f935e6619ba3f2b1704e3c rhpvorderman parents: 91 diff changeset	114 echo "---------------- creating new IMGT zips ----------------<br />" >> $log
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	115
95 d63eff357515 planemo upload commit d96a736dcd6da34137f79861fbc6369716c332f1 rhpvorderman parents: 94 diff changeset	116 python $dir/split_imgt_file.py --outdir $outdir "$input" $outdir/merged.txt \
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	117 --prefix "${NEW_IMGT_PREFIX}" \
92 cf8ad181628f planemo upload commit 36be3b053802693392f935e6619ba3f2b1704e3c rhpvorderman parents: 91 diff changeset	118 - IGA IGA1 IGA2 IGG IGG1 IGG2 IGG3 IGG4 IGM IGE
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	119
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	120
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	121 echo "---------------- shm_csr.r ----------------"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	122 echo "---------------- shm_csr.r ----------------<br />" >> $log
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	123
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	124 classes="IGA,IGA1,IGA2,IGG,IGG1,IGG2,IGG3,IGG4,IGM,IGE,unmatched"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	125 echo "R mutation analysis"
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	126 Rscript $dir/shm_csr.r $outdir/merged.txt $classes $outdir ${empty_region_filter}
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	127
92 cf8ad181628f planemo upload commit 36be3b053802693392f935e6619ba3f2b1704e3c rhpvorderman parents: 91 diff changeset	128 echo "---------- Split naive memory IGM ---------"
cf8ad181628f planemo upload commit 36be3b053802693392f935e6619ba3f2b1704e3c rhpvorderman parents: 91 diff changeset	129 echo "---------- Split naive memory IGM ---------<br />" >> $log
cf8ad181628f planemo upload commit 36be3b053802693392f935e6619ba3f2b1704e3c rhpvorderman parents: 91 diff changeset	130
cf8ad181628f planemo upload commit 36be3b053802693392f935e6619ba3f2b1704e3c rhpvorderman parents: 91 diff changeset	131 python $dir/igm_naive_mutations.py $outdir/scatter.txt $outdir/igm_naive_mutations.txt \
cf8ad181628f planemo upload commit 36be3b053802693392f935e6619ba3f2b1704e3c rhpvorderman parents: 91 diff changeset	132 $outdir/igm_naive_memory_mutations.txt
cf8ad181628f planemo upload commit 36be3b053802693392f935e6619ba3f2b1704e3c rhpvorderman parents: 91 diff changeset	133
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	134 python $dir/split_imgt_file.py --outdir $outdir $outdir/${NEW_IMGT_PREFIX}_IGM.txz \
92 cf8ad181628f planemo upload commit 36be3b053802693392f935e6619ba3f2b1704e3c rhpvorderman parents: 91 diff changeset	135 $outdir/igm_naive_mutations.txt \
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	136 --prefix "${NEW_IMGT_PREFIX}_IGM_NAIVE" -
92 cf8ad181628f planemo upload commit 36be3b053802693392f935e6619ba3f2b1704e3c rhpvorderman parents: 91 diff changeset	137
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	138 python $dir/split_imgt_file.py --outdir $outdir $outdir/${NEW_IMGT_PREFIX}_IGM.txz \
92 cf8ad181628f planemo upload commit 36be3b053802693392f935e6619ba3f2b1704e3c rhpvorderman parents: 91 diff changeset	139 $outdir/igm_naive_memory_mutations.txt \
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	140 --prefix "${NEW_IMGT_PREFIX}_IGM_NAIVE_MEMORY" -
92 cf8ad181628f planemo upload commit 36be3b053802693392f935e6619ba3f2b1704e3c rhpvorderman parents: 91 diff changeset	141
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	142 echo "---------------- plot_pdfs.r ----------------"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	143 echo "---------------- plot_pdfs.r ----------------<br />" >> $log
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	144
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	145 echo "Rscript $dir/shm_csr.r $outdir/pdfplots.RData $outdir"
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	146
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	147 Rscript $dir/plot_pdf.r "$outdir/pdfplots.RData" "$outdir"
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	148
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	149 echo "---------------- shm_csr.py ----------------"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	150 echo "---------------- shm_csr.py ----------------<br />" >> $log
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	151
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	152 python $dir/shm_csr.py --input $outdir/merged.txt --genes $classes --empty_region_filter "${empty_region_filter}" --output $outdir/hotspot_analysis.txt
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	153
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	154 echo "---------------- aa_histogram.r ----------------"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	155 echo "---------------- aa_histogram.r ----------------<br />" >> $log
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	156
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	157 Rscript $dir/aa_histogram.r \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	158 $outdir/aa_id_mutations.txt \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	159 $outdir/absent_aa_id.txt "IGA,IGG,IGM,IGE" \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	160 $outdir/
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	161
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	162 if [ -e "$outdir/aa_histogram_.png" ]; then
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	163 mv $outdir/aa_histogram_.png $outdir/aa_histogram.png
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	164 mv $outdir/aa_histogram_.pdf $outdir/aa_histogram.pdf
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	165 mv $outdir/aa_histogram_.txt $outdir/aa_histogram.txt
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	166 mv $outdir/aa_histogram_absent_.txt $outdir/aa_histogram_absent.txt
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	167 mv $outdir/aa_histogram_count_.txt $outdir/aa_histogram_count.txt
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	168 mv $outdir/aa_histogram_sum_.txt $outdir/aa_histogram_sum.txt
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	169 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	170
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	171 genes=(IGA IGA1 IGA2 IGG IGG1 IGG2 IGG3 IGG4 IGM IGE)
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	172
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	173 funcs=(sum mean median)
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	174 funcs=(sum)
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	175
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	176 echo "---------------- sequence_overview.r ----------------"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	177 echo "---------------- sequence_overview.r ----------------<br />" >> $log
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	178
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	179 mkdir $outdir/sequence_overview
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	180
92 cf8ad181628f planemo upload commit 36be3b053802693392f935e6619ba3f2b1704e3c rhpvorderman parents: 91 diff changeset	181 python $dir/sequence_overview.py --before-unique $outdir/before_unique_filter.txt \
cf8ad181628f planemo upload commit 36be3b053802693392f935e6619ba3f2b1704e3c rhpvorderman parents: 91 diff changeset	182 --outdir $outdir/sequence_overview --empty-region-filter ${empty_region_filter}
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	183 Rscript $dir/nt_overview.r \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	184 $outdir/merged.txt \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	185 $outdir/sequence_overview \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	186 $classes \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	187 $outdir/hotspot_analysis_sum.txt \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	188 ${empty_region_filter}
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	189
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	190 echo "<table border='1'>" > $outdir/base_overview.html
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	191
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	192 while IFS=$'\t' read ID class seq A C G T
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	193 do
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	194 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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	195 done < $outdir/sequence_overview/ntoverview.txt
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	196
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	197 echo "<html><center><h1>$title</h1></center>" > $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	198 echo "<meta name='viewport' content='width=device-width, initial-scale=1'>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	199 echo "<script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	200 echo "<script type='text/javascript' src='tabber.js'></script>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	201 echo "<script type='text/javascript' src='script.js'></script>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	202 echo "<link rel='stylesheet' type='text/css' href='style.css'>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	203 echo "<link rel='stylesheet' type='text/css' href='pure-min.css'>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	204
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	205 matched_count="`cat $outdir/merged.txt \| grep -v 'unmatched' \| tail -n +2 \| wc -l`"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	206 unmatched_count="`cat $outdir/unmatched.txt \| tail -n +2 \| wc -l`"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	207 total_count=$((matched_count + unmatched_count))
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	208 perc_count=$((unmatched_count / total_count * 100))
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	209 perc_count=`bc -l <<< "scale=2; ${unmatched_count} / ${total_count} * 100"`
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	210 perc_count=`bc -l <<< "scale=2; (${unmatched_count} / ${total_count} * 100 ) / 1"`
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	211
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	212 echo "<center><h2>Total: ${total_count}</h2></center>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	213 echo "<center><h2>Matched: ${matched_count} Unmatched: ${unmatched_count}</h2></center>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	214 echo "<center><h2>Percentage unmatched: ${perc_count}</h2></center>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	215
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	216 echo "---------------- main tables ----------------"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	217 echo "---------------- main tables ----------------<br />" >> $log
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	218
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	219 echo "<div class='tabber'>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	220 echo "<div class='tabbertab' title='SHM Overview' style='width: 3000px;'>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	221
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	222 for func in ${funcs[@]}
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	223 do
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	224
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	225 echo "---------------- $func table ----------------"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	226 echo "---------------- $func table ----------------<br />" >> $log
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	227
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	228 cat $outdir/mutations_${func}.txt $outdir/shm_overview_tandem_row.txt $outdir/hotspot_analysis_${func}.txt > $outdir/data_${func}.txt
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	229
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	230 echo "---------------- pattern_plots.r ----------------"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	231 echo "---------------- pattern_plots.r ----------------<br />" >> $log
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	232
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	233 Rscript $dir/pattern_plots.r \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	234 $outdir/data_${func}.txt \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	235 $outdir/aid_motives \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	236 $outdir/relative_mutations \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	237 $outdir/absolute_mutations \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	238 $outdir/shm_overview.txt
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	239
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	240 echo "<table class='pure-table pure-table-striped'>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	241 echo "<thead><tr><th>info</th>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	242
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	243 if [ "${class_filter}" != "101_101_all" ] ; then
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	244
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	245 for gene in ${genes[@]}
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	246 do
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	247 tmp=`cat $outdir/${gene}_${func}_n.txt`
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	248 echo "<th><a href='matched_${gene}_${func}.txt'>${gene} (N = $tmp)</a></th>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	249 done
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	250
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	251 tmp=`cat $outdir/all_${func}_n.txt`
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	252 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	253 tmp=`cat $outdir/unmatched_${func}_n.txt`
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	254 echo "<th><a href='unmatched.txt'>unmatched (N = ${unmatched_count})</a></th><tr></thead>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	255
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	256 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	257 do
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	258 if [ "$name" == "FR R/S (ratio)" ] \|\| [ "$name" == "CDR R/S (ratio)" ] \|\| [ "$name" == "Tandems/Expected (ratio)" ] ; then #meh
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	259 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>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	260 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	261 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>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	262 else
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	263 echo "<tr><td>$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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	264 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	265 done < $outdir/data_${func}.txt
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	266
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	267 else
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	268 tmp=`cat $outdir/all_${func}_n.txt`
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	269 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	270
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	271 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	272 do
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	273 if [ "$name" == "FR R/S (ratio)" ] \|\| [ "$name" == "CDR R/S (ratio)" ] ; then #meh
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	274 echo "<tr><td>$name</td><td>${allx}/${ally}</td></tr>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	275 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	276 echo "<tr><td>$name</td><td>${allz}%</td></tr>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	277 else
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	278 echo "<tr><td>$name</td><td>${allx}/${ally} (${allz}%)</td></tr>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	279 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	280 done < $outdir/data_${func}.txt
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	281
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	282 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	283 echo "</table>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	284 #echo "<a href='data_${func}.txt'>Download data</a>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	285 done
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	286
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	287 echo "<a href='aid_motives.pdf'><img src='aid_motives.png' /></a><br />" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	288 echo "<a href='relative_mutations.pdf'><img src='relative_mutations.png' /></a><br />" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	289 echo "<a href='absolute_mutations.pdf'><img src='absolute_mutations.png' /></a><br />" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	290 echo "<br />" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	291 cat $dir/shm_overview.htm >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	292 echo "</div>" >> $output #SHM overview tab end
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	293
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	294 echo "---------------- images ----------------"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	295 echo "---------------- images ----------------<br />" >> $log
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	296
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	297 echo "<div class='tabbertab' title='SHM Frequency' style='width: 3000px;'></a>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	298
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	299 if [ -a $outdir/scatter.png ]
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	300 then
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	301 echo "<a href='scatter.pdf'><img src='scatter.png'/><br />" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	302 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	303 if [ -a $outdir/frequency_ranges.png ]
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	304 then
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	305 echo "<a href='frequency_ranges.pdf'><img src='frequency_ranges.png'/></a><br />" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	306 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	307
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	308 echo "<br />" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	309 cat $dir/shm_frequency.htm >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	310
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	311 echo "</div>" >> $output #SHM frequency tab end
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	312
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	313 echo "<div class='tabbertab' title='Transition tables' style='width: 3000px;'>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	314
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	315 echo "<table border='0'>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	316
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	317 for gene in ${genes[@]}
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	318 do
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	319 echo "<tr>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	320 echo "<td><h1>${gene}</h1></td>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	321
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	322 if [ -e $outdir/transitions_heatmap_${gene}.png ]
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	323 then
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	324 echo "<td><a href='transitions_heatmap_${gene}.pdf'><img src='transitions_heatmap_${gene}.png' /></a></td>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	325 else
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	326 echo "<td></td>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	327 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	328
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	329 if [ -e $outdir/transitions_stacked_${gene}.png ]
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	330 then
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	331 echo "<td><a href='transitions_stacked_${gene}.pdf'><img src='transitions_stacked_${gene}.png' /></a></td>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	332 else
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	333 echo "<td></td>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	334 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	335
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	336 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	337 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	338 first="true"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	339 while IFS=, read from a c g t
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	340 do
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	341 if [ "$first" == "true" ] ; then
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	342 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	343 first="false"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	344 else
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	345 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	346 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	347 done < $outdir/transitions_${gene}_sum.txt
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	348 echo "</table></td>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	349
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	350 echo "</tr>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	351 done
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	352
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	353 echo "<tr>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	354 echo "<td><h1>All</h1></td>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	355 echo "<td><a href='transitions_heatmap_all.pdf'><img src='transitions_heatmap_all.png' /></a></td>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	356 echo "<td><a href='transitions_stacked_all.pdf'><img src='transitions_stacked_all.png' /></a></td>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	357 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	358 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	359 first="true"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	360 while IFS=, read from a c g t
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	361 do
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	362 if [ "$first" == "true" ] ; then
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	363 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	364 first="false"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	365 else
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	366 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	367 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	368 done < $outdir/transitions_all_sum.txt
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	369 echo "</table></td>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	370
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	371 echo "</tr>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	372
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	373 echo "</table>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	374
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	375 echo "<br />" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	376 cat $dir/shm_transition.htm >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	377
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	378 echo "</div>" >> $output #transition tables tab end
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	379
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	380 echo "<div class='tabbertab' title='Antigen Selection'>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	381
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	382 if [ -e $outdir/aa_histogram.png ]
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	383 then
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	384 echo "<a href='aa_histogram.pdf'><img src='aa_histogram.png'/></a><br />" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	385 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	386
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	387 if [ -e $outdir/aa_histogram_IGA.png ]
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	388 then
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	389 echo "<a href='aa_histogram_IGA.pdf'><img src='aa_histogram_IGA.png'/></a><br />" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	390 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	391
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	392 if [ -e $outdir/aa_histogram_IGG.png ]
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	393 then
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	394 echo "<a href='aa_histogram_IGG.pdf'><img src='aa_histogram_IGG.png'/></a><br />" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	395 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	396
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	397 if [ -e $outdir/aa_histogram_IGM.png ]
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	398 then
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	399 echo "<a href='aa_histogram_IGM.pdf'><img src='aa_histogram_IGM.png'/></a><br />" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	400 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	401
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	402 if [ -e $outdir/aa_histogram_IGE.png ]
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	403 then
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	404 echo "<a href='aa_histogram_IGE.pdf'><img src='aa_histogram_IGE.png'/></a><br />" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	405 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	406
92 cf8ad181628f planemo upload commit 36be3b053802693392f935e6619ba3f2b1704e3c rhpvorderman parents: 91 diff changeset	407 count_imgt_lines () {
cf8ad181628f planemo upload commit 36be3b053802693392f935e6619ba3f2b1704e3c rhpvorderman parents: 91 diff changeset	408 tar -xJf $1 1_Summary.txt
cf8ad181628f planemo upload commit 36be3b053802693392f935e6619ba3f2b1704e3c rhpvorderman parents: 91 diff changeset	409 # Use a pipe so wc -l does not display the filename
cf8ad181628f planemo upload commit 36be3b053802693392f935e6619ba3f2b1704e3c rhpvorderman parents: 91 diff changeset	410 wc -l < 1_Summary.txt
cf8ad181628f planemo upload commit 36be3b053802693392f935e6619ba3f2b1704e3c rhpvorderman parents: 91 diff changeset	411 rm 1_Summary.txt
cf8ad181628f planemo upload commit 36be3b053802693392f935e6619ba3f2b1704e3c rhpvorderman parents: 91 diff changeset	412 }
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	413
98 d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf rhpvorderman parents: 96 diff changeset	414 if [[ "$run_baseline" == "yes" ]] ; then
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	415
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	416
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	417
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	418 echo "---------------- baseline ----------------"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	419 echo "---------------- baseline ----------------<br />" >> $log
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	420 tmp="$PWD"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	421
83 729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57" rhpvorderman parents: 81 diff changeset	422 mkdir -p $outdir/baseline
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	423
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	424 echo "<center><h1>BASELINe</h1>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	425 header_substring="Based on CDR1, FR2, CDR2, FR3 (27:27:38:55:65:104:-)"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	426
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	427 baseline_boundaries="27:27:38:55:65:104:-"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	428
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	429 if [[ "${empty_region_filter}" == "leader" ]] ; then
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	430 baseline_boundaries="1:26:38:55:65:104:-"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	431 header_substring="Based on FR1, CDR1, FR2, CDR2, FR3 (1:26:38:55:65:104,-)"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	432 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	433
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	434 echo "<p>${header_substring}</p></center>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	435
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	436 mkdir $outdir/baseline/IGA_IGG_IGM
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	437 if [[ "$(count_imgt_lines $outdir/${NEW_IMGT_PREFIX}.txz)" -gt "1" ]]; then
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	438 cd $outdir/baseline/IGA_IGG_IGM
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	439 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/${NEW_IMGT_PREFIX}.txz "IGA_IGG_IGM_IGE" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt"
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	440 else
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	441 echo "No sequences" > "$outdir/baseline.txt"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	442 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	443
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	444 mkdir $outdir/baseline/IGA
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	445 if [[ "$(count_imgt_lines $outdir/${NEW_IMGT_PREFIX}_IGA.txz)" -gt "1" ]]; then
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	446 cd $outdir/baseline/IGA
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	447 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/${NEW_IMGT_PREFIX}_IGA.txz "IGA" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGA.pdf" "Sequence.ID" "$outdir/baseline_IGA.txt"
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	448 else
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	449 echo "No IGA sequences" > "$outdir/baseline_IGA.txt"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	450 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	451
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	452 mkdir $outdir/baseline/IGG
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	453 if [[ "$(count_imgt_lines $outdir/${NEW_IMGT_PREFIX}_IGG.txz)" -gt "1" ]]; then
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	454 cd $outdir/baseline/IGG
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	455 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/${NEW_IMGT_PREFIX}_IGG.txz "IGG" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGG.pdf" "Sequence.ID" "$outdir/baseline_IGG.txt"
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	456 else
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	457 echo "No IGG sequences" > "$outdir/baseline_IGG.txt"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	458 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	459
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	460 mkdir $outdir/baseline/IGM
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	461 if [[ "$(count_imgt_lines $outdir/${NEW_IMGT_PREFIX}_IGM.txz)" -gt "1" ]]; then
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	462 cd $outdir/baseline/IGM
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	463 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/${NEW_IMGT_PREFIX}_IGM.txz "IGM" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGM.pdf" "Sequence.ID" "$outdir/baseline_IGM.txt"
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	464 else
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	465 echo "No IGM sequences" > "$outdir/baseline_IGM.txt"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	466 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	467
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	468 mkdir $outdir/baseline/IGE
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	469 if [[ "$(count_imgt_lines $outdir/${NEW_IMGT_PREFIX}_IGE.txz)" -gt "1" ]]; then
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	470 cd $outdir/baseline/IGE
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	471 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/${NEW_IMGT_PREFIX}_IGE.txz "IGE" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGE.pdf" "Sequence.ID" "$outdir/baseline_IGE.txt"
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	472 else
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	473 echo "No IGE sequences" > "$outdir/baseline_IGE.txt"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	474 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	475
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	476 cd $tmp
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	477
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	478 echo "Cleaning up *.RData files"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	479 find $outdir/baseline -name "*.RData" -type f -delete
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	480
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	481 if [ -e $outdir/baseline.pdf ]
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	482 then
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	483 echo "<embed src='baseline.pdf' width='700px' height='1000px'>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	484 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	485
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	486 if [ -e $outdir/baseline_IGA.pdf ]
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	487 then
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	488 echo "<embed src='baseline_IGA.pdf' width='700px' height='1000px'>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	489 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	490
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	491 if [ -e $outdir/baseline_IGG.pdf ]
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	492 then
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	493 echo "<embed src='baseline_IGG.pdf' width='700px' height='1000px'>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	494 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	495
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	496 if [ -e $outdir/baseline_IGM.pdf ]
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	497 then
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	498 echo "<embed src='baseline_IGM.pdf' width='700px' height='1000px'>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	499 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	500
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	501 if [ -e $outdir/baseline_IGE.pdf ]
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	502 then
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	503 echo "<embed src='baseline_IGE.pdf' width='700px' height='1000px'>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	504 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	505 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	506
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	507 echo "<br />" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	508 cat $dir/shm_selection.htm >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	509
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	510 echo "</div>" >> $output #antigen selection tab end
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	511
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	512 echo "<div class='tabbertab' title='CSR'>" >> $output #CSR tab
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	513
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	514 if [ -e $outdir/IGA.png ]
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	515 then
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	516 echo "<a href='IGA.pdf'><img src='IGA.png'/></a><br />" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	517 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	518 if [ -e $outdir/IGG.png ]
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	519 then
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	520 echo "<a href='IGG.pdf'><img src='IGG.png'/></a><br />" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	521 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	522
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	523 echo "<br />" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	524 cat $dir/shm_csr.htm >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	525
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	526 echo "</div>" >> $output #CSR tab end
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	527
98 d714f5ea83d7 planemo upload commit 1a01065a084a817382872154f779b94090a35ebf rhpvorderman parents: 96 diff changeset	528 if [[ "$run_changeo" == "yes" ]] ; then
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	529
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	530 echo "---------------- change-o MakeDB ----------------"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	531
83 729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57" rhpvorderman parents: 81 diff changeset	532 mkdir -p $outdir/change_o
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	533
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	534 tmp="$PWD"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	535
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	536 cd $outdir/change_o
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	537
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	538 bash $dir/change_o/makedb.sh $outdir/${NEW_IMGT_PREFIX}.txz false false false $outdir/change_o/change-o-db.txt
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	539 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
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	540 Rscript $dir/change_o/select_first_in_clone.r \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	541 $outdir/change_o/change-o-db-defined_clones.txt \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	542 $outdir/change_o/change-o-db-defined_first_clones.txt
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	543
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	544 python $dir/split_imgt_file.py --outdir $outdir --prefix ${NEW_IMGT_PREFIX}_first_seq_of_clone \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	545 $outdir/${NEW_IMGT_PREFIX}.txz $outdir/change_o/change-o-db-defined_first_clones.txt \
92 cf8ad181628f planemo upload commit 36be3b053802693392f935e6619ba3f2b1704e3c rhpvorderman parents: 91 diff changeset	546 "-"
cf8ad181628f planemo upload commit 36be3b053802693392f935e6619ba3f2b1704e3c rhpvorderman parents: 91 diff changeset	547
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	548 Rscript $dir/merge.r \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	549 $outdir/change_o/change-o-db-defined_clones.txt \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	550 $outdir/merged.txt \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	551 "all" "Sequence.ID,best_match" "SEQUENCE_ID" "Sequence.ID" \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	552 $outdir/change_o/change-o-db-defined_clones.txt
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	553 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' $outdir/change_o/change-o-db-defined_clones.txt"
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	554
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	555 if [[ "$(count_imgt_lines $outdir/${NEW_IMGT_PREFIX}_IGA.txz)" -gt "1" ]]; then
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	556 bash $dir/change_o/makedb.sh $outdir/${NEW_IMGT_PREFIX}_IGA.txz false false false $outdir/change_o/change-o-db-IGA.txt
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	557 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
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	558 Rscript $dir/change_o/select_first_in_clone.r \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	559 $outdir/change_o/change-o-db-defined_clones-IGA.txt \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	560 $outdir/change_o/change-o-db-defined_first_clones-IGA.txt
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	561
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	562 python $dir/split_imgt_file.py --outdir $outdir --prefix ${NEW_IMGT_PREFIX}_IGA_first_seq_of_clone \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	563 $outdir/${NEW_IMGT_PREFIX}.txz $outdir/change_o/change-o-db-defined_first_clones-IGA.txt \
92 cf8ad181628f planemo upload commit 36be3b053802693392f935e6619ba3f2b1704e3c rhpvorderman parents: 91 diff changeset	564 "-"
cf8ad181628f planemo upload commit 36be3b053802693392f935e6619ba3f2b1704e3c rhpvorderman parents: 91 diff changeset	565
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	566 else
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	567 echo "No IGA sequences" > "$outdir/change_o/change-o-db-defined_clones-IGA.txt"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	568 echo "No IGA sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGA.txt"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	569 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	570
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	571 if [[ "$(count_imgt_lines $outdir/${NEW_IMGT_PREFIX}_IGG.txz)" -gt "1" ]]; then
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	572 bash $dir/change_o/makedb.sh $outdir/${NEW_IMGT_PREFIX}_IGG.txz false false false $outdir/change_o/change-o-db-IGG.txt
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	573 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
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	574 Rscript $dir/change_o/select_first_in_clone.r \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	575 $outdir/change_o/change-o-db-defined_clones-IGG.txt \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	576 $outdir/change_o/change-o-db-defined_first_clones-IGG.txt
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	577
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	578 python $dir/split_imgt_file.py --outdir $outdir --prefix ${NEW_IMGT_PREFIX}_IGG_first_seq_of_clone \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	579 $outdir/${NEW_IMGT_PREFIX}.txz $outdir/change_o/change-o-db-defined_first_clones-IGG.txt \
92 cf8ad181628f planemo upload commit 36be3b053802693392f935e6619ba3f2b1704e3c rhpvorderman parents: 91 diff changeset	580 "-"
cf8ad181628f planemo upload commit 36be3b053802693392f935e6619ba3f2b1704e3c rhpvorderman parents: 91 diff changeset	581
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	582 else
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	583 echo "No IGG sequences" > "$outdir/change_o/change-o-db-defined_clones-IGG.txt"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	584 echo "No IGG sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGG.txt"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	585 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	586
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	587 if [[ "$(count_imgt_lines $outdir/${NEW_IMGT_PREFIX}_IGM.txz)" -gt "1" ]]; then
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	588 bash $dir/change_o/makedb.sh $outdir/${NEW_IMGT_PREFIX}_IGM.txz false false false $outdir/change_o/change-o-db-IGM.txt
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	589 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
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	590 Rscript $dir/change_o/select_first_in_clone.r \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	591 $outdir/change_o/change-o-db-defined_clones-IGM.txt \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	592 $outdir/change_o/change-o-db-defined_first_clones-IGM.txt
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	593
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	594 python $dir/split_imgt_file.py --outdir $outdir --prefix ${NEW_IMGT_PREFIX}_IGM_first_seq_of_clone \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	595 $outdir/${NEW_IMGT_PREFIX}.txz $outdir/change_o/change-o-db-defined_first_clones-IGM.txt \
92 cf8ad181628f planemo upload commit 36be3b053802693392f935e6619ba3f2b1704e3c rhpvorderman parents: 91 diff changeset	596 "-"
cf8ad181628f planemo upload commit 36be3b053802693392f935e6619ba3f2b1704e3c rhpvorderman parents: 91 diff changeset	597
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	598 else
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	599 echo "No IGM sequences" > "$outdir/change_o/change-o-db-defined_clones-IGM.txt"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	600 echo "No IGM sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGM.txt"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	601 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	602
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	603 if [[ "$(count_imgt_lines $outdir/${NEW_IMGT_PREFIX}_IGE.txz)" -gt "1" ]]; then
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	604 bash $dir/change_o/makedb.sh $outdir/${NEW_IMGT_PREFIX}_IGE.txz false false false $outdir/change_o/change-o-db-IGE.txt
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	605 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
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	606 Rscript $dir/change_o/select_first_in_clone.r \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	607 $outdir/change_o/change-o-db-defined_clones-IGE.txt \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	608 $outdir/change_o/change-o-db-defined_first_clones-IGE.txt
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	609
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	610 python $dir/split_imgt_file.py --outdir $outdir --prefix ${NEW_IMGT_PREFIX}_IGE_first_seq_of_clone \
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	611 $outdir/${NEW_IMGT_PREFIX}.txz $outdir/change_o/change-o-db-defined_first_clones-IGE.txt \
92 cf8ad181628f planemo upload commit 36be3b053802693392f935e6619ba3f2b1704e3c rhpvorderman parents: 91 diff changeset	612 "-"
cf8ad181628f planemo upload commit 36be3b053802693392f935e6619ba3f2b1704e3c rhpvorderman parents: 91 diff changeset	613
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	614 else
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	615 echo "No IGE sequences" > "$outdir/change_o/change-o-db-defined_clones-IGE.txt"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	616 echo "No IGE sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGE.txt"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	617 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	618
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	619 cd "$tmp"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	620
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	621 echo "<div class='tabbertab' title='Clonal Relation' style='width: 7000px;'>" >> $output #clonality tab
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	622
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	623 function clonality_table {
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	624 local infile=$1
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	625 local outfile=$2
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	626
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	627 echo "<table class='pure-table pure-table-striped'>" >> $outfile
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	628 echo "<thead><tr><th>Clone size</th><th>Nr of clones</th><th>Nr of sequences</th></tr></thead>" >> $outfile
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	629
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	630 first='true'
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	631
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	632 while read size clones seqs
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	633 do
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	634 if [[ "$first" == "true" ]]; then
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	635 first="false"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	636 continue
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	637 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	638 echo "<tr><td>$size</td><td>$clones</td><td>$seqs</td></tr>" >> $outfile
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	639 done < $infile
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	640
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	641 echo "</table>" >> $outfile
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	642 }
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	643 echo "<div class='tabber'>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	644
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	645 echo "<div class='tabbertab' title='All'>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	646 clonality_table $outdir/change_o/change-o-defined_clones-summary.txt $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	647 echo "</div>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	648
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	649 echo "<div class='tabbertab' title='IGA'>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	650 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGA.txt $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	651 echo "</div>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	652
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	653 echo "<div class='tabbertab' title='IGG'>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	654 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGG.txt $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	655 echo "</div>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	656
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	657 echo "<div class='tabbertab' title='IGM'>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	658 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	659 echo "</div>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	660
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	661 echo "<div class='tabbertab' title='IGE'>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	662 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	663 echo "</div>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	664
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	665 echo "<div class='tabbertab' title='Overlap' style='width: 7000px;'>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	666 cat "$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/..."
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	667 echo "</div>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	668
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	669 echo "</div>" >> $output #clonality tabber end
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	670
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	671 echo "<br />" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	672 cat $dir/shm_clonality.htm >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	673
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	674 echo "</div>" >> $output #clonality tab end
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	675
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	676 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	677
91 f387cc1580c6 "planemo upload commit 6f5bdb4189fcc9028c90365d8edf8d1d7c1cf690" rhpvorderman parents: 90 diff changeset	678 # Use python's zipfile utility to prevent needing another dependency in the
f387cc1580c6 "planemo upload commit 6f5bdb4189fcc9028c90365d8edf8d1d7c1cf690" rhpvorderman parents: 90 diff changeset	679 # container.
f387cc1580c6 "planemo upload commit 6f5bdb4189fcc9028c90365d8edf8d1d7c1cf690" rhpvorderman parents: 90 diff changeset	680 current_dir=$(pwd)
f387cc1580c6 "planemo upload commit 6f5bdb4189fcc9028c90365d8edf8d1d7c1cf690" rhpvorderman parents: 90 diff changeset	681 cd $outdir
f387cc1580c6 "planemo upload commit 6f5bdb4189fcc9028c90365d8edf8d1d7c1cf690" rhpvorderman parents: 90 diff changeset	682 python -m zipfile -c all_outputs.zip \
f387cc1580c6 "planemo upload commit 6f5bdb4189fcc9028c90365d8edf8d1d7c1cf690" rhpvorderman parents: 90 diff changeset	683 merged.txt filtered.txt unmatched.txt shm_overview.txt motif_per_seq.txt \
f387cc1580c6 "planemo upload commit 6f5bdb4189fcc9028c90365d8edf8d1d7c1cf690" rhpvorderman parents: 90 diff changeset	684 mutation_by_id.txt base_overview.html aid_motives.txt relative_mutations.txt \
f387cc1580c6 "planemo upload commit 6f5bdb4189fcc9028c90365d8edf8d1d7c1cf690" rhpvorderman parents: 90 diff changeset	685 absolute_mutations.txt tandems_by_id.txt scatter.txt frequency_ranges_class.txt \
f387cc1580c6 "planemo upload commit 6f5bdb4189fcc9028c90365d8edf8d1d7c1cf690" rhpvorderman parents: 90 diff changeset	686 frequency_ranges_subclasses.txt transitions_all_sum.txt transitions_IGA_sum.txt \
f387cc1580c6 "planemo upload commit 6f5bdb4189fcc9028c90365d8edf8d1d7c1cf690" rhpvorderman parents: 90 diff changeset	687 transitions_IGA1_sum.txt transitions_IGA2_sum.txt transitions_IGG_sum.txt \
f387cc1580c6 "planemo upload commit 6f5bdb4189fcc9028c90365d8edf8d1d7c1cf690" rhpvorderman parents: 90 diff changeset	688 transitions_IGG1_sum.txt transitions_IGG2_sum.txt transitions_IGG3_sum.txt \
f387cc1580c6 "planemo upload commit 6f5bdb4189fcc9028c90365d8edf8d1d7c1cf690" rhpvorderman parents: 90 diff changeset	689 transitions_IGG4_sum.txt transitions_IGM_sum.txt transitions_IGE_sum.txt \
f387cc1580c6 "planemo upload commit 6f5bdb4189fcc9028c90365d8edf8d1d7c1cf690" rhpvorderman parents: 90 diff changeset	690 aa_id_mutations.txt absent_aa_id.txt aa_histogram_sum.txt \
f387cc1580c6 "planemo upload commit 6f5bdb4189fcc9028c90365d8edf8d1d7c1cf690" rhpvorderman parents: 90 diff changeset	691 aa_histogram_sum_IGA.txt aa_histogram_sum_IGG.txt aa_histogram_sum_IGM.txt \
f387cc1580c6 "planemo upload commit 6f5bdb4189fcc9028c90365d8edf8d1d7c1cf690" rhpvorderman parents: 90 diff changeset	692 aa_histogram_sum_IGE.txt baseline.txt baseline_IGA.pdf baseline_IGA.txt \
f387cc1580c6 "planemo upload commit 6f5bdb4189fcc9028c90365d8edf8d1d7c1cf690" rhpvorderman parents: 90 diff changeset	693 baseline_IGG.pdf baseline_IGG.txt baseline_IGM.pdf baseline_IGM.txt \
f387cc1580c6 "planemo upload commit 6f5bdb4189fcc9028c90365d8edf8d1d7c1cf690" rhpvorderman parents: 90 diff changeset	694 baseline_IGE.pdf baseline_IGE.txt IGA_pie.txt IGG_pie.txt \
f387cc1580c6 "planemo upload commit 6f5bdb4189fcc9028c90365d8edf8d1d7c1cf690" rhpvorderman parents: 90 diff changeset	695 sequence_overview/index.html change_o/change-o-db-defined_clones*.txt \
f387cc1580c6 "planemo upload commit 6f5bdb4189fcc9028c90365d8edf8d1d7c1cf690" rhpvorderman parents: 90 diff changeset	696 *.txz
f387cc1580c6 "planemo upload commit 6f5bdb4189fcc9028c90365d8edf8d1d7c1cf690" rhpvorderman parents: 90 diff changeset	697
f387cc1580c6 "planemo upload commit 6f5bdb4189fcc9028c90365d8edf8d1d7c1cf690" rhpvorderman parents: 90 diff changeset	698 cd $current_dir
f387cc1580c6 "planemo upload commit 6f5bdb4189fcc9028c90365d8edf8d1d7c1cf690" rhpvorderman parents: 90 diff changeset	699
f387cc1580c6 "planemo upload commit 6f5bdb4189fcc9028c90365d8edf8d1d7c1cf690" rhpvorderman parents: 90 diff changeset	700
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	701 echo "<div class='tabbertab' title='Downloads'>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	702
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	703 echo "<table class='pure-table pure-table-striped'>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	704 echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output
91 f387cc1580c6 "planemo upload commit 6f5bdb4189fcc9028c90365d8edf8d1d7c1cf690" rhpvorderman parents: 90 diff changeset	705 echo "<tr><td>All output files in a zip file</td><td><a href='all_outputs.zip' download='all_outputs.zip' >Download</a></td></tr>" >> $output
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	706 echo "<tr><td>The complete dataset</td><td><a href='merged.txt' download='merged.txt' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	707 echo "<tr><td>The filtered dataset</td><td><a href='filtered.txt' download='filtered.txt' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	708 echo "<tr><td>The alignment info on the unmatched sequences</td><td><a href='unmatched.txt' download='unmatched.txt' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	709
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	710 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Overview</td></tr>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	711 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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	712 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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	713 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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	714 echo "<tr><td>Base count for every sequence</td><td><a href='base_overview.html'>View</a></td></tr>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	715 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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	716 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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	717 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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	718 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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	719
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	720 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Frequency</td></tr>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	721 echo "<tr><td>The data generate the frequency scatter plot</td><td><a href='scatter.txt' download='scatter.txt' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	722 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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	723 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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	724
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	725 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Transition Tables</td></tr>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	726 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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	727 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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	728 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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	729 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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	730 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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	731 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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	732 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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	733 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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	734 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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	735 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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	736 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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	737
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	738 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Antigen Selection</td></tr>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	739 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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	740 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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	741
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	742 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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	743 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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	744 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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	745 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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	746 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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	747
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	748 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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	749 echo "<tr><td>Baseline data</td><td><a href='baseline.txt' download='baseline.txt' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	750 echo "<tr><td>Baseline IGA PDF</td><td><a href='baseline_IGA.pdf' download='baseline_IGA.pdf' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	751 echo "<tr><td>Baseline IGA data</td><td><a href='baseline_IGA.txt' download='baseline_IGA.txt' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	752 echo "<tr><td>Baseline IGG PDF</td><td><a href='baseline_IGG.pdf' download='baseline_IGG.pdf' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	753 echo "<tr><td>Baseline IGG data</td><td><a href='baseline_IGG.txt' download='baseline_IGG.txt' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	754 echo "<tr><td>Baseline IGM PDF</td><td><a href='baseline_IGM.pdf' download='baseline_IGM.pdf' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	755 echo "<tr><td>Baseline IGM data</td><td><a href='baseline_IGM.txt' download='baseline_IGM.txt' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	756 echo "<tr><td>Baseline IGE PDF</td><td><a href='baseline_IGE.pdf' download='baseline_IGE.pdf' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	757 echo "<tr><td>Baseline IGE data</td><td><a href='baseline_IGE.txt' download='baseline_IGE.txt' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	758
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	759 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>CSR</td></tr>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	760 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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	761 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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	762
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	763
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	764 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Clonal Relation</td></tr>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	765 echo "<tr><td>Sequence overlap between subclasses</td><td><a href='sequence_overview/index.html'>View</a></td></tr>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	766 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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	767 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>" >> $output
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	768 echo "<tr><td>An IMGT archive with just just the first sequence of a clone</td><td><a href='${NEW_IMGT_PREFIX}_first_seq_of_clone.txz' download='${NEW_IMGT_PREFIX}_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	769
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	770 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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	771 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>" >> $output
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	772 echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGA)</td><td><a href='${NEW_IMGT_PREFIX}_IGA_first_seq_of_clone.txz' download='${NEW_IMGT_PREFIX}_IGA_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	773
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	774 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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	775 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>" >> $output
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	776 echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGG)</td><td><a href='${NEW_IMGT_PREFIX}_IGG_first_seq_of_clone.txz' download='${NEW_IMGT_PREFIX}_IGG_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	777
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	778 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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	779 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>" >> $output
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	780 echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGM)</td><td><a href='${NEW_IMGT_PREFIX}_IGM_first_seq_of_clone.txz' download='${NEW_IMGT_PREFIX}_IGM_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	781
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	782 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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	783 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>" >> $output
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	784 echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGE)</td><td><a href='${NEW_IMGT_PREFIX}_IGE_first_seq_of_clone.txz' download='${NEW_IMGT_PREFIX}_IGE_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	785
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	786 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Filtered IMGT output files</td></tr>" >> $output
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	787 echo "<tr><td>An IMGT archive with just the matched and filtered sequences</td><td><a href='${NEW_IMGT_PREFIX}.txz' download='${NEW_IMGT_PREFIX}.txz' >Download</a></td></tr>" >> $output
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	788 echo "<tr><td>An IMGT archive with just the matched and filtered IGA sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGA.txz' download='${NEW_IMGT_PREFIX}_IGA.txz' >Download</a></td></tr>" >> $output
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	789 echo "<tr><td>An IMGT archive with just the matched and filtered IGA1 sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGA1.txz' download='${NEW_IMGT_PREFIX}_IGA1.txz' >Download</a></td></tr>" >> $output
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	790 echo "<tr><td>An IMGT archive with just the matched and filtered IGA2 sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGA2.txz' download='${NEW_IMGT_PREFIX}_IGA2.txz' >Download</a></td></tr>" >> $output
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	791 echo "<tr><td>An IMGT archive with just the matched and filtered IGG sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGG.txz' download='${NEW_IMGT_PREFIX}_IGG.txz' >Download</a></td></tr>" >> $output
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	792 echo "<tr><td>An IMGT archive with just the matched and filtered IGG1 sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGG1.txz' download='${NEW_IMGT_PREFIX}_IGG1.txz' >Download</a></td></tr>" >> $output
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	793 echo "<tr><td>An IMGT archive with just the matched and filtered IGG2 sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGG2.txz' download='${NEW_IMGT_PREFIX}_IGG2.txz' >Download</a></td></tr>" >> $output
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	794 echo "<tr><td>An IMGT archive with just the matched and filtered IGG3 sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGG3.txz' download='${NEW_IMGT_PREFIX}_IGG3.txz' >Download</a></td></tr>" >> $output
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	795 echo "<tr><td>An IMGT archive with just the matched and filtered IGG4 sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGG4.txz' download='${NEW_IMGT_PREFIX}_IGG4.txz' >Download</a></td></tr>" >> $output
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	796 echo "<tr><td>An IMGT archive with just the matched and filtered IGM sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGM.txz' download='${NEW_IMGT_PREFIX}_IGM.txz' >Download</a></td></tr>" >> $output
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	797 echo "<tr><td>An IMGT archive with just the matched and filtered IGE sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGE.txz' download='${NEW_IMGT_PREFIX}_IGE.txz' >Download</a></td></tr>" >> $output
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	798 echo "<tr><td>An IMGT archive with just the matched and filtered naive IGM sequences (mutations below 2%)</td><td><a href='${NEW_IMGT_PREFIX}_IGM_NAIVE.txz' download='${NEW_IMGT_PREFIX}_IGM_NAIVE.txz' >Download</a></td></tr>" >> $output
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	799 echo "<tr><td>An IMGT archive with just the matched and filtered naive memory IGM sequences (mutations 2% or higher)</td><td><a href='${NEW_IMGT_PREFIX}_IGM_NAIVE_MEMORY.txz' download='${NEW_IMGT_PREFIX}_IGM_NAIVE_MEMORY.txz' >Download</a></td></tr>" >> $output
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	800 echo "</table>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	801
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	802 echo "<br />" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	803 cat $dir/shm_downloads.htm >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	804
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	805 echo "</div>" >> $output #downloads tab end
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	806
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	807 echo "</div>" >> $output #tabs end
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	808
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	809 echo "</html>" >> $output
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	810
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	811
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	812 echo "---------------- naive_output.r ----------------"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	813 echo "---------------- naive_output.r ----------------<br />" >> $log
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	814
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	815 if [[ "$naive_output" == "yes" ]]
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	816 then
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	817 echo "output naive output"
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	818 if [[ "${class_filter}" == "101_101_all" ]]
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	819 then
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	820 echo "copy ${NEW_IMGT_PREFIX}.txz to ${naive_output_all}"
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	821 cp $outdir/${NEW_IMGT_PREFIX}.txz ${naive_output_all}
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	822 else
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	823 echo "copy for classes"
93 8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	824 cp $outdir/${NEW_IMGT_PREFIX}_IGA.txz ${naive_output_ca}
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	825 cp $outdir/${NEW_IMGT_PREFIX}_IGG.txz ${naive_output_cg}
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	826 cp $outdir/${NEW_IMGT_PREFIX}_IGM.txz ${naive_output_cm}
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c rhpvorderman parents: 92 diff changeset	827 cp $outdir/${NEW_IMGT_PREFIX}_IGE.txz ${naive_output_ce}
94 84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140" rhpvorderman parents: 93 diff changeset	828 cp $outdir/${NEW_IMGT_PREFIX}_IGM_NAIVE.txz ${naive_output_igm_naive}
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140" rhpvorderman parents: 93 diff changeset	829 cp $outdir/${NEW_IMGT_PREFIX}_IGM_NAIVE_MEMORY.txz ${naive_output_igm_naive_memory}
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	830 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	831 fi
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	832
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	833 echo "</table>" >> $outdir/base_overview.html
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	834
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	835 mv $log $outdir/log.html
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	836
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	837 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
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	838 echo "<table border = 1>" >> $log
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	839 echo "<thead><tr><th>Info</th><th>Sequences</th><th>Percentage</th></tr></thead>" >> $log
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	840 tIFS="$TMP"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	841 IFS=$'\t'
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	842 while read step seq perc
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	843 do
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	844 echo "<tr>" >> $log
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	845 echo "<td>$step</td>" >> $log
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	846 echo "<td>$seq</td>" >> $log
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	847 echo "<td>${perc}%</td>" >> $log
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	848 echo "</tr>" >> $log
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	849 done < $outdir/filtering_steps.txt
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	850 echo "</table>" >> $log
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	851 echo "<br />" >> $log
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	852 cat $dir/shm_first.htm >> $log
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	853 echo "</center></html>" >> $log
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	854
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	855 IFS="$tIFS"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	856
84 4db34e32dd47 "planemo upload commit 78ace939ed7437b8b360588032449a99aad949eb" rhpvorderman parents: 83 diff changeset	857 echo "---------------- remove_files----------------"
4db34e32dd47 "planemo upload commit 78ace939ed7437b8b360588032449a99aad949eb" rhpvorderman parents: 83 diff changeset	858 echo "---------------- remove_files----------------<br />" >> $log
4db34e32dd47 "planemo upload commit 78ace939ed7437b8b360588032449a99aad949eb" rhpvorderman parents: 83 diff changeset	859
90 6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26" rhpvorderman parents: 89 diff changeset	860 rm -r -v -f $outdir/baseline
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26" rhpvorderman parents: 89 diff changeset	861 rm -r -v -f $PWD/files
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26" rhpvorderman parents: 89 diff changeset	862 rm -v $PWD/aa.txt
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26" rhpvorderman parents: 89 diff changeset	863 rm -v $PWD/aa_change_stats.txt
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26" rhpvorderman parents: 89 diff changeset	864 rm -v $PWD/gapped_aa.txt
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26" rhpvorderman parents: 89 diff changeset	865 rm -v $PWD/gapped_nt.txt
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26" rhpvorderman parents: 89 diff changeset	866 rm -v $PWD/hotspots.txt
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26" rhpvorderman parents: 89 diff changeset	867 rm -v $PWD/junction.txt
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26" rhpvorderman parents: 89 diff changeset	868 rm -v $PWD/mutationanalysis.txt
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26" rhpvorderman parents: 89 diff changeset	869 rm -v $PWD/mutationstats.txt
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26" rhpvorderman parents: 89 diff changeset	870 rm -v $PWD/sequences.txt
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26" rhpvorderman parents: 89 diff changeset	871 rm -v $PWD/summary.txt
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26" rhpvorderman parents: 89 diff changeset	872 rm -v $PWD/Rplots.pdf
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26" rhpvorderman parents: 89 diff changeset	873
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26" rhpvorderman parents: 89 diff changeset	874 filename="$dir/remove_files.txt"
84 4db34e32dd47 "planemo upload commit 78ace939ed7437b8b360588032449a99aad949eb" rhpvorderman parents: 83 diff changeset	875
4db34e32dd47 "planemo upload commit 78ace939ed7437b8b360588032449a99aad949eb" rhpvorderman parents: 83 diff changeset	876 while read file; do
90 6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26" rhpvorderman parents: 89 diff changeset	877 rm -v -f $outdir/$file
84 4db34e32dd47 "planemo upload commit 78ace939ed7437b8b360588032449a99aad949eb" rhpvorderman parents: 83 diff changeset	878 done < "$filename"
4db34e32dd47 "planemo upload commit 78ace939ed7437b8b360588032449a99aad949eb" rhpvorderman parents: 83 diff changeset	879
81 b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	880 echo "---------------- Done! ----------------"
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	881 echo "---------------- Done! ----------------<br />" >> $outdir/log.html
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	882
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	883
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	884
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	885
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	886
b6f9a640e098 Uploaded davidvanzessen parents: diff changeset	887

Mercurial > repos > davidvanzessen > shm_csr

annotate wrapper.sh @ 98:d714f5ea83d7 draft default tip