shm_csr: wrapper.sh annotate

annotate wrapper.sh @ 94:84e9e5c8c101 draft

"planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"

author	rhpvorderman
date	Fri, 24 Mar 2023 16:58:28 +0000
parents	8fcf31272f6e
children	d63eff357515

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

Mercurial > repos > davidvanzessen > shm_csr

annotate wrapper.sh @ 94:84e9e5c8c101 draft