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0
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1 #!/bin/bash
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2 #set -e
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3 dir="$(cd "$(dirname "$0")" && pwd)"
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4 input=$1
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5 method=$2
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6 log=$3 #becomes the main html page at the end
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7 outdir=$4
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8 output="$outdir/index.html" #copied to $log location at the end
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9 title=$5
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10 include_fr1=$6
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11 functionality=$7
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12 unique=$8
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28
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13 naive_output=$9
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14 naive_output_ca=${10}
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15 naive_output_cg=${11}
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16 naive_output_cm=${12}
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17 naive_output_ce=${13}
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18 naive_output_all=${14}
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19 filter_unique=${15}
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20 class_filter=${16}
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21 empty_region_filter=${17}
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22 fast=${18}
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0
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23 mkdir $outdir
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24
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25 tar -xzf $dir/style.tar.gz -C $outdir
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26
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27 echo "---------------- read parameters ----------------"
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28 echo "---------------- read parameters ----------------<br />" > $log
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29
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30 echo "unpacking IMGT file"
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31
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32 type="`file $input`"
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33 if [[ "$type" == *"Zip archive"* ]] ; then
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34 echo "Zip archive"
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35 echo "unzip $input -d $PWD/files/"
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36 unzip $input -d $PWD/files/
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37 elif [[ "$type" == *"XZ compressed data"* ]] ; then
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38 echo "ZX archive"
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39 echo "tar -xJf $input -C $PWD/files/"
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40 mkdir -p $PWD/files/$title
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41 tar -xJf $input -C $PWD/files/$title
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42 fi
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43
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44 cat `find $PWD/files/ -name "1_*"` > $PWD/summary.txt
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45 cat `find $PWD/files/ -name "3_*"` > $PWD/sequences.txt
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46 cat `find $PWD/files/ -name "5_*"` > $PWD/aa.txt
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47 cat `find $PWD/files/ -name "6_*"` > $PWD/junction.txt
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48 cat `find $PWD/files/ -name "7_*"` > $PWD/mutationanalysis.txt
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49 cat `find $PWD/files/ -name "8_*"` > $PWD/mutationstats.txt
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50 cat `find $PWD/files/ -name "10_*"` > $PWD/hotspots.txt
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51
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52 if [[ ${#BLASTN_DIR} -ge 5 ]] ; then
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53 echo "On server, using BLASTN_DIR env: ${BLASTN_DIR}"
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54 else
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55 BLASTN_DIR="/home/galaxy/Downloads/ncbi-blast-2.4.0+/bin"
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56 echo "Dev Galaxy set BLASTN_DIR to: ${BLASTN_DIR}"
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57 fi
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58
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59 echo "---------------- class identification ----------------"
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60 echo "---------------- class identification ----------------<br />" >> $log
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61
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62 python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt
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63
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64 echo "---------------- merge_and_filter.r ----------------"
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65 echo "---------------- merge_and_filter.r ----------------<br />" >> $log
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66
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14
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67 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $PWD/aa.txt $outdir/identified_genes.txt $outdir/merged.txt $outdir/before_unique_filter.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${class_filter} ${empty_region_filter} 2>&1
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0
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68
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5
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69 if [[ "$fast" == "no" ]] ; then
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0
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70
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5
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71 echo "---------------- creating new IMGT zips ----------------"
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72 echo "---------------- creating new IMGT zips ----------------<br />" >> $log
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73
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74 mkdir $outdir/new_IMGT
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75
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5
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76 cat `find $PWD/files/ -name "1_*"` > "$outdir/new_IMGT/1_Summary.txt"
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77 cat `find $PWD/files/ -name "2_*"` > "$outdir/new_IMGT/2_IMGT-gapped-nt-sequences.txt"
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78 cat `find $PWD/files/ -name "3_*"` > "$outdir/new_IMGT/3_Nt-sequences.txt"
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79 cat `find $PWD/files/ -name "4_*"` > "$outdir/new_IMGT/4_IMGT-gapped-AA-sequences.txt"
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80 cat `find $PWD/files/ -name "5_*"` > "$outdir/new_IMGT/5_AA-sequences.txt"
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81 cat `find $PWD/files/ -name "6_*"` > "$outdir/new_IMGT/6_Junction.txt"
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82 cat `find $PWD/files/ -name "7_*"` > "$outdir/new_IMGT/7_V-REGION-mutation-and-AA-change-table.txt"
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83 cat `find $PWD/files/ -name "8_*"` > "$outdir/new_IMGT/8_V-REGION-nt-mutation-statistics.txt"
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84 cat `find $PWD/files/ -name "9_*"` > "$outdir/new_IMGT/9_V-REGION-AA-change-statistics.txt"
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85 cat `find $PWD/files/ -name "10_*"` > "$outdir/new_IMGT/10_V-REGION-mutation-hotspots.txt"
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0
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86
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5
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87 mkdir $outdir/new_IMGT_IGA
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88 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA
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89
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5
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90 mkdir $outdir/new_IMGT_IGA1
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91 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA1
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0
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92
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5
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93 mkdir $outdir/new_IMGT_IGA2
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94 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA2
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0
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95
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5
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96 mkdir $outdir/new_IMGT_IGG
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97 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG
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0
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98
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5
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99 mkdir $outdir/new_IMGT_IGG1
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100 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG1
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0
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101
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5
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102 mkdir $outdir/new_IMGT_IGG2
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103 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG2
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0
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104
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5
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105 mkdir $outdir/new_IMGT_IGG3
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106 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG3
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0
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107
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5
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108 mkdir $outdir/new_IMGT_IGG4
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109 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG4
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110
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111 mkdir $outdir/new_IMGT_IGM
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112 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGM
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0
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113
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5
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114 mkdir $outdir/new_IMGT_IGE
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115 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGE
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0
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116
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5
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117 Rscript $dir/new_imgt.r $outdir/new_IMGT/ $outdir/merged.txt "-" 2>&1
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118
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119 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA/ $outdir/merged.txt "IGA" 2>&1
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120 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA1/ $outdir/merged.txt "IGA1" 2>&1
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121 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA2/ $outdir/merged.txt "IGA2" 2>&1
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0
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122
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5
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123 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG/ $outdir/merged.txt "IGG" 2>&1
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124 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG1/ $outdir/merged.txt "IGG1" 2>&1
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125 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG2/ $outdir/merged.txt "IGG2" 2>&1
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126 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG3/ $outdir/merged.txt "IGG3" 2>&1
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127 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG4/ $outdir/merged.txt "IGG4" 2>&1
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0
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128
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5
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129 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGM/ $outdir/merged.txt "IGM" 2>&1
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0
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130
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5
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131 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGE/ $outdir/merged.txt "IGE" 2>&1
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0
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132
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133
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5
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134 tmp="$PWD"
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135 cd $outdir/new_IMGT/ #tar weirdness...
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136 tar -cJf ../new_IMGT.txz *
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0
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137
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5
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138 cd $outdir/new_IMGT_IGA/
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139 tar -cJf ../new_IMGT_IGA.txz *
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140
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5
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141 cd $outdir/new_IMGT_IGA1/
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142 tar -cJf ../new_IMGT_IGA1.txz *
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0
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143
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5
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144 cd $outdir/new_IMGT_IGA2/
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145 tar -cJf ../new_IMGT_IGA2.txz *
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0
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146
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5
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147 cd $outdir/new_IMGT_IGG/
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148 tar -cJf ../new_IMGT_IGG.txz *
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0
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149
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5
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150 cd $outdir/new_IMGT_IGG1/
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151 tar -cJf ../new_IMGT_IGG1.txz *
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0
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152
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5
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153 cd $outdir/new_IMGT_IGG2/
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154 tar -cJf ../new_IMGT_IGG2.txz *
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155
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156 cd $outdir/new_IMGT_IGG3/
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157 tar -cJf ../new_IMGT_IGG3.txz *
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0
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158
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5
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159 cd $outdir/new_IMGT_IGG4/
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160 tar -cJf ../new_IMGT_IGG4.txz *
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161
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162 cd $outdir/new_IMGT_IGM/
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163 tar -cJf ../new_IMGT_IGM.txz *
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0
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164
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5
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165 cd $outdir/new_IMGT_IGE/
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166 tar -cJf ../new_IMGT_IGE.txz *
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0
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167
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5
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168 cd $tmp
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169 fi
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0
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170
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171 echo "---------------- shm_csr.r ----------------"
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172 echo "---------------- shm_csr.r ----------------<br />" >> $log
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173
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5
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174 classes="IGA,IGA1,IGA2,IGG,IGG1,IGG2,IGG3,IGG4,IGM,IGE,unmatched"
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175 echo "R mutation analysis"
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1
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176 Rscript $dir/shm_csr.r $outdir/merged.txt $classes $outdir ${empty_region_filter} 2>&1
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0
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177
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178 echo "---------------- shm_csr.py ----------------"
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179 echo "---------------- shm_csr.py ----------------<br />" >> $log
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180
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1
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181 python $dir/shm_csr.py --input $outdir/merged.txt --genes $classes --empty_region_filter "${empty_region_filter}" --output $outdir/hotspot_analysis.txt
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182
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183 echo "---------------- aa_histogram.r ----------------"
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184 echo "---------------- aa_histogram.r ----------------<br />" >> $log
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185
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5
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186 Rscript $dir/aa_histogram.r $outdir/aa_id_mutations.txt $outdir/absent_aa_id.txt "IGA,IGG,IGM,IGE" $outdir/ 2>&1
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187 if [ -e "$outdir/aa_histogram_.png" ]; then
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188 mv $outdir/aa_histogram_.png $outdir/aa_histogram.png
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189 mv $outdir/aa_histogram_.txt $outdir/aa_histogram.txt
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29
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190 mv $outdir/aa_histogram_absent_.txt $outdir/aa_histogram_absent.txt
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191 mv $outdir/aa_histogram_count_.txt $outdir/aa_histogram_count.txt
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192 mv $outdir/aa_histogram_sum_.txt $outdir/aa_histogram_sum.txt
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0
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193 fi
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194
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5
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195 genes=(IGA IGA1 IGA2 IGG IGG1 IGG2 IGG3 IGG4 IGM IGE)
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0
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196
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197 funcs=(sum mean median)
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198 funcs=(sum)
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199
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200 echo "---------------- sequence_overview.r ----------------"
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201 echo "---------------- sequence_overview.r ----------------<br />" >> $log
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202
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203 mkdir $outdir/sequence_overview
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204
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7
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205 Rscript $dir/sequence_overview.r $outdir/before_unique_filter.txt $outdir/merged.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt ${empty_region_filter} 2>&1
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206
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207 echo "<table border='1'>" > $outdir/base_overview.html
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208
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209 while IFS=$'\t' read ID class seq A C G T
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210 do
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211 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
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212 done < $outdir/sequence_overview/ntoverview.txt
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213
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214 echo "<html><center><h1>$title</h1></center>" > $output
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215 echo "<meta name='viewport' content='width=device-width, initial-scale=1'>" >> $output
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216 echo "<script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $output
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217 echo "<script type='text/javascript' src='tabber.js'></script>" >> $output
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218 echo "<script type='text/javascript' src='script.js'></script>" >> $output
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219 echo "<link rel='stylesheet' type='text/css' href='style.css'>" >> $output
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220 echo "<link rel='stylesheet' type='text/css' href='pure-min.css'>" >> $output
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221
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222 matched_count="`cat $outdir/merged.txt | grep -v 'unmatched' | tail -n +2 | wc -l`"
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223 unmatched_count="`cat $outdir/unmatched.txt | tail -n +2 | wc -l`"
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224 total_count=$((matched_count + unmatched_count))
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225 perc_count=$((unmatched_count / total_count * 100))
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226 perc_count=`bc -l <<< "scale=2; ${unmatched_count} / ${total_count} * 100"`
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227 perc_count=`bc -l <<< "scale=2; (${unmatched_count} / ${total_count} * 100 ) / 1"`
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228
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229 echo "<center><h2>Total: ${total_count}</h2></center>" >> $output
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230 echo "<center><h2>Matched: ${matched_count} Unmatched: ${unmatched_count}</h2></center>" >> $output
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231 echo "<center><h2>Percentage unmatched: ${perc_count}</h2></center>" >> $output
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232
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233 echo "---------------- main tables ----------------"
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234 echo "---------------- main tables ----------------<br />" >> $log
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235
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236 echo "<div class='tabber'>" >> $output
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23
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237 echo "<div class='tabbertab' title='SHM Overview' style='width: 3000px;'>" >> $output
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0
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238
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239 for func in ${funcs[@]}
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240 do
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241
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242 echo "---------------- $func table ----------------"
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243 echo "---------------- $func table ----------------<br />" >> $log
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244
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245 cat $outdir/mutations_${func}.txt $outdir/hotspot_analysis_${func}.txt > $outdir/data_${func}.txt
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246
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247 echo "---------------- pattern_plots.r ----------------"
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248 echo "---------------- pattern_plots.r ----------------<br />" >> $log
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249
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23
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250 Rscript $dir/pattern_plots.r $outdir/data_${func}.txt $outdir/plot1 $outdir/plot2 $outdir/plot3 $outdir/shm_overview.txt 2>&1
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0
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251
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252 echo "<table class='pure-table pure-table-striped'>" >> $output
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253 echo "<thead><tr><th>info</th>" >> $output
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254
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255 if [ "${class_filter}" != "101_101" ] ; then
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256
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257 for gene in ${genes[@]}
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258 do
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259 tmp=`cat $outdir/${gene}_${func}_n.txt`
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260 echo "<th><a href='matched_${gene}_${func}.txt'>${gene} (N = $tmp)</a></th>" >> $output
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261 done
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262
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263 tmp=`cat $outdir/all_${func}_n.txt`
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264 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
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265 tmp=`cat $outdir/unmatched_${func}_n.txt`
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266 echo "<th><a href='unmatched.txt'>unmatched (N = ${unmatched_count})</a></th><tr></thead>" >> $output
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267
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5
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268 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
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0
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269 do
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270 if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] ; then #meh
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5
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271 echo "<tr><td>$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>" >> $output
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0
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272 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
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5
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273 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>" >> $output
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0
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274 else
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5
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275 echo "<tr><td>$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
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0
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276 fi
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277 done < $outdir/data_${func}.txt
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278
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279 else
|
|
3
|
280 tmp=`cat $outdir/all_${func}_n.txt`
|
|
0
|
281 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
|
|
|
282
|
|
5
|
283 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
|
|
0
|
284 do
|
|
|
285 if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] ; then #meh
|
|
3
|
286 echo "<tr><td>$name</td><td>${allx}/${ally}</td></tr>" >> $output
|
|
0
|
287 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
|
|
3
|
288 echo "<tr><td>$name</td><td>${allz}%</td></tr>" >> $output
|
|
0
|
289 else
|
|
3
|
290 echo "<tr><td>$name</td><td>${allx}/${ally} (${allz}%)</td></tr>" >> $output
|
|
0
|
291 fi
|
|
|
292 done < $outdir/data_${func}.txt
|
|
|
293
|
|
|
294 fi
|
|
|
295 echo "</table>" >> $output
|
|
|
296 #echo "<a href='data_${func}.txt'>Download data</a>" >> $output
|
|
|
297 done
|
|
|
298
|
|
|
299 echo "<img src='plot1.png' /><br />" >> $output
|
|
|
300 echo "<img src='plot2.png' /><br />" >> $output
|
|
|
301 echo "<img src='plot3.png' /><br />" >> $output
|
|
|
302
|
|
|
303 echo "</div>" >> $output #SHM overview tab end
|
|
|
304
|
|
|
305 echo "---------------- images ----------------"
|
|
|
306 echo "---------------- images ----------------<br />" >> $log
|
|
|
307
|
|
23
|
308 echo "<div class='tabbertab' title='SHM Frequency' style='width: 3000px;'>" >> $output
|
|
0
|
309
|
|
|
310 if [ -a $outdir/scatter.png ]
|
|
|
311 then
|
|
|
312 echo "<img src='scatter.png'/><br />" >> $output
|
|
|
313 fi
|
|
|
314 if [ -a $outdir/frequency_ranges.png ]
|
|
|
315 then
|
|
|
316 echo "<img src='frequency_ranges.png'/><br />" >> $output
|
|
|
317 fi
|
|
|
318
|
|
|
319 echo "</div>" >> $output #SHM frequency tab end
|
|
|
320
|
|
23
|
321 echo "<div class='tabbertab' title='Transition tables' style='width: 3000px;'>" >> $output
|
|
0
|
322
|
|
|
323 echo "<table border='0'>" >> $output
|
|
|
324
|
|
|
325 for gene in ${genes[@]}
|
|
|
326 do
|
|
|
327 echo "<tr>" >> $output
|
|
|
328 echo "<td><h1>${gene}</h1></td>" >> $output
|
|
23
|
329
|
|
|
330 if [ -e $outdir/transitions_heatmap_${gene}.png ]
|
|
|
331 then
|
|
|
332 echo "<td><img src='transitions_heatmap_${gene}.png' /></td>" >> $output
|
|
|
333 else
|
|
|
334 echo "<td></td>" >> $output
|
|
|
335 fi
|
|
|
336
|
|
|
337 if [ -e $outdir/transitions_stacked_${gene}.png ]
|
|
|
338 then
|
|
|
339 echo "<td><img src='transitions_stacked_${gene}.png' /></td>" >> $output
|
|
|
340 else
|
|
|
341 echo "<td></td>" >> $output
|
|
|
342 fi
|
|
|
343
|
|
0
|
344 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
|
|
|
345 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
|
|
|
346 first="true"
|
|
|
347 while IFS=, read from a c g t
|
|
|
348 do
|
|
|
349 if [ "$first" == "true" ] ; then
|
|
|
350 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
|
|
|
351 first="false"
|
|
|
352 else
|
|
|
353 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
|
|
|
354 fi
|
|
|
355 done < $outdir/transitions_${gene}_sum.txt
|
|
|
356 echo "</table></td>" >> $output
|
|
|
357
|
|
|
358 echo "</tr>" >> $output
|
|
|
359 done
|
|
|
360
|
|
|
361 echo "<tr>" >> $output
|
|
|
362 echo "<td><h1>All</h1></td>" >> $output
|
|
|
363 echo "<td><img src='transitions_heatmap_all.png' /></td>" >> $output
|
|
|
364 echo "<td><img src='transitions_stacked_all.png' /></td>" >> $output
|
|
|
365 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
|
|
|
366 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
|
|
|
367 first="true"
|
|
|
368 while IFS=, read from a c g t
|
|
|
369 do
|
|
|
370 if [ "$first" == "true" ] ; then
|
|
|
371 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
|
|
|
372 first="false"
|
|
|
373 else
|
|
|
374 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
|
|
|
375 fi
|
|
|
376 done < $outdir/transitions_all_sum.txt
|
|
|
377 echo "</table></td>" >> $output
|
|
|
378
|
|
|
379 echo "</tr>" >> $output
|
|
|
380
|
|
|
381 echo "</table>" >> $output
|
|
|
382
|
|
|
383 echo "</div>" >> $output #transition tables tab end
|
|
|
384
|
|
|
385 echo "<div class='tabbertab' title='Antigen Selection'>" >> $output
|
|
|
386
|
|
23
|
387 if [ -e $outdir/aa_histogram.png ]
|
|
0
|
388 then
|
|
|
389 echo "<img src='aa_histogram.png'/><br />" >> $output
|
|
23
|
390 fi
|
|
|
391
|
|
|
392 if [ -e $outdir/aa_histogram_IGA.png ]
|
|
|
393 then
|
|
0
|
394 echo "<img src='aa_histogram_IGA.png'/><br />" >> $output
|
|
23
|
395 fi
|
|
|
396
|
|
|
397 if [ -e $outdir/aa_histogram_IGG.png ]
|
|
|
398 then
|
|
0
|
399 echo "<img src='aa_histogram_IGG.png'/><br />" >> $output
|
|
23
|
400 fi
|
|
|
401
|
|
|
402 if [ -e $outdir/aa_histogram_IGM.png ]
|
|
|
403 then
|
|
0
|
404 echo "<img src='aa_histogram_IGM.png'/><br />" >> $output
|
|
23
|
405 fi
|
|
|
406
|
|
|
407 if [ -e $outdir/aa_histogram_IGE.png ]
|
|
|
408 then
|
|
6
|
409 echo "<img src='aa_histogram_IGE.png'/><br />" >> $output
|
|
0
|
410 fi
|
|
|
411
|
|
23
|
412
|
|
33
|
413
|
|
|
414 if [[ "$fast" == "no" ]] ; then
|
|
|
415
|
|
|
416 echo "---------------- baseline ----------------"
|
|
|
417 echo "---------------- baseline ----------------<br />" >> $log
|
|
|
418 tmp="$PWD"
|
|
|
419
|
|
|
420 mkdir $outdir/baseline
|
|
|
421
|
|
23
|
422
|
|
33
|
423 mkdir $outdir/baseline/IGA_IGG_IGM
|
|
|
424 if [[ $(wc -l < $outdir/new_IMGT/1_Summary.txt) -gt "1" ]]; then
|
|
|
425 cd $outdir/baseline/IGA_IGG_IGM
|
|
|
426 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT.txz "IGA_IGG_IGM" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt"
|
|
|
427 else
|
|
|
428 echo "No sequences" > "$outdir/baseline.txt"
|
|
|
429 fi
|
|
|
430
|
|
|
431 mkdir $outdir/baseline/IGA
|
|
|
432 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
|
|
|
433 cd $outdir/baseline/IGA
|
|
|
434 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGA.txz "IGA" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGA.pdf" "Sequence.ID" "$outdir/baseline_IGA.txt"
|
|
|
435 else
|
|
|
436 echo "No IGA sequences" > "$outdir/baseline_IGA.txt"
|
|
|
437 fi
|
|
|
438
|
|
|
439 mkdir $outdir/baseline/IGG
|
|
|
440 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
|
|
|
441 cd $outdir/baseline/IGG
|
|
|
442 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGG.txz "cg" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGG.pdf" "Sequence.ID" "$outdir/baseline_IGG.txt"
|
|
|
443 else
|
|
|
444 echo "No IGG sequences" > "$outdir/baseline_IGG.txt"
|
|
|
445 fi
|
|
23
|
446
|
|
33
|
447 mkdir $outdir/baseline/IGM
|
|
|
448 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
|
|
|
449 cd $outdir/baseline/IGM
|
|
|
450 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGM.txz "IGM" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGM.pdf" "Sequence.ID" "$outdir/baseline_IGM.txt"
|
|
|
451 else
|
|
|
452 echo "No IGM sequences" > "$outdir/baseline_IGM.txt"
|
|
|
453 fi
|
|
|
454
|
|
|
455 mkdir $outdir/baseline/IGE
|
|
|
456 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
|
|
|
457 cd $outdir/baseline/IGE
|
|
|
458 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGE.txz "IGE" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGE.pdf" "Sequence.ID" "$outdir/baseline_IGE.txt"
|
|
|
459 else
|
|
|
460 echo "No IGE sequences" > "$outdir/baseline_IGE.txt"
|
|
|
461 fi
|
|
|
462
|
|
|
463 cd $tmp
|
|
23
|
464
|
|
33
|
465 echo "Cleaning up *.RData files"
|
|
|
466 find $outdir/baseline -name "*.RData" -type f -delete
|
|
|
467
|
|
|
468 if [ -e $outdir/baseline.pdf ]
|
|
|
469 then
|
|
|
470 echo "<embed src='baseline.pdf' width='700px' height='1000px'>" >> $output
|
|
|
471 fi
|
|
|
472
|
|
|
473 if [ -e $outdir/baseline_IGA.pdf ]
|
|
|
474 then
|
|
|
475 echo "<embed src='baseline_IGA.pdf' width='700px' height='1000px'>" >> $output
|
|
|
476 fi
|
|
23
|
477
|
|
33
|
478 if [ -e $outdir/baseline_IGG.pdf ]
|
|
|
479 then
|
|
|
480 echo "<embed src='baseline_IGG.pdf' width='700px' height='1000px'>" >> $output
|
|
|
481 fi
|
|
|
482
|
|
|
483 if [ -e $outdir/baseline_IGM.pdf ]
|
|
|
484 then
|
|
|
485 echo "<embed src='baseline_IGM.pdf' width='700px' height='1000px'>" >> $output
|
|
|
486 fi
|
|
|
487
|
|
|
488 if [ -e $outdir/baseline_IGE.pdf ]
|
|
|
489 then
|
|
|
490 echo "<embed src='baseline_IGE.pdf' width='700px' height='1000px'>" >> $output
|
|
|
491 fi
|
|
23
|
492 fi
|
|
0
|
493
|
|
|
494 echo "</div>" >> $output #antigen selection tab end
|
|
|
495
|
|
|
496 echo "<div class='tabbertab' title='CSR'>" >> $output #CSR tab
|
|
|
497
|
|
23
|
498 if [ -e $outdir/IGA.png ]
|
|
0
|
499 then
|
|
|
500 echo "<img src='IGA.png'/><br />" >> $output
|
|
|
501 fi
|
|
23
|
502 if [ -e $outdir/IGG.png ]
|
|
0
|
503 then
|
|
|
504 echo "<img src='IGG.png'/><br />" >> $output
|
|
|
505 fi
|
|
|
506
|
|
|
507 echo "</div>" >> $output #CSR tab end
|
|
|
508
|
|
5
|
509 if [[ "$fast" == "no" ]] ; then
|
|
|
510
|
|
|
511 echo "---------------- change-o MakeDB ----------------"
|
|
0
|
512
|
|
5
|
513 mkdir $outdir/change_o
|
|
0
|
514
|
|
5
|
515 tmp="$PWD"
|
|
0
|
516
|
|
5
|
517 cd $outdir/change_o
|
|
0
|
518
|
|
5
|
519 bash $dir/change_o/makedb.sh $outdir/new_IMGT.txz false false false $outdir/change_o/change-o-db.txt
|
|
|
520 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
|
|
0
|
521
|
|
5
|
522 Rscript $dir/merge.r $outdir/change_o/change-o-db-defined_clones.txt $outdir/merged.txt "all" "Sequence.ID,best_match" "SEQUENCE_ID" "Sequence.ID" $outdir/change_o/change-o-db-defined_clones.txt 2>&1
|
|
0
|
523
|
|
5
|
524 echo "Rscript $dir/merge.r $outdir/change_o/change-o-db-defined_clones.txt $outdir/$outdir/merged.txt 'all' 'Sequence.ID,best_match' 'Sequence.ID' 'Sequence.ID' '\t' $outdir/change_o/change-o-db-defined_clones.txt 2>&1"
|
|
0
|
525
|
|
5
|
526 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
|
|
|
527 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGA.txz false false false $outdir/change_o/change-o-db-IGA.txt
|
|
|
528 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 $outdir/change_o/change-o-defined_clones-summary-IGA.txt
|
|
|
529 else
|
|
|
530 echo "No IGA sequences" > "$outdir/change_o/change-o-db-defined_clones-IGA.txt"
|
|
|
531 echo "No IGA sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGA.txt"
|
|
|
532 fi
|
|
0
|
533
|
|
5
|
534 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
|
|
|
535 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGG.txz false false false $outdir/change_o/change-o-db-IGG.txt
|
|
|
536 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 $outdir/change_o/change-o-defined_clones-summary-IGG.txt
|
|
|
537 else
|
|
|
538 echo "No IGG sequences" > "$outdir/change_o/change-o-db-defined_clones-IGG.txt"
|
|
|
539 echo "No IGG sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGG.txt"
|
|
|
540 fi
|
|
0
|
541
|
|
5
|
542 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
|
|
|
543 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGM.txz false false false $outdir/change_o/change-o-db-IGM.txt
|
|
|
544 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 $outdir/change_o/change-o-defined_clones-summary-IGM.txt
|
|
|
545 else
|
|
|
546 echo "No IGM sequences" > "$outdir/change_o/change-o-db-defined_clones-IGM.txt"
|
|
|
547 echo "No IGM sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGM.txt"
|
|
|
548 fi
|
|
0
|
549
|
|
6
|
550 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
|
|
|
551 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGE.txz false false false $outdir/change_o/change-o-db-IGE.txt
|
|
|
552 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 $outdir/change_o/change-o-defined_clones-summary-IGE.txt
|
|
|
553 else
|
|
|
554 echo "No IGE sequences" > "$outdir/change_o/change-o-db-defined_clones-IGE.txt"
|
|
|
555 echo "No IGE sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGE.txt"
|
|
|
556 fi
|
|
|
557
|
|
5
|
558 PWD="$tmp"
|
|
0
|
559
|
|
16
|
560 echo "<div class='tabbertab' title='Clonality'>" >> $output #clonality tab
|
|
0
|
561
|
|
16
|
562 function clonality_table {
|
|
|
563 local infile=$1
|
|
|
564 local outfile=$2
|
|
|
565
|
|
|
566 echo "<table class='pure-table pure-table-striped'>" >> $outfile
|
|
|
567 echo "<thead><tr><th>Clone size</th><th>Nr of clones</th><th>Nr of sequences</th></tr></thead>" >> $outfile
|
|
|
568
|
|
|
569 first='true'
|
|
|
570
|
|
|
571 while read size clones seqs
|
|
|
572 do
|
|
|
573 if [[ "$first" == "true" ]]; then
|
|
|
574 first="false"
|
|
|
575 continue
|
|
|
576 fi
|
|
|
577 echo "<tr><td>$size</td><td>$clones</td><td>$seqs</td></tr>" >> $outfile
|
|
|
578 done < $infile
|
|
|
579
|
|
|
580 echo "</table>" >> $outfile
|
|
|
581 }
|
|
|
582 echo "<div class='tabber'>" >> $output
|
|
0
|
583
|
|
16
|
584 echo "<div class='tabbertab' title='All'>" >> $output
|
|
|
585 clonality_table $outdir/change_o/change-o-defined_clones-summary.txt $output
|
|
|
586 echo "</div>" >> $output
|
|
0
|
587
|
|
16
|
588 echo "<div class='tabbertab' title='IGA'>" >> $output
|
|
|
589 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGA.txt $output
|
|
|
590 echo "</div>" >> $output
|
|
0
|
591
|
|
16
|
592 echo "<div class='tabbertab' title='IGG'>" >> $output
|
|
|
593 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGG.txt $output
|
|
|
594 echo "</div>" >> $output
|
|
0
|
595
|
|
16
|
596 echo "<div class='tabbertab' title='IGM'>" >> $output
|
|
|
597 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
|
|
|
598 echo "</div>" >> $output
|
|
6
|
599
|
|
16
|
600 echo "<div class='tabbertab' title='IGE'>" >> $output
|
|
|
601 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
|
|
|
602 echo "</div>" >> $output
|
|
0
|
603
|
|
23
|
604 echo "<div class='tabbertab' title='Overlap'>" >> $output
|
|
31
|
605 cat "$outdir/sequence_overview/index.html" | sed "s%href='\(.*\).html%href='sequence_overview/\1.html%g" >> $output # rewrite href to 'sequence_overview/..."
|
|
16
|
606 echo "</div>" >> $output
|
|
0
|
607
|
|
|
608
|
|
16
|
609 echo "</div>" >> $output #clonality tabber end
|
|
0
|
610
|
|
16
|
611 echo "</div>" >> $output #clonality tab end
|
|
0
|
612
|
|
5
|
613 fi
|
|
|
614
|
|
0
|
615 echo "<div class='tabbertab' title='Downloads'>" >> $output
|
|
|
616
|
|
|
617 echo "<table class='pure-table pure-table-striped'>" >> $output
|
|
|
618 echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output
|
|
|
619 echo "<tr><td>The complete dataset</td><td><a href='merged.txt' download='merged.txt' >Download</a></td></tr>" >> $output
|
|
|
620 echo "<tr><td>The filtered dataset</td><td><a href='filtered.txt' download='filtered.txt' >Download</a></td></tr>" >> $output
|
|
|
621 echo "<tr><td>The alignment info on the unmatched sequences</td><td><a href='unmatched.txt' download='unmatched.txt' >Download</a></td></tr>" >> $output
|
|
|
622
|
|
2
|
623 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Overview</td></tr>" >> $output
|
|
23
|
624 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
|
|
2
|
625 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
|
|
|
626 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
|
|
|
627 echo "<tr><td>Base count for every sequence</td><td><a href='base_overview.html'>View</a></td></tr>" >> $output
|
|
|
628 echo "<tr><td>The data used to generate the RGYW/WRCY and TW/WA plot</td><td><a href='plot1.txt' download='plot1.txt' >Download</a></td></tr>" >> $output
|
|
|
629 echo "<tr><td>The data used to generate the relative transition and transversion plot</td><td><a href='plot2.txt' download='plot2.txt' >Download</a></td></tr>" >> $output
|
|
|
630 echo "<tr><td>The data used to generate the absolute transition and transversion plot</td><td><a href='plot3.txt' download='plot3.txt' >Download</a></td></tr>" >> $output
|
|
|
631
|
|
|
632 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Frequency</td></tr>" >> $output
|
|
0
|
633 echo "<tr><td>The data generate the frequency scatter plot</td><td><a href='scatter.txt' download='scatter.txt' >Download</a></td></tr>" >> $output
|
|
|
634 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
|
|
|
635 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
|
|
|
636
|
|
2
|
637 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Transition Tables</td></tr>" >> $output
|
|
23
|
638 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
|
|
|
639 echo "<tr><td>The data for the 'IGA' transition plot</td><td><a href='transitions_IGA_sum.txt' download='transitions_all_sum.txt' >Download</a></td></tr>" >> $output
|
|
|
640 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
|
|
30
|
641 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
|
|
23
|
642 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
|
|
|
643 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
|
|
|
644 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
|
|
|
645 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
|
|
|
646 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
|
|
|
647 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
|
|
|
648 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
|
|
0
|
649
|
|
2
|
650 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Antigen Selection</td></tr>" >> $output
|
|
0
|
651 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
|
|
|
652 echo "<tr><td>Absent AA location data per sequence ID</td><td><a href='absent_aa_id.txt' download='absent_aa_id.txt' >Download</a></td></tr>" >> $output
|
|
|
653
|
|
29
|
654 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
|
|
|
655 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
|
|
|
656 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
|
|
|
657 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
|
|
|
658 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
|
|
|
659
|
|
0
|
660 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
|
|
|
661 echo "<tr><td>Baseline data</td><td><a href='baseline.txt' download='baseline.txt' >Download</a></td></tr>" >> $output
|
|
|
662 echo "<tr><td>Baseline IGA PDF</td><td><a href='baseline_IGA.pdf' download='baseline_IGA.pdf' >Download</a></td></tr>" >> $output
|
|
|
663 echo "<tr><td>Baseline IGA data</td><td><a href='baseline_IGA.txt' download='baseline_IGA.txt' >Download</a></td></tr>" >> $output
|
|
|
664 echo "<tr><td>Baseline IGG PDF</td><td><a href='baseline_IGG.pdf' download='baseline_IGG.pdf' >Download</a></td></tr>" >> $output
|
|
|
665 echo "<tr><td>Baseline IGG data</td><td><a href='baseline_IGG.txt' download='baseline_IGG.txt' >Download</a></td></tr>" >> $output
|
|
|
666 echo "<tr><td>Baseline IGM PDF</td><td><a href='baseline_IGM.pdf' download='baseline_IGM.pdf' >Download</a></td></tr>" >> $output
|
|
|
667 echo "<tr><td>Baseline IGM data</td><td><a href='baseline_IGM.txt' download='baseline_IGM.txt' >Download</a></td></tr>" >> $output
|
|
31
|
668 echo "<tr><td>Baseline IGE PDF</td><td><a href='baseline_IGE.pdf' download='baseline_IGE.pdf' >Download</a></td></tr>" >> $output
|
|
6
|
669 echo "<tr><td>Baseline IGE data</td><td><a href='baseline_IGE.txt' download='baseline_IGE.txt' >Download</a></td></tr>" >> $output
|
|
0
|
670
|
|
2
|
671 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>CSR</td></tr>" >> $output
|
|
|
672 echo "<tr><td>The data for the CSR IGA pie plot</td><td><a href='IGA_pie.txt' download='IGA_pie.txt' >Download</a></td></tr>" >> $output
|
|
|
673 echo "<tr><td>The data for the CSR IGG pie plot</td><td><a href='IGG_pie.txt' download='IGG_pie.txt' >Download</a></td></tr>" >> $output
|
|
|
674
|
|
|
675 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Clonality</td></tr>" >> $output
|
|
|
676 echo "<tr><td>Sequence overlap between subclasses</td><td><a href='sequence_overview/index.html'>View</a></td></tr>" >> $output
|
|
|
677 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
|
|
|
678 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
|
|
|
679 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
|
|
|
680 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
|
|
|
681 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
|
|
|
682 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
|
|
|
683 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
|
|
|
684 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
|
|
6
|
685 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
|
|
|
686 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
|
|
2
|
687
|
|
|
688 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Filtered IMGT output files</td></tr>" >> $output
|
|
0
|
689 echo "<tr><td>An IMGT archive with just the matched and filtered sequences</td><td><a href='new_IMGT.txz' download='new_IMGT.txz' >Download</a></td></tr>" >> $output
|
|
|
690 echo "<tr><td>An IMGT archive with just the matched and filtered IGA sequences</td><td><a href='new_IMGT_IGA.txz' download='new_IMGT_IGA.txz' >Download</a></td></tr>" >> $output
|
|
|
691 echo "<tr><td>An IMGT archive with just the matched and filtered IGA1 sequences</td><td><a href='new_IMGT_IGA1.txz' download='new_IMGT_IGA1.txz' >Download</a></td></tr>" >> $output
|
|
|
692 echo "<tr><td>An IMGT archive with just the matched and filtered IGA2 sequences</td><td><a href='new_IMGT_IGA2.txz' download='new_IMGT_IGA2.txz' >Download</a></td></tr>" >> $output
|
|
|
693 echo "<tr><td>An IMGT archive with just the matched and filtered IGG sequences</td><td><a href='new_IMGT_IGG.txz' download='new_IMGT_IGG.txz' >Download</a></td></tr>" >> $output
|
|
|
694 echo "<tr><td>An IMGT archive with just the matched and filtered IGG1 sequences</td><td><a href='new_IMGT_IGG1.txz' download='new_IMGT_IGG1.txz' >Download</a></td></tr>" >> $output
|
|
|
695 echo "<tr><td>An IMGT archive with just the matched and filtered IGG2 sequences</td><td><a href='new_IMGT_IGG2.txz' download='new_IMGT_IGG2.txz' >Download</a></td></tr>" >> $output
|
|
|
696 echo "<tr><td>An IMGT archive with just the matched and filtered IGG3 sequences</td><td><a href='new_IMGT_IGG3.txz' download='new_IMGT_IGG3.txz' >Download</a></td></tr>" >> $output
|
|
|
697 echo "<tr><td>An IMGT archive with just the matched and filtered IGG4 sequences</td><td><a href='new_IMGT_IGG4.txz' download='new_IMGT_IGG4.txz' >Download</a></td></tr>" >> $output
|
|
|
698 echo "<tr><td>An IMGT archive with just the matched and filtered IGM sequences</td><td><a href='new_IMGT_IGM.txz' download='new_IMGT_IGM.txz' >Download</a></td></tr>" >> $output
|
|
31
|
699 echo "<tr><td>An IMGT archive with just the matched and filtered IGE sequences</td><td><a href='new_IMGT_IGE.txz' download='new_IMGT_IGE.txz' >Download</a></td></tr>" >> $output
|
|
0
|
700
|
|
|
701 echo "</table>" >> $output
|
|
|
702
|
|
|
703 echo "</div>" >> $output #downloads tab end
|
|
|
704
|
|
|
705 echo "</div>" >> $output #tabs end
|
|
|
706
|
|
|
707 echo "</html>" >> $output
|
|
|
708
|
|
5
|
709
|
|
0
|
710 echo "---------------- naive_output.r ----------------"
|
|
|
711 echo "---------------- naive_output.r ----------------<br />" >> $log
|
|
|
712
|
|
5
|
713 if [[ "$naive_output" == "yes" ]]
|
|
0
|
714 then
|
|
28
|
715 echo "output naive output"
|
|
18
|
716 if [[ "${class_filter}" == "101_101" ]]
|
|
|
717 then
|
|
28
|
718 echo "copy new_IMGT.txz to ${naive_output_all}"
|
|
21
|
719 cp $outdir/new_IMGT.txz ${naive_output_all}
|
|
18
|
720 else
|
|
28
|
721 echo "copy for classes"
|
|
18
|
722 cp $outdir/new_IMGT_IGA.txz ${naive_output_ca}
|
|
|
723 cp $outdir/new_IMGT_IGG.txz ${naive_output_cg}
|
|
|
724 cp $outdir/new_IMGT_IGM.txz ${naive_output_cm}
|
|
|
725 cp $outdir/new_IMGT_IGE.txz ${naive_output_ce}
|
|
|
726 fi
|
|
0
|
727 fi
|
|
|
728
|
|
|
729 echo "</table>" >> $outdir/base_overview.html
|
|
|
730
|
|
|
731 mv $log $outdir/log.html
|
|
|
732
|
|
|
733 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
|
|
|
734 echo "<table border = 1>" >> $log
|
|
|
735 echo "<thead><tr><th>Info</th><th>Sequences</th><th>Percentage</th></tr></thead>" >> $log
|
|
|
736 tIFS="$TMP"
|
|
|
737 IFS=$'\t'
|
|
|
738 while read step seq perc
|
|
|
739 do
|
|
|
740 echo "<tr>" >> $log
|
|
|
741 echo "<td>$step</td>" >> $log
|
|
|
742 echo "<td>$seq</td>" >> $log
|
|
|
743 echo "<td>${perc}%</td>" >> $log
|
|
|
744 echo "</tr>" >> $log
|
|
|
745 done < $outdir/filtering_steps.txt
|
|
|
746 echo "</table border></center></html>" >> $log
|
|
|
747
|
|
|
748 IFS="$tIFS"
|
|
|
749
|
|
|
750
|
|
|
751 echo "---------------- Done! ----------------"
|
|
|
752 echo "---------------- Done! ----------------<br />" >> $outdir/log.html
|
|
|
753
|
|
|
754
|
|
|
755
|
|
|
756
|
|
|
757
|
|
|
758
|
|
|
759
|
|
|
760
|
|
|
761
|
|
|
762
|
|
|
763
|
|
|
764
|
|
|
765
|
|
|
766
|
|
|
767
|
|
|
768
|
|
|
769
|
|
|
770
|
|
|
771
|
|
|
772
|
|
|
773
|
