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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
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|
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
|
|
|
413 if [ -e $outdir/baseline.png ]
|
|
|
414 then
|
|
|
415 echo "<embed src='baseline.pdf' width='700px' height='1000px'>" >> $output
|
|
|
416 fi
|
|
|
417
|
|
|
418 if [ -e $outdir/baseline_IGA.png ]
|
|
|
419 then
|
|
|
420 echo "<embed src='baseline_IGA.pdf' width='700px' height='1000px'>" >> $output
|
|
|
421 fi
|
|
|
422
|
|
|
423 if [ -e $outdir/baseline_IGG.png ]
|
|
|
424 then
|
|
|
425 echo "<embed src='baseline_IGG.pdf' width='700px' height='1000px'>" >> $output
|
|
|
426 fi
|
|
|
427
|
|
|
428 if [ -e $outdir/baseline_IGM.png ]
|
|
|
429 then
|
|
|
430 echo "<embed src='baseline_IGM.pdf' width='700px' height='1000px'>" >> $output
|
|
|
431 fi
|
|
|
432
|
|
|
433 if [ -e $outdir/baseline_IGE.png ]
|
|
|
434 then
|
|
|
435 echo "<embed src='baseline_IGE.pdf' width='700px' height='1000px'>" >> $output
|
|
|
436 fi
|
|
0
|
437
|
|
|
438 echo "</div>" >> $output #antigen selection tab end
|
|
|
439
|
|
|
440 echo "<div class='tabbertab' title='CSR'>" >> $output #CSR tab
|
|
|
441
|
|
23
|
442 if [ -e $outdir/IGA.png ]
|
|
0
|
443 then
|
|
|
444 echo "<img src='IGA.png'/><br />" >> $output
|
|
|
445 fi
|
|
23
|
446 if [ -e $outdir/IGG.png ]
|
|
0
|
447 then
|
|
|
448 echo "<img src='IGG.png'/><br />" >> $output
|
|
|
449 fi
|
|
|
450
|
|
|
451 echo "</div>" >> $output #CSR tab end
|
|
|
452
|
|
5
|
453 if [[ "$fast" == "no" ]] ; then
|
|
|
454
|
|
|
455 echo "---------------- change-o MakeDB ----------------"
|
|
0
|
456
|
|
5
|
457 mkdir $outdir/change_o
|
|
0
|
458
|
|
5
|
459 tmp="$PWD"
|
|
0
|
460
|
|
5
|
461 cd $outdir/change_o
|
|
0
|
462
|
|
5
|
463 bash $dir/change_o/makedb.sh $outdir/new_IMGT.txz false false false $outdir/change_o/change-o-db.txt
|
|
|
464 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
|
465
|
|
5
|
466 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
|
467
|
|
5
|
468 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
|
469
|
|
5
|
470 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
|
|
|
471 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGA.txz false false false $outdir/change_o/change-o-db-IGA.txt
|
|
|
472 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 $outdir/change_o/change-o-defined_clones-summary-IGA.txt
|
|
|
473 else
|
|
|
474 echo "No IGA sequences" > "$outdir/change_o/change-o-db-defined_clones-IGA.txt"
|
|
|
475 echo "No IGA sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGA.txt"
|
|
|
476 fi
|
|
0
|
477
|
|
5
|
478 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
|
|
|
479 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGG.txz false false false $outdir/change_o/change-o-db-IGG.txt
|
|
|
480 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 $outdir/change_o/change-o-defined_clones-summary-IGG.txt
|
|
|
481 else
|
|
|
482 echo "No IGG sequences" > "$outdir/change_o/change-o-db-defined_clones-IGG.txt"
|
|
|
483 echo "No IGG sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGG.txt"
|
|
|
484 fi
|
|
0
|
485
|
|
5
|
486 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
|
|
|
487 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGM.txz false false false $outdir/change_o/change-o-db-IGM.txt
|
|
|
488 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 $outdir/change_o/change-o-defined_clones-summary-IGM.txt
|
|
|
489 else
|
|
|
490 echo "No IGM sequences" > "$outdir/change_o/change-o-db-defined_clones-IGM.txt"
|
|
|
491 echo "No IGM sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGM.txt"
|
|
|
492 fi
|
|
0
|
493
|
|
6
|
494 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
|
|
|
495 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGE.txz false false false $outdir/change_o/change-o-db-IGE.txt
|
|
|
496 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 $outdir/change_o/change-o-defined_clones-summary-IGE.txt
|
|
|
497 else
|
|
|
498 echo "No IGE sequences" > "$outdir/change_o/change-o-db-defined_clones-IGE.txt"
|
|
|
499 echo "No IGE sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGE.txt"
|
|
|
500 fi
|
|
|
501
|
|
5
|
502 PWD="$tmp"
|
|
0
|
503
|
|
16
|
504 echo "<div class='tabbertab' title='Clonality'>" >> $output #clonality tab
|
|
0
|
505
|
|
16
|
506 function clonality_table {
|
|
|
507 local infile=$1
|
|
|
508 local outfile=$2
|
|
|
509
|
|
|
510 echo "<table class='pure-table pure-table-striped'>" >> $outfile
|
|
|
511 echo "<thead><tr><th>Clone size</th><th>Nr of clones</th><th>Nr of sequences</th></tr></thead>" >> $outfile
|
|
|
512
|
|
|
513 first='true'
|
|
|
514
|
|
|
515 while read size clones seqs
|
|
|
516 do
|
|
|
517 if [[ "$first" == "true" ]]; then
|
|
|
518 first="false"
|
|
|
519 continue
|
|
|
520 fi
|
|
|
521 echo "<tr><td>$size</td><td>$clones</td><td>$seqs</td></tr>" >> $outfile
|
|
|
522 done < $infile
|
|
|
523
|
|
|
524 echo "</table>" >> $outfile
|
|
|
525 }
|
|
|
526 echo "<div class='tabber'>" >> $output
|
|
0
|
527
|
|
16
|
528 echo "<div class='tabbertab' title='All'>" >> $output
|
|
|
529 clonality_table $outdir/change_o/change-o-defined_clones-summary.txt $output
|
|
|
530 echo "</div>" >> $output
|
|
0
|
531
|
|
16
|
532 echo "<div class='tabbertab' title='IGA'>" >> $output
|
|
|
533 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGA.txt $output
|
|
|
534 echo "</div>" >> $output
|
|
0
|
535
|
|
16
|
536 echo "<div class='tabbertab' title='IGG'>" >> $output
|
|
|
537 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGG.txt $output
|
|
|
538 echo "</div>" >> $output
|
|
0
|
539
|
|
16
|
540 echo "<div class='tabbertab' title='IGM'>" >> $output
|
|
|
541 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
|
|
|
542 echo "</div>" >> $output
|
|
6
|
543
|
|
16
|
544 echo "<div class='tabbertab' title='IGE'>" >> $output
|
|
|
545 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
|
|
|
546 echo "</div>" >> $output
|
|
0
|
547
|
|
23
|
548 echo "<div class='tabbertab' title='Overlap'>" >> $output
|
|
16
|
549 cat "$outdir/sequence_overview/index.html" >> $output
|
|
|
550 echo "</div>" >> $output
|
|
0
|
551
|
|
|
552
|
|
16
|
553 echo "</div>" >> $output #clonality tabber end
|
|
0
|
554
|
|
16
|
555 echo "</div>" >> $output #clonality tab end
|
|
0
|
556
|
|
5
|
557 fi
|
|
|
558
|
|
0
|
559 echo "<div class='tabbertab' title='Downloads'>" >> $output
|
|
|
560
|
|
|
561 echo "<table class='pure-table pure-table-striped'>" >> $output
|
|
|
562 echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output
|
|
|
563 echo "<tr><td>The complete dataset</td><td><a href='merged.txt' download='merged.txt' >Download</a></td></tr>" >> $output
|
|
|
564 echo "<tr><td>The filtered dataset</td><td><a href='filtered.txt' download='filtered.txt' >Download</a></td></tr>" >> $output
|
|
|
565 echo "<tr><td>The alignment info on the unmatched sequences</td><td><a href='unmatched.txt' download='unmatched.txt' >Download</a></td></tr>" >> $output
|
|
|
566
|
|
2
|
567 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Overview</td></tr>" >> $output
|
|
23
|
568 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
|
569 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
|
|
|
570 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
|
|
|
571 echo "<tr><td>Base count for every sequence</td><td><a href='base_overview.html'>View</a></td></tr>" >> $output
|
|
|
572 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
|
|
|
573 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
|
|
|
574 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
|
|
|
575
|
|
|
576 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Frequency</td></tr>" >> $output
|
|
0
|
577 echo "<tr><td>The data generate the frequency scatter plot</td><td><a href='scatter.txt' download='scatter.txt' >Download</a></td></tr>" >> $output
|
|
|
578 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
|
|
|
579 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
|
|
|
580
|
|
2
|
581 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Transition Tables</td></tr>" >> $output
|
|
23
|
582 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
|
|
|
583 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
|
|
|
584 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
|
|
26
|
585 echo "<tr><td>The data for the 'IGA1' transition plot</td><td><a href='transitions_IGA2_sum.txt' download='transitions_IGA2_sum.txt' >Download</a></td></tr>" >> $output
|
|
23
|
586 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
|
|
|
587 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
|
|
|
588 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
|
|
|
589 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
|
|
|
590 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
|
|
|
591 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
|
|
|
592 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
|
593
|
|
2
|
594 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Antigen Selection</td></tr>" >> $output
|
|
0
|
595 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
|
|
|
596 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
|
|
|
597
|
|
29
|
598 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
|
|
|
599 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
|
|
|
600 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
|
|
|
601 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
|
|
|
602 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
|
|
|
603
|
|
0
|
604 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
|
|
|
605 echo "<tr><td>Baseline data</td><td><a href='baseline.txt' download='baseline.txt' >Download</a></td></tr>" >> $output
|
|
|
606 echo "<tr><td>Baseline IGA PDF</td><td><a href='baseline_IGA.pdf' download='baseline_IGA.pdf' >Download</a></td></tr>" >> $output
|
|
|
607 echo "<tr><td>Baseline IGA data</td><td><a href='baseline_IGA.txt' download='baseline_IGA.txt' >Download</a></td></tr>" >> $output
|
|
|
608 echo "<tr><td>Baseline IGG PDF</td><td><a href='baseline_IGG.pdf' download='baseline_IGG.pdf' >Download</a></td></tr>" >> $output
|
|
|
609 echo "<tr><td>Baseline IGG data</td><td><a href='baseline_IGG.txt' download='baseline_IGG.txt' >Download</a></td></tr>" >> $output
|
|
|
610 echo "<tr><td>Baseline IGM PDF</td><td><a href='baseline_IGM.pdf' download='baseline_IGM.pdf' >Download</a></td></tr>" >> $output
|
|
|
611 echo "<tr><td>Baseline IGM data</td><td><a href='baseline_IGM.txt' download='baseline_IGM.txt' >Download</a></td></tr>" >> $output
|
|
6
|
612 echo "<tr><td>Baseline IGE data</td><td><a href='baseline_IGE.txt' download='baseline_IGE.txt' >Download</a></td></tr>" >> $output
|
|
0
|
613
|
|
2
|
614 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>CSR</td></tr>" >> $output
|
|
|
615 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
|
|
|
616 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
|
|
|
617
|
|
|
618 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Clonality</td></tr>" >> $output
|
|
|
619 echo "<tr><td>Sequence overlap between subclasses</td><td><a href='sequence_overview/index.html'>View</a></td></tr>" >> $output
|
|
|
620 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
|
|
|
621 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
|
|
|
622 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
|
|
|
623 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
|
|
|
624 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
|
|
|
625 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
|
|
|
626 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
|
|
|
627 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
|
628 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
|
|
|
629 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
|
630
|
|
|
631 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Filtered IMGT output files</td></tr>" >> $output
|
|
0
|
632 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
|
|
|
633 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
|
|
|
634 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
|
|
|
635 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
|
|
|
636 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
|
|
|
637 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
|
|
|
638 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
|
|
|
639 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
|
|
|
640 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
|
|
|
641 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
|
|
6
|
642 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_IGM.txz' >Download</a></td></tr>" >> $output
|
|
0
|
643
|
|
|
644 echo "</table>" >> $output
|
|
|
645
|
|
|
646 echo "</div>" >> $output #downloads tab end
|
|
|
647
|
|
|
648 echo "</div>" >> $output #tabs end
|
|
|
649
|
|
|
650 echo "</html>" >> $output
|
|
|
651
|
|
5
|
652
|
|
|
653 if [[ "$fast" == "no" ]] ; then
|
|
0
|
654
|
|
5
|
655 echo "---------------- baseline ----------------"
|
|
|
656 echo "---------------- baseline ----------------<br />" >> $log
|
|
|
657 tmp="$PWD"
|
|
|
658
|
|
|
659 mkdir $outdir/baseline
|
|
0
|
660
|
|
|
661
|
|
5
|
662 mkdir $outdir/baseline/IGA_IGG_IGM
|
|
|
663 if [[ $(wc -l < $outdir/new_IMGT/1_Summary.txt) -gt "1" ]]; then
|
|
|
664 cd $outdir/baseline/IGA_IGG_IGM
|
|
|
665 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/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt"
|
|
|
666 else
|
|
|
667 echo "No sequences" > "$outdir/baseline.txt"
|
|
|
668 fi
|
|
0
|
669
|
|
5
|
670 mkdir $outdir/baseline/IGA
|
|
|
671 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
|
|
|
672 cd $outdir/baseline/IGA
|
|
|
673 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/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_IGA.pdf" "Sequence.ID" "$outdir/baseline_IGA.txt"
|
|
|
674 else
|
|
|
675 echo "No IGA sequences" > "$outdir/baseline_IGA.txt"
|
|
|
676 fi
|
|
0
|
677
|
|
5
|
678 mkdir $outdir/baseline/IGG
|
|
|
679 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
|
|
|
680 cd $outdir/baseline/IGG
|
|
|
681 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/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_IGG.pdf" "Sequence.ID" "$outdir/baseline_IGG.txt"
|
|
|
682 else
|
|
|
683 echo "No IGG sequences" > "$outdir/baseline_IGG.txt"
|
|
|
684 fi
|
|
0
|
685
|
|
5
|
686 mkdir $outdir/baseline/IGM
|
|
|
687 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
|
|
|
688 cd $outdir/baseline/IGM
|
|
|
689 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/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_IGM.pdf" "Sequence.ID" "$outdir/baseline_IGM.txt"
|
|
|
690 else
|
|
|
691 echo "No IGM sequences" > "$outdir/baseline_IGM.txt"
|
|
|
692 fi
|
|
|
693
|
|
6
|
694 mkdir $outdir/baseline/IGE
|
|
|
695 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
|
|
|
696 cd $outdir/baseline/IGE
|
|
|
697 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/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_IGE.pdf" "Sequence.ID" "$outdir/baseline_IGE.txt"
|
|
|
698 else
|
|
|
699 echo "No IGE sequences" > "$outdir/baseline_IGE.txt"
|
|
|
700 fi
|
|
|
701
|
|
5
|
702 cd $tmp
|
|
|
703
|
|
|
704 echo "Cleaning up *.RData files"
|
|
|
705 find $outdir/baseline -name "*.RData" -type f -delete
|
|
|
706
|
|
0
|
707 fi
|
|
|
708
|
|
|
709 echo "---------------- naive_output.r ----------------"
|
|
|
710 echo "---------------- naive_output.r ----------------<br />" >> $log
|
|
|
711
|
|
5
|
712 if [[ "$naive_output" == "yes" ]]
|
|
0
|
713 then
|
|
28
|
714 echo "output naive output"
|
|
18
|
715 if [[ "${class_filter}" == "101_101" ]]
|
|
|
716 then
|
|
28
|
717 echo "copy new_IMGT.txz to ${naive_output_all}"
|
|
21
|
718 cp $outdir/new_IMGT.txz ${naive_output_all}
|
|
18
|
719 else
|
|
28
|
720 echo "copy for classes"
|
|
18
|
721 cp $outdir/new_IMGT_IGA.txz ${naive_output_ca}
|
|
|
722 cp $outdir/new_IMGT_IGG.txz ${naive_output_cg}
|
|
|
723 cp $outdir/new_IMGT_IGM.txz ${naive_output_cm}
|
|
|
724 cp $outdir/new_IMGT_IGE.txz ${naive_output_ce}
|
|
|
725 fi
|
|
0
|
726 fi
|
|
|
727
|
|
|
728 echo "</table>" >> $outdir/base_overview.html
|
|
|
729
|
|
|
730 mv $log $outdir/log.html
|
|
|
731
|
|
|
732 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
|
|
|
733 echo "<table border = 1>" >> $log
|
|
|
734 echo "<thead><tr><th>Info</th><th>Sequences</th><th>Percentage</th></tr></thead>" >> $log
|
|
|
735 tIFS="$TMP"
|
|
|
736 IFS=$'\t'
|
|
|
737 while read step seq perc
|
|
|
738 do
|
|
|
739 echo "<tr>" >> $log
|
|
|
740 echo "<td>$step</td>" >> $log
|
|
|
741 echo "<td>$seq</td>" >> $log
|
|
|
742 echo "<td>${perc}%</td>" >> $log
|
|
|
743 echo "</tr>" >> $log
|
|
|
744 done < $outdir/filtering_steps.txt
|
|
|
745 echo "</table border></center></html>" >> $log
|
|
|
746
|
|
|
747 IFS="$tIFS"
|
|
|
748
|
|
|
749
|
|
|
750 echo "---------------- Done! ----------------"
|
|
|
751 echo "---------------- Done! ----------------<br />" >> $outdir/log.html
|
|
|
752
|
|
|
753
|
|
|
754
|
|
|
755
|
|
|
756
|
|
|
757
|
|
|
758
|
|
|
759
|
|
|
760
|
|
|
761
|
|
|
762
|
|
|
763
|
|
|
764
|
|
|
765
|
|
|
766
|
|
|
767
|
|
|
768
|
|
|
769
|
|
|
770
|
|
|
771
|
|
|
772
|
