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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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13 naive_output_ca=$9
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14 naive_output_cg=${10}
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15 naive_output_cm=${11}
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6
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16 naive_output_ce=${12}
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20
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17 naive_output_all=${13}
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18 filter_unique=${14}
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19 class_filter=${15}
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20 empty_region_filter=${16}
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21 fast=${17}
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0
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22 mkdir $outdir
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23
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24 tar -xzf $dir/style.tar.gz -C $outdir
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25
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26 echo "---------------- read parameters ----------------"
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27 echo "---------------- read parameters ----------------<br />" > $log
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28
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29 echo "unpacking IMGT file"
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30
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31 type="`file $input`"
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32 if [[ "$type" == *"Zip archive"* ]] ; then
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33 echo "Zip archive"
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34 echo "unzip $input -d $PWD/files/"
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35 unzip $input -d $PWD/files/
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36 elif [[ "$type" == *"XZ compressed data"* ]] ; then
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37 echo "ZX archive"
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38 echo "tar -xJf $input -C $PWD/files/"
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39 mkdir -p $PWD/files/$title
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40 tar -xJf $input -C $PWD/files/$title
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41 fi
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42
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43 cat `find $PWD/files/ -name "1_*"` > $PWD/summary.txt
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44 cat `find $PWD/files/ -name "3_*"` > $PWD/sequences.txt
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45 cat `find $PWD/files/ -name "5_*"` > $PWD/aa.txt
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46 cat `find $PWD/files/ -name "6_*"` > $PWD/junction.txt
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47 cat `find $PWD/files/ -name "7_*"` > $PWD/mutationanalysis.txt
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48 cat `find $PWD/files/ -name "8_*"` > $PWD/mutationstats.txt
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49 cat `find $PWD/files/ -name "10_*"` > $PWD/hotspots.txt
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50
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51 if [[ ${#BLASTN_DIR} -ge 5 ]] ; then
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52 echo "On server, using BLASTN_DIR env: ${BLASTN_DIR}"
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53 else
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54 BLASTN_DIR="/home/galaxy/Downloads/ncbi-blast-2.4.0+/bin"
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55 echo "Dev Galaxy set BLASTN_DIR to: ${BLASTN_DIR}"
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56 fi
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57
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58 echo "---------------- class identification ----------------"
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59 echo "---------------- class identification ----------------<br />" >> $log
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60
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61 python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt
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62
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63 echo "---------------- merge_and_filter.r ----------------"
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64 echo "---------------- merge_and_filter.r ----------------<br />" >> $log
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65
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14
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66 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} ${empty_region_filter} 2>&1
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0
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67
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5
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68 if [[ "$fast" == "no" ]] ; then
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0
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69
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5
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70 echo "---------------- creating new IMGT zips ----------------"
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71 echo "---------------- creating new IMGT zips ----------------<br />" >> $log
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72
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73 mkdir $outdir/new_IMGT
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74
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5
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75 cat `find $PWD/files/ -name "1_*"` > "$outdir/new_IMGT/1_Summary.txt"
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76 cat `find $PWD/files/ -name "2_*"` > "$outdir/new_IMGT/2_IMGT-gapped-nt-sequences.txt"
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77 cat `find $PWD/files/ -name "3_*"` > "$outdir/new_IMGT/3_Nt-sequences.txt"
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78 cat `find $PWD/files/ -name "4_*"` > "$outdir/new_IMGT/4_IMGT-gapped-AA-sequences.txt"
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79 cat `find $PWD/files/ -name "5_*"` > "$outdir/new_IMGT/5_AA-sequences.txt"
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80 cat `find $PWD/files/ -name "6_*"` > "$outdir/new_IMGT/6_Junction.txt"
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81 cat `find $PWD/files/ -name "7_*"` > "$outdir/new_IMGT/7_V-REGION-mutation-and-AA-change-table.txt"
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82 cat `find $PWD/files/ -name "8_*"` > "$outdir/new_IMGT/8_V-REGION-nt-mutation-statistics.txt"
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83 cat `find $PWD/files/ -name "9_*"` > "$outdir/new_IMGT/9_V-REGION-AA-change-statistics.txt"
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84 cat `find $PWD/files/ -name "10_*"` > "$outdir/new_IMGT/10_V-REGION-mutation-hotspots.txt"
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0
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85
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5
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86 mkdir $outdir/new_IMGT_IGA
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87 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA
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88
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5
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89 mkdir $outdir/new_IMGT_IGA1
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90 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA1
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91
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5
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92 mkdir $outdir/new_IMGT_IGA2
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93 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA2
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94
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5
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95 mkdir $outdir/new_IMGT_IGG
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96 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG
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0
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97
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5
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98 mkdir $outdir/new_IMGT_IGG1
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99 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG1
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0
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100
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5
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101 mkdir $outdir/new_IMGT_IGG2
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102 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG2
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103
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5
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104 mkdir $outdir/new_IMGT_IGG3
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105 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG3
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106
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5
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107 mkdir $outdir/new_IMGT_IGG4
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108 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG4
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109
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110 mkdir $outdir/new_IMGT_IGM
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111 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGM
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112
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5
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113 mkdir $outdir/new_IMGT_IGE
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114 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGE
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115
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5
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116 Rscript $dir/new_imgt.r $outdir/new_IMGT/ $outdir/merged.txt "-" 2>&1
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117
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118 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA/ $outdir/merged.txt "IGA" 2>&1
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119 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA1/ $outdir/merged.txt "IGA1" 2>&1
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120 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA2/ $outdir/merged.txt "IGA2" 2>&1
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0
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121
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5
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122 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG/ $outdir/merged.txt "IGG" 2>&1
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123 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG1/ $outdir/merged.txt "IGG1" 2>&1
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124 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG2/ $outdir/merged.txt "IGG2" 2>&1
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125 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG3/ $outdir/merged.txt "IGG3" 2>&1
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126 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG4/ $outdir/merged.txt "IGG4" 2>&1
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0
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127
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5
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128 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGM/ $outdir/merged.txt "IGM" 2>&1
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0
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129
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5
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130 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGE/ $outdir/merged.txt "IGE" 2>&1
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0
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131
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132
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5
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133 tmp="$PWD"
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134 cd $outdir/new_IMGT/ #tar weirdness...
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135 tar -cJf ../new_IMGT.txz *
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136
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5
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137 cd $outdir/new_IMGT_IGA/
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138 tar -cJf ../new_IMGT_IGA.txz *
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139
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5
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140 cd $outdir/new_IMGT_IGA1/
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141 tar -cJf ../new_IMGT_IGA1.txz *
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142
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5
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143 cd $outdir/new_IMGT_IGA2/
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144 tar -cJf ../new_IMGT_IGA2.txz *
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0
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145
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5
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146 cd $outdir/new_IMGT_IGG/
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147 tar -cJf ../new_IMGT_IGG.txz *
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0
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148
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5
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149 cd $outdir/new_IMGT_IGG1/
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150 tar -cJf ../new_IMGT_IGG1.txz *
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151
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5
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152 cd $outdir/new_IMGT_IGG2/
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153 tar -cJf ../new_IMGT_IGG2.txz *
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154
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155 cd $outdir/new_IMGT_IGG3/
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156 tar -cJf ../new_IMGT_IGG3.txz *
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157
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5
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158 cd $outdir/new_IMGT_IGG4/
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159 tar -cJf ../new_IMGT_IGG4.txz *
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160
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161 cd $outdir/new_IMGT_IGM/
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162 tar -cJf ../new_IMGT_IGM.txz *
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0
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163
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5
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164 cd $outdir/new_IMGT_IGE/
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165 tar -cJf ../new_IMGT_IGE.txz *
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0
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166
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5
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167 cd $tmp
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168 fi
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0
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169
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170 echo "---------------- shm_csr.r ----------------"
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171 echo "---------------- shm_csr.r ----------------<br />" >> $log
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172
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5
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173 classes="IGA,IGA1,IGA2,IGG,IGG1,IGG2,IGG3,IGG4,IGM,IGE,unmatched"
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174 echo "R mutation analysis"
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1
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175 Rscript $dir/shm_csr.r $outdir/merged.txt $classes $outdir ${empty_region_filter} 2>&1
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0
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176
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177 echo "---------------- shm_csr.py ----------------"
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178 echo "---------------- shm_csr.py ----------------<br />" >> $log
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179
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1
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180 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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181
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182 echo "---------------- aa_histogram.r ----------------"
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183 echo "---------------- aa_histogram.r ----------------<br />" >> $log
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184
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5
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185 Rscript $dir/aa_histogram.r $outdir/aa_id_mutations.txt $outdir/absent_aa_id.txt "IGA,IGG,IGM,IGE" $outdir/ 2>&1
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186 if [ -e "$outdir/aa_histogram_.png" ]; then
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187 mv $outdir/aa_histogram_.png $outdir/aa_histogram.png
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188 mv $outdir/aa_histogram_.txt $outdir/aa_histogram.txt
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189 fi
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190
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5
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191 genes=(IGA IGA1 IGA2 IGG IGG1 IGG2 IGG3 IGG4 IGM IGE)
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0
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192
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193 funcs=(sum mean median)
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194 funcs=(sum)
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195
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196 echo "---------------- sequence_overview.r ----------------"
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197 echo "---------------- sequence_overview.r ----------------<br />" >> $log
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198
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199 mkdir $outdir/sequence_overview
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200
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7
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201 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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202
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203 echo "<table border='1'>" > $outdir/base_overview.html
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204
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205 while IFS=$'\t' read ID class seq A C G T
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206 do
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207 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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208 done < $outdir/sequence_overview/ntoverview.txt
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209
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210 echo "<html><center><h1>$title</h1></center>" > $output
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211 echo "<meta name='viewport' content='width=device-width, initial-scale=1'>" >> $output
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212 echo "<script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $output
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213 echo "<script type='text/javascript' src='tabber.js'></script>" >> $output
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214 echo "<script type='text/javascript' src='script.js'></script>" >> $output
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215 echo "<link rel='stylesheet' type='text/css' href='style.css'>" >> $output
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216 echo "<link rel='stylesheet' type='text/css' href='pure-min.css'>" >> $output
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217
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218 matched_count="`cat $outdir/merged.txt | grep -v 'unmatched' | tail -n +2 | wc -l`"
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219 unmatched_count="`cat $outdir/unmatched.txt | tail -n +2 | wc -l`"
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220 total_count=$((matched_count + unmatched_count))
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221 perc_count=$((unmatched_count / total_count * 100))
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222 perc_count=`bc -l <<< "scale=2; ${unmatched_count} / ${total_count} * 100"`
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223 perc_count=`bc -l <<< "scale=2; (${unmatched_count} / ${total_count} * 100 ) / 1"`
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224
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225 echo "<center><h2>Total: ${total_count}</h2></center>" >> $output
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226 echo "<center><h2>Matched: ${matched_count} Unmatched: ${unmatched_count}</h2></center>" >> $output
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227 echo "<center><h2>Percentage unmatched: ${perc_count}</h2></center>" >> $output
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228
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229 echo "---------------- main tables ----------------"
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230 echo "---------------- main tables ----------------<br />" >> $log
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231
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232 echo "<div class='tabber'>" >> $output
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233 echo "<div class='tabbertab' title='SHM Overview'>" >> $output
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234
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235 for func in ${funcs[@]}
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236 do
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237
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238 echo "---------------- $func table ----------------"
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239 echo "---------------- $func table ----------------<br />" >> $log
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240
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241 cat $outdir/mutations_${func}.txt $outdir/hotspot_analysis_${func}.txt > $outdir/data_${func}.txt
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242
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243 echo "---------------- pattern_plots.r ----------------"
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244 echo "---------------- pattern_plots.r ----------------<br />" >> $log
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245
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246 Rscript $dir/pattern_plots.r $outdir/data_${func}.txt $outdir/plot1 $outdir/plot2 $outdir/plot3 2>&1
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247
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248 echo "<table class='pure-table pure-table-striped'>" >> $output
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249 echo "<thead><tr><th>info</th>" >> $output
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250
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251 if [ "${class_filter}" != "101_101" ] ; then
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252
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253 for gene in ${genes[@]}
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254 do
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255 tmp=`cat $outdir/${gene}_${func}_n.txt`
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256 echo "<th><a href='matched_${gene}_${func}.txt'>${gene} (N = $tmp)</a></th>" >> $output
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257 done
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258
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259 tmp=`cat $outdir/all_${func}_n.txt`
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260 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
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261 tmp=`cat $outdir/unmatched_${func}_n.txt`
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262 echo "<th><a href='unmatched.txt'>unmatched (N = ${unmatched_count})</a></th><tr></thead>" >> $output
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263
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5
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264 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
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0
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265 do
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266 if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] ; then #meh
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267 echo "<tr><td>$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>" >> $output
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268 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
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5
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269 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>" >> $output
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0
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270 else
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5
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271 echo "<tr><td>$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 fi
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273 done < $outdir/data_${func}.txt
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274
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275 else
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3
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276 tmp=`cat $outdir/all_${func}_n.txt`
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0
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277 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
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278
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5
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279 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
|
|
0
|
280 do
|
|
|
281 if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] ; then #meh
|
|
3
|
282 echo "<tr><td>$name</td><td>${allx}/${ally}</td></tr>" >> $output
|
|
0
|
283 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
|
|
3
|
284 echo "<tr><td>$name</td><td>${allz}%</td></tr>" >> $output
|
|
0
|
285 else
|
|
3
|
286 echo "<tr><td>$name</td><td>${allx}/${ally} (${allz}%)</td></tr>" >> $output
|
|
0
|
287 fi
|
|
|
288 done < $outdir/data_${func}.txt
|
|
|
289
|
|
|
290 fi
|
|
|
291 echo "</table>" >> $output
|
|
|
292 #echo "<a href='data_${func}.txt'>Download data</a>" >> $output
|
|
|
293 done
|
|
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294
|
|
|
295 echo "<img src='plot1.png' /><br />" >> $output
|
|
|
296 echo "<img src='plot2.png' /><br />" >> $output
|
|
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297 echo "<img src='plot3.png' /><br />" >> $output
|
|
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298
|
|
|
299 echo "</div>" >> $output #SHM overview tab end
|
|
|
300
|
|
|
301 echo "---------------- images ----------------"
|
|
|
302 echo "---------------- images ----------------<br />" >> $log
|
|
|
303
|
|
|
304 echo "<div class='tabbertab' title='SHM Frequency'>" >> $output
|
|
|
305
|
|
|
306 if [ -a $outdir/scatter.png ]
|
|
|
307 then
|
|
|
308 echo "<img src='scatter.png'/><br />" >> $output
|
|
|
309 fi
|
|
|
310 if [ -a $outdir/frequency_ranges.png ]
|
|
|
311 then
|
|
|
312 echo "<img src='frequency_ranges.png'/><br />" >> $output
|
|
|
313 fi
|
|
|
314
|
|
|
315 echo "</div>" >> $output #SHM frequency tab end
|
|
|
316
|
|
|
317 echo "<div class='tabbertab' title='Transition tables'>" >> $output
|
|
|
318
|
|
|
319 echo "<table border='0'>" >> $output
|
|
|
320
|
|
|
321 for gene in ${genes[@]}
|
|
|
322 do
|
|
|
323 echo "<tr>" >> $output
|
|
|
324 echo "<td><h1>${gene}</h1></td>" >> $output
|
|
|
325 echo "<td><img src='transitions_heatmap_${gene}.png' /></td>" >> $output
|
|
|
326 echo "<td><img src='transitions_stacked_${gene}.png' /></td>" >> $output
|
|
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327 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
|
|
|
328 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
|
|
|
329 first="true"
|
|
|
330 while IFS=, read from a c g t
|
|
|
331 do
|
|
|
332 if [ "$first" == "true" ] ; then
|
|
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333 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
|
|
|
334 first="false"
|
|
|
335 else
|
|
|
336 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
|
|
|
337 fi
|
|
|
338 done < $outdir/transitions_${gene}_sum.txt
|
|
|
339 echo "</table></td>" >> $output
|
|
|
340
|
|
|
341 echo "</tr>" >> $output
|
|
|
342 done
|
|
|
343
|
|
|
344 echo "<tr>" >> $output
|
|
|
345 echo "<td><h1>All</h1></td>" >> $output
|
|
|
346 echo "<td><img src='transitions_heatmap_all.png' /></td>" >> $output
|
|
|
347 echo "<td><img src='transitions_stacked_all.png' /></td>" >> $output
|
|
|
348 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
|
|
|
349 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
|
|
|
350 first="true"
|
|
|
351 while IFS=, read from a c g t
|
|
|
352 do
|
|
|
353 if [ "$first" == "true" ] ; then
|
|
|
354 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
|
|
|
355 first="false"
|
|
|
356 else
|
|
|
357 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
|
|
|
358 fi
|
|
|
359 done < $outdir/transitions_all_sum.txt
|
|
|
360 echo "</table></td>" >> $output
|
|
|
361
|
|
|
362 echo "</tr>" >> $output
|
|
|
363
|
|
|
364 echo "</table>" >> $output
|
|
|
365
|
|
|
366 echo "</div>" >> $output #transition tables tab end
|
|
|
367
|
|
|
368 echo "<div class='tabbertab' title='Antigen Selection'>" >> $output
|
|
|
369
|
|
|
370 if [ -a $outdir/aa_histogram.png ]
|
|
|
371 then
|
|
|
372 echo "<img src='aa_histogram.png'/><br />" >> $output
|
|
|
373 echo "<img src='aa_histogram_IGA.png'/><br />" >> $output
|
|
|
374 echo "<img src='aa_histogram_IGG.png'/><br />" >> $output
|
|
|
375 echo "<img src='aa_histogram_IGM.png'/><br />" >> $output
|
|
6
|
376 echo "<img src='aa_histogram_IGE.png'/><br />" >> $output
|
|
0
|
377 fi
|
|
|
378
|
|
|
379 echo "<embed src='baseline.pdf' width='700px' height='1000px'>" >> $output
|
|
|
380 echo "<embed src='baseline_IGA.pdf' width='700px' height='1000px'>" >> $output
|
|
|
381 echo "<embed src='baseline_IGG.pdf' width='700px' height='1000px'>" >> $output
|
|
|
382 echo "<embed src='baseline_IGM.pdf' width='700px' height='1000px'>" >> $output
|
|
6
|
383 echo "<embed src='baseline_IGE.pdf' width='700px' height='1000px'>" >> $output
|
|
0
|
384
|
|
|
385 echo "</div>" >> $output #antigen selection tab end
|
|
|
386
|
|
|
387 echo "<div class='tabbertab' title='CSR'>" >> $output #CSR tab
|
|
|
388
|
|
|
389 if [ -a $outdir/IGA.png ]
|
|
|
390 then
|
|
|
391 echo "<img src='IGA.png'/><br />" >> $output
|
|
|
392 fi
|
|
|
393 if [ -a $outdir/IGG.png ]
|
|
|
394 then
|
|
|
395 echo "<img src='IGG.png'/><br />" >> $output
|
|
|
396 fi
|
|
|
397
|
|
|
398 echo "</div>" >> $output #CSR tab end
|
|
|
399
|
|
5
|
400 if [[ "$fast" == "no" ]] ; then
|
|
|
401
|
|
|
402 echo "---------------- change-o MakeDB ----------------"
|
|
0
|
403
|
|
5
|
404 mkdir $outdir/change_o
|
|
0
|
405
|
|
5
|
406 tmp="$PWD"
|
|
0
|
407
|
|
5
|
408 cd $outdir/change_o
|
|
0
|
409
|
|
5
|
410 bash $dir/change_o/makedb.sh $outdir/new_IMGT.txz false false false $outdir/change_o/change-o-db.txt
|
|
|
411 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
|
412
|
|
5
|
413 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
|
414
|
|
5
|
415 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
|
416
|
|
5
|
417 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
|
|
|
418 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGA.txz false false false $outdir/change_o/change-o-db-IGA.txt
|
|
|
419 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 $outdir/change_o/change-o-defined_clones-summary-IGA.txt
|
|
|
420 else
|
|
|
421 echo "No IGA sequences" > "$outdir/change_o/change-o-db-defined_clones-IGA.txt"
|
|
|
422 echo "No IGA sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGA.txt"
|
|
|
423 fi
|
|
0
|
424
|
|
5
|
425 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
|
|
|
426 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGG.txz false false false $outdir/change_o/change-o-db-IGG.txt
|
|
|
427 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 $outdir/change_o/change-o-defined_clones-summary-IGG.txt
|
|
|
428 else
|
|
|
429 echo "No IGG sequences" > "$outdir/change_o/change-o-db-defined_clones-IGG.txt"
|
|
|
430 echo "No IGG sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGG.txt"
|
|
|
431 fi
|
|
0
|
432
|
|
5
|
433 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
|
|
|
434 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGM.txz false false false $outdir/change_o/change-o-db-IGM.txt
|
|
|
435 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 $outdir/change_o/change-o-defined_clones-summary-IGM.txt
|
|
|
436 else
|
|
|
437 echo "No IGM sequences" > "$outdir/change_o/change-o-db-defined_clones-IGM.txt"
|
|
|
438 echo "No IGM sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGM.txt"
|
|
|
439 fi
|
|
0
|
440
|
|
6
|
441 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
|
|
|
442 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGE.txz false false false $outdir/change_o/change-o-db-IGE.txt
|
|
|
443 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 $outdir/change_o/change-o-defined_clones-summary-IGE.txt
|
|
|
444 else
|
|
|
445 echo "No IGE sequences" > "$outdir/change_o/change-o-db-defined_clones-IGE.txt"
|
|
|
446 echo "No IGE sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGE.txt"
|
|
|
447 fi
|
|
|
448
|
|
5
|
449 PWD="$tmp"
|
|
0
|
450
|
|
16
|
451 echo "<div class='tabbertab' title='Clonality'>" >> $output #clonality tab
|
|
0
|
452
|
|
16
|
453 function clonality_table {
|
|
|
454 local infile=$1
|
|
|
455 local outfile=$2
|
|
|
456
|
|
|
457 echo "<table class='pure-table pure-table-striped'>" >> $outfile
|
|
|
458 echo "<thead><tr><th>Clone size</th><th>Nr of clones</th><th>Nr of sequences</th></tr></thead>" >> $outfile
|
|
|
459
|
|
|
460 first='true'
|
|
|
461
|
|
|
462 while read size clones seqs
|
|
|
463 do
|
|
|
464 if [[ "$first" == "true" ]]; then
|
|
|
465 first="false"
|
|
|
466 continue
|
|
|
467 fi
|
|
|
468 echo "<tr><td>$size</td><td>$clones</td><td>$seqs</td></tr>" >> $outfile
|
|
|
469 done < $infile
|
|
|
470
|
|
|
471 echo "</table>" >> $outfile
|
|
|
472 }
|
|
|
473 echo "<div class='tabber'>" >> $output
|
|
0
|
474
|
|
16
|
475 echo "<div class='tabbertab' title='All'>" >> $output
|
|
|
476 clonality_table $outdir/change_o/change-o-defined_clones-summary.txt $output
|
|
|
477 echo "</div>" >> $output
|
|
0
|
478
|
|
16
|
479 echo "<div class='tabbertab' title='IGA'>" >> $output
|
|
|
480 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGA.txt $output
|
|
|
481 echo "</div>" >> $output
|
|
0
|
482
|
|
16
|
483 echo "<div class='tabbertab' title='IGG'>" >> $output
|
|
|
484 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGG.txt $output
|
|
|
485 echo "</div>" >> $output
|
|
0
|
486
|
|
16
|
487 echo "<div class='tabbertab' title='IGM'>" >> $output
|
|
|
488 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
|
|
|
489 echo "</div>" >> $output
|
|
6
|
490
|
|
16
|
491 echo "<div class='tabbertab' title='IGE'>" >> $output
|
|
|
492 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
|
|
|
493 echo "</div>" >> $output
|
|
0
|
494
|
|
16
|
495 echo "<div class='tabbertab' title='Overview'>" >> $output
|
|
|
496 cat "$outdir/sequence_overview/index.html" >> $output
|
|
|
497 echo "</div>" >> $output
|
|
0
|
498
|
|
|
499
|
|
16
|
500 echo "</div>" >> $output #clonality tabber end
|
|
0
|
501
|
|
16
|
502 echo "</div>" >> $output #clonality tab end
|
|
0
|
503
|
|
5
|
504 fi
|
|
|
505
|
|
0
|
506 echo "<div class='tabbertab' title='Downloads'>" >> $output
|
|
|
507
|
|
|
508 echo "<table class='pure-table pure-table-striped'>" >> $output
|
|
|
509 echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output
|
|
|
510 echo "<tr><td>The complete dataset</td><td><a href='merged.txt' download='merged.txt' >Download</a></td></tr>" >> $output
|
|
|
511 echo "<tr><td>The filtered dataset</td><td><a href='filtered.txt' download='filtered.txt' >Download</a></td></tr>" >> $output
|
|
|
512 echo "<tr><td>The alignment info on the unmatched sequences</td><td><a href='unmatched.txt' download='unmatched.txt' >Download</a></td></tr>" >> $output
|
|
|
513
|
|
2
|
514 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Overview</td></tr>" >> $output
|
|
|
515 echo "<tr><td>The SHM Overview table as a dataset</td><td><a href='data_sum.txt' download='data_sum.txt' >Download</a></td></tr>" >> $output
|
|
|
516 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
|
|
|
517 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
|
|
|
518 echo "<tr><td>Base count for every sequence</td><td><a href='base_overview.html'>View</a></td></tr>" >> $output
|
|
|
519 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
|
|
|
520 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
|
|
|
521 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
|
|
|
522
|
|
|
523 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Frequency</td></tr>" >> $output
|
|
0
|
524 echo "<tr><td>The data generate the frequency scatter plot</td><td><a href='scatter.txt' download='scatter.txt' >Download</a></td></tr>" >> $output
|
|
|
525 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
|
|
|
526 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
|
|
|
527
|
|
2
|
528 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Transition Tables</td></tr>" >> $output
|
|
|
529 echo "<tr><td>The data for the 'all' transition plot</td><td><a href='transition_all_sum.txt' download='transition_all_sum.txt' >Download</a></td></tr>" >> $output
|
|
|
530 echo "<tr><td>The data for the 'IGA' transition plot</td><td><a href='transition_IGA_sum.txt' download='transition_all_sum.txt' >Download</a></td></tr>" >> $output
|
|
|
531 echo "<tr><td>The data for the 'IGA1' transition plot</td><td><a href='transition_IGA1_sum.txt' download='transition_IGA1_sum.txt' >Download</a></td></tr>" >> $output
|
|
|
532 echo "<tr><td>The data for the 'IGA1' transition plot</td><td><a href='transition_IGA1_sum.txt' download='transition_IGA1_sum.txt' >Download</a></td></tr>" >> $output
|
|
|
533 echo "<tr><td>The data for the 'IGG' transition plot</td><td><a href='transition_IGG_sum.txt' download='transition_IGG_sum.txt' >Download</a></td></tr>" >> $output
|
|
|
534 echo "<tr><td>The data for the 'IGG1' transition plot</td><td><a href='transition_IGG1_sum.txt' download='transition_IGG1_sum.txt' >Download</a></td></tr>" >> $output
|
|
|
535 echo "<tr><td>The data for the 'IGG2' transition plot</td><td><a href='transition_IGG2_sum.txt' download='transition_IGG2_sum.txt' >Download</a></td></tr>" >> $output
|
|
|
536 echo "<tr><td>The data for the 'IGG3' transition plot</td><td><a href='transition_IGG3_sum.txt' download='transition_IGG3_sum.txt' >Download</a></td></tr>" >> $output
|
|
|
537 echo "<tr><td>The data for the 'IGG4' transition plot</td><td><a href='transition_IGG4_sum.txt' download='transition_IGG4_sum.txt' >Download</a></td></tr>" >> $output
|
|
|
538 echo "<tr><td>The data for the 'IGM' transition plot</td><td><a href='transition_IGM_sum.txt' download='transition_IGM_sum.txt' >Download</a></td></tr>" >> $output
|
|
6
|
539 echo "<tr><td>The data for the 'IGE' transition plot</td><td><a href='transition_IGE_sum.txt' download='transition_IGE_sum.txt' >Download</a></td></tr>" >> $output
|
|
0
|
540
|
|
2
|
541 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Antigen Selection</td></tr>" >> $output
|
|
0
|
542 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
|
|
|
543 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
|
|
|
544
|
|
|
545 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
|
|
|
546 echo "<tr><td>Baseline data</td><td><a href='baseline.txt' download='baseline.txt' >Download</a></td></tr>" >> $output
|
|
|
547 echo "<tr><td>Baseline IGA PDF</td><td><a href='baseline_IGA.pdf' download='baseline_IGA.pdf' >Download</a></td></tr>" >> $output
|
|
|
548 echo "<tr><td>Baseline IGA data</td><td><a href='baseline_IGA.txt' download='baseline_IGA.txt' >Download</a></td></tr>" >> $output
|
|
|
549 echo "<tr><td>Baseline IGG PDF</td><td><a href='baseline_IGG.pdf' download='baseline_IGG.pdf' >Download</a></td></tr>" >> $output
|
|
|
550 echo "<tr><td>Baseline IGG data</td><td><a href='baseline_IGG.txt' download='baseline_IGG.txt' >Download</a></td></tr>" >> $output
|
|
|
551 echo "<tr><td>Baseline IGM PDF</td><td><a href='baseline_IGM.pdf' download='baseline_IGM.pdf' >Download</a></td></tr>" >> $output
|
|
|
552 echo "<tr><td>Baseline IGM data</td><td><a href='baseline_IGM.txt' download='baseline_IGM.txt' >Download</a></td></tr>" >> $output
|
|
6
|
553 echo "<tr><td>Baseline IGE data</td><td><a href='baseline_IGE.txt' download='baseline_IGE.txt' >Download</a></td></tr>" >> $output
|
|
0
|
554
|
|
2
|
555 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>CSR</td></tr>" >> $output
|
|
|
556 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
|
|
|
557 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
|
|
|
558
|
|
|
559 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Clonality</td></tr>" >> $output
|
|
|
560 echo "<tr><td>Sequence overlap between subclasses</td><td><a href='sequence_overview/index.html'>View</a></td></tr>" >> $output
|
|
|
561 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
|
|
|
562 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
|
|
|
563 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
|
|
|
564 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
|
|
|
565 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
|
|
|
566 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
|
|
|
567 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
|
|
|
568 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
|
569 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
|
|
|
570 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
|
571
|
|
|
572 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Filtered IMGT output files</td></tr>" >> $output
|
|
0
|
573 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
|
|
|
574 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
|
|
|
575 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
|
|
|
576 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
|
|
|
577 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
|
|
|
578 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
|
|
|
579 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
|
|
|
580 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
|
|
|
581 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
|
|
|
582 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
|
583 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
|
584
|
|
|
585 echo "</table>" >> $output
|
|
|
586
|
|
|
587 echo "</div>" >> $output #downloads tab end
|
|
|
588
|
|
|
589 echo "</div>" >> $output #tabs end
|
|
|
590
|
|
|
591 echo "</html>" >> $output
|
|
|
592
|
|
5
|
593
|
|
|
594 if [[ "$fast" == "no" ]] ; then
|
|
0
|
595
|
|
5
|
596 echo "---------------- baseline ----------------"
|
|
|
597 echo "---------------- baseline ----------------<br />" >> $log
|
|
|
598 tmp="$PWD"
|
|
|
599
|
|
|
600 mkdir $outdir/baseline
|
|
0
|
601
|
|
|
602
|
|
5
|
603 mkdir $outdir/baseline/IGA_IGG_IGM
|
|
|
604 if [[ $(wc -l < $outdir/new_IMGT/1_Summary.txt) -gt "1" ]]; then
|
|
|
605 cd $outdir/baseline/IGA_IGG_IGM
|
|
|
606 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"
|
|
|
607 else
|
|
|
608 echo "No sequences" > "$outdir/baseline.txt"
|
|
|
609 fi
|
|
0
|
610
|
|
5
|
611 mkdir $outdir/baseline/IGA
|
|
|
612 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
|
|
|
613 cd $outdir/baseline/IGA
|
|
|
614 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"
|
|
|
615 else
|
|
|
616 echo "No IGA sequences" > "$outdir/baseline_IGA.txt"
|
|
|
617 fi
|
|
0
|
618
|
|
5
|
619 mkdir $outdir/baseline/IGG
|
|
|
620 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
|
|
|
621 cd $outdir/baseline/IGG
|
|
|
622 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"
|
|
|
623 else
|
|
|
624 echo "No IGG sequences" > "$outdir/baseline_IGG.txt"
|
|
|
625 fi
|
|
0
|
626
|
|
5
|
627 mkdir $outdir/baseline/IGM
|
|
|
628 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
|
|
|
629 cd $outdir/baseline/IGM
|
|
|
630 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"
|
|
|
631 else
|
|
|
632 echo "No IGM sequences" > "$outdir/baseline_IGM.txt"
|
|
|
633 fi
|
|
|
634
|
|
6
|
635 mkdir $outdir/baseline/IGE
|
|
|
636 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
|
|
|
637 cd $outdir/baseline/IGE
|
|
|
638 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"
|
|
|
639 else
|
|
|
640 echo "No IGE sequences" > "$outdir/baseline_IGE.txt"
|
|
|
641 fi
|
|
|
642
|
|
5
|
643 cd $tmp
|
|
|
644
|
|
|
645 echo "Cleaning up *.RData files"
|
|
|
646 find $outdir/baseline -name "*.RData" -type f -delete
|
|
|
647
|
|
0
|
648 fi
|
|
|
649
|
|
|
650 echo "---------------- naive_output.r ----------------"
|
|
|
651 echo "---------------- naive_output.r ----------------<br />" >> $log
|
|
|
652
|
|
5
|
653 if [[ "$naive_output" == "yes" ]]
|
|
0
|
654 then
|
|
18
|
655 if [[ "${class_filter}" == "101_101" ]]
|
|
|
656 then
|
|
|
657 cp $outdir/new_IMGT.txz ${naive_output_ca}
|
|
|
658 else
|
|
|
659 cp $outdir/new_IMGT_IGA.txz ${naive_output_ca}
|
|
|
660 cp $outdir/new_IMGT_IGG.txz ${naive_output_cg}
|
|
|
661 cp $outdir/new_IMGT_IGM.txz ${naive_output_cm}
|
|
|
662 cp $outdir/new_IMGT_IGE.txz ${naive_output_ce}
|
|
|
663 fi
|
|
0
|
664 fi
|
|
|
665
|
|
|
666 echo "</table>" >> $outdir/base_overview.html
|
|
|
667
|
|
|
668 mv $log $outdir/log.html
|
|
|
669
|
|
|
670 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
|
|
|
671 echo "<table border = 1>" >> $log
|
|
|
672 echo "<thead><tr><th>Info</th><th>Sequences</th><th>Percentage</th></tr></thead>" >> $log
|
|
|
673 tIFS="$TMP"
|
|
|
674 IFS=$'\t'
|
|
|
675 while read step seq perc
|
|
|
676 do
|
|
|
677 echo "<tr>" >> $log
|
|
|
678 echo "<td>$step</td>" >> $log
|
|
|
679 echo "<td>$seq</td>" >> $log
|
|
|
680 echo "<td>${perc}%</td>" >> $log
|
|
|
681 echo "</tr>" >> $log
|
|
|
682 done < $outdir/filtering_steps.txt
|
|
|
683 echo "</table border></center></html>" >> $log
|
|
|
684
|
|
|
685 IFS="$tIFS"
|
|
|
686
|
|
|
687
|
|
|
688 echo "---------------- Done! ----------------"
|
|
|
689 echo "---------------- Done! ----------------<br />" >> $outdir/log.html
|
|
|
690
|
|
|
691
|
|
|
692
|
|
|
693
|
|
|
694
|
|
|
695
|
|
|
696
|
|
|
697
|
|
|
698
|
|
|
699
|
|
|
700
|
|
|
701
|
|
|
702
|
|
|
703
|
|
|
704
|
|
|
705
|
|
|
706
|
|
|
707
|
|
|
708
|
|
|
709
|
|
|
710
|
