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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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34
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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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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 $PWD/files/"
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34
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40 mkdir -p "$PWD/files/$title"
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41 tar -xJf $input -C "$PWD/files/$title"
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0
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42 fi
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43
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35
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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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40
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46 cat "`find $PWD/files/ -name "4_*"`" > $PWD/gapped_aa.txt
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35
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47 cat "`find $PWD/files/ -name "5_*"`" > $PWD/aa.txt
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48 cat "`find $PWD/files/ -name "6_*"`" > $PWD/junction.txt
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49 cat "`find $PWD/files/ -name "7_*"`" > $PWD/mutationanalysis.txt
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50 cat "`find $PWD/files/ -name "8_*"`" > $PWD/mutationstats.txt
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51 cat "`find $PWD/files/ -name "10_*"`" > $PWD/hotspots.txt
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0
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52
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53 if [[ ${#BLASTN_DIR} -ge 5 ]] ; then
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54 echo "On server, using BLASTN_DIR env: ${BLASTN_DIR}"
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55 else
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56 BLASTN_DIR="/home/galaxy/Downloads/ncbi-blast-2.4.0+/bin"
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57 echo "Dev Galaxy set BLASTN_DIR to: ${BLASTN_DIR}"
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58 fi
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59
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60 echo "---------------- class identification ----------------"
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61 echo "---------------- class identification ----------------<br />" >> $log
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62
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63 python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt
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64
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65 echo "---------------- merge_and_filter.r ----------------"
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66 echo "---------------- merge_and_filter.r ----------------<br />" >> $log
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67
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40
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68 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt "$PWD/gapped_aa.txt" $outdir/identified_genes.txt $outdir/merged.txt $outdir/before_unique_filter.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${class_filter} ${empty_region_filter} 2>&1
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0
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69
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5
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70 if [[ "$fast" == "no" ]] ; then
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71
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5
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72 echo "---------------- creating new IMGT zips ----------------"
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73 echo "---------------- creating new IMGT zips ----------------<br />" >> $log
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74
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75 mkdir $outdir/new_IMGT
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76
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36
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77 cat "`find $PWD/files/ -name "1_*"`" > "$outdir/new_IMGT/1_Summary.txt"
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78 cat "`find $PWD/files/ -name "2_*"`" > "$outdir/new_IMGT/2_IMGT-gapped-nt-sequences.txt"
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79 cat "`find $PWD/files/ -name "3_*"`" > "$outdir/new_IMGT/3_Nt-sequences.txt"
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80 cat "`find $PWD/files/ -name "4_*"`" > "$outdir/new_IMGT/4_IMGT-gapped-AA-sequences.txt"
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81 cat "`find $PWD/files/ -name "5_*"`" > "$outdir/new_IMGT/5_AA-sequences.txt"
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82 cat "`find $PWD/files/ -name "6_*"`" > "$outdir/new_IMGT/6_Junction.txt"
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83 cat "`find $PWD/files/ -name "7_*"`" > "$outdir/new_IMGT/7_V-REGION-mutation-and-AA-change-table.txt"
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84 cat "`find $PWD/files/ -name "8_*"`" > "$outdir/new_IMGT/8_V-REGION-nt-mutation-statistics.txt"
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85 cat "`find $PWD/files/ -name "9_*"`" > "$outdir/new_IMGT/9_V-REGION-AA-change-statistics.txt"
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86 cat "`find $PWD/files/ -name "10_*"`" > "$outdir/new_IMGT/10_V-REGION-mutation-hotspots.txt"
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0
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87
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5
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88 mkdir $outdir/new_IMGT_IGA
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89 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA
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90
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5
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91 mkdir $outdir/new_IMGT_IGA1
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92 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA1
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93
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5
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94 mkdir $outdir/new_IMGT_IGA2
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95 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA2
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96
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5
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97 mkdir $outdir/new_IMGT_IGG
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98 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG
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0
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99
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5
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100 mkdir $outdir/new_IMGT_IGG1
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101 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG1
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0
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102
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5
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103 mkdir $outdir/new_IMGT_IGG2
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104 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG2
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0
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105
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5
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106 mkdir $outdir/new_IMGT_IGG3
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107 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG3
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0
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108
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5
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109 mkdir $outdir/new_IMGT_IGG4
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110 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG4
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111
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112 mkdir $outdir/new_IMGT_IGM
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113 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGM
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0
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114
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5
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115 mkdir $outdir/new_IMGT_IGE
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116 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGE
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117
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5
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118 Rscript $dir/new_imgt.r $outdir/new_IMGT/ $outdir/merged.txt "-" 2>&1
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119
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120 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA/ $outdir/merged.txt "IGA" 2>&1
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121 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA1/ $outdir/merged.txt "IGA1" 2>&1
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122 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA2/ $outdir/merged.txt "IGA2" 2>&1
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0
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123
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5
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124 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG/ $outdir/merged.txt "IGG" 2>&1
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125 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG1/ $outdir/merged.txt "IGG1" 2>&1
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126 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG2/ $outdir/merged.txt "IGG2" 2>&1
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127 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG3/ $outdir/merged.txt "IGG3" 2>&1
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128 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG4/ $outdir/merged.txt "IGG4" 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_IGM/ $outdir/merged.txt "IGM" 2>&1
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131
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5
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132 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGE/ $outdir/merged.txt "IGE" 2>&1
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0
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133
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134
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5
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135 tmp="$PWD"
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136 cd $outdir/new_IMGT/ #tar weirdness...
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137 tar -cJf ../new_IMGT.txz *
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138
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5
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139 cd $outdir/new_IMGT_IGA/
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140 tar -cJf ../new_IMGT_IGA.txz *
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141
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5
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142 cd $outdir/new_IMGT_IGA1/
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143 tar -cJf ../new_IMGT_IGA1.txz *
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144
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5
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145 cd $outdir/new_IMGT_IGA2/
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146 tar -cJf ../new_IMGT_IGA2.txz *
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147
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5
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148 cd $outdir/new_IMGT_IGG/
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149 tar -cJf ../new_IMGT_IGG.txz *
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150
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5
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151 cd $outdir/new_IMGT_IGG1/
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152 tar -cJf ../new_IMGT_IGG1.txz *
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153
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5
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154 cd $outdir/new_IMGT_IGG2/
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155 tar -cJf ../new_IMGT_IGG2.txz *
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156
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157 cd $outdir/new_IMGT_IGG3/
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158 tar -cJf ../new_IMGT_IGG3.txz *
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159
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5
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160 cd $outdir/new_IMGT_IGG4/
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161 tar -cJf ../new_IMGT_IGG4.txz *
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162
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163 cd $outdir/new_IMGT_IGM/
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164 tar -cJf ../new_IMGT_IGM.txz *
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0
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165
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5
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166 cd $outdir/new_IMGT_IGE/
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167 tar -cJf ../new_IMGT_IGE.txz *
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0
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168
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5
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169 cd $tmp
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170 fi
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171
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172 echo "---------------- shm_csr.r ----------------"
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173 echo "---------------- shm_csr.r ----------------<br />" >> $log
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174
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5
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175 classes="IGA,IGA1,IGA2,IGG,IGG1,IGG2,IGG3,IGG4,IGM,IGE,unmatched"
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176 echo "R mutation analysis"
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1
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177 Rscript $dir/shm_csr.r $outdir/merged.txt $classes $outdir ${empty_region_filter} 2>&1
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0
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178
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179 echo "---------------- shm_csr.py ----------------"
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180 echo "---------------- shm_csr.py ----------------<br />" >> $log
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181
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1
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182 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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183
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184 echo "---------------- aa_histogram.r ----------------"
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185 echo "---------------- aa_histogram.r ----------------<br />" >> $log
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186
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5
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187 Rscript $dir/aa_histogram.r $outdir/aa_id_mutations.txt $outdir/absent_aa_id.txt "IGA,IGG,IGM,IGE" $outdir/ 2>&1
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188 if [ -e "$outdir/aa_histogram_.png" ]; then
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189 mv $outdir/aa_histogram_.png $outdir/aa_histogram.png
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42
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190 mv $outdir/aa_histogram_.pdf $outdir/aa_histogram.pdf
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191 mv $outdir/aa_histogram_.txt $outdir/aa_histogram.txt
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29
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192 mv $outdir/aa_histogram_absent_.txt $outdir/aa_histogram_absent.txt
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193 mv $outdir/aa_histogram_count_.txt $outdir/aa_histogram_count.txt
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194 mv $outdir/aa_histogram_sum_.txt $outdir/aa_histogram_sum.txt
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0
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195 fi
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196
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5
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197 genes=(IGA IGA1 IGA2 IGG IGG1 IGG2 IGG3 IGG4 IGM IGE)
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198
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199 funcs=(sum mean median)
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200 funcs=(sum)
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201
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202 echo "---------------- sequence_overview.r ----------------"
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203 echo "---------------- sequence_overview.r ----------------<br />" >> $log
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204
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205 mkdir $outdir/sequence_overview
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206
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7
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207 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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208
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209 echo "<table border='1'>" > $outdir/base_overview.html
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210
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211 while IFS=$'\t' read ID class seq A C G T
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212 do
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213 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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214 done < $outdir/sequence_overview/ntoverview.txt
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215
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216 echo "<html><center><h1>$title</h1></center>" > $output
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217 echo "<meta name='viewport' content='width=device-width, initial-scale=1'>" >> $output
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218 echo "<script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $output
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219 echo "<script type='text/javascript' src='tabber.js'></script>" >> $output
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220 echo "<script type='text/javascript' src='script.js'></script>" >> $output
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221 echo "<link rel='stylesheet' type='text/css' href='style.css'>" >> $output
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222 echo "<link rel='stylesheet' type='text/css' href='pure-min.css'>" >> $output
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223
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224 matched_count="`cat $outdir/merged.txt | grep -v 'unmatched' | tail -n +2 | wc -l`"
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225 unmatched_count="`cat $outdir/unmatched.txt | tail -n +2 | wc -l`"
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226 total_count=$((matched_count + unmatched_count))
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227 perc_count=$((unmatched_count / total_count * 100))
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228 perc_count=`bc -l <<< "scale=2; ${unmatched_count} / ${total_count} * 100"`
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229 perc_count=`bc -l <<< "scale=2; (${unmatched_count} / ${total_count} * 100 ) / 1"`
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230
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231 echo "<center><h2>Total: ${total_count}</h2></center>" >> $output
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232 echo "<center><h2>Matched: ${matched_count} Unmatched: ${unmatched_count}</h2></center>" >> $output
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233 echo "<center><h2>Percentage unmatched: ${perc_count}</h2></center>" >> $output
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234
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235 echo "---------------- main tables ----------------"
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236 echo "---------------- main tables ----------------<br />" >> $log
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237
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238 echo "<div class='tabber'>" >> $output
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23
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239 echo "<div class='tabbertab' title='SHM Overview' style='width: 3000px;'>" >> $output
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240
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241 for func in ${funcs[@]}
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242 do
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243
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244 echo "---------------- $func table ----------------"
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245 echo "---------------- $func table ----------------<br />" >> $log
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246
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247 cat $outdir/mutations_${func}.txt $outdir/hotspot_analysis_${func}.txt > $outdir/data_${func}.txt
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248
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249 echo "---------------- pattern_plots.r ----------------"
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250 echo "---------------- pattern_plots.r ----------------<br />" >> $log
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251
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39
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252 Rscript $dir/pattern_plots.r $outdir/data_${func}.txt $outdir/aid_motives $outdir/relative_mutations $outdir/abolute_mutations $outdir/shm_overview.txt 2>&1
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253
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254 echo "<table class='pure-table pure-table-striped'>" >> $output
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255 echo "<thead><tr><th>info</th>" >> $output
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256
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257 if [ "${class_filter}" != "101_101" ] ; then
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258
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259 for gene in ${genes[@]}
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260 do
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261 tmp=`cat $outdir/${gene}_${func}_n.txt`
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262 echo "<th><a href='matched_${gene}_${func}.txt'>${gene} (N = $tmp)</a></th>" >> $output
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263 done
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264
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265 tmp=`cat $outdir/all_${func}_n.txt`
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266 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
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267 tmp=`cat $outdir/unmatched_${func}_n.txt`
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268 echo "<th><a href='unmatched.txt'>unmatched (N = ${unmatched_count})</a></th><tr></thead>" >> $output
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269
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5
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270 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
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0
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271 do
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272 if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] ; then #meh
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5
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273 echo "<tr><td>$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>" >> $output
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0
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274 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
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5
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275 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>" >> $output
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0
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276 else
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5
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277 echo "<tr><td>$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
|
|
0
|
278 fi
|
|
|
279 done < $outdir/data_${func}.txt
|
|
|
280
|
|
|
281 else
|
|
3
|
282 tmp=`cat $outdir/all_${func}_n.txt`
|
|
0
|
283 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
|
|
|
284
|
|
5
|
285 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
|
|
0
|
286 do
|
|
|
287 if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] ; then #meh
|
|
3
|
288 echo "<tr><td>$name</td><td>${allx}/${ally}</td></tr>" >> $output
|
|
0
|
289 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
|
|
3
|
290 echo "<tr><td>$name</td><td>${allz}%</td></tr>" >> $output
|
|
0
|
291 else
|
|
3
|
292 echo "<tr><td>$name</td><td>${allx}/${ally} (${allz}%)</td></tr>" >> $output
|
|
0
|
293 fi
|
|
|
294 done < $outdir/data_${func}.txt
|
|
|
295
|
|
|
296 fi
|
|
|
297 echo "</table>" >> $output
|
|
|
298 #echo "<a href='data_${func}.txt'>Download data</a>" >> $output
|
|
|
299 done
|
|
|
300
|
|
42
|
301 echo "<a href='aid_motives.pdf'><img src='aid_motives.png' /></a><br />" >> $output
|
|
|
302 echo "<a href='relative_mutations.pdf'><img src='relative_mutations.png' /></a><br />" >> $output
|
|
|
303 echo "<a href='abolute_mutations.pdf'><img src='abolute_mutations.png' /></a><br />" >> $output
|
|
39
|
304 echo "<br />" >> $output
|
|
|
305 cat $dir/shm_overview.htm >> $output
|
|
0
|
306 echo "</div>" >> $output #SHM overview tab end
|
|
|
307
|
|
|
308 echo "---------------- images ----------------"
|
|
|
309 echo "---------------- images ----------------<br />" >> $log
|
|
|
310
|
|
42
|
311 echo "<div class='tabbertab' title='SHM Frequency' style='width: 3000px;'></a>" >> $output
|
|
0
|
312
|
|
|
313 if [ -a $outdir/scatter.png ]
|
|
|
314 then
|
|
42
|
315 echo "<a href='scatter.pdf'><img src='scatter.png'/><br />" >> $output
|
|
0
|
316 fi
|
|
|
317 if [ -a $outdir/frequency_ranges.png ]
|
|
|
318 then
|
|
42
|
319 echo "<a href='frequency_ranges.pdf'><img src='frequency_ranges.png'/></a><br />" >> $output
|
|
0
|
320 fi
|
|
|
321
|
|
39
|
322 echo "<br />" >> $output
|
|
|
323 cat $dir/shm_frequency.htm >> $output
|
|
|
324
|
|
0
|
325 echo "</div>" >> $output #SHM frequency tab end
|
|
|
326
|
|
23
|
327 echo "<div class='tabbertab' title='Transition tables' style='width: 3000px;'>" >> $output
|
|
0
|
328
|
|
|
329 echo "<table border='0'>" >> $output
|
|
|
330
|
|
|
331 for gene in ${genes[@]}
|
|
|
332 do
|
|
|
333 echo "<tr>" >> $output
|
|
|
334 echo "<td><h1>${gene}</h1></td>" >> $output
|
|
23
|
335
|
|
|
336 if [ -e $outdir/transitions_heatmap_${gene}.png ]
|
|
|
337 then
|
|
42
|
338 echo "<td><a href='transitions_heatmap_${gene}.pdf'><img src='transitions_heatmap_${gene}.png' /></a></td>" >> $output
|
|
23
|
339 else
|
|
|
340 echo "<td></td>" >> $output
|
|
|
341 fi
|
|
|
342
|
|
|
343 if [ -e $outdir/transitions_stacked_${gene}.png ]
|
|
|
344 then
|
|
42
|
345 echo "<td><a href='transitions_stacked_${gene}.pdf'><img src='transitions_stacked_${gene}.png' /></a></td>" >> $output
|
|
23
|
346 else
|
|
|
347 echo "<td></td>" >> $output
|
|
|
348 fi
|
|
|
349
|
|
0
|
350 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
|
|
|
351 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
|
|
|
352 first="true"
|
|
|
353 while IFS=, read from a c g t
|
|
|
354 do
|
|
|
355 if [ "$first" == "true" ] ; then
|
|
|
356 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
|
|
|
357 first="false"
|
|
|
358 else
|
|
|
359 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
|
|
|
360 fi
|
|
|
361 done < $outdir/transitions_${gene}_sum.txt
|
|
|
362 echo "</table></td>" >> $output
|
|
|
363
|
|
|
364 echo "</tr>" >> $output
|
|
|
365 done
|
|
|
366
|
|
|
367 echo "<tr>" >> $output
|
|
|
368 echo "<td><h1>All</h1></td>" >> $output
|
|
42
|
369 echo "<td><a href='transitions_heatmap_all.pdf'><img src='transitions_heatmap_all.png' /></a></td>" >> $output
|
|
|
370 echo "<td><a href='transitions_stacked_all.pdf'><img src='transitions_stacked_all.png' /></a></td>" >> $output
|
|
0
|
371 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
|
|
|
372 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
|
|
|
373 first="true"
|
|
|
374 while IFS=, read from a c g t
|
|
|
375 do
|
|
|
376 if [ "$first" == "true" ] ; then
|
|
|
377 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
|
|
|
378 first="false"
|
|
|
379 else
|
|
|
380 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
|
|
|
381 fi
|
|
|
382 done < $outdir/transitions_all_sum.txt
|
|
|
383 echo "</table></td>" >> $output
|
|
|
384
|
|
|
385 echo "</tr>" >> $output
|
|
|
386
|
|
|
387 echo "</table>" >> $output
|
|
|
388
|
|
39
|
389 echo "<br />" >> $output
|
|
|
390 cat $dir/shm_transition.htm >> $output
|
|
|
391
|
|
0
|
392 echo "</div>" >> $output #transition tables tab end
|
|
|
393
|
|
|
394 echo "<div class='tabbertab' title='Antigen Selection'>" >> $output
|
|
|
395
|
|
23
|
396 if [ -e $outdir/aa_histogram.png ]
|
|
0
|
397 then
|
|
42
|
398 echo "<a href='aa_histogram.pdf'><img src='aa_histogram.png'/></a><br />" >> $output
|
|
23
|
399 fi
|
|
|
400
|
|
|
401 if [ -e $outdir/aa_histogram_IGA.png ]
|
|
|
402 then
|
|
42
|
403 echo "<a href='aa_histogram_IGA.pdf'><img src='aa_histogram_IGA.png'/></a><br />" >> $output
|
|
23
|
404 fi
|
|
|
405
|
|
|
406 if [ -e $outdir/aa_histogram_IGG.png ]
|
|
|
407 then
|
|
42
|
408 echo "<a href='aa_histogram_IGG.pdf'><img src='aa_histogram_IGG.png'/></a><br />" >> $output
|
|
23
|
409 fi
|
|
|
410
|
|
|
411 if [ -e $outdir/aa_histogram_IGM.png ]
|
|
|
412 then
|
|
42
|
413 echo "<a href='aa_histogram_IGM.pdf'><img src='aa_histogram_IGM.png'/></a><br />" >> $output
|
|
23
|
414 fi
|
|
|
415
|
|
|
416 if [ -e $outdir/aa_histogram_IGE.png ]
|
|
|
417 then
|
|
42
|
418 echo "<a href='aa_histogram_IGE.pdf'><img src='aa_histogram_IGE.png'/></a><br />" >> $output
|
|
0
|
419 fi
|
|
|
420
|
|
23
|
421
|
|
33
|
422
|
|
|
423 if [[ "$fast" == "no" ]] ; then
|
|
|
424
|
|
41
|
425
|
|
|
426
|
|
33
|
427 echo "---------------- baseline ----------------"
|
|
|
428 echo "---------------- baseline ----------------<br />" >> $log
|
|
|
429 tmp="$PWD"
|
|
|
430
|
|
|
431 mkdir $outdir/baseline
|
|
37
|
432
|
|
41
|
433 echo "<center><h1>BASELINe</h1>" >> $output
|
|
|
434 header_substring="Based on CDR1, FR2, CDR2, FR3 (27:27:38:55:65:104:-)"
|
|
|
435
|
|
37
|
436 baseline_boundaries="27:27:38:55:65:104:-"
|
|
|
437
|
|
|
438 if [[ "${empty_region_filter}" == "leader" ]] ; then
|
|
|
439 baseline_boundaries="1:26:38:55:65:104:-"
|
|
41
|
440 header_substring="Based on FR1, CDR1, FR2, CDR2, FR3 (1:26:38:55:65:104,-)"
|
|
37
|
441 fi
|
|
41
|
442
|
|
|
443 echo "<p>${header_substring}</p></center>" >> $output
|
|
23
|
444
|
|
33
|
445 mkdir $outdir/baseline/IGA_IGG_IGM
|
|
|
446 if [[ $(wc -l < $outdir/new_IMGT/1_Summary.txt) -gt "1" ]]; then
|
|
|
447 cd $outdir/baseline/IGA_IGG_IGM
|
|
41
|
448 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT.txz "IGA_IGG_IGM_IGE" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt"
|
|
33
|
449 else
|
|
|
450 echo "No sequences" > "$outdir/baseline.txt"
|
|
|
451 fi
|
|
|
452
|
|
|
453 mkdir $outdir/baseline/IGA
|
|
|
454 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
|
|
|
455 cd $outdir/baseline/IGA
|
|
37
|
456 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT_IGA.txz "IGA" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGA.pdf" "Sequence.ID" "$outdir/baseline_IGA.txt"
|
|
33
|
457 else
|
|
|
458 echo "No IGA sequences" > "$outdir/baseline_IGA.txt"
|
|
|
459 fi
|
|
|
460
|
|
|
461 mkdir $outdir/baseline/IGG
|
|
|
462 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
|
|
|
463 cd $outdir/baseline/IGG
|
|
37
|
464 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT_IGG.txz "IGG" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGG.pdf" "Sequence.ID" "$outdir/baseline_IGG.txt"
|
|
33
|
465 else
|
|
|
466 echo "No IGG sequences" > "$outdir/baseline_IGG.txt"
|
|
|
467 fi
|
|
23
|
468
|
|
33
|
469 mkdir $outdir/baseline/IGM
|
|
|
470 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
|
|
|
471 cd $outdir/baseline/IGM
|
|
37
|
472 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT_IGM.txz "IGM" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGM.pdf" "Sequence.ID" "$outdir/baseline_IGM.txt"
|
|
33
|
473 else
|
|
|
474 echo "No IGM sequences" > "$outdir/baseline_IGM.txt"
|
|
|
475 fi
|
|
|
476
|
|
|
477 mkdir $outdir/baseline/IGE
|
|
|
478 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
|
|
|
479 cd $outdir/baseline/IGE
|
|
37
|
480 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT_IGE.txz "IGE" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGE.pdf" "Sequence.ID" "$outdir/baseline_IGE.txt"
|
|
33
|
481 else
|
|
|
482 echo "No IGE sequences" > "$outdir/baseline_IGE.txt"
|
|
|
483 fi
|
|
|
484
|
|
|
485 cd $tmp
|
|
23
|
486
|
|
33
|
487 echo "Cleaning up *.RData files"
|
|
|
488 find $outdir/baseline -name "*.RData" -type f -delete
|
|
|
489
|
|
|
490 if [ -e $outdir/baseline.pdf ]
|
|
|
491 then
|
|
|
492 echo "<embed src='baseline.pdf' width='700px' height='1000px'>" >> $output
|
|
|
493 fi
|
|
|
494
|
|
|
495 if [ -e $outdir/baseline_IGA.pdf ]
|
|
|
496 then
|
|
|
497 echo "<embed src='baseline_IGA.pdf' width='700px' height='1000px'>" >> $output
|
|
|
498 fi
|
|
23
|
499
|
|
33
|
500 if [ -e $outdir/baseline_IGG.pdf ]
|
|
|
501 then
|
|
|
502 echo "<embed src='baseline_IGG.pdf' width='700px' height='1000px'>" >> $output
|
|
|
503 fi
|
|
|
504
|
|
|
505 if [ -e $outdir/baseline_IGM.pdf ]
|
|
|
506 then
|
|
|
507 echo "<embed src='baseline_IGM.pdf' width='700px' height='1000px'>" >> $output
|
|
|
508 fi
|
|
|
509
|
|
|
510 if [ -e $outdir/baseline_IGE.pdf ]
|
|
|
511 then
|
|
|
512 echo "<embed src='baseline_IGE.pdf' width='700px' height='1000px'>" >> $output
|
|
|
513 fi
|
|
23
|
514 fi
|
|
0
|
515
|
|
39
|
516 echo "<br />" >> $output
|
|
|
517 cat $dir/shm_selection.htm >> $output
|
|
|
518
|
|
0
|
519 echo "</div>" >> $output #antigen selection tab end
|
|
|
520
|
|
|
521 echo "<div class='tabbertab' title='CSR'>" >> $output #CSR tab
|
|
|
522
|
|
23
|
523 if [ -e $outdir/IGA.png ]
|
|
0
|
524 then
|
|
42
|
525 echo "<a href='IGA.pdf'><img src='IGA.png'/></a><br />" >> $output
|
|
0
|
526 fi
|
|
23
|
527 if [ -e $outdir/IGG.png ]
|
|
0
|
528 then
|
|
42
|
529 echo "<a href='IGG.pdf'><img src='IGG.png'/></a><br />" >> $output
|
|
0
|
530 fi
|
|
|
531
|
|
39
|
532 echo "<br />" >> $output
|
|
|
533 cat $dir/shm_csr.htm >> $output
|
|
|
534
|
|
0
|
535 echo "</div>" >> $output #CSR tab end
|
|
|
536
|
|
5
|
537 if [[ "$fast" == "no" ]] ; then
|
|
|
538
|
|
|
539 echo "---------------- change-o MakeDB ----------------"
|
|
0
|
540
|
|
5
|
541 mkdir $outdir/change_o
|
|
0
|
542
|
|
5
|
543 tmp="$PWD"
|
|
0
|
544
|
|
5
|
545 cd $outdir/change_o
|
|
0
|
546
|
|
5
|
547 bash $dir/change_o/makedb.sh $outdir/new_IMGT.txz false false false $outdir/change_o/change-o-db.txt
|
|
|
548 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
|
549
|
|
5
|
550 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
|
551
|
|
5
|
552 echo "Rscript $dir/merge.r $outdir/change_o/change-o-db-defined_clones.txt $outdir/$outdir/merged.txt 'all' 'Sequence.ID,best_match' 'Sequence.ID' 'Sequence.ID' '\t' $outdir/change_o/change-o-db-defined_clones.txt 2>&1"
|
|
0
|
553
|
|
5
|
554 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
|
|
|
555 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGA.txz false false false $outdir/change_o/change-o-db-IGA.txt
|
|
|
556 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGA.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGA.txt $outdir/change_o/change-o-defined_clones-summary-IGA.txt
|
|
|
557 else
|
|
|
558 echo "No IGA sequences" > "$outdir/change_o/change-o-db-defined_clones-IGA.txt"
|
|
|
559 echo "No IGA sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGA.txt"
|
|
|
560 fi
|
|
0
|
561
|
|
5
|
562 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
|
|
|
563 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGG.txz false false false $outdir/change_o/change-o-db-IGG.txt
|
|
|
564 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 $outdir/change_o/change-o-defined_clones-summary-IGG.txt
|
|
|
565 else
|
|
|
566 echo "No IGG sequences" > "$outdir/change_o/change-o-db-defined_clones-IGG.txt"
|
|
|
567 echo "No IGG sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGG.txt"
|
|
|
568 fi
|
|
0
|
569
|
|
5
|
570 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
|
|
|
571 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGM.txz false false false $outdir/change_o/change-o-db-IGM.txt
|
|
|
572 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 $outdir/change_o/change-o-defined_clones-summary-IGM.txt
|
|
|
573 else
|
|
|
574 echo "No IGM sequences" > "$outdir/change_o/change-o-db-defined_clones-IGM.txt"
|
|
|
575 echo "No IGM sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGM.txt"
|
|
|
576 fi
|
|
0
|
577
|
|
6
|
578 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
|
|
|
579 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGE.txz false false false $outdir/change_o/change-o-db-IGE.txt
|
|
|
580 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 $outdir/change_o/change-o-defined_clones-summary-IGE.txt
|
|
|
581 else
|
|
|
582 echo "No IGE sequences" > "$outdir/change_o/change-o-db-defined_clones-IGE.txt"
|
|
|
583 echo "No IGE sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGE.txt"
|
|
|
584 fi
|
|
|
585
|
|
5
|
586 PWD="$tmp"
|
|
0
|
587
|
|
39
|
588 echo "<div class='tabbertab' title='Clonal Relation' style='width: 7000px;'>" >> $output #clonality tab
|
|
0
|
589
|
|
16
|
590 function clonality_table {
|
|
|
591 local infile=$1
|
|
|
592 local outfile=$2
|
|
|
593
|
|
|
594 echo "<table class='pure-table pure-table-striped'>" >> $outfile
|
|
|
595 echo "<thead><tr><th>Clone size</th><th>Nr of clones</th><th>Nr of sequences</th></tr></thead>" >> $outfile
|
|
|
596
|
|
|
597 first='true'
|
|
|
598
|
|
|
599 while read size clones seqs
|
|
|
600 do
|
|
|
601 if [[ "$first" == "true" ]]; then
|
|
|
602 first="false"
|
|
|
603 continue
|
|
|
604 fi
|
|
|
605 echo "<tr><td>$size</td><td>$clones</td><td>$seqs</td></tr>" >> $outfile
|
|
|
606 done < $infile
|
|
|
607
|
|
|
608 echo "</table>" >> $outfile
|
|
|
609 }
|
|
|
610 echo "<div class='tabber'>" >> $output
|
|
0
|
611
|
|
16
|
612 echo "<div class='tabbertab' title='All'>" >> $output
|
|
|
613 clonality_table $outdir/change_o/change-o-defined_clones-summary.txt $output
|
|
|
614 echo "</div>" >> $output
|
|
0
|
615
|
|
16
|
616 echo "<div class='tabbertab' title='IGA'>" >> $output
|
|
|
617 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGA.txt $output
|
|
|
618 echo "</div>" >> $output
|
|
0
|
619
|
|
16
|
620 echo "<div class='tabbertab' title='IGG'>" >> $output
|
|
|
621 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGG.txt $output
|
|
|
622 echo "</div>" >> $output
|
|
0
|
623
|
|
16
|
624 echo "<div class='tabbertab' title='IGM'>" >> $output
|
|
|
625 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
|
|
|
626 echo "</div>" >> $output
|
|
6
|
627
|
|
16
|
628 echo "<div class='tabbertab' title='IGE'>" >> $output
|
|
|
629 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
|
|
|
630 echo "</div>" >> $output
|
|
0
|
631
|
|
39
|
632 echo "<div class='tabbertab' title='Overlap' style='width: 7000px;'>" >> $output
|
|
|
633 cat "$outdir/sequence_overview/index.html" | sed -e 's:</td>:</td>\n:g' | sed "s:href='\(.*\).html:href='sequence_overview/\1.html:g" >> $output # rewrite href to 'sequence_overview/..."
|
|
16
|
634 echo "</div>" >> $output
|
|
39
|
635
|
|
16
|
636 echo "</div>" >> $output #clonality tabber end
|
|
39
|
637
|
|
|
638 echo "<br />" >> $output
|
|
|
639 cat $dir/shm_clonality.htm >> $output
|
|
|
640
|
|
16
|
641 echo "</div>" >> $output #clonality tab end
|
|
0
|
642
|
|
5
|
643 fi
|
|
|
644
|
|
0
|
645 echo "<div class='tabbertab' title='Downloads'>" >> $output
|
|
|
646
|
|
|
647 echo "<table class='pure-table pure-table-striped'>" >> $output
|
|
|
648 echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output
|
|
|
649 echo "<tr><td>The complete dataset</td><td><a href='merged.txt' download='merged.txt' >Download</a></td></tr>" >> $output
|
|
|
650 echo "<tr><td>The filtered dataset</td><td><a href='filtered.txt' download='filtered.txt' >Download</a></td></tr>" >> $output
|
|
|
651 echo "<tr><td>The alignment info on the unmatched sequences</td><td><a href='unmatched.txt' download='unmatched.txt' >Download</a></td></tr>" >> $output
|
|
|
652
|
|
2
|
653 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Overview</td></tr>" >> $output
|
|
23
|
654 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
|
655 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
|
|
|
656 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
|
|
|
657 echo "<tr><td>Base count for every sequence</td><td><a href='base_overview.html'>View</a></td></tr>" >> $output
|
|
39
|
658 echo "<tr><td>The data used to generate the percentage of mutations in AID and pol eta motives plot</td><td><a href='aid_motives.txt' download='aid_motives.txt' >Download</a></td></tr>" >> $output
|
|
|
659 echo "<tr><td>The data used to generate the relative mutation patterns plot</td><td><a href='relative_mutations.txt' download='relative_mutations.txt' >Download</a></td></tr>" >> $output
|
|
|
660 echo "<tr><td>The data used to generate the absolute mutation patterns plot</td><td><a href='absolute_mutations.txt' download='abolute_mutations.txt' >Download</a></td></tr>" >> $output
|
|
2
|
661
|
|
|
662 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Frequency</td></tr>" >> $output
|
|
0
|
663 echo "<tr><td>The data generate the frequency scatter plot</td><td><a href='scatter.txt' download='scatter.txt' >Download</a></td></tr>" >> $output
|
|
|
664 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
|
|
|
665 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
|
|
|
666
|
|
2
|
667 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Transition Tables</td></tr>" >> $output
|
|
23
|
668 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
|
|
|
669 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
|
|
|
670 echo "<tr><td>The data for the 'IGA1' transition plot</td><td><a href='transitions_IGA1_sum.txt' download='transitions_IGA1_sum.txt' >Download</a></td></tr>" >> $output
|
|
30
|
671 echo "<tr><td>The data for the 'IGA2' transition plot</td><td><a href='transitions_IGA2_sum.txt' download='transitions_IGA2_sum.txt' >Download</a></td></tr>" >> $output
|
|
23
|
672 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
|
|
|
673 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
|
|
|
674 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
|
|
|
675 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
|
|
|
676 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
|
|
|
677 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
|
|
|
678 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
|
679
|
|
2
|
680 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Antigen Selection</td></tr>" >> $output
|
|
0
|
681 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
|
|
39
|
682 echo "<tr><td>Presence of AA per sequence ID</td><td><a href='absent_aa_id.txt' download='absent_aa_id.txt' >Download</a></td></tr>" >> $output
|
|
0
|
683
|
|
29
|
684 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
|
|
|
685 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
|
|
|
686 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
|
|
|
687 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
|
|
|
688 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
|
|
|
689
|
|
0
|
690 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
|
|
|
691 echo "<tr><td>Baseline data</td><td><a href='baseline.txt' download='baseline.txt' >Download</a></td></tr>" >> $output
|
|
|
692 echo "<tr><td>Baseline IGA PDF</td><td><a href='baseline_IGA.pdf' download='baseline_IGA.pdf' >Download</a></td></tr>" >> $output
|
|
|
693 echo "<tr><td>Baseline IGA data</td><td><a href='baseline_IGA.txt' download='baseline_IGA.txt' >Download</a></td></tr>" >> $output
|
|
|
694 echo "<tr><td>Baseline IGG PDF</td><td><a href='baseline_IGG.pdf' download='baseline_IGG.pdf' >Download</a></td></tr>" >> $output
|
|
|
695 echo "<tr><td>Baseline IGG data</td><td><a href='baseline_IGG.txt' download='baseline_IGG.txt' >Download</a></td></tr>" >> $output
|
|
|
696 echo "<tr><td>Baseline IGM PDF</td><td><a href='baseline_IGM.pdf' download='baseline_IGM.pdf' >Download</a></td></tr>" >> $output
|
|
|
697 echo "<tr><td>Baseline IGM data</td><td><a href='baseline_IGM.txt' download='baseline_IGM.txt' >Download</a></td></tr>" >> $output
|
|
31
|
698 echo "<tr><td>Baseline IGE PDF</td><td><a href='baseline_IGE.pdf' download='baseline_IGE.pdf' >Download</a></td></tr>" >> $output
|
|
6
|
699 echo "<tr><td>Baseline IGE data</td><td><a href='baseline_IGE.txt' download='baseline_IGE.txt' >Download</a></td></tr>" >> $output
|
|
0
|
700
|
|
2
|
701 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>CSR</td></tr>" >> $output
|
|
39
|
702 echo "<tr><td>The data for the IGA subclass distribution plot</td><td><a href='IGA_pie.txt' download='IGA_pie.txt' >Download</a></td></tr>" >> $output
|
|
|
703 echo "<tr><td>The data for the IGG subclass distribution plot</td><td><a href='IGG_pie.txt' download='IGG_pie.txt' >Download</a></td></tr>" >> $output
|
|
2
|
704
|
|
39
|
705 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Clonal Relation</td></tr>" >> $output
|
|
2
|
706 echo "<tr><td>Sequence overlap between subclasses</td><td><a href='sequence_overview/index.html'>View</a></td></tr>" >> $output
|
|
|
707 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
|
|
|
708 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
|
|
|
709 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
|
|
|
710 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
|
|
|
711 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
|
|
|
712 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
|
|
|
713 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
|
|
|
714 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
|
715 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
|
|
|
716 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
|
717
|
|
|
718 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Filtered IMGT output files</td></tr>" >> $output
|
|
0
|
719 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
|
|
|
720 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
|
|
|
721 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
|
|
|
722 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
|
|
|
723 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
|
|
|
724 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
|
|
|
725 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
|
|
|
726 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
|
|
|
727 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
|
|
|
728 echo "<tr><td>An IMGT archive with just the matched and filtered IGM sequences</td><td><a href='new_IMGT_IGM.txz' download='new_IMGT_IGM.txz' >Download</a></td></tr>" >> $output
|
|
31
|
729 echo "<tr><td>An IMGT archive with just the matched and filtered IGE sequences</td><td><a href='new_IMGT_IGE.txz' download='new_IMGT_IGE.txz' >Download</a></td></tr>" >> $output
|
|
0
|
730
|
|
|
731 echo "</table>" >> $output
|
|
|
732
|
|
39
|
733 echo "<br />" >> $output
|
|
|
734 cat $dir/shm_downloads.htm >> $output
|
|
|
735
|
|
0
|
736 echo "</div>" >> $output #downloads tab end
|
|
|
737
|
|
|
738 echo "</div>" >> $output #tabs end
|
|
|
739
|
|
|
740 echo "</html>" >> $output
|
|
|
741
|
|
5
|
742
|
|
0
|
743 echo "---------------- naive_output.r ----------------"
|
|
|
744 echo "---------------- naive_output.r ----------------<br />" >> $log
|
|
|
745
|
|
5
|
746 if [[ "$naive_output" == "yes" ]]
|
|
0
|
747 then
|
|
28
|
748 echo "output naive output"
|
|
18
|
749 if [[ "${class_filter}" == "101_101" ]]
|
|
|
750 then
|
|
28
|
751 echo "copy new_IMGT.txz to ${naive_output_all}"
|
|
21
|
752 cp $outdir/new_IMGT.txz ${naive_output_all}
|
|
18
|
753 else
|
|
28
|
754 echo "copy for classes"
|
|
18
|
755 cp $outdir/new_IMGT_IGA.txz ${naive_output_ca}
|
|
|
756 cp $outdir/new_IMGT_IGG.txz ${naive_output_cg}
|
|
|
757 cp $outdir/new_IMGT_IGM.txz ${naive_output_cm}
|
|
|
758 cp $outdir/new_IMGT_IGE.txz ${naive_output_ce}
|
|
|
759 fi
|
|
0
|
760 fi
|
|
|
761
|
|
|
762 echo "</table>" >> $outdir/base_overview.html
|
|
|
763
|
|
|
764 mv $log $outdir/log.html
|
|
|
765
|
|
|
766 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
|
|
|
767 echo "<table border = 1>" >> $log
|
|
|
768 echo "<thead><tr><th>Info</th><th>Sequences</th><th>Percentage</th></tr></thead>" >> $log
|
|
|
769 tIFS="$TMP"
|
|
|
770 IFS=$'\t'
|
|
|
771 while read step seq perc
|
|
|
772 do
|
|
|
773 echo "<tr>" >> $log
|
|
|
774 echo "<td>$step</td>" >> $log
|
|
|
775 echo "<td>$seq</td>" >> $log
|
|
|
776 echo "<td>${perc}%</td>" >> $log
|
|
|
777 echo "</tr>" >> $log
|
|
|
778 done < $outdir/filtering_steps.txt
|
|
39
|
779 echo "</table>" >> $log
|
|
|
780 echo "<br />" >> $log
|
|
|
781 cat $dir/shm_first.htm >> $log
|
|
|
782 echo "</center></html>" >> $log
|
|
0
|
783
|
|
|
784 IFS="$tIFS"
|
|
|
785
|
|
|
786
|
|
|
787 echo "---------------- Done! ----------------"
|
|
|
788 echo "---------------- Done! ----------------<br />" >> $outdir/log.html
|
|
|
789
|
|
|
790
|
|
|
791
|
|
|
792
|
|
|
793
|
|
|
794
|
|
|
795
|
|
|
796
|
|
|
797
|
|
|
798
|
|
|
799
|
|
|
800
|
|
|
801
|
|
|
802
|
|
|
803
|
|
|
804
|
|
|
805
|
|
|
806
|
|
|
807
|
|
|
808
|
|
|
809
|
