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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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0
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23 mkdir $outdir
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24
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25 tar -xzf $dir/style.tar.gz -C $outdir
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26
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27 echo "---------------- read parameters ----------------"
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28 echo "---------------- read parameters ----------------<br />" > $log
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29
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30 echo "unpacking IMGT file"
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31
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32 type="`file $input`"
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33 if [[ "$type" == *"Zip archive"* ]] ; then
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34 echo "Zip archive"
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35 echo "unzip $input -d $PWD/files/"
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36 unzip $input -d $PWD/files/
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37 elif [[ "$type" == *"XZ compressed data"* ]] ; then
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38 echo "ZX archive"
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39 echo "tar -xJf $input -C $PWD/files/"
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34
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40 mkdir -p "$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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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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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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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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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/ $outdir/merged.txt "IGE" 2>&1
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133
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134
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135 tmp="$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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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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190 mv $outdir/aa_histogram_.txt $outdir/aa_histogram.txt
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29
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191 mv $outdir/aa_histogram_absent_.txt $outdir/aa_histogram_absent.txt
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192 mv $outdir/aa_histogram_count_.txt $outdir/aa_histogram_count.txt
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193 mv $outdir/aa_histogram_sum_.txt $outdir/aa_histogram_sum.txt
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0
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194 fi
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195
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5
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196 genes=(IGA IGA1 IGA2 IGG IGG1 IGG2 IGG3 IGG4 IGM IGE)
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0
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197
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198 funcs=(sum mean median)
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199 funcs=(sum)
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200
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201 echo "---------------- sequence_overview.r ----------------"
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202 echo "---------------- sequence_overview.r ----------------<br />" >> $log
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203
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204 mkdir $outdir/sequence_overview
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205
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7
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206 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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207
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208 echo "<table border='1'>" > $outdir/base_overview.html
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209
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210 while IFS=$'\t' read ID class seq A C G T
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211 do
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212 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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213 done < $outdir/sequence_overview/ntoverview.txt
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214
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215 echo "<html><center><h1>$title</h1></center>" > $output
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216 echo "<meta name='viewport' content='width=device-width, initial-scale=1'>" >> $output
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217 echo "<script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $output
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218 echo "<script type='text/javascript' src='tabber.js'></script>" >> $output
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219 echo "<script type='text/javascript' src='script.js'></script>" >> $output
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220 echo "<link rel='stylesheet' type='text/css' href='style.css'>" >> $output
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221 echo "<link rel='stylesheet' type='text/css' href='pure-min.css'>" >> $output
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222
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223 matched_count="`cat $outdir/merged.txt | grep -v 'unmatched' | tail -n +2 | wc -l`"
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224 unmatched_count="`cat $outdir/unmatched.txt | tail -n +2 | wc -l`"
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225 total_count=$((matched_count + unmatched_count))
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226 perc_count=$((unmatched_count / total_count * 100))
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227 perc_count=`bc -l <<< "scale=2; ${unmatched_count} / ${total_count} * 100"`
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228 perc_count=`bc -l <<< "scale=2; (${unmatched_count} / ${total_count} * 100 ) / 1"`
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229
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230 echo "<center><h2>Total: ${total_count}</h2></center>" >> $output
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231 echo "<center><h2>Matched: ${matched_count} Unmatched: ${unmatched_count}</h2></center>" >> $output
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232 echo "<center><h2>Percentage unmatched: ${perc_count}</h2></center>" >> $output
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233
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234 echo "---------------- main tables ----------------"
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235 echo "---------------- main tables ----------------<br />" >> $log
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236
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237 echo "<div class='tabber'>" >> $output
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23
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238 echo "<div class='tabbertab' title='SHM Overview' style='width: 3000px;'>" >> $output
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239
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240 for func in ${funcs[@]}
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241 do
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242
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243 echo "---------------- $func table ----------------"
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244 echo "---------------- $func table ----------------<br />" >> $log
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245
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246 cat $outdir/mutations_${func}.txt $outdir/hotspot_analysis_${func}.txt > $outdir/data_${func}.txt
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247
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248 echo "---------------- pattern_plots.r ----------------"
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249 echo "---------------- pattern_plots.r ----------------<br />" >> $log
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250
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39
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251 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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252
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253 echo "<table class='pure-table pure-table-striped'>" >> $output
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254 echo "<thead><tr><th>info</th>" >> $output
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255
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256 if [ "${class_filter}" != "101_101" ] ; then
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257
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258 for gene in ${genes[@]}
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259 do
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260 tmp=`cat $outdir/${gene}_${func}_n.txt`
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261 echo "<th><a href='matched_${gene}_${func}.txt'>${gene} (N = $tmp)</a></th>" >> $output
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262 done
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263
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264 tmp=`cat $outdir/all_${func}_n.txt`
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265 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
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266 tmp=`cat $outdir/unmatched_${func}_n.txt`
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267 echo "<th><a href='unmatched.txt'>unmatched (N = ${unmatched_count})</a></th><tr></thead>" >> $output
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268
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5
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269 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
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0
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270 do
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271 if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] ; then #meh
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5
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272 echo "<tr><td>$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>" >> $output
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0
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273 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
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5
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274 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>" >> $output
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0
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275 else
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5
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276 echo "<tr><td>$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
|
277 fi
|
|
|
278 done < $outdir/data_${func}.txt
|
|
|
279
|
|
|
280 else
|
|
3
|
281 tmp=`cat $outdir/all_${func}_n.txt`
|
|
0
|
282 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
|
|
|
283
|
|
5
|
284 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
|
|
0
|
285 do
|
|
|
286 if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] ; then #meh
|
|
3
|
287 echo "<tr><td>$name</td><td>${allx}/${ally}</td></tr>" >> $output
|
|
0
|
288 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
|
|
3
|
289 echo "<tr><td>$name</td><td>${allz}%</td></tr>" >> $output
|
|
0
|
290 else
|
|
3
|
291 echo "<tr><td>$name</td><td>${allx}/${ally} (${allz}%)</td></tr>" >> $output
|
|
0
|
292 fi
|
|
|
293 done < $outdir/data_${func}.txt
|
|
|
294
|
|
|
295 fi
|
|
|
296 echo "</table>" >> $output
|
|
|
297 #echo "<a href='data_${func}.txt'>Download data</a>" >> $output
|
|
|
298 done
|
|
|
299
|
|
39
|
300 echo "<img src='aid_motives.png' /><br />" >> $output
|
|
|
301 echo "<img src='relative_mutations.png' /><br />" >> $output
|
|
|
302 echo "<img src='abolute_mutations.png' /><br />" >> $output
|
|
|
303 echo "<br />" >> $output
|
|
|
304 cat $dir/shm_overview.htm >> $output
|
|
0
|
305 echo "</div>" >> $output #SHM overview tab end
|
|
|
306
|
|
|
307 echo "---------------- images ----------------"
|
|
|
308 echo "---------------- images ----------------<br />" >> $log
|
|
|
309
|
|
23
|
310 echo "<div class='tabbertab' title='SHM Frequency' style='width: 3000px;'>" >> $output
|
|
0
|
311
|
|
|
312 if [ -a $outdir/scatter.png ]
|
|
|
313 then
|
|
|
314 echo "<img src='scatter.png'/><br />" >> $output
|
|
|
315 fi
|
|
|
316 if [ -a $outdir/frequency_ranges.png ]
|
|
|
317 then
|
|
|
318 echo "<img src='frequency_ranges.png'/><br />" >> $output
|
|
|
319 fi
|
|
|
320
|
|
39
|
321 echo "<br />" >> $output
|
|
|
322 cat $dir/shm_frequency.htm >> $output
|
|
|
323
|
|
0
|
324 echo "</div>" >> $output #SHM frequency tab end
|
|
|
325
|
|
23
|
326 echo "<div class='tabbertab' title='Transition tables' style='width: 3000px;'>" >> $output
|
|
0
|
327
|
|
|
328 echo "<table border='0'>" >> $output
|
|
|
329
|
|
|
330 for gene in ${genes[@]}
|
|
|
331 do
|
|
|
332 echo "<tr>" >> $output
|
|
|
333 echo "<td><h1>${gene}</h1></td>" >> $output
|
|
23
|
334
|
|
|
335 if [ -e $outdir/transitions_heatmap_${gene}.png ]
|
|
|
336 then
|
|
|
337 echo "<td><img src='transitions_heatmap_${gene}.png' /></td>" >> $output
|
|
|
338 else
|
|
|
339 echo "<td></td>" >> $output
|
|
|
340 fi
|
|
|
341
|
|
|
342 if [ -e $outdir/transitions_stacked_${gene}.png ]
|
|
|
343 then
|
|
|
344 echo "<td><img src='transitions_stacked_${gene}.png' /></td>" >> $output
|
|
|
345 else
|
|
|
346 echo "<td></td>" >> $output
|
|
|
347 fi
|
|
|
348
|
|
0
|
349 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
|
|
|
350 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
|
|
|
351 first="true"
|
|
|
352 while IFS=, read from a c g t
|
|
|
353 do
|
|
|
354 if [ "$first" == "true" ] ; then
|
|
|
355 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
|
|
|
356 first="false"
|
|
|
357 else
|
|
|
358 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
|
|
|
359 fi
|
|
|
360 done < $outdir/transitions_${gene}_sum.txt
|
|
|
361 echo "</table></td>" >> $output
|
|
|
362
|
|
|
363 echo "</tr>" >> $output
|
|
|
364 done
|
|
|
365
|
|
|
366 echo "<tr>" >> $output
|
|
|
367 echo "<td><h1>All</h1></td>" >> $output
|
|
|
368 echo "<td><img src='transitions_heatmap_all.png' /></td>" >> $output
|
|
|
369 echo "<td><img src='transitions_stacked_all.png' /></td>" >> $output
|
|
|
370 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
|
|
|
371 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
|
|
|
372 first="true"
|
|
|
373 while IFS=, read from a c g t
|
|
|
374 do
|
|
|
375 if [ "$first" == "true" ] ; then
|
|
|
376 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
|
|
|
377 first="false"
|
|
|
378 else
|
|
|
379 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
|
|
|
380 fi
|
|
|
381 done < $outdir/transitions_all_sum.txt
|
|
|
382 echo "</table></td>" >> $output
|
|
|
383
|
|
|
384 echo "</tr>" >> $output
|
|
|
385
|
|
|
386 echo "</table>" >> $output
|
|
|
387
|
|
39
|
388 echo "<br />" >> $output
|
|
|
389 cat $dir/shm_transition.htm >> $output
|
|
|
390
|
|
0
|
391 echo "</div>" >> $output #transition tables tab end
|
|
|
392
|
|
|
393 echo "<div class='tabbertab' title='Antigen Selection'>" >> $output
|
|
|
394
|
|
23
|
395 if [ -e $outdir/aa_histogram.png ]
|
|
0
|
396 then
|
|
|
397 echo "<img src='aa_histogram.png'/><br />" >> $output
|
|
23
|
398 fi
|
|
|
399
|
|
|
400 if [ -e $outdir/aa_histogram_IGA.png ]
|
|
|
401 then
|
|
0
|
402 echo "<img src='aa_histogram_IGA.png'/><br />" >> $output
|
|
23
|
403 fi
|
|
|
404
|
|
|
405 if [ -e $outdir/aa_histogram_IGG.png ]
|
|
|
406 then
|
|
0
|
407 echo "<img src='aa_histogram_IGG.png'/><br />" >> $output
|
|
23
|
408 fi
|
|
|
409
|
|
|
410 if [ -e $outdir/aa_histogram_IGM.png ]
|
|
|
411 then
|
|
0
|
412 echo "<img src='aa_histogram_IGM.png'/><br />" >> $output
|
|
23
|
413 fi
|
|
|
414
|
|
|
415 if [ -e $outdir/aa_histogram_IGE.png ]
|
|
|
416 then
|
|
6
|
417 echo "<img src='aa_histogram_IGE.png'/><br />" >> $output
|
|
0
|
418 fi
|
|
|
419
|
|
23
|
420
|
|
33
|
421
|
|
|
422 if [[ "$fast" == "no" ]] ; then
|
|
|
423
|
|
|
424 echo "---------------- baseline ----------------"
|
|
|
425 echo "---------------- baseline ----------------<br />" >> $log
|
|
|
426 tmp="$PWD"
|
|
|
427
|
|
|
428 mkdir $outdir/baseline
|
|
37
|
429
|
|
|
430 baseline_boundaries="27:27:38:55:65:104:-"
|
|
|
431
|
|
|
432 if [[ "${empty_region_filter}" == "leader" ]] ; then
|
|
|
433 baseline_boundaries="1:26:38:55:65:104:-"
|
|
|
434 fi
|
|
23
|
435
|
|
33
|
436 mkdir $outdir/baseline/IGA_IGG_IGM
|
|
|
437 if [[ $(wc -l < $outdir/new_IMGT/1_Summary.txt) -gt "1" ]]; then
|
|
|
438 cd $outdir/baseline/IGA_IGG_IGM
|
|
39
|
439 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
|
440 else
|
|
|
441 echo "No sequences" > "$outdir/baseline.txt"
|
|
|
442 fi
|
|
|
443
|
|
|
444 mkdir $outdir/baseline/IGA
|
|
|
445 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
|
|
|
446 cd $outdir/baseline/IGA
|
|
37
|
447 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
|
448 else
|
|
|
449 echo "No IGA sequences" > "$outdir/baseline_IGA.txt"
|
|
|
450 fi
|
|
|
451
|
|
|
452 mkdir $outdir/baseline/IGG
|
|
|
453 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
|
|
|
454 cd $outdir/baseline/IGG
|
|
37
|
455 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
|
456 else
|
|
|
457 echo "No IGG sequences" > "$outdir/baseline_IGG.txt"
|
|
|
458 fi
|
|
23
|
459
|
|
33
|
460 mkdir $outdir/baseline/IGM
|
|
|
461 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
|
|
|
462 cd $outdir/baseline/IGM
|
|
37
|
463 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
|
464 else
|
|
|
465 echo "No IGM sequences" > "$outdir/baseline_IGM.txt"
|
|
|
466 fi
|
|
|
467
|
|
|
468 mkdir $outdir/baseline/IGE
|
|
|
469 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
|
|
|
470 cd $outdir/baseline/IGE
|
|
37
|
471 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
|
472 else
|
|
|
473 echo "No IGE sequences" > "$outdir/baseline_IGE.txt"
|
|
|
474 fi
|
|
|
475
|
|
|
476 cd $tmp
|
|
23
|
477
|
|
33
|
478 echo "Cleaning up *.RData files"
|
|
|
479 find $outdir/baseline -name "*.RData" -type f -delete
|
|
|
480
|
|
|
481 if [ -e $outdir/baseline.pdf ]
|
|
|
482 then
|
|
|
483 echo "<embed src='baseline.pdf' width='700px' height='1000px'>" >> $output
|
|
|
484 fi
|
|
|
485
|
|
|
486 if [ -e $outdir/baseline_IGA.pdf ]
|
|
|
487 then
|
|
|
488 echo "<embed src='baseline_IGA.pdf' width='700px' height='1000px'>" >> $output
|
|
|
489 fi
|
|
23
|
490
|
|
33
|
491 if [ -e $outdir/baseline_IGG.pdf ]
|
|
|
492 then
|
|
|
493 echo "<embed src='baseline_IGG.pdf' width='700px' height='1000px'>" >> $output
|
|
|
494 fi
|
|
|
495
|
|
|
496 if [ -e $outdir/baseline_IGM.pdf ]
|
|
|
497 then
|
|
|
498 echo "<embed src='baseline_IGM.pdf' width='700px' height='1000px'>" >> $output
|
|
|
499 fi
|
|
|
500
|
|
|
501 if [ -e $outdir/baseline_IGE.pdf ]
|
|
|
502 then
|
|
|
503 echo "<embed src='baseline_IGE.pdf' width='700px' height='1000px'>" >> $output
|
|
|
504 fi
|
|
23
|
505 fi
|
|
0
|
506
|
|
39
|
507 echo "<br />" >> $output
|
|
|
508 cat $dir/shm_selection.htm >> $output
|
|
|
509
|
|
0
|
510 echo "</div>" >> $output #antigen selection tab end
|
|
|
511
|
|
|
512 echo "<div class='tabbertab' title='CSR'>" >> $output #CSR tab
|
|
|
513
|
|
23
|
514 if [ -e $outdir/IGA.png ]
|
|
0
|
515 then
|
|
|
516 echo "<img src='IGA.png'/><br />" >> $output
|
|
|
517 fi
|
|
23
|
518 if [ -e $outdir/IGG.png ]
|
|
0
|
519 then
|
|
|
520 echo "<img src='IGG.png'/><br />" >> $output
|
|
|
521 fi
|
|
|
522
|
|
39
|
523 echo "<br />" >> $output
|
|
|
524 cat $dir/shm_csr.htm >> $output
|
|
|
525
|
|
0
|
526 echo "</div>" >> $output #CSR tab end
|
|
|
527
|
|
5
|
528 if [[ "$fast" == "no" ]] ; then
|
|
|
529
|
|
|
530 echo "---------------- change-o MakeDB ----------------"
|
|
0
|
531
|
|
5
|
532 mkdir $outdir/change_o
|
|
0
|
533
|
|
5
|
534 tmp="$PWD"
|
|
0
|
535
|
|
5
|
536 cd $outdir/change_o
|
|
0
|
537
|
|
5
|
538 bash $dir/change_o/makedb.sh $outdir/new_IMGT.txz false false false $outdir/change_o/change-o-db.txt
|
|
|
539 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
|
540
|
|
5
|
541 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
|
542
|
|
5
|
543 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
|
544
|
|
5
|
545 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
|
|
|
546 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGA.txz false false false $outdir/change_o/change-o-db-IGA.txt
|
|
|
547 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 $outdir/change_o/change-o-defined_clones-summary-IGA.txt
|
|
|
548 else
|
|
|
549 echo "No IGA sequences" > "$outdir/change_o/change-o-db-defined_clones-IGA.txt"
|
|
|
550 echo "No IGA sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGA.txt"
|
|
|
551 fi
|
|
0
|
552
|
|
5
|
553 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
|
|
|
554 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGG.txz false false false $outdir/change_o/change-o-db-IGG.txt
|
|
|
555 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 $outdir/change_o/change-o-defined_clones-summary-IGG.txt
|
|
|
556 else
|
|
|
557 echo "No IGG sequences" > "$outdir/change_o/change-o-db-defined_clones-IGG.txt"
|
|
|
558 echo "No IGG sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGG.txt"
|
|
|
559 fi
|
|
0
|
560
|
|
5
|
561 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
|
|
|
562 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGM.txz false false false $outdir/change_o/change-o-db-IGM.txt
|
|
|
563 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 $outdir/change_o/change-o-defined_clones-summary-IGM.txt
|
|
|
564 else
|
|
|
565 echo "No IGM sequences" > "$outdir/change_o/change-o-db-defined_clones-IGM.txt"
|
|
|
566 echo "No IGM sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGM.txt"
|
|
|
567 fi
|
|
0
|
568
|
|
6
|
569 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
|
|
|
570 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGE.txz false false false $outdir/change_o/change-o-db-IGE.txt
|
|
|
571 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 $outdir/change_o/change-o-defined_clones-summary-IGE.txt
|
|
|
572 else
|
|
|
573 echo "No IGE sequences" > "$outdir/change_o/change-o-db-defined_clones-IGE.txt"
|
|
|
574 echo "No IGE sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGE.txt"
|
|
|
575 fi
|
|
|
576
|
|
5
|
577 PWD="$tmp"
|
|
0
|
578
|
|
39
|
579 echo "<div class='tabbertab' title='Clonal Relation' style='width: 7000px;'>" >> $output #clonality tab
|
|
0
|
580
|
|
16
|
581 function clonality_table {
|
|
|
582 local infile=$1
|
|
|
583 local outfile=$2
|
|
|
584
|
|
|
585 echo "<table class='pure-table pure-table-striped'>" >> $outfile
|
|
|
586 echo "<thead><tr><th>Clone size</th><th>Nr of clones</th><th>Nr of sequences</th></tr></thead>" >> $outfile
|
|
|
587
|
|
|
588 first='true'
|
|
|
589
|
|
|
590 while read size clones seqs
|
|
|
591 do
|
|
|
592 if [[ "$first" == "true" ]]; then
|
|
|
593 first="false"
|
|
|
594 continue
|
|
|
595 fi
|
|
|
596 echo "<tr><td>$size</td><td>$clones</td><td>$seqs</td></tr>" >> $outfile
|
|
|
597 done < $infile
|
|
|
598
|
|
|
599 echo "</table>" >> $outfile
|
|
|
600 }
|
|
|
601 echo "<div class='tabber'>" >> $output
|
|
0
|
602
|
|
16
|
603 echo "<div class='tabbertab' title='All'>" >> $output
|
|
|
604 clonality_table $outdir/change_o/change-o-defined_clones-summary.txt $output
|
|
|
605 echo "</div>" >> $output
|
|
0
|
606
|
|
16
|
607 echo "<div class='tabbertab' title='IGA'>" >> $output
|
|
|
608 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGA.txt $output
|
|
|
609 echo "</div>" >> $output
|
|
0
|
610
|
|
16
|
611 echo "<div class='tabbertab' title='IGG'>" >> $output
|
|
|
612 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGG.txt $output
|
|
|
613 echo "</div>" >> $output
|
|
0
|
614
|
|
16
|
615 echo "<div class='tabbertab' title='IGM'>" >> $output
|
|
|
616 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
|
|
|
617 echo "</div>" >> $output
|
|
6
|
618
|
|
16
|
619 echo "<div class='tabbertab' title='IGE'>" >> $output
|
|
|
620 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
|
|
|
621 echo "</div>" >> $output
|
|
0
|
622
|
|
39
|
623 echo "<div class='tabbertab' title='Overlap' style='width: 7000px;'>" >> $output
|
|
|
624 cat "$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
|
625 echo "</div>" >> $output
|
|
39
|
626
|
|
16
|
627 echo "</div>" >> $output #clonality tabber end
|
|
39
|
628
|
|
|
629 echo "<br />" >> $output
|
|
|
630 cat $dir/shm_clonality.htm >> $output
|
|
|
631
|
|
16
|
632 echo "</div>" >> $output #clonality tab end
|
|
0
|
633
|
|
5
|
634 fi
|
|
|
635
|
|
0
|
636 echo "<div class='tabbertab' title='Downloads'>" >> $output
|
|
|
637
|
|
|
638 echo "<table class='pure-table pure-table-striped'>" >> $output
|
|
|
639 echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output
|
|
|
640 echo "<tr><td>The complete dataset</td><td><a href='merged.txt' download='merged.txt' >Download</a></td></tr>" >> $output
|
|
|
641 echo "<tr><td>The filtered dataset</td><td><a href='filtered.txt' download='filtered.txt' >Download</a></td></tr>" >> $output
|
|
|
642 echo "<tr><td>The alignment info on the unmatched sequences</td><td><a href='unmatched.txt' download='unmatched.txt' >Download</a></td></tr>" >> $output
|
|
|
643
|
|
2
|
644 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Overview</td></tr>" >> $output
|
|
23
|
645 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
|
646 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
|
|
|
647 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
|
|
|
648 echo "<tr><td>Base count for every sequence</td><td><a href='base_overview.html'>View</a></td></tr>" >> $output
|
|
39
|
649 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
|
|
|
650 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
|
|
|
651 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
|
652
|
|
|
653 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Frequency</td></tr>" >> $output
|
|
0
|
654 echo "<tr><td>The data generate the frequency scatter plot</td><td><a href='scatter.txt' download='scatter.txt' >Download</a></td></tr>" >> $output
|
|
|
655 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
|
|
|
656 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
|
|
|
657
|
|
2
|
658 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Transition Tables</td></tr>" >> $output
|
|
23
|
659 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
|
|
|
660 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
|
|
|
661 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
|
662 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
|
663 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
|
|
|
664 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
|
|
|
665 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
|
|
|
666 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
|
|
|
667 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
|
|
|
668 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
|
|
|
669 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
|
670
|
|
2
|
671 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Antigen Selection</td></tr>" >> $output
|
|
0
|
672 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
|
673 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
|
674
|
|
29
|
675 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
|
|
|
676 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
|
|
|
677 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
|
|
|
678 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
|
|
|
679 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
|
|
|
680
|
|
0
|
681 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
|
|
|
682 echo "<tr><td>Baseline data</td><td><a href='baseline.txt' download='baseline.txt' >Download</a></td></tr>" >> $output
|
|
|
683 echo "<tr><td>Baseline IGA PDF</td><td><a href='baseline_IGA.pdf' download='baseline_IGA.pdf' >Download</a></td></tr>" >> $output
|
|
|
684 echo "<tr><td>Baseline IGA data</td><td><a href='baseline_IGA.txt' download='baseline_IGA.txt' >Download</a></td></tr>" >> $output
|
|
|
685 echo "<tr><td>Baseline IGG PDF</td><td><a href='baseline_IGG.pdf' download='baseline_IGG.pdf' >Download</a></td></tr>" >> $output
|
|
|
686 echo "<tr><td>Baseline IGG data</td><td><a href='baseline_IGG.txt' download='baseline_IGG.txt' >Download</a></td></tr>" >> $output
|
|
|
687 echo "<tr><td>Baseline IGM PDF</td><td><a href='baseline_IGM.pdf' download='baseline_IGM.pdf' >Download</a></td></tr>" >> $output
|
|
|
688 echo "<tr><td>Baseline IGM data</td><td><a href='baseline_IGM.txt' download='baseline_IGM.txt' >Download</a></td></tr>" >> $output
|
|
31
|
689 echo "<tr><td>Baseline IGE PDF</td><td><a href='baseline_IGE.pdf' download='baseline_IGE.pdf' >Download</a></td></tr>" >> $output
|
|
6
|
690 echo "<tr><td>Baseline IGE data</td><td><a href='baseline_IGE.txt' download='baseline_IGE.txt' >Download</a></td></tr>" >> $output
|
|
0
|
691
|
|
2
|
692 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>CSR</td></tr>" >> $output
|
|
39
|
693 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
|
|
|
694 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
|
695
|
|
39
|
696 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Clonal Relation</td></tr>" >> $output
|
|
2
|
697 echo "<tr><td>Sequence overlap between subclasses</td><td><a href='sequence_overview/index.html'>View</a></td></tr>" >> $output
|
|
|
698 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
|
|
|
699 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
|
|
|
700 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
|
|
|
701 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
|
|
|
702 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
|
|
|
703 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
|
|
|
704 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
|
|
|
705 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
|
706 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
|
|
|
707 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
|
708
|
|
|
709 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Filtered IMGT output files</td></tr>" >> $output
|
|
0
|
710 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
|
|
|
711 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
|
|
|
712 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
|
|
|
713 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
|
|
|
714 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
|
|
|
715 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
|
|
|
716 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
|
|
|
717 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
|
|
|
718 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
|
|
|
719 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
|
720 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
|
721
|
|
|
722 echo "</table>" >> $output
|
|
|
723
|
|
39
|
724 echo "<br />" >> $output
|
|
|
725 cat $dir/shm_downloads.htm >> $output
|
|
|
726
|
|
0
|
727 echo "</div>" >> $output #downloads tab end
|
|
|
728
|
|
|
729 echo "</div>" >> $output #tabs end
|
|
|
730
|
|
|
731 echo "</html>" >> $output
|
|
|
732
|
|
5
|
733
|
|
0
|
734 echo "---------------- naive_output.r ----------------"
|
|
|
735 echo "---------------- naive_output.r ----------------<br />" >> $log
|
|
|
736
|
|
5
|
737 if [[ "$naive_output" == "yes" ]]
|
|
0
|
738 then
|
|
28
|
739 echo "output naive output"
|
|
18
|
740 if [[ "${class_filter}" == "101_101" ]]
|
|
|
741 then
|
|
28
|
742 echo "copy new_IMGT.txz to ${naive_output_all}"
|
|
21
|
743 cp $outdir/new_IMGT.txz ${naive_output_all}
|
|
18
|
744 else
|
|
28
|
745 echo "copy for classes"
|
|
18
|
746 cp $outdir/new_IMGT_IGA.txz ${naive_output_ca}
|
|
|
747 cp $outdir/new_IMGT_IGG.txz ${naive_output_cg}
|
|
|
748 cp $outdir/new_IMGT_IGM.txz ${naive_output_cm}
|
|
|
749 cp $outdir/new_IMGT_IGE.txz ${naive_output_ce}
|
|
|
750 fi
|
|
0
|
751 fi
|
|
|
752
|
|
|
753 echo "</table>" >> $outdir/base_overview.html
|
|
|
754
|
|
|
755 mv $log $outdir/log.html
|
|
|
756
|
|
|
757 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
|
|
|
758 echo "<table border = 1>" >> $log
|
|
|
759 echo "<thead><tr><th>Info</th><th>Sequences</th><th>Percentage</th></tr></thead>" >> $log
|
|
|
760 tIFS="$TMP"
|
|
|
761 IFS=$'\t'
|
|
|
762 while read step seq perc
|
|
|
763 do
|
|
|
764 echo "<tr>" >> $log
|
|
|
765 echo "<td>$step</td>" >> $log
|
|
|
766 echo "<td>$seq</td>" >> $log
|
|
|
767 echo "<td>${perc}%</td>" >> $log
|
|
|
768 echo "</tr>" >> $log
|
|
|
769 done < $outdir/filtering_steps.txt
|
|
39
|
770 echo "</table>" >> $log
|
|
|
771 echo "<br />" >> $log
|
|
|
772 cat $dir/shm_first.htm >> $log
|
|
|
773 echo "</center></html>" >> $log
|
|
0
|
774
|
|
|
775 IFS="$tIFS"
|
|
|
776
|
|
|
777
|
|
|
778 echo "---------------- Done! ----------------"
|
|
|
779 echo "---------------- Done! ----------------<br />" >> $outdir/log.html
|
|
|
780
|
|
|
781
|
|
|
782
|
|
|
783
|
|
|
784
|
|
|
785
|
|
|
786
|
|
|
787
|
|
|
788
|
|
|
789
|
|
|
790
|
|
|
791
|
|
|
792
|
|
|
793
|
|
|
794
|
|
|
795
|
|
|
796
|
|
|
797
|
|
|
798
|
|
|
799
|
|
|
800
|
