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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
|
|
41
|
424
|
|
|
425
|
|
33
|
426 echo "---------------- baseline ----------------"
|
|
|
427 echo "---------------- baseline ----------------<br />" >> $log
|
|
|
428 tmp="$PWD"
|
|
|
429
|
|
|
430 mkdir $outdir/baseline
|
|
37
|
431
|
|
41
|
432 echo "<center><h1>BASELINe</h1>" >> $output
|
|
|
433 header_substring="Based on CDR1, FR2, CDR2, FR3 (27:27:38:55:65:104:-)"
|
|
|
434
|
|
37
|
435 baseline_boundaries="27:27:38:55:65:104:-"
|
|
|
436
|
|
|
437 if [[ "${empty_region_filter}" == "leader" ]] ; then
|
|
|
438 baseline_boundaries="1:26:38:55:65:104:-"
|
|
41
|
439 header_substring="Based on FR1, CDR1, FR2, CDR2, FR3 (1:26:38:55:65:104,-)"
|
|
37
|
440 fi
|
|
41
|
441
|
|
|
442 echo "<p>${header_substring}</p></center>" >> $output
|
|
23
|
443
|
|
33
|
444 mkdir $outdir/baseline/IGA_IGG_IGM
|
|
|
445 if [[ $(wc -l < $outdir/new_IMGT/1_Summary.txt) -gt "1" ]]; then
|
|
|
446 cd $outdir/baseline/IGA_IGG_IGM
|
|
41
|
447 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
|
448 else
|
|
|
449 echo "No sequences" > "$outdir/baseline.txt"
|
|
|
450 fi
|
|
|
451
|
|
|
452 mkdir $outdir/baseline/IGA
|
|
|
453 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
|
|
|
454 cd $outdir/baseline/IGA
|
|
37
|
455 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
|
456 else
|
|
|
457 echo "No IGA sequences" > "$outdir/baseline_IGA.txt"
|
|
|
458 fi
|
|
|
459
|
|
|
460 mkdir $outdir/baseline/IGG
|
|
|
461 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
|
|
|
462 cd $outdir/baseline/IGG
|
|
37
|
463 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
|
464 else
|
|
|
465 echo "No IGG sequences" > "$outdir/baseline_IGG.txt"
|
|
|
466 fi
|
|
23
|
467
|
|
33
|
468 mkdir $outdir/baseline/IGM
|
|
|
469 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
|
|
|
470 cd $outdir/baseline/IGM
|
|
37
|
471 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
|
472 else
|
|
|
473 echo "No IGM sequences" > "$outdir/baseline_IGM.txt"
|
|
|
474 fi
|
|
|
475
|
|
|
476 mkdir $outdir/baseline/IGE
|
|
|
477 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
|
|
|
478 cd $outdir/baseline/IGE
|
|
37
|
479 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
|
480 else
|
|
|
481 echo "No IGE sequences" > "$outdir/baseline_IGE.txt"
|
|
|
482 fi
|
|
|
483
|
|
|
484 cd $tmp
|
|
23
|
485
|
|
33
|
486 echo "Cleaning up *.RData files"
|
|
|
487 find $outdir/baseline -name "*.RData" -type f -delete
|
|
|
488
|
|
|
489 if [ -e $outdir/baseline.pdf ]
|
|
|
490 then
|
|
|
491 echo "<embed src='baseline.pdf' width='700px' height='1000px'>" >> $output
|
|
|
492 fi
|
|
|
493
|
|
|
494 if [ -e $outdir/baseline_IGA.pdf ]
|
|
|
495 then
|
|
|
496 echo "<embed src='baseline_IGA.pdf' width='700px' height='1000px'>" >> $output
|
|
|
497 fi
|
|
23
|
498
|
|
33
|
499 if [ -e $outdir/baseline_IGG.pdf ]
|
|
|
500 then
|
|
|
501 echo "<embed src='baseline_IGG.pdf' width='700px' height='1000px'>" >> $output
|
|
|
502 fi
|
|
|
503
|
|
|
504 if [ -e $outdir/baseline_IGM.pdf ]
|
|
|
505 then
|
|
|
506 echo "<embed src='baseline_IGM.pdf' width='700px' height='1000px'>" >> $output
|
|
|
507 fi
|
|
|
508
|
|
|
509 if [ -e $outdir/baseline_IGE.pdf ]
|
|
|
510 then
|
|
|
511 echo "<embed src='baseline_IGE.pdf' width='700px' height='1000px'>" >> $output
|
|
|
512 fi
|
|
23
|
513 fi
|
|
0
|
514
|
|
39
|
515 echo "<br />" >> $output
|
|
|
516 cat $dir/shm_selection.htm >> $output
|
|
|
517
|
|
0
|
518 echo "</div>" >> $output #antigen selection tab end
|
|
|
519
|
|
|
520 echo "<div class='tabbertab' title='CSR'>" >> $output #CSR tab
|
|
|
521
|
|
23
|
522 if [ -e $outdir/IGA.png ]
|
|
0
|
523 then
|
|
|
524 echo "<img src='IGA.png'/><br />" >> $output
|
|
|
525 fi
|
|
23
|
526 if [ -e $outdir/IGG.png ]
|
|
0
|
527 then
|
|
|
528 echo "<img src='IGG.png'/><br />" >> $output
|
|
|
529 fi
|
|
|
530
|
|
39
|
531 echo "<br />" >> $output
|
|
|
532 cat $dir/shm_csr.htm >> $output
|
|
|
533
|
|
0
|
534 echo "</div>" >> $output #CSR tab end
|
|
|
535
|
|
5
|
536 if [[ "$fast" == "no" ]] ; then
|
|
|
537
|
|
|
538 echo "---------------- change-o MakeDB ----------------"
|
|
0
|
539
|
|
5
|
540 mkdir $outdir/change_o
|
|
0
|
541
|
|
5
|
542 tmp="$PWD"
|
|
0
|
543
|
|
5
|
544 cd $outdir/change_o
|
|
0
|
545
|
|
5
|
546 bash $dir/change_o/makedb.sh $outdir/new_IMGT.txz false false false $outdir/change_o/change-o-db.txt
|
|
|
547 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
|
548
|
|
5
|
549 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
|
550
|
|
5
|
551 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
|
552
|
|
5
|
553 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
|
|
|
554 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGA.txz false false false $outdir/change_o/change-o-db-IGA.txt
|
|
|
555 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 $outdir/change_o/change-o-defined_clones-summary-IGA.txt
|
|
|
556 else
|
|
|
557 echo "No IGA sequences" > "$outdir/change_o/change-o-db-defined_clones-IGA.txt"
|
|
|
558 echo "No IGA sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGA.txt"
|
|
|
559 fi
|
|
0
|
560
|
|
5
|
561 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
|
|
|
562 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGG.txz false false false $outdir/change_o/change-o-db-IGG.txt
|
|
|
563 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 $outdir/change_o/change-o-defined_clones-summary-IGG.txt
|
|
|
564 else
|
|
|
565 echo "No IGG sequences" > "$outdir/change_o/change-o-db-defined_clones-IGG.txt"
|
|
|
566 echo "No IGG sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGG.txt"
|
|
|
567 fi
|
|
0
|
568
|
|
5
|
569 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
|
|
|
570 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGM.txz false false false $outdir/change_o/change-o-db-IGM.txt
|
|
|
571 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 $outdir/change_o/change-o-defined_clones-summary-IGM.txt
|
|
|
572 else
|
|
|
573 echo "No IGM sequences" > "$outdir/change_o/change-o-db-defined_clones-IGM.txt"
|
|
|
574 echo "No IGM sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGM.txt"
|
|
|
575 fi
|
|
0
|
576
|
|
6
|
577 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
|
|
|
578 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGE.txz false false false $outdir/change_o/change-o-db-IGE.txt
|
|
|
579 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 $outdir/change_o/change-o-defined_clones-summary-IGE.txt
|
|
|
580 else
|
|
|
581 echo "No IGE sequences" > "$outdir/change_o/change-o-db-defined_clones-IGE.txt"
|
|
|
582 echo "No IGE sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGE.txt"
|
|
|
583 fi
|
|
|
584
|
|
5
|
585 PWD="$tmp"
|
|
0
|
586
|
|
39
|
587 echo "<div class='tabbertab' title='Clonal Relation' style='width: 7000px;'>" >> $output #clonality tab
|
|
0
|
588
|
|
16
|
589 function clonality_table {
|
|
|
590 local infile=$1
|
|
|
591 local outfile=$2
|
|
|
592
|
|
|
593 echo "<table class='pure-table pure-table-striped'>" >> $outfile
|
|
|
594 echo "<thead><tr><th>Clone size</th><th>Nr of clones</th><th>Nr of sequences</th></tr></thead>" >> $outfile
|
|
|
595
|
|
|
596 first='true'
|
|
|
597
|
|
|
598 while read size clones seqs
|
|
|
599 do
|
|
|
600 if [[ "$first" == "true" ]]; then
|
|
|
601 first="false"
|
|
|
602 continue
|
|
|
603 fi
|
|
|
604 echo "<tr><td>$size</td><td>$clones</td><td>$seqs</td></tr>" >> $outfile
|
|
|
605 done < $infile
|
|
|
606
|
|
|
607 echo "</table>" >> $outfile
|
|
|
608 }
|
|
|
609 echo "<div class='tabber'>" >> $output
|
|
0
|
610
|
|
16
|
611 echo "<div class='tabbertab' title='All'>" >> $output
|
|
|
612 clonality_table $outdir/change_o/change-o-defined_clones-summary.txt $output
|
|
|
613 echo "</div>" >> $output
|
|
0
|
614
|
|
16
|
615 echo "<div class='tabbertab' title='IGA'>" >> $output
|
|
|
616 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGA.txt $output
|
|
|
617 echo "</div>" >> $output
|
|
0
|
618
|
|
16
|
619 echo "<div class='tabbertab' title='IGG'>" >> $output
|
|
|
620 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGG.txt $output
|
|
|
621 echo "</div>" >> $output
|
|
0
|
622
|
|
16
|
623 echo "<div class='tabbertab' title='IGM'>" >> $output
|
|
|
624 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
|
|
|
625 echo "</div>" >> $output
|
|
6
|
626
|
|
16
|
627 echo "<div class='tabbertab' title='IGE'>" >> $output
|
|
|
628 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
|
|
|
629 echo "</div>" >> $output
|
|
0
|
630
|
|
39
|
631 echo "<div class='tabbertab' title='Overlap' style='width: 7000px;'>" >> $output
|
|
|
632 cat "$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
|
633 echo "</div>" >> $output
|
|
39
|
634
|
|
16
|
635 echo "</div>" >> $output #clonality tabber end
|
|
39
|
636
|
|
|
637 echo "<br />" >> $output
|
|
|
638 cat $dir/shm_clonality.htm >> $output
|
|
|
639
|
|
16
|
640 echo "</div>" >> $output #clonality tab end
|
|
0
|
641
|
|
5
|
642 fi
|
|
|
643
|
|
0
|
644 echo "<div class='tabbertab' title='Downloads'>" >> $output
|
|
|
645
|
|
|
646 echo "<table class='pure-table pure-table-striped'>" >> $output
|
|
|
647 echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output
|
|
|
648 echo "<tr><td>The complete dataset</td><td><a href='merged.txt' download='merged.txt' >Download</a></td></tr>" >> $output
|
|
|
649 echo "<tr><td>The filtered dataset</td><td><a href='filtered.txt' download='filtered.txt' >Download</a></td></tr>" >> $output
|
|
|
650 echo "<tr><td>The alignment info on the unmatched sequences</td><td><a href='unmatched.txt' download='unmatched.txt' >Download</a></td></tr>" >> $output
|
|
|
651
|
|
2
|
652 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Overview</td></tr>" >> $output
|
|
23
|
653 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
|
654 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
|
|
|
655 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
|
|
|
656 echo "<tr><td>Base count for every sequence</td><td><a href='base_overview.html'>View</a></td></tr>" >> $output
|
|
39
|
657 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
|
|
|
658 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
|
|
|
659 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
|
660
|
|
|
661 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Frequency</td></tr>" >> $output
|
|
0
|
662 echo "<tr><td>The data generate the frequency scatter plot</td><td><a href='scatter.txt' download='scatter.txt' >Download</a></td></tr>" >> $output
|
|
|
663 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
|
|
|
664 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
|
|
|
665
|
|
2
|
666 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Transition Tables</td></tr>" >> $output
|
|
23
|
667 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
|
|
|
668 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
|
|
|
669 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
|
670 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
|
671 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
|
|
|
672 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
|
|
|
673 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
|
|
|
674 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
|
|
|
675 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
|
|
|
676 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
|
|
|
677 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
|
678
|
|
2
|
679 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Antigen Selection</td></tr>" >> $output
|
|
0
|
680 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
|
681 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
|
682
|
|
29
|
683 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
|
|
|
684 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
|
|
|
685 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
|
|
|
686 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
|
|
|
687 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
|
|
|
688
|
|
0
|
689 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
|
|
|
690 echo "<tr><td>Baseline data</td><td><a href='baseline.txt' download='baseline.txt' >Download</a></td></tr>" >> $output
|
|
|
691 echo "<tr><td>Baseline IGA PDF</td><td><a href='baseline_IGA.pdf' download='baseline_IGA.pdf' >Download</a></td></tr>" >> $output
|
|
|
692 echo "<tr><td>Baseline IGA data</td><td><a href='baseline_IGA.txt' download='baseline_IGA.txt' >Download</a></td></tr>" >> $output
|
|
|
693 echo "<tr><td>Baseline IGG PDF</td><td><a href='baseline_IGG.pdf' download='baseline_IGG.pdf' >Download</a></td></tr>" >> $output
|
|
|
694 echo "<tr><td>Baseline IGG data</td><td><a href='baseline_IGG.txt' download='baseline_IGG.txt' >Download</a></td></tr>" >> $output
|
|
|
695 echo "<tr><td>Baseline IGM PDF</td><td><a href='baseline_IGM.pdf' download='baseline_IGM.pdf' >Download</a></td></tr>" >> $output
|
|
|
696 echo "<tr><td>Baseline IGM data</td><td><a href='baseline_IGM.txt' download='baseline_IGM.txt' >Download</a></td></tr>" >> $output
|
|
31
|
697 echo "<tr><td>Baseline IGE PDF</td><td><a href='baseline_IGE.pdf' download='baseline_IGE.pdf' >Download</a></td></tr>" >> $output
|
|
6
|
698 echo "<tr><td>Baseline IGE data</td><td><a href='baseline_IGE.txt' download='baseline_IGE.txt' >Download</a></td></tr>" >> $output
|
|
0
|
699
|
|
2
|
700 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>CSR</td></tr>" >> $output
|
|
39
|
701 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
|
|
|
702 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
|
703
|
|
39
|
704 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Clonal Relation</td></tr>" >> $output
|
|
2
|
705 echo "<tr><td>Sequence overlap between subclasses</td><td><a href='sequence_overview/index.html'>View</a></td></tr>" >> $output
|
|
|
706 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
|
|
|
707 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
|
|
|
708 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
|
|
|
709 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
|
|
|
710 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
|
|
|
711 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
|
|
|
712 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
|
|
|
713 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
|
714 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
|
|
|
715 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
|
716
|
|
|
717 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Filtered IMGT output files</td></tr>" >> $output
|
|
0
|
718 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
|
|
|
719 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
|
|
|
720 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
|
|
|
721 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
|
|
|
722 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
|
|
|
723 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
|
|
|
724 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
|
|
|
725 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
|
|
|
726 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
|
|
|
727 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
|
728 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
|
729
|
|
|
730 echo "</table>" >> $output
|
|
|
731
|
|
39
|
732 echo "<br />" >> $output
|
|
|
733 cat $dir/shm_downloads.htm >> $output
|
|
|
734
|
|
0
|
735 echo "</div>" >> $output #downloads tab end
|
|
|
736
|
|
|
737 echo "</div>" >> $output #tabs end
|
|
|
738
|
|
|
739 echo "</html>" >> $output
|
|
|
740
|
|
5
|
741
|
|
0
|
742 echo "---------------- naive_output.r ----------------"
|
|
|
743 echo "---------------- naive_output.r ----------------<br />" >> $log
|
|
|
744
|
|
5
|
745 if [[ "$naive_output" == "yes" ]]
|
|
0
|
746 then
|
|
28
|
747 echo "output naive output"
|
|
18
|
748 if [[ "${class_filter}" == "101_101" ]]
|
|
|
749 then
|
|
28
|
750 echo "copy new_IMGT.txz to ${naive_output_all}"
|
|
21
|
751 cp $outdir/new_IMGT.txz ${naive_output_all}
|
|
18
|
752 else
|
|
28
|
753 echo "copy for classes"
|
|
18
|
754 cp $outdir/new_IMGT_IGA.txz ${naive_output_ca}
|
|
|
755 cp $outdir/new_IMGT_IGG.txz ${naive_output_cg}
|
|
|
756 cp $outdir/new_IMGT_IGM.txz ${naive_output_cm}
|
|
|
757 cp $outdir/new_IMGT_IGE.txz ${naive_output_ce}
|
|
|
758 fi
|
|
0
|
759 fi
|
|
|
760
|
|
|
761 echo "</table>" >> $outdir/base_overview.html
|
|
|
762
|
|
|
763 mv $log $outdir/log.html
|
|
|
764
|
|
|
765 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
|
|
|
766 echo "<table border = 1>" >> $log
|
|
|
767 echo "<thead><tr><th>Info</th><th>Sequences</th><th>Percentage</th></tr></thead>" >> $log
|
|
|
768 tIFS="$TMP"
|
|
|
769 IFS=$'\t'
|
|
|
770 while read step seq perc
|
|
|
771 do
|
|
|
772 echo "<tr>" >> $log
|
|
|
773 echo "<td>$step</td>" >> $log
|
|
|
774 echo "<td>$seq</td>" >> $log
|
|
|
775 echo "<td>${perc}%</td>" >> $log
|
|
|
776 echo "</tr>" >> $log
|
|
|
777 done < $outdir/filtering_steps.txt
|
|
39
|
778 echo "</table>" >> $log
|
|
|
779 echo "<br />" >> $log
|
|
|
780 cat $dir/shm_first.htm >> $log
|
|
|
781 echo "</center></html>" >> $log
|
|
0
|
782
|
|
|
783 IFS="$tIFS"
|
|
|
784
|
|
|
785
|
|
|
786 echo "---------------- Done! ----------------"
|
|
|
787 echo "---------------- Done! ----------------<br />" >> $outdir/log.html
|
|
|
788
|
|
|
789
|
|
|
790
|
|
|
791
|
|
|
792
|
|
|
793
|
|
|
794
|
|
|
795
|
|
|
796
|
|
|
797
|
|
|
798
|
|
|
799
|
|
|
800
|
|
|
801
|
|
|
802
|
|
|
803
|
|
|
804
|
|
|
805
|
|
|
806
|
|
|
807
|
|
|
808
|
