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0
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1 #!/bin/bash
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2 #set -e
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3 dir="$(cd "$(dirname "$0")" && pwd)"
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4 input=$1
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5 method=$2
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6 log=$3 #becomes the main html page at the end
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7 outdir=$4
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8 output="$outdir/index.html" #copied to $log location at the end
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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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46 cat "`find $PWD/files/ -name "5_*"`" > $PWD/aa.txt
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47 cat "`find $PWD/files/ -name "6_*"`" > $PWD/junction.txt
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48 cat "`find $PWD/files/ -name "7_*"`" > $PWD/mutationanalysis.txt
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49 cat "`find $PWD/files/ -name "8_*"`" > $PWD/mutationstats.txt
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50 cat "`find $PWD/files/ -name "10_*"`" > $PWD/hotspots.txt
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0
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51
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52 if [[ ${#BLASTN_DIR} -ge 5 ]] ; then
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53 echo "On server, using BLASTN_DIR env: ${BLASTN_DIR}"
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54 else
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55 BLASTN_DIR="/home/galaxy/Downloads/ncbi-blast-2.4.0+/bin"
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56 echo "Dev Galaxy set BLASTN_DIR to: ${BLASTN_DIR}"
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57 fi
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58
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59 echo "---------------- class identification ----------------"
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60 echo "---------------- class identification ----------------<br />" >> $log
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61
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62 python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt
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63
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64 echo "---------------- merge_and_filter.r ----------------"
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65 echo "---------------- merge_and_filter.r ----------------<br />" >> $log
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66
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14
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67 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $PWD/aa.txt $outdir/identified_genes.txt $outdir/merged.txt $outdir/before_unique_filter.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${class_filter} ${empty_region_filter} 2>&1
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0
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68
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5
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69 if [[ "$fast" == "no" ]] ; then
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0
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70
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5
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71 echo "---------------- creating new IMGT zips ----------------"
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72 echo "---------------- creating new IMGT zips ----------------<br />" >> $log
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73
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74 mkdir $outdir/new_IMGT
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75
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36
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76 cat "`find $PWD/files/ -name "1_*"`" > "$outdir/new_IMGT/1_Summary.txt"
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77 cat "`find $PWD/files/ -name "2_*"`" > "$outdir/new_IMGT/2_IMGT-gapped-nt-sequences.txt"
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78 cat "`find $PWD/files/ -name "3_*"`" > "$outdir/new_IMGT/3_Nt-sequences.txt"
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79 cat "`find $PWD/files/ -name "4_*"`" > "$outdir/new_IMGT/4_IMGT-gapped-AA-sequences.txt"
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80 cat "`find $PWD/files/ -name "5_*"`" > "$outdir/new_IMGT/5_AA-sequences.txt"
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81 cat "`find $PWD/files/ -name "6_*"`" > "$outdir/new_IMGT/6_Junction.txt"
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82 cat "`find $PWD/files/ -name "7_*"`" > "$outdir/new_IMGT/7_V-REGION-mutation-and-AA-change-table.txt"
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83 cat "`find $PWD/files/ -name "8_*"`" > "$outdir/new_IMGT/8_V-REGION-nt-mutation-statistics.txt"
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84 cat "`find $PWD/files/ -name "9_*"`" > "$outdir/new_IMGT/9_V-REGION-AA-change-statistics.txt"
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85 cat "`find $PWD/files/ -name "10_*"`" > "$outdir/new_IMGT/10_V-REGION-mutation-hotspots.txt"
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0
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86
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5
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87 mkdir $outdir/new_IMGT_IGA
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88 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA
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89
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5
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90 mkdir $outdir/new_IMGT_IGA1
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91 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA1
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0
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92
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5
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93 mkdir $outdir/new_IMGT_IGA2
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94 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA2
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0
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95
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5
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96 mkdir $outdir/new_IMGT_IGG
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97 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG
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0
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98
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5
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99 mkdir $outdir/new_IMGT_IGG1
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100 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG1
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0
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101
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5
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102 mkdir $outdir/new_IMGT_IGG2
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103 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG2
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0
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104
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5
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105 mkdir $outdir/new_IMGT_IGG3
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106 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG3
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0
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107
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5
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108 mkdir $outdir/new_IMGT_IGG4
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109 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG4
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110
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111 mkdir $outdir/new_IMGT_IGM
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112 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGM
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0
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113
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5
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114 mkdir $outdir/new_IMGT_IGE
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115 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGE
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0
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116
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5
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117 Rscript $dir/new_imgt.r $outdir/new_IMGT/ $outdir/merged.txt "-" 2>&1
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118
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119 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA/ $outdir/merged.txt "IGA" 2>&1
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120 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA1/ $outdir/merged.txt "IGA1" 2>&1
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121 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA2/ $outdir/merged.txt "IGA2" 2>&1
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0
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122
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5
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123 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG/ $outdir/merged.txt "IGG" 2>&1
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124 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG1/ $outdir/merged.txt "IGG1" 2>&1
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125 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG2/ $outdir/merged.txt "IGG2" 2>&1
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126 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG3/ $outdir/merged.txt "IGG3" 2>&1
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127 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG4/ $outdir/merged.txt "IGG4" 2>&1
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0
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128
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5
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129 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGM/ $outdir/merged.txt "IGM" 2>&1
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0
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130
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5
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131 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGE/ $outdir/merged.txt "IGE" 2>&1
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0
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132
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133
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5
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134 tmp="$PWD"
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135 cd $outdir/new_IMGT/ #tar weirdness...
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136 tar -cJf ../new_IMGT.txz *
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0
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137
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5
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138 cd $outdir/new_IMGT_IGA/
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139 tar -cJf ../new_IMGT_IGA.txz *
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0
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140
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5
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141 cd $outdir/new_IMGT_IGA1/
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142 tar -cJf ../new_IMGT_IGA1.txz *
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0
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143
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5
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144 cd $outdir/new_IMGT_IGA2/
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145 tar -cJf ../new_IMGT_IGA2.txz *
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0
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146
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5
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147 cd $outdir/new_IMGT_IGG/
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148 tar -cJf ../new_IMGT_IGG.txz *
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0
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149
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5
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150 cd $outdir/new_IMGT_IGG1/
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151 tar -cJf ../new_IMGT_IGG1.txz *
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0
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152
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5
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153 cd $outdir/new_IMGT_IGG2/
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154 tar -cJf ../new_IMGT_IGG2.txz *
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155
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156 cd $outdir/new_IMGT_IGG3/
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157 tar -cJf ../new_IMGT_IGG3.txz *
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0
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158
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5
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159 cd $outdir/new_IMGT_IGG4/
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160 tar -cJf ../new_IMGT_IGG4.txz *
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161
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162 cd $outdir/new_IMGT_IGM/
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163 tar -cJf ../new_IMGT_IGM.txz *
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0
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164
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5
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165 cd $outdir/new_IMGT_IGE/
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166 tar -cJf ../new_IMGT_IGE.txz *
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0
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167
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5
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168 cd $tmp
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169 fi
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0
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170
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171 echo "---------------- shm_csr.r ----------------"
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172 echo "---------------- shm_csr.r ----------------<br />" >> $log
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173
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5
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174 classes="IGA,IGA1,IGA2,IGG,IGG1,IGG2,IGG3,IGG4,IGM,IGE,unmatched"
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0
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175 echo "R mutation analysis"
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1
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176 Rscript $dir/shm_csr.r $outdir/merged.txt $classes $outdir ${empty_region_filter} 2>&1
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0
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177
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178 echo "---------------- shm_csr.py ----------------"
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179 echo "---------------- shm_csr.py ----------------<br />" >> $log
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180
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1
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181 python $dir/shm_csr.py --input $outdir/merged.txt --genes $classes --empty_region_filter "${empty_region_filter}" --output $outdir/hotspot_analysis.txt
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182
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183 echo "---------------- aa_histogram.r ----------------"
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184 echo "---------------- aa_histogram.r ----------------<br />" >> $log
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185
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5
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186 Rscript $dir/aa_histogram.r $outdir/aa_id_mutations.txt $outdir/absent_aa_id.txt "IGA,IGG,IGM,IGE" $outdir/ 2>&1
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187 if [ -e "$outdir/aa_histogram_.png" ]; then
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188 mv $outdir/aa_histogram_.png $outdir/aa_histogram.png
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189 mv $outdir/aa_histogram_.txt $outdir/aa_histogram.txt
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29
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190 mv $outdir/aa_histogram_absent_.txt $outdir/aa_histogram_absent.txt
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191 mv $outdir/aa_histogram_count_.txt $outdir/aa_histogram_count.txt
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192 mv $outdir/aa_histogram_sum_.txt $outdir/aa_histogram_sum.txt
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0
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193 fi
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194
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5
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195 genes=(IGA IGA1 IGA2 IGG IGG1 IGG2 IGG3 IGG4 IGM IGE)
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0
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196
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197 funcs=(sum mean median)
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198 funcs=(sum)
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199
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200 echo "---------------- sequence_overview.r ----------------"
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201 echo "---------------- sequence_overview.r ----------------<br />" >> $log
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202
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203 mkdir $outdir/sequence_overview
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204
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7
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205 Rscript $dir/sequence_overview.r $outdir/before_unique_filter.txt $outdir/merged.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt ${empty_region_filter} 2>&1
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0
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206
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207 echo "<table border='1'>" > $outdir/base_overview.html
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208
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209 while IFS=$'\t' read ID class seq A C G T
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210 do
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211 echo "<tr><td>$ID</td><td>$seq</td><td>$class</td><td>$A</td><td>$C</td><td>$G</td><td>$T</td></tr>" >> $outdir/base_overview.html
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212 done < $outdir/sequence_overview/ntoverview.txt
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213
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214 echo "<html><center><h1>$title</h1></center>" > $output
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215 echo "<meta name='viewport' content='width=device-width, initial-scale=1'>" >> $output
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216 echo "<script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $output
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217 echo "<script type='text/javascript' src='tabber.js'></script>" >> $output
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218 echo "<script type='text/javascript' src='script.js'></script>" >> $output
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219 echo "<link rel='stylesheet' type='text/css' href='style.css'>" >> $output
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220 echo "<link rel='stylesheet' type='text/css' href='pure-min.css'>" >> $output
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221
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222 matched_count="`cat $outdir/merged.txt | grep -v 'unmatched' | tail -n +2 | wc -l`"
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223 unmatched_count="`cat $outdir/unmatched.txt | tail -n +2 | wc -l`"
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224 total_count=$((matched_count + unmatched_count))
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225 perc_count=$((unmatched_count / total_count * 100))
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226 perc_count=`bc -l <<< "scale=2; ${unmatched_count} / ${total_count} * 100"`
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227 perc_count=`bc -l <<< "scale=2; (${unmatched_count} / ${total_count} * 100 ) / 1"`
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228
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229 echo "<center><h2>Total: ${total_count}</h2></center>" >> $output
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230 echo "<center><h2>Matched: ${matched_count} Unmatched: ${unmatched_count}</h2></center>" >> $output
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231 echo "<center><h2>Percentage unmatched: ${perc_count}</h2></center>" >> $output
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232
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233 echo "---------------- main tables ----------------"
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234 echo "---------------- main tables ----------------<br />" >> $log
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235
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236 echo "<div class='tabber'>" >> $output
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23
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237 echo "<div class='tabbertab' title='SHM Overview' style='width: 3000px;'>" >> $output
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0
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238
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239 for func in ${funcs[@]}
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240 do
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241
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242 echo "---------------- $func table ----------------"
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243 echo "---------------- $func table ----------------<br />" >> $log
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244
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245 cat $outdir/mutations_${func}.txt $outdir/hotspot_analysis_${func}.txt > $outdir/data_${func}.txt
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246
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247 echo "---------------- pattern_plots.r ----------------"
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248 echo "---------------- pattern_plots.r ----------------<br />" >> $log
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249
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39
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250 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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0
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251
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252 echo "<table class='pure-table pure-table-striped'>" >> $output
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253 echo "<thead><tr><th>info</th>" >> $output
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254
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255 if [ "${class_filter}" != "101_101" ] ; then
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256
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257 for gene in ${genes[@]}
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258 do
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259 tmp=`cat $outdir/${gene}_${func}_n.txt`
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260 echo "<th><a href='matched_${gene}_${func}.txt'>${gene} (N = $tmp)</a></th>" >> $output
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261 done
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262
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263 tmp=`cat $outdir/all_${func}_n.txt`
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264 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
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265 tmp=`cat $outdir/unmatched_${func}_n.txt`
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266 echo "<th><a href='unmatched.txt'>unmatched (N = ${unmatched_count})</a></th><tr></thead>" >> $output
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267
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5
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268 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
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0
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269 do
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270 if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] ; then #meh
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5
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271 echo "<tr><td>$name</td><td>${cax}/${cay} (${caz})</td><td>${ca1x}/${ca1y} (${ca1z})</td><td>${ca2x}/${ca2y} (${ca2z})</td><td>${cgx}/${cgy} (${cgz})</td><td>${cg1x}/${cg1y} (${cg1z})</td><td>${cg2x}/${cg2y} (${cg2z})</td><td>${cg3x}/${cg3y} (${cg3z})</td><td>${cg4x}/${cg4y} (${cg4z})</td><td>${cmx}/${cmy} (${cmz})</td><td>${cex}/${cey} (${cez})</td><td>${allx}/${ally} (${allz})</td><td>${unx}/${uny} (${unz})</td></tr>" >> $output
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0
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272 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
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5
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273 echo "<tr><td>$name</td><td>${caz}%</td><td>${ca1z}%</td><td>${ca2z}%</td><td>${cgz}%</td><td>${cg1z}%</td><td>${cg2z}%</td><td>${cg3z}%</td><td>${cg4z}%</td><td>${cmz}%</td><td>${cez}%</td><td>${allz}%</td><td>${unz}%</td></tr>" >> $output
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0
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274 else
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5
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275 echo "<tr><td>$name</td><td>${cax}/${cay} (${caz}%)</td><td>${ca1x}/${ca1y} (${ca1z}%)</td><td>${ca2x}/${ca2y} (${ca2z}%)</td><td>${cgx}/${cgy} (${cgz}%)</td><td>${cg1x}/${cg1y} (${cg1z}%)</td><td>${cg2x}/${cg2y} (${cg2z}%)</td><td>${cg3x}/${cg3y} (${cg3z}%)</td><td>${cg4x}/${cg4y} (${cg4z}%)</td><td>${cmx}/${cmy} (${cmz}%)</td><td>${cex}/${cey} (${cez}%)</td><td>${allx}/${ally} (${allz}%)</td><td>${unx}/${uny} (${unz}%)</td></tr>" >> $output
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0
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276 fi
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|
277 done < $outdir/data_${func}.txt
|
|
|
278
|
|
|
279 else
|
|
3
|
280 tmp=`cat $outdir/all_${func}_n.txt`
|
|
0
|
281 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
|
|
|
282
|
|
5
|
283 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
|
|
0
|
284 do
|
|
|
285 if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] ; then #meh
|
|
3
|
286 echo "<tr><td>$name</td><td>${allx}/${ally}</td></tr>" >> $output
|
|
0
|
287 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
|
|
3
|
288 echo "<tr><td>$name</td><td>${allz}%</td></tr>" >> $output
|
|
0
|
289 else
|
|
3
|
290 echo "<tr><td>$name</td><td>${allx}/${ally} (${allz}%)</td></tr>" >> $output
|
|
0
|
291 fi
|
|
|
292 done < $outdir/data_${func}.txt
|
|
|
293
|
|
|
294 fi
|
|
|
295 echo "</table>" >> $output
|
|
|
296 #echo "<a href='data_${func}.txt'>Download data</a>" >> $output
|
|
|
297 done
|
|
|
298
|
|
39
|
299 echo "<img src='aid_motives.png' /><br />" >> $output
|
|
|
300 echo "<img src='relative_mutations.png' /><br />" >> $output
|
|
|
301 echo "<img src='abolute_mutations.png' /><br />" >> $output
|
|
|
302 echo "<br />" >> $output
|
|
|
303 cat $dir/shm_overview.htm >> $output
|
|
0
|
304 echo "</div>" >> $output #SHM overview tab end
|
|
|
305
|
|
|
306 echo "---------------- images ----------------"
|
|
|
307 echo "---------------- images ----------------<br />" >> $log
|
|
|
308
|
|
23
|
309 echo "<div class='tabbertab' title='SHM Frequency' style='width: 3000px;'>" >> $output
|
|
0
|
310
|
|
|
311 if [ -a $outdir/scatter.png ]
|
|
|
312 then
|
|
|
313 echo "<img src='scatter.png'/><br />" >> $output
|
|
|
314 fi
|
|
|
315 if [ -a $outdir/frequency_ranges.png ]
|
|
|
316 then
|
|
|
317 echo "<img src='frequency_ranges.png'/><br />" >> $output
|
|
|
318 fi
|
|
|
319
|
|
39
|
320 echo "<br />" >> $output
|
|
|
321 cat $dir/shm_frequency.htm >> $output
|
|
|
322
|
|
0
|
323 echo "</div>" >> $output #SHM frequency tab end
|
|
|
324
|
|
23
|
325 echo "<div class='tabbertab' title='Transition tables' style='width: 3000px;'>" >> $output
|
|
0
|
326
|
|
|
327 echo "<table border='0'>" >> $output
|
|
|
328
|
|
|
329 for gene in ${genes[@]}
|
|
|
330 do
|
|
|
331 echo "<tr>" >> $output
|
|
|
332 echo "<td><h1>${gene}</h1></td>" >> $output
|
|
23
|
333
|
|
|
334 if [ -e $outdir/transitions_heatmap_${gene}.png ]
|
|
|
335 then
|
|
|
336 echo "<td><img src='transitions_heatmap_${gene}.png' /></td>" >> $output
|
|
|
337 else
|
|
|
338 echo "<td></td>" >> $output
|
|
|
339 fi
|
|
|
340
|
|
|
341 if [ -e $outdir/transitions_stacked_${gene}.png ]
|
|
|
342 then
|
|
|
343 echo "<td><img src='transitions_stacked_${gene}.png' /></td>" >> $output
|
|
|
344 else
|
|
|
345 echo "<td></td>" >> $output
|
|
|
346 fi
|
|
|
347
|
|
0
|
348 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
|
|
|
349 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
|
|
|
350 first="true"
|
|
|
351 while IFS=, read from a c g t
|
|
|
352 do
|
|
|
353 if [ "$first" == "true" ] ; then
|
|
|
354 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
|
|
|
355 first="false"
|
|
|
356 else
|
|
|
357 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
|
|
|
358 fi
|
|
|
359 done < $outdir/transitions_${gene}_sum.txt
|
|
|
360 echo "</table></td>" >> $output
|
|
|
361
|
|
|
362 echo "</tr>" >> $output
|
|
|
363 done
|
|
|
364
|
|
|
365 echo "<tr>" >> $output
|
|
|
366 echo "<td><h1>All</h1></td>" >> $output
|
|
|
367 echo "<td><img src='transitions_heatmap_all.png' /></td>" >> $output
|
|
|
368 echo "<td><img src='transitions_stacked_all.png' /></td>" >> $output
|
|
|
369 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
|
|
|
370 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
|
|
|
371 first="true"
|
|
|
372 while IFS=, read from a c g t
|
|
|
373 do
|
|
|
374 if [ "$first" == "true" ] ; then
|
|
|
375 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
|
|
|
376 first="false"
|
|
|
377 else
|
|
|
378 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
|
|
|
379 fi
|
|
|
380 done < $outdir/transitions_all_sum.txt
|
|
|
381 echo "</table></td>" >> $output
|
|
|
382
|
|
|
383 echo "</tr>" >> $output
|
|
|
384
|
|
|
385 echo "</table>" >> $output
|
|
|
386
|
|
39
|
387 echo "<br />" >> $output
|
|
|
388 cat $dir/shm_transition.htm >> $output
|
|
|
389
|
|
0
|
390 echo "</div>" >> $output #transition tables tab end
|
|
|
391
|
|
|
392 echo "<div class='tabbertab' title='Antigen Selection'>" >> $output
|
|
|
393
|
|
23
|
394 if [ -e $outdir/aa_histogram.png ]
|
|
0
|
395 then
|
|
|
396 echo "<img src='aa_histogram.png'/><br />" >> $output
|
|
23
|
397 fi
|
|
|
398
|
|
|
399 if [ -e $outdir/aa_histogram_IGA.png ]
|
|
|
400 then
|
|
0
|
401 echo "<img src='aa_histogram_IGA.png'/><br />" >> $output
|
|
23
|
402 fi
|
|
|
403
|
|
|
404 if [ -e $outdir/aa_histogram_IGG.png ]
|
|
|
405 then
|
|
0
|
406 echo "<img src='aa_histogram_IGG.png'/><br />" >> $output
|
|
23
|
407 fi
|
|
|
408
|
|
|
409 if [ -e $outdir/aa_histogram_IGM.png ]
|
|
|
410 then
|
|
0
|
411 echo "<img src='aa_histogram_IGM.png'/><br />" >> $output
|
|
23
|
412 fi
|
|
|
413
|
|
|
414 if [ -e $outdir/aa_histogram_IGE.png ]
|
|
|
415 then
|
|
6
|
416 echo "<img src='aa_histogram_IGE.png'/><br />" >> $output
|
|
0
|
417 fi
|
|
|
418
|
|
23
|
419
|
|
33
|
420
|
|
|
421 if [[ "$fast" == "no" ]] ; then
|
|
|
422
|
|
|
423 echo "---------------- baseline ----------------"
|
|
|
424 echo "---------------- baseline ----------------<br />" >> $log
|
|
|
425 tmp="$PWD"
|
|
|
426
|
|
|
427 mkdir $outdir/baseline
|
|
37
|
428
|
|
|
429 baseline_boundaries="27:27:38:55:65:104:-"
|
|
|
430
|
|
|
431 if [[ "${empty_region_filter}" == "leader" ]] ; then
|
|
|
432 baseline_boundaries="1:26:38:55:65:104:-"
|
|
|
433 fi
|
|
23
|
434
|
|
33
|
435 mkdir $outdir/baseline/IGA_IGG_IGM
|
|
|
436 if [[ $(wc -l < $outdir/new_IMGT/1_Summary.txt) -gt "1" ]]; then
|
|
|
437 cd $outdir/baseline/IGA_IGG_IGM
|
|
39
|
438 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
|
439 else
|
|
|
440 echo "No sequences" > "$outdir/baseline.txt"
|
|
|
441 fi
|
|
|
442
|
|
|
443 mkdir $outdir/baseline/IGA
|
|
|
444 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
|
|
|
445 cd $outdir/baseline/IGA
|
|
37
|
446 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
|
447 else
|
|
|
448 echo "No IGA sequences" > "$outdir/baseline_IGA.txt"
|
|
|
449 fi
|
|
|
450
|
|
|
451 mkdir $outdir/baseline/IGG
|
|
|
452 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
|
|
|
453 cd $outdir/baseline/IGG
|
|
37
|
454 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
|
455 else
|
|
|
456 echo "No IGG sequences" > "$outdir/baseline_IGG.txt"
|
|
|
457 fi
|
|
23
|
458
|
|
33
|
459 mkdir $outdir/baseline/IGM
|
|
|
460 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
|
|
|
461 cd $outdir/baseline/IGM
|
|
37
|
462 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
|
463 else
|
|
|
464 echo "No IGM sequences" > "$outdir/baseline_IGM.txt"
|
|
|
465 fi
|
|
|
466
|
|
|
467 mkdir $outdir/baseline/IGE
|
|
|
468 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
|
|
|
469 cd $outdir/baseline/IGE
|
|
37
|
470 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
|
471 else
|
|
|
472 echo "No IGE sequences" > "$outdir/baseline_IGE.txt"
|
|
|
473 fi
|
|
|
474
|
|
|
475 cd $tmp
|
|
23
|
476
|
|
33
|
477 echo "Cleaning up *.RData files"
|
|
|
478 find $outdir/baseline -name "*.RData" -type f -delete
|
|
|
479
|
|
|
480 if [ -e $outdir/baseline.pdf ]
|
|
|
481 then
|
|
|
482 echo "<embed src='baseline.pdf' width='700px' height='1000px'>" >> $output
|
|
|
483 fi
|
|
|
484
|
|
|
485 if [ -e $outdir/baseline_IGA.pdf ]
|
|
|
486 then
|
|
|
487 echo "<embed src='baseline_IGA.pdf' width='700px' height='1000px'>" >> $output
|
|
|
488 fi
|
|
23
|
489
|
|
33
|
490 if [ -e $outdir/baseline_IGG.pdf ]
|
|
|
491 then
|
|
|
492 echo "<embed src='baseline_IGG.pdf' width='700px' height='1000px'>" >> $output
|
|
|
493 fi
|
|
|
494
|
|
|
495 if [ -e $outdir/baseline_IGM.pdf ]
|
|
|
496 then
|
|
|
497 echo "<embed src='baseline_IGM.pdf' width='700px' height='1000px'>" >> $output
|
|
|
498 fi
|
|
|
499
|
|
|
500 if [ -e $outdir/baseline_IGE.pdf ]
|
|
|
501 then
|
|
|
502 echo "<embed src='baseline_IGE.pdf' width='700px' height='1000px'>" >> $output
|
|
|
503 fi
|
|
23
|
504 fi
|
|
0
|
505
|
|
39
|
506 echo "<br />" >> $output
|
|
|
507 cat $dir/shm_selection.htm >> $output
|
|
|
508
|
|
0
|
509 echo "</div>" >> $output #antigen selection tab end
|
|
|
510
|
|
|
511 echo "<div class='tabbertab' title='CSR'>" >> $output #CSR tab
|
|
|
512
|
|
23
|
513 if [ -e $outdir/IGA.png ]
|
|
0
|
514 then
|
|
|
515 echo "<img src='IGA.png'/><br />" >> $output
|
|
|
516 fi
|
|
23
|
517 if [ -e $outdir/IGG.png ]
|
|
0
|
518 then
|
|
|
519 echo "<img src='IGG.png'/><br />" >> $output
|
|
|
520 fi
|
|
|
521
|
|
39
|
522 echo "<br />" >> $output
|
|
|
523 cat $dir/shm_csr.htm >> $output
|
|
|
524
|
|
0
|
525 echo "</div>" >> $output #CSR tab end
|
|
|
526
|
|
5
|
527 if [[ "$fast" == "no" ]] ; then
|
|
|
528
|
|
|
529 echo "---------------- change-o MakeDB ----------------"
|
|
0
|
530
|
|
5
|
531 mkdir $outdir/change_o
|
|
0
|
532
|
|
5
|
533 tmp="$PWD"
|
|
0
|
534
|
|
5
|
535 cd $outdir/change_o
|
|
0
|
536
|
|
5
|
537 bash $dir/change_o/makedb.sh $outdir/new_IMGT.txz false false false $outdir/change_o/change-o-db.txt
|
|
|
538 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
|
539
|
|
5
|
540 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
|
541
|
|
5
|
542 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
|
543
|
|
5
|
544 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
|
|
|
545 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGA.txz false false false $outdir/change_o/change-o-db-IGA.txt
|
|
|
546 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 $outdir/change_o/change-o-defined_clones-summary-IGA.txt
|
|
|
547 else
|
|
|
548 echo "No IGA sequences" > "$outdir/change_o/change-o-db-defined_clones-IGA.txt"
|
|
|
549 echo "No IGA sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGA.txt"
|
|
|
550 fi
|
|
0
|
551
|
|
5
|
552 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
|
|
|
553 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGG.txz false false false $outdir/change_o/change-o-db-IGG.txt
|
|
|
554 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 $outdir/change_o/change-o-defined_clones-summary-IGG.txt
|
|
|
555 else
|
|
|
556 echo "No IGG sequences" > "$outdir/change_o/change-o-db-defined_clones-IGG.txt"
|
|
|
557 echo "No IGG sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGG.txt"
|
|
|
558 fi
|
|
0
|
559
|
|
5
|
560 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
|
|
|
561 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGM.txz false false false $outdir/change_o/change-o-db-IGM.txt
|
|
|
562 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 $outdir/change_o/change-o-defined_clones-summary-IGM.txt
|
|
|
563 else
|
|
|
564 echo "No IGM sequences" > "$outdir/change_o/change-o-db-defined_clones-IGM.txt"
|
|
|
565 echo "No IGM sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGM.txt"
|
|
|
566 fi
|
|
0
|
567
|
|
6
|
568 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
|
|
|
569 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGE.txz false false false $outdir/change_o/change-o-db-IGE.txt
|
|
|
570 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 $outdir/change_o/change-o-defined_clones-summary-IGE.txt
|
|
|
571 else
|
|
|
572 echo "No IGE sequences" > "$outdir/change_o/change-o-db-defined_clones-IGE.txt"
|
|
|
573 echo "No IGE sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGE.txt"
|
|
|
574 fi
|
|
|
575
|
|
5
|
576 PWD="$tmp"
|
|
0
|
577
|
|
39
|
578 echo "<div class='tabbertab' title='Clonal Relation' style='width: 7000px;'>" >> $output #clonality tab
|
|
0
|
579
|
|
16
|
580 function clonality_table {
|
|
|
581 local infile=$1
|
|
|
582 local outfile=$2
|
|
|
583
|
|
|
584 echo "<table class='pure-table pure-table-striped'>" >> $outfile
|
|
|
585 echo "<thead><tr><th>Clone size</th><th>Nr of clones</th><th>Nr of sequences</th></tr></thead>" >> $outfile
|
|
|
586
|
|
|
587 first='true'
|
|
|
588
|
|
|
589 while read size clones seqs
|
|
|
590 do
|
|
|
591 if [[ "$first" == "true" ]]; then
|
|
|
592 first="false"
|
|
|
593 continue
|
|
|
594 fi
|
|
|
595 echo "<tr><td>$size</td><td>$clones</td><td>$seqs</td></tr>" >> $outfile
|
|
|
596 done < $infile
|
|
|
597
|
|
|
598 echo "</table>" >> $outfile
|
|
|
599 }
|
|
|
600 echo "<div class='tabber'>" >> $output
|
|
0
|
601
|
|
16
|
602 echo "<div class='tabbertab' title='All'>" >> $output
|
|
|
603 clonality_table $outdir/change_o/change-o-defined_clones-summary.txt $output
|
|
|
604 echo "</div>" >> $output
|
|
0
|
605
|
|
16
|
606 echo "<div class='tabbertab' title='IGA'>" >> $output
|
|
|
607 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGA.txt $output
|
|
|
608 echo "</div>" >> $output
|
|
0
|
609
|
|
16
|
610 echo "<div class='tabbertab' title='IGG'>" >> $output
|
|
|
611 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGG.txt $output
|
|
|
612 echo "</div>" >> $output
|
|
0
|
613
|
|
16
|
614 echo "<div class='tabbertab' title='IGM'>" >> $output
|
|
|
615 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
|
|
|
616 echo "</div>" >> $output
|
|
6
|
617
|
|
16
|
618 echo "<div class='tabbertab' title='IGE'>" >> $output
|
|
|
619 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
|
|
|
620 echo "</div>" >> $output
|
|
0
|
621
|
|
39
|
622 echo "<div class='tabbertab' title='Overlap' style='width: 7000px;'>" >> $output
|
|
|
623 cat "$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
|
624 echo "</div>" >> $output
|
|
39
|
625
|
|
16
|
626 echo "</div>" >> $output #clonality tabber end
|
|
39
|
627
|
|
|
628 echo "<br />" >> $output
|
|
|
629 cat $dir/shm_clonality.htm >> $output
|
|
|
630
|
|
16
|
631 echo "</div>" >> $output #clonality tab end
|
|
0
|
632
|
|
5
|
633 fi
|
|
|
634
|
|
0
|
635 echo "<div class='tabbertab' title='Downloads'>" >> $output
|
|
|
636
|
|
|
637 echo "<table class='pure-table pure-table-striped'>" >> $output
|
|
|
638 echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output
|
|
|
639 echo "<tr><td>The complete dataset</td><td><a href='merged.txt' download='merged.txt' >Download</a></td></tr>" >> $output
|
|
|
640 echo "<tr><td>The filtered dataset</td><td><a href='filtered.txt' download='filtered.txt' >Download</a></td></tr>" >> $output
|
|
|
641 echo "<tr><td>The alignment info on the unmatched sequences</td><td><a href='unmatched.txt' download='unmatched.txt' >Download</a></td></tr>" >> $output
|
|
|
642
|
|
2
|
643 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Overview</td></tr>" >> $output
|
|
23
|
644 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
|
645 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
|
|
|
646 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
|
|
|
647 echo "<tr><td>Base count for every sequence</td><td><a href='base_overview.html'>View</a></td></tr>" >> $output
|
|
39
|
648 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
|
|
|
649 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
|
|
|
650 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
|
651
|
|
|
652 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Frequency</td></tr>" >> $output
|
|
0
|
653 echo "<tr><td>The data generate the frequency scatter plot</td><td><a href='scatter.txt' download='scatter.txt' >Download</a></td></tr>" >> $output
|
|
|
654 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
|
|
|
655 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
|
|
|
656
|
|
2
|
657 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Transition Tables</td></tr>" >> $output
|
|
23
|
658 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
|
|
|
659 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
|
|
|
660 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
|
661 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
|
662 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
|
|
|
663 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
|
|
|
664 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
|
|
|
665 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
|
|
|
666 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
|
|
|
667 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
|
|
|
668 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
|
669
|
|
2
|
670 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Antigen Selection</td></tr>" >> $output
|
|
0
|
671 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
|
672 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
|
673
|
|
29
|
674 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
|
|
|
675 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
|
|
|
676 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
|
|
|
677 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
|
|
|
678 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
|
|
|
679
|
|
0
|
680 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
|
|
|
681 echo "<tr><td>Baseline data</td><td><a href='baseline.txt' download='baseline.txt' >Download</a></td></tr>" >> $output
|
|
|
682 echo "<tr><td>Baseline IGA PDF</td><td><a href='baseline_IGA.pdf' download='baseline_IGA.pdf' >Download</a></td></tr>" >> $output
|
|
|
683 echo "<tr><td>Baseline IGA data</td><td><a href='baseline_IGA.txt' download='baseline_IGA.txt' >Download</a></td></tr>" >> $output
|
|
|
684 echo "<tr><td>Baseline IGG PDF</td><td><a href='baseline_IGG.pdf' download='baseline_IGG.pdf' >Download</a></td></tr>" >> $output
|
|
|
685 echo "<tr><td>Baseline IGG data</td><td><a href='baseline_IGG.txt' download='baseline_IGG.txt' >Download</a></td></tr>" >> $output
|
|
|
686 echo "<tr><td>Baseline IGM PDF</td><td><a href='baseline_IGM.pdf' download='baseline_IGM.pdf' >Download</a></td></tr>" >> $output
|
|
|
687 echo "<tr><td>Baseline IGM data</td><td><a href='baseline_IGM.txt' download='baseline_IGM.txt' >Download</a></td></tr>" >> $output
|
|
31
|
688 echo "<tr><td>Baseline IGE PDF</td><td><a href='baseline_IGE.pdf' download='baseline_IGE.pdf' >Download</a></td></tr>" >> $output
|
|
6
|
689 echo "<tr><td>Baseline IGE data</td><td><a href='baseline_IGE.txt' download='baseline_IGE.txt' >Download</a></td></tr>" >> $output
|
|
0
|
690
|
|
2
|
691 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>CSR</td></tr>" >> $output
|
|
39
|
692 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
|
|
|
693 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
|
694
|
|
39
|
695 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Clonal Relation</td></tr>" >> $output
|
|
2
|
696 echo "<tr><td>Sequence overlap between subclasses</td><td><a href='sequence_overview/index.html'>View</a></td></tr>" >> $output
|
|
|
697 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
|
|
|
698 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
|
|
|
699 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
|
|
|
700 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
|
|
|
701 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
|
|
|
702 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
|
|
|
703 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
|
|
|
704 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
|
705 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
|
|
|
706 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
|
707
|
|
|
708 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Filtered IMGT output files</td></tr>" >> $output
|
|
0
|
709 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
|
|
|
710 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
|
|
|
711 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
|
|
|
712 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
|
|
|
713 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
|
|
|
714 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
|
|
|
715 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
|
|
|
716 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
|
|
|
717 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
|
|
|
718 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
|
719 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
|
720
|
|
|
721 echo "</table>" >> $output
|
|
|
722
|
|
39
|
723 echo "<br />" >> $output
|
|
|
724 cat $dir/shm_downloads.htm >> $output
|
|
|
725
|
|
0
|
726 echo "</div>" >> $output #downloads tab end
|
|
|
727
|
|
|
728 echo "</div>" >> $output #tabs end
|
|
|
729
|
|
|
730 echo "</html>" >> $output
|
|
|
731
|
|
5
|
732
|
|
0
|
733 echo "---------------- naive_output.r ----------------"
|
|
|
734 echo "---------------- naive_output.r ----------------<br />" >> $log
|
|
|
735
|
|
5
|
736 if [[ "$naive_output" == "yes" ]]
|
|
0
|
737 then
|
|
28
|
738 echo "output naive output"
|
|
18
|
739 if [[ "${class_filter}" == "101_101" ]]
|
|
|
740 then
|
|
28
|
741 echo "copy new_IMGT.txz to ${naive_output_all}"
|
|
21
|
742 cp $outdir/new_IMGT.txz ${naive_output_all}
|
|
18
|
743 else
|
|
28
|
744 echo "copy for classes"
|
|
18
|
745 cp $outdir/new_IMGT_IGA.txz ${naive_output_ca}
|
|
|
746 cp $outdir/new_IMGT_IGG.txz ${naive_output_cg}
|
|
|
747 cp $outdir/new_IMGT_IGM.txz ${naive_output_cm}
|
|
|
748 cp $outdir/new_IMGT_IGE.txz ${naive_output_ce}
|
|
|
749 fi
|
|
0
|
750 fi
|
|
|
751
|
|
|
752 echo "</table>" >> $outdir/base_overview.html
|
|
|
753
|
|
|
754 mv $log $outdir/log.html
|
|
|
755
|
|
|
756 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
|
|
|
757 echo "<table border = 1>" >> $log
|
|
|
758 echo "<thead><tr><th>Info</th><th>Sequences</th><th>Percentage</th></tr></thead>" >> $log
|
|
|
759 tIFS="$TMP"
|
|
|
760 IFS=$'\t'
|
|
|
761 while read step seq perc
|
|
|
762 do
|
|
|
763 echo "<tr>" >> $log
|
|
|
764 echo "<td>$step</td>" >> $log
|
|
|
765 echo "<td>$seq</td>" >> $log
|
|
|
766 echo "<td>${perc}%</td>" >> $log
|
|
|
767 echo "</tr>" >> $log
|
|
|
768 done < $outdir/filtering_steps.txt
|
|
39
|
769 echo "</table>" >> $log
|
|
|
770 echo "<br />" >> $log
|
|
|
771 cat $dir/shm_first.htm >> $log
|
|
|
772 echo "</center></html>" >> $log
|
|
0
|
773
|
|
|
774 IFS="$tIFS"
|
|
|
775
|
|
|
776
|
|
|
777 echo "---------------- Done! ----------------"
|
|
|
778 echo "---------------- Done! ----------------<br />" >> $outdir/log.html
|
|
|
779
|
|
|
780
|
|
|
781
|
|
|
782
|
|
|
783
|
|
|
784
|
|
|
785
|
|
|
786
|
|
|
787
|
|
|
788
|
|
|
789
|
|
|
790
|
|
|
791
|
|
|
792
|
|
|
793
|
|
|
794
|
|
|
795
|
|
|
796
|
|
|
797
|
|
|
798
|
|
|
799
|
