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1 #!/bin/bash
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2 #set -e
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3 dir="$(cd "$(dirname "$0")" && pwd)"
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4 input=$1
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5 method=$2
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6 log=$3 #becomes the main html page at the end
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7 outdir=$4
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8 output="$outdir/index.html" #copied to $log location at the end
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9 title=$5
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10 include_fr1=$6
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11 functionality=$7
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12 unique=$8
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13 naive_output_ca=$9
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14 naive_output_cg=${10}
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15 naive_output_cm=${11}
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16 filter_unique=${12}
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17 class_filter=${13}
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18 empty_region_filter=${14}
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5
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19 fast=${15}
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0
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20 mkdir $outdir
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21
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22 tar -xzf $dir/style.tar.gz -C $outdir
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23
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24 echo "---------------- read parameters ----------------"
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25 echo "---------------- read parameters ----------------<br />" > $log
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26
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27 echo "unpacking IMGT file"
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28
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29 type="`file $input`"
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30 if [[ "$type" == *"Zip archive"* ]] ; then
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31 echo "Zip archive"
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32 echo "unzip $input -d $PWD/files/"
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33 unzip $input -d $PWD/files/
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34 elif [[ "$type" == *"XZ compressed data"* ]] ; then
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35 echo "ZX archive"
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36 echo "tar -xJf $input -C $PWD/files/"
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37 mkdir -p $PWD/files/$title
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38 tar -xJf $input -C $PWD/files/$title
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39 fi
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40
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41 cat `find $PWD/files/ -name "1_*"` > $PWD/summary.txt
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42 cat `find $PWD/files/ -name "3_*"` > $PWD/sequences.txt
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43 cat `find $PWD/files/ -name "5_*"` > $PWD/aa.txt
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44 cat `find $PWD/files/ -name "6_*"` > $PWD/junction.txt
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45 cat `find $PWD/files/ -name "7_*"` > $PWD/mutationanalysis.txt
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46 cat `find $PWD/files/ -name "8_*"` > $PWD/mutationstats.txt
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47 cat `find $PWD/files/ -name "10_*"` > $PWD/hotspots.txt
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48
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49 if [[ ${#BLASTN_DIR} -ge 5 ]] ; then
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50 echo "On server, using BLASTN_DIR env: ${BLASTN_DIR}"
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51 else
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52 BLASTN_DIR="/home/galaxy/Downloads/ncbi-blast-2.4.0+/bin"
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53 echo "Dev Galaxy set BLASTN_DIR to: ${BLASTN_DIR}"
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54 fi
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55
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56 echo "---------------- class identification ----------------"
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57 echo "---------------- class identification ----------------<br />" >> $log
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58
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59 python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt
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60
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61 echo "---------------- merge_and_filter.r ----------------"
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62 echo "---------------- merge_and_filter.r ----------------<br />" >> $log
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63
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64 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $outdir/identified_genes.txt $outdir/merged.txt $outdir/before_unique_filter.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${class_filter} ${empty_region_filter} 2>&1
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65
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5
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66 if [[ "$fast" == "no" ]] ; then
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0
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67
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5
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68 echo "---------------- creating new IMGT zips ----------------"
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69 echo "---------------- creating new IMGT zips ----------------<br />" >> $log
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70
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71 mkdir $outdir/new_IMGT
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0
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72
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5
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73 cat `find $PWD/files/ -name "1_*"` > "$outdir/new_IMGT/1_Summary.txt"
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74 cat `find $PWD/files/ -name "2_*"` > "$outdir/new_IMGT/2_IMGT-gapped-nt-sequences.txt"
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75 cat `find $PWD/files/ -name "3_*"` > "$outdir/new_IMGT/3_Nt-sequences.txt"
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76 cat `find $PWD/files/ -name "4_*"` > "$outdir/new_IMGT/4_IMGT-gapped-AA-sequences.txt"
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77 cat `find $PWD/files/ -name "5_*"` > "$outdir/new_IMGT/5_AA-sequences.txt"
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78 cat `find $PWD/files/ -name "6_*"` > "$outdir/new_IMGT/6_Junction.txt"
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79 cat `find $PWD/files/ -name "7_*"` > "$outdir/new_IMGT/7_V-REGION-mutation-and-AA-change-table.txt"
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80 cat `find $PWD/files/ -name "8_*"` > "$outdir/new_IMGT/8_V-REGION-nt-mutation-statistics.txt"
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81 cat `find $PWD/files/ -name "9_*"` > "$outdir/new_IMGT/9_V-REGION-AA-change-statistics.txt"
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82 cat `find $PWD/files/ -name "10_*"` > "$outdir/new_IMGT/10_V-REGION-mutation-hotspots.txt"
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0
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83
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5
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84 mkdir $outdir/new_IMGT_IGA
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85 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA
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86
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5
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87 mkdir $outdir/new_IMGT_IGA1
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88 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA1
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0
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89
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5
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90 mkdir $outdir/new_IMGT_IGA2
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91 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA2
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0
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92
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5
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93 mkdir $outdir/new_IMGT_IGG
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94 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG
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0
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95
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5
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96 mkdir $outdir/new_IMGT_IGG1
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97 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG1
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0
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98
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5
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99 mkdir $outdir/new_IMGT_IGG2
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100 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG2
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0
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101
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5
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102 mkdir $outdir/new_IMGT_IGG3
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103 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG3
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0
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104
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5
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105 mkdir $outdir/new_IMGT_IGG4
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106 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG4
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107
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108 mkdir $outdir/new_IMGT_IGM
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109 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGM
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0
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110
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5
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111 mkdir $outdir/new_IMGT_IGE
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112 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGE
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0
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113
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5
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114 Rscript $dir/new_imgt.r $outdir/new_IMGT/ $outdir/merged.txt "-" 2>&1
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115
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116 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA/ $outdir/merged.txt "IGA" 2>&1
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117 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA1/ $outdir/merged.txt "IGA1" 2>&1
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118 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA2/ $outdir/merged.txt "IGA2" 2>&1
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0
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119
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5
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120 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG/ $outdir/merged.txt "IGG" 2>&1
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121 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG1/ $outdir/merged.txt "IGG1" 2>&1
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122 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG2/ $outdir/merged.txt "IGG2" 2>&1
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123 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG3/ $outdir/merged.txt "IGG3" 2>&1
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124 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG4/ $outdir/merged.txt "IGG4" 2>&1
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0
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125
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5
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126 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGM/ $outdir/merged.txt "IGM" 2>&1
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0
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127
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5
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128 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGE/ $outdir/merged.txt "IGE" 2>&1
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0
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129
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130
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5
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131 tmp="$PWD"
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132 cd $outdir/new_IMGT/ #tar weirdness...
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133 tar -cJf ../new_IMGT.txz *
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0
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134
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5
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135 cd $outdir/new_IMGT_IGA/
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136 tar -cJf ../new_IMGT_IGA.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_IGA1/
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139 tar -cJf ../new_IMGT_IGA1.txz *
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140
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5
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141 cd $outdir/new_IMGT_IGA2/
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142 tar -cJf ../new_IMGT_IGA2.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_IGG/
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145 tar -cJf ../new_IMGT_IGG.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_IGG1/
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148 tar -cJf ../new_IMGT_IGG1.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_IGG2/
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151 tar -cJf ../new_IMGT_IGG2.txz *
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152
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153 cd $outdir/new_IMGT_IGG3/
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154 tar -cJf ../new_IMGT_IGG3.txz *
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155
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5
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156 cd $outdir/new_IMGT_IGG4/
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157 tar -cJf ../new_IMGT_IGG4.txz *
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158
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159 cd $outdir/new_IMGT_IGM/
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160 tar -cJf ../new_IMGT_IGM.txz *
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0
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161
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5
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162 cd $outdir/new_IMGT_IGE/
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163 tar -cJf ../new_IMGT_IGE.txz *
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0
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164
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5
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165 cd $tmp
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166 fi
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0
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167
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168 echo "---------------- shm_csr.r ----------------"
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169 echo "---------------- shm_csr.r ----------------<br />" >> $log
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170
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5
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171 classes="IGA,IGA1,IGA2,IGG,IGG1,IGG2,IGG3,IGG4,IGM,IGE,unmatched"
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0
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172 echo "R mutation analysis"
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1
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173 Rscript $dir/shm_csr.r $outdir/merged.txt $classes $outdir ${empty_region_filter} 2>&1
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0
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174
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175 echo "---------------- shm_csr.py ----------------"
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176 echo "---------------- shm_csr.py ----------------<br />" >> $log
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177
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1
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178 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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179
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180 echo "---------------- aa_histogram.r ----------------"
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181 echo "---------------- aa_histogram.r ----------------<br />" >> $log
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182
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5
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183 Rscript $dir/aa_histogram.r $outdir/aa_id_mutations.txt $outdir/absent_aa_id.txt "IGA,IGG,IGM,IGE" $outdir/ 2>&1
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184 if [ -e "$outdir/aa_histogram_.png" ]; then
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185 mv $outdir/aa_histogram_.png $outdir/aa_histogram.png
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186 mv $outdir/aa_histogram_.txt $outdir/aa_histogram.txt
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187 fi
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188
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5
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189 genes=(IGA IGA1 IGA2 IGG IGG1 IGG2 IGG3 IGG4 IGM IGE)
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0
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190
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191 funcs=(sum mean median)
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192 funcs=(sum)
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193
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194 echo "---------------- sequence_overview.r ----------------"
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195 echo "---------------- sequence_overview.r ----------------<br />" >> $log
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196
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197 mkdir $outdir/sequence_overview
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198
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199 Rscript $dir/sequence_overview.r $outdir/before_unique_filter.txt $outdir/merged.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt 2>&1
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200
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201 echo "<table border='1'>" > $outdir/base_overview.html
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202
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203 while IFS=$'\t' read ID class seq A C G T
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204 do
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205 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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206 done < $outdir/sequence_overview/ntoverview.txt
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207
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208 echo "<html><center><h1>$title</h1></center>" > $output
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209 echo "<meta name='viewport' content='width=device-width, initial-scale=1'>" >> $output
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210 echo "<script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $output
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211 echo "<script type='text/javascript' src='tabber.js'></script>" >> $output
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212 echo "<script type='text/javascript' src='script.js'></script>" >> $output
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213 echo "<link rel='stylesheet' type='text/css' href='style.css'>" >> $output
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214 echo "<link rel='stylesheet' type='text/css' href='pure-min.css'>" >> $output
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215
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216 matched_count="`cat $outdir/merged.txt | grep -v 'unmatched' | tail -n +2 | wc -l`"
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217 unmatched_count="`cat $outdir/unmatched.txt | tail -n +2 | wc -l`"
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218 total_count=$((matched_count + unmatched_count))
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219 perc_count=$((unmatched_count / total_count * 100))
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220 perc_count=`bc -l <<< "scale=2; ${unmatched_count} / ${total_count} * 100"`
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221 perc_count=`bc -l <<< "scale=2; (${unmatched_count} / ${total_count} * 100 ) / 1"`
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222
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223 echo "<center><h2>Total: ${total_count}</h2></center>" >> $output
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224 echo "<center><h2>Matched: ${matched_count} Unmatched: ${unmatched_count}</h2></center>" >> $output
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225 echo "<center><h2>Percentage unmatched: ${perc_count}</h2></center>" >> $output
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226
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227 echo "---------------- main tables ----------------"
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228 echo "---------------- main tables ----------------<br />" >> $log
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229
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230 echo "<div class='tabber'>" >> $output
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231 echo "<div class='tabbertab' title='SHM Overview'>" >> $output
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232
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233 for func in ${funcs[@]}
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234 do
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235
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236 echo "---------------- $func table ----------------"
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237 echo "---------------- $func table ----------------<br />" >> $log
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238
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239 cat $outdir/mutations_${func}.txt $outdir/hotspot_analysis_${func}.txt > $outdir/data_${func}.txt
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240
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241 echo "---------------- pattern_plots.r ----------------"
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242 echo "---------------- pattern_plots.r ----------------<br />" >> $log
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243
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244 Rscript $dir/pattern_plots.r $outdir/data_${func}.txt $outdir/plot1 $outdir/plot2 $outdir/plot3 2>&1
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245
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246 echo "<table class='pure-table pure-table-striped'>" >> $output
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247 echo "<thead><tr><th>info</th>" >> $output
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248
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249 if [ "${class_filter}" != "101_101" ] ; then
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250
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251 for gene in ${genes[@]}
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252 do
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253 tmp=`cat $outdir/${gene}_${func}_n.txt`
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254 echo "<th><a href='matched_${gene}_${func}.txt'>${gene} (N = $tmp)</a></th>" >> $output
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255 done
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256
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257 tmp=`cat $outdir/all_${func}_n.txt`
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258 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
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259 tmp=`cat $outdir/unmatched_${func}_n.txt`
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260 echo "<th><a href='unmatched.txt'>unmatched (N = ${unmatched_count})</a></th><tr></thead>" >> $output
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261
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5
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262 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
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0
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263 do
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264 if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] ; then #meh
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265 echo "<tr><td>$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>" >> $output
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266 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
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5
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267 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>" >> $output
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0
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268 else
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5
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269 echo "<tr><td>$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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270 fi
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271 done < $outdir/data_${func}.txt
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272
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273 else
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3
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274 tmp=`cat $outdir/all_${func}_n.txt`
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0
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275 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
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276
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5
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277 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
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0
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278 do
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279 if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] ; then #meh
|
|
3
|
280 echo "<tr><td>$name</td><td>${allx}/${ally}</td></tr>" >> $output
|
|
0
|
281 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
|
|
3
|
282 echo "<tr><td>$name</td><td>${allz}%</td></tr>" >> $output
|
|
0
|
283 else
|
|
3
|
284 echo "<tr><td>$name</td><td>${allx}/${ally} (${allz}%)</td></tr>" >> $output
|
|
0
|
285 fi
|
|
|
286 done < $outdir/data_${func}.txt
|
|
|
287
|
|
|
288 fi
|
|
|
289 echo "</table>" >> $output
|
|
|
290 #echo "<a href='data_${func}.txt'>Download data</a>" >> $output
|
|
|
291 done
|
|
|
292
|
|
|
293 echo "<img src='plot1.png' /><br />" >> $output
|
|
|
294 echo "<img src='plot2.png' /><br />" >> $output
|
|
|
295 echo "<img src='plot3.png' /><br />" >> $output
|
|
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296
|
|
|
297 echo "</div>" >> $output #SHM overview tab end
|
|
|
298
|
|
|
299 echo "---------------- images ----------------"
|
|
|
300 echo "---------------- images ----------------<br />" >> $log
|
|
|
301
|
|
|
302 echo "<div class='tabbertab' title='SHM Frequency'>" >> $output
|
|
|
303
|
|
|
304 if [ -a $outdir/scatter.png ]
|
|
|
305 then
|
|
|
306 echo "<img src='scatter.png'/><br />" >> $output
|
|
|
307 fi
|
|
|
308 if [ -a $outdir/frequency_ranges.png ]
|
|
|
309 then
|
|
|
310 echo "<img src='frequency_ranges.png'/><br />" >> $output
|
|
|
311 fi
|
|
|
312
|
|
|
313 echo "</div>" >> $output #SHM frequency tab end
|
|
|
314
|
|
|
315 echo "<div class='tabbertab' title='Transition tables'>" >> $output
|
|
|
316
|
|
|
317 echo "<table border='0'>" >> $output
|
|
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318
|
|
|
319 for gene in ${genes[@]}
|
|
|
320 do
|
|
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321 echo "<tr>" >> $output
|
|
|
322 echo "<td><h1>${gene}</h1></td>" >> $output
|
|
|
323 echo "<td><img src='transitions_heatmap_${gene}.png' /></td>" >> $output
|
|
|
324 echo "<td><img src='transitions_stacked_${gene}.png' /></td>" >> $output
|
|
|
325 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
|
|
|
326 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
|
|
|
327 first="true"
|
|
|
328 while IFS=, read from a c g t
|
|
|
329 do
|
|
|
330 if [ "$first" == "true" ] ; then
|
|
|
331 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
|
|
|
332 first="false"
|
|
|
333 else
|
|
|
334 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
|
|
|
335 fi
|
|
|
336 done < $outdir/transitions_${gene}_sum.txt
|
|
|
337 echo "</table></td>" >> $output
|
|
|
338
|
|
|
339 echo "</tr>" >> $output
|
|
|
340 done
|
|
|
341
|
|
|
342 echo "<tr>" >> $output
|
|
|
343 echo "<td><h1>All</h1></td>" >> $output
|
|
|
344 echo "<td><img src='transitions_heatmap_all.png' /></td>" >> $output
|
|
|
345 echo "<td><img src='transitions_stacked_all.png' /></td>" >> $output
|
|
|
346 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
|
|
|
347 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
|
|
|
348 first="true"
|
|
|
349 while IFS=, read from a c g t
|
|
|
350 do
|
|
|
351 if [ "$first" == "true" ] ; then
|
|
|
352 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
|
|
|
353 first="false"
|
|
|
354 else
|
|
|
355 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
|
|
|
356 fi
|
|
|
357 done < $outdir/transitions_all_sum.txt
|
|
|
358 echo "</table></td>" >> $output
|
|
|
359
|
|
|
360 echo "</tr>" >> $output
|
|
|
361
|
|
|
362 echo "</table>" >> $output
|
|
|
363
|
|
|
364 echo "</div>" >> $output #transition tables tab end
|
|
|
365
|
|
|
366 echo "<div class='tabbertab' title='Antigen Selection'>" >> $output
|
|
|
367
|
|
|
368 if [ -a $outdir/aa_histogram.png ]
|
|
|
369 then
|
|
|
370 echo "<img src='aa_histogram.png'/><br />" >> $output
|
|
|
371 echo "<img src='aa_histogram_IGA.png'/><br />" >> $output
|
|
|
372 echo "<img src='aa_histogram_IGG.png'/><br />" >> $output
|
|
|
373 echo "<img src='aa_histogram_IGM.png'/><br />" >> $output
|
|
|
374 fi
|
|
|
375
|
|
|
376 echo "<embed src='baseline.pdf' width='700px' height='1000px'>" >> $output
|
|
|
377 echo "<embed src='baseline_IGA.pdf' width='700px' height='1000px'>" >> $output
|
|
|
378 echo "<embed src='baseline_IGG.pdf' width='700px' height='1000px'>" >> $output
|
|
|
379 echo "<embed src='baseline_IGM.pdf' width='700px' height='1000px'>" >> $output
|
|
|
380
|
|
|
381 echo "</div>" >> $output #antigen selection tab end
|
|
|
382
|
|
|
383 echo "<div class='tabbertab' title='CSR'>" >> $output #CSR tab
|
|
|
384
|
|
|
385 if [ -a $outdir/IGA.png ]
|
|
|
386 then
|
|
|
387 echo "<img src='IGA.png'/><br />" >> $output
|
|
|
388 fi
|
|
|
389 if [ -a $outdir/IGG.png ]
|
|
|
390 then
|
|
|
391 echo "<img src='IGG.png'/><br />" >> $output
|
|
|
392 fi
|
|
|
393
|
|
|
394 echo "</div>" >> $output #CSR tab end
|
|
|
395
|
|
5
|
396 if [[ "$fast" == "no" ]] ; then
|
|
|
397
|
|
|
398 echo "---------------- change-o MakeDB ----------------"
|
|
0
|
399
|
|
5
|
400 mkdir $outdir/change_o
|
|
0
|
401
|
|
5
|
402 tmp="$PWD"
|
|
0
|
403
|
|
5
|
404 cd $outdir/change_o
|
|
0
|
405
|
|
5
|
406 bash $dir/change_o/makedb.sh $outdir/new_IMGT.txz false false false $outdir/change_o/change-o-db.txt
|
|
|
407 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
|
408
|
|
5
|
409 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
|
410
|
|
5
|
411 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
|
412
|
|
5
|
413 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
|
|
|
414 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGA.txz false false false $outdir/change_o/change-o-db-IGA.txt
|
|
|
415 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 $outdir/change_o/change-o-defined_clones-summary-IGA.txt
|
|
|
416 else
|
|
|
417 echo "No IGA sequences" > "$outdir/change_o/change-o-db-defined_clones-IGA.txt"
|
|
|
418 echo "No IGA sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGA.txt"
|
|
|
419 fi
|
|
0
|
420
|
|
5
|
421 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
|
|
|
422 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGG.txz false false false $outdir/change_o/change-o-db-IGG.txt
|
|
|
423 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 $outdir/change_o/change-o-defined_clones-summary-IGG.txt
|
|
|
424 else
|
|
|
425 echo "No IGG sequences" > "$outdir/change_o/change-o-db-defined_clones-IGG.txt"
|
|
|
426 echo "No IGG sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGG.txt"
|
|
|
427 fi
|
|
0
|
428
|
|
5
|
429 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
|
|
|
430 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGM.txz false false false $outdir/change_o/change-o-db-IGM.txt
|
|
|
431 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 $outdir/change_o/change-o-defined_clones-summary-IGM.txt
|
|
|
432 else
|
|
|
433 echo "No IGM sequences" > "$outdir/change_o/change-o-db-defined_clones-IGM.txt"
|
|
|
434 echo "No IGM sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGM.txt"
|
|
|
435 fi
|
|
0
|
436
|
|
5
|
437 PWD="$tmp"
|
|
0
|
438
|
|
|
439 echo "<div class='tabbertab' title='Clonality'>" >> $output #clonality tab
|
|
|
440
|
|
|
441 function clonality_table {
|
|
|
442 local infile=$1
|
|
|
443 local outfile=$2
|
|
|
444
|
|
|
445 echo "<table class='pure-table pure-table-striped'>" >> $outfile
|
|
|
446 echo "<thead><tr><th>Clone size</th><th>Nr of clones</th><th>Nr of sequences</th></tr></thead>" >> $outfile
|
|
|
447
|
|
|
448 first='true'
|
|
|
449
|
|
|
450 while read size clones seqs
|
|
|
451 do
|
|
|
452 if [[ "$first" == "true" ]]; then
|
|
|
453 first="false"
|
|
|
454 continue
|
|
|
455 fi
|
|
|
456 echo "<tr><td>$size</td><td>$clones</td><td>$seqs</td></tr>" >> $outfile
|
|
|
457 done < $infile
|
|
|
458
|
|
|
459 echo "</table>" >> $outfile
|
|
|
460 }
|
|
|
461 echo "<div class='tabber'>" >> $output
|
|
|
462
|
|
|
463 echo "<div class='tabbertab' title='All'>" >> $output
|
|
|
464 clonality_table $outdir/change_o/change-o-defined_clones-summary.txt $output
|
|
|
465 echo "</div>" >> $output
|
|
|
466
|
|
|
467 echo "<div class='tabbertab' title='Ca'>" >> $output
|
|
|
468 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGA.txt $output
|
|
|
469 echo "</div>" >> $output
|
|
|
470
|
|
|
471 echo "<div class='tabbertab' title='Cg'>" >> $output
|
|
|
472 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGG.txt $output
|
|
|
473 echo "</div>" >> $output
|
|
|
474
|
|
|
475 echo "<div class='tabbertab' title='Cm'>" >> $output
|
|
|
476 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
|
|
|
477 echo "</div>" >> $output
|
|
|
478
|
|
|
479 echo "<div class='tabbertab' title='Overview'>" >> $output
|
|
|
480 cat "$outdir/sequence_overview/index.html" >> $output
|
|
|
481 echo "</div>" >> $output
|
|
|
482
|
|
|
483
|
|
|
484 echo "</div>" >> $output #clonality tabber end
|
|
|
485
|
|
|
486 echo "</div>" >> $output #clonality tab end
|
|
|
487
|
|
5
|
488 fi
|
|
|
489
|
|
0
|
490 echo "<div class='tabbertab' title='Downloads'>" >> $output
|
|
|
491
|
|
|
492 echo "<table class='pure-table pure-table-striped'>" >> $output
|
|
|
493 echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output
|
|
|
494 echo "<tr><td>The complete dataset</td><td><a href='merged.txt' download='merged.txt' >Download</a></td></tr>" >> $output
|
|
|
495 echo "<tr><td>The filtered dataset</td><td><a href='filtered.txt' download='filtered.txt' >Download</a></td></tr>" >> $output
|
|
|
496 echo "<tr><td>The alignment info on the unmatched sequences</td><td><a href='unmatched.txt' download='unmatched.txt' >Download</a></td></tr>" >> $output
|
|
|
497
|
|
2
|
498 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Overview</td></tr>" >> $output
|
|
|
499 echo "<tr><td>The SHM Overview table as a dataset</td><td><a href='data_sum.txt' download='data_sum.txt' >Download</a></td></tr>" >> $output
|
|
|
500 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
|
|
|
501 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
|
|
|
502 echo "<tr><td>Base count for every sequence</td><td><a href='base_overview.html'>View</a></td></tr>" >> $output
|
|
|
503 echo "<tr><td>The data used to generate the RGYW/WRCY and TW/WA plot</td><td><a href='plot1.txt' download='plot1.txt' >Download</a></td></tr>" >> $output
|
|
|
504 echo "<tr><td>The data used to generate the relative transition and transversion plot</td><td><a href='plot2.txt' download='plot2.txt' >Download</a></td></tr>" >> $output
|
|
|
505 echo "<tr><td>The data used to generate the absolute transition and transversion plot</td><td><a href='plot3.txt' download='plot3.txt' >Download</a></td></tr>" >> $output
|
|
|
506
|
|
|
507 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Frequency</td></tr>" >> $output
|
|
0
|
508 echo "<tr><td>The data generate the frequency scatter plot</td><td><a href='scatter.txt' download='scatter.txt' >Download</a></td></tr>" >> $output
|
|
|
509 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
|
|
|
510 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
|
|
|
511
|
|
2
|
512 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Transition Tables</td></tr>" >> $output
|
|
|
513 echo "<tr><td>The data for the 'all' transition plot</td><td><a href='transition_all_sum.txt' download='transition_all_sum.txt' >Download</a></td></tr>" >> $output
|
|
|
514 echo "<tr><td>The data for the 'IGA' transition plot</td><td><a href='transition_IGA_sum.txt' download='transition_all_sum.txt' >Download</a></td></tr>" >> $output
|
|
|
515 echo "<tr><td>The data for the 'IGA1' transition plot</td><td><a href='transition_IGA1_sum.txt' download='transition_IGA1_sum.txt' >Download</a></td></tr>" >> $output
|
|
|
516 echo "<tr><td>The data for the 'IGA1' transition plot</td><td><a href='transition_IGA1_sum.txt' download='transition_IGA1_sum.txt' >Download</a></td></tr>" >> $output
|
|
|
517 echo "<tr><td>The data for the 'IGG' transition plot</td><td><a href='transition_IGG_sum.txt' download='transition_IGG_sum.txt' >Download</a></td></tr>" >> $output
|
|
|
518 echo "<tr><td>The data for the 'IGG1' transition plot</td><td><a href='transition_IGG1_sum.txt' download='transition_IGG1_sum.txt' >Download</a></td></tr>" >> $output
|
|
|
519 echo "<tr><td>The data for the 'IGG2' transition plot</td><td><a href='transition_IGG2_sum.txt' download='transition_IGG2_sum.txt' >Download</a></td></tr>" >> $output
|
|
|
520 echo "<tr><td>The data for the 'IGG3' transition plot</td><td><a href='transition_IGG3_sum.txt' download='transition_IGG3_sum.txt' >Download</a></td></tr>" >> $output
|
|
|
521 echo "<tr><td>The data for the 'IGG4' transition plot</td><td><a href='transition_IGG4_sum.txt' download='transition_IGG4_sum.txt' >Download</a></td></tr>" >> $output
|
|
|
522 echo "<tr><td>The data for the 'IGM' transition plot</td><td><a href='transition_IGM_sum.txt' download='transition_IGM_sum.txt' >Download</a></td></tr>" >> $output
|
|
0
|
523
|
|
2
|
524 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Antigen Selection</td></tr>" >> $output
|
|
0
|
525 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
|
|
|
526 echo "<tr><td>Absent AA location data per sequence ID</td><td><a href='absent_aa_id.txt' download='absent_aa_id.txt' >Download</a></td></tr>" >> $output
|
|
|
527
|
|
|
528 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
|
|
|
529 echo "<tr><td>Baseline data</td><td><a href='baseline.txt' download='baseline.txt' >Download</a></td></tr>" >> $output
|
|
|
530 echo "<tr><td>Baseline IGA PDF</td><td><a href='baseline_IGA.pdf' download='baseline_IGA.pdf' >Download</a></td></tr>" >> $output
|
|
|
531 echo "<tr><td>Baseline IGA data</td><td><a href='baseline_IGA.txt' download='baseline_IGA.txt' >Download</a></td></tr>" >> $output
|
|
|
532 echo "<tr><td>Baseline IGG PDF</td><td><a href='baseline_IGG.pdf' download='baseline_IGG.pdf' >Download</a></td></tr>" >> $output
|
|
|
533 echo "<tr><td>Baseline IGG data</td><td><a href='baseline_IGG.txt' download='baseline_IGG.txt' >Download</a></td></tr>" >> $output
|
|
|
534 echo "<tr><td>Baseline IGM PDF</td><td><a href='baseline_IGM.pdf' download='baseline_IGM.pdf' >Download</a></td></tr>" >> $output
|
|
|
535 echo "<tr><td>Baseline IGM data</td><td><a href='baseline_IGM.txt' download='baseline_IGM.txt' >Download</a></td></tr>" >> $output
|
|
|
536
|
|
2
|
537 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>CSR</td></tr>" >> $output
|
|
|
538 echo "<tr><td>The data for the CSR IGA pie plot</td><td><a href='IGA_pie.txt' download='IGA_pie.txt' >Download</a></td></tr>" >> $output
|
|
|
539 echo "<tr><td>The data for the CSR IGG pie plot</td><td><a href='IGG_pie.txt' download='IGG_pie.txt' >Download</a></td></tr>" >> $output
|
|
|
540
|
|
|
541 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Clonality</td></tr>" >> $output
|
|
|
542 echo "<tr><td>Sequence overlap between subclasses</td><td><a href='sequence_overview/index.html'>View</a></td></tr>" >> $output
|
|
|
543 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
|
|
|
544 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
|
|
|
545 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
|
|
|
546 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
|
|
|
547 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
|
|
|
548 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
|
|
|
549 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
|
|
|
550 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
|
|
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551
|
|
|
552 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Filtered IMGT output files</td></tr>" >> $output
|
|
0
|
553 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
|
|
|
554 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
|
|
|
555 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
|
|
|
556 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
|
|
|
557 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
|
|
|
558 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
|
|
|
559 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
|
|
|
560 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
|
|
|
561 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
|
|
|
562 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
|
|
|
563
|
|
|
564 echo "</table>" >> $output
|
|
|
565
|
|
|
566 echo "</div>" >> $output #downloads tab end
|
|
|
567
|
|
|
568 echo "</div>" >> $output #tabs end
|
|
|
569
|
|
|
570 echo "</html>" >> $output
|
|
|
571
|
|
5
|
572
|
|
|
573 if [[ "$fast" == "no" ]] ; then
|
|
0
|
574
|
|
5
|
575 echo "---------------- baseline ----------------"
|
|
|
576 echo "---------------- baseline ----------------<br />" >> $log
|
|
|
577 tmp="$PWD"
|
|
|
578
|
|
|
579 mkdir $outdir/baseline
|
|
0
|
580
|
|
|
581
|
|
5
|
582 mkdir $outdir/baseline/IGA_IGG_IGM
|
|
|
583 if [[ $(wc -l < $outdir/new_IMGT/1_Summary.txt) -gt "1" ]]; then
|
|
|
584 cd $outdir/baseline/IGA_IGG_IGM
|
|
|
585 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT.txz "IGA_IGG_IGM" "$dir/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt"
|
|
|
586 else
|
|
|
587 echo "No sequences" > "$outdir/baseline.txt"
|
|
|
588 fi
|
|
0
|
589
|
|
5
|
590 mkdir $outdir/baseline/IGA
|
|
|
591 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
|
|
|
592 cd $outdir/baseline/IGA
|
|
|
593 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGA.txz "IGA" "$dir/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_IGA.pdf" "Sequence.ID" "$outdir/baseline_IGA.txt"
|
|
|
594 else
|
|
|
595 echo "No IGA sequences" > "$outdir/baseline_IGA.txt"
|
|
|
596 fi
|
|
0
|
597
|
|
5
|
598 mkdir $outdir/baseline/IGG
|
|
|
599 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
|
|
|
600 cd $outdir/baseline/IGG
|
|
|
601 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGG.txz "cg" "$dir/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_IGG.pdf" "Sequence.ID" "$outdir/baseline_IGG.txt"
|
|
|
602 else
|
|
|
603 echo "No IGG sequences" > "$outdir/baseline_IGG.txt"
|
|
|
604 fi
|
|
0
|
605
|
|
5
|
606 mkdir $outdir/baseline/IGM
|
|
|
607 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
|
|
|
608 cd $outdir/baseline/IGM
|
|
|
609 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGM.txz "IGM" "$dir/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_IGM.pdf" "Sequence.ID" "$outdir/baseline_IGM.txt"
|
|
|
610 else
|
|
|
611 echo "No IGM sequences" > "$outdir/baseline_IGM.txt"
|
|
|
612 fi
|
|
|
613
|
|
|
614 cd $tmp
|
|
|
615
|
|
|
616 echo "Cleaning up *.RData files"
|
|
|
617 find $outdir/baseline -name "*.RData" -type f -delete
|
|
|
618
|
|
0
|
619 fi
|
|
|
620
|
|
|
621 echo "---------------- naive_output.r ----------------"
|
|
|
622 echo "---------------- naive_output.r ----------------<br />" >> $log
|
|
|
623
|
|
5
|
624 if [[ "$naive_output" == "yes" ]]
|
|
0
|
625 then
|
|
|
626 cp $outdir/new_IMGT_IGA.txz ${naive_output_ca}
|
|
|
627 cp $outdir/new_IMGT_IGG.txz ${naive_output_cg}
|
|
|
628 cp $outdir/new_IMGT_IGM.txz ${naive_output_cm}
|
|
|
629 fi
|
|
|
630
|
|
|
631 echo "</table>" >> $outdir/base_overview.html
|
|
|
632
|
|
|
633 mv $log $outdir/log.html
|
|
|
634
|
|
|
635 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
|
|
|
636 echo "<table border = 1>" >> $log
|
|
|
637 echo "<thead><tr><th>Info</th><th>Sequences</th><th>Percentage</th></tr></thead>" >> $log
|
|
|
638 tIFS="$TMP"
|
|
|
639 IFS=$'\t'
|
|
|
640 while read step seq perc
|
|
|
641 do
|
|
|
642 echo "<tr>" >> $log
|
|
|
643 echo "<td>$step</td>" >> $log
|
|
|
644 echo "<td>$seq</td>" >> $log
|
|
|
645 echo "<td>${perc}%</td>" >> $log
|
|
|
646 echo "</tr>" >> $log
|
|
|
647 done < $outdir/filtering_steps.txt
|
|
|
648 echo "</table border></center></html>" >> $log
|
|
|
649
|
|
|
650 IFS="$tIFS"
|
|
|
651
|
|
|
652
|
|
|
653 echo "---------------- Done! ----------------"
|
|
|
654 echo "---------------- Done! ----------------<br />" >> $outdir/log.html
|
|
|
655
|
|
|
656
|
|
|
657
|
|
|
658
|
|
|
659
|
|
|
660
|
|
|
661
|
|
|
662
|
|
|
663
|
|
|
664
|
|
|
665
|
|
|
666
|
|
|
667
|
|
|
668
|
|
|
669
|
|
|
670
|
|
|
671
|
|
|
672
|
|
|
673
|
|
|
674
|
|
|
675
|
