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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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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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40 mkdir -p $PWD/files/$title
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41 tar -xJf $input -C $PWD/files/$title
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42 fi
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43
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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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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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5
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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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0
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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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0
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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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190 fi
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191
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5
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192 genes=(IGA IGA1 IGA2 IGG IGG1 IGG2 IGG3 IGG4 IGM IGE)
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0
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193
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194 funcs=(sum mean median)
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195 funcs=(sum)
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196
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197 echo "---------------- sequence_overview.r ----------------"
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198 echo "---------------- sequence_overview.r ----------------<br />" >> $log
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199
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200 mkdir $outdir/sequence_overview
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201
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7
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202 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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203
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204 echo "<table border='1'>" > $outdir/base_overview.html
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205
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206 while IFS=$'\t' read ID class seq A C G T
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207 do
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208 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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209 done < $outdir/sequence_overview/ntoverview.txt
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210
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211 echo "<html><center><h1>$title</h1></center>" > $output
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212 echo "<meta name='viewport' content='width=device-width, initial-scale=1'>" >> $output
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213 echo "<script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $output
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214 echo "<script type='text/javascript' src='tabber.js'></script>" >> $output
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215 echo "<script type='text/javascript' src='script.js'></script>" >> $output
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216 echo "<link rel='stylesheet' type='text/css' href='style.css'>" >> $output
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217 echo "<link rel='stylesheet' type='text/css' href='pure-min.css'>" >> $output
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218
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219 matched_count="`cat $outdir/merged.txt | grep -v 'unmatched' | tail -n +2 | wc -l`"
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220 unmatched_count="`cat $outdir/unmatched.txt | tail -n +2 | wc -l`"
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221 total_count=$((matched_count + unmatched_count))
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222 perc_count=$((unmatched_count / total_count * 100))
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223 perc_count=`bc -l <<< "scale=2; ${unmatched_count} / ${total_count} * 100"`
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224 perc_count=`bc -l <<< "scale=2; (${unmatched_count} / ${total_count} * 100 ) / 1"`
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225
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226 echo "<center><h2>Total: ${total_count}</h2></center>" >> $output
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227 echo "<center><h2>Matched: ${matched_count} Unmatched: ${unmatched_count}</h2></center>" >> $output
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228 echo "<center><h2>Percentage unmatched: ${perc_count}</h2></center>" >> $output
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229
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230 echo "---------------- main tables ----------------"
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231 echo "---------------- main tables ----------------<br />" >> $log
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232
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233 echo "<div class='tabber'>" >> $output
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23
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234 echo "<div class='tabbertab' title='SHM Overview' style='width: 3000px;'>" >> $output
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0
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235
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236 for func in ${funcs[@]}
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237 do
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238
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239 echo "---------------- $func table ----------------"
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240 echo "---------------- $func table ----------------<br />" >> $log
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241
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242 cat $outdir/mutations_${func}.txt $outdir/hotspot_analysis_${func}.txt > $outdir/data_${func}.txt
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243
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244 echo "---------------- pattern_plots.r ----------------"
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245 echo "---------------- pattern_plots.r ----------------<br />" >> $log
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246
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23
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247 Rscript $dir/pattern_plots.r $outdir/data_${func}.txt $outdir/plot1 $outdir/plot2 $outdir/plot3 $outdir/shm_overview.txt 2>&1
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0
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248
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249 echo "<table class='pure-table pure-table-striped'>" >> $output
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250 echo "<thead><tr><th>info</th>" >> $output
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251
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252 if [ "${class_filter}" != "101_101" ] ; then
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253
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254 for gene in ${genes[@]}
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255 do
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256 tmp=`cat $outdir/${gene}_${func}_n.txt`
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257 echo "<th><a href='matched_${gene}_${func}.txt'>${gene} (N = $tmp)</a></th>" >> $output
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258 done
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259
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260 tmp=`cat $outdir/all_${func}_n.txt`
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261 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
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262 tmp=`cat $outdir/unmatched_${func}_n.txt`
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263 echo "<th><a href='unmatched.txt'>unmatched (N = ${unmatched_count})</a></th><tr></thead>" >> $output
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264
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5
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265 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
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0
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266 do
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267 if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] ; then #meh
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5
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268 echo "<tr><td>$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>" >> $output
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0
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269 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
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5
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270 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>" >> $output
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0
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271 else
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5
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272 echo "<tr><td>$name</td><td>${cax}/${cay} (${caz}%)</td><td>${ca1x}/${ca1y} (${ca1z}%)</td><td>${ca2x}/${ca2y} (${ca2z}%)</td><td>${cgx}/${cgy} (${cgz}%)</td><td>${cg1x}/${cg1y} (${cg1z}%)</td><td>${cg2x}/${cg2y} (${cg2z}%)</td><td>${cg3x}/${cg3y} (${cg3z}%)</td><td>${cg4x}/${cg4y} (${cg4z}%)</td><td>${cmx}/${cmy} (${cmz}%)</td><td>${cex}/${cey} (${cez}%)</td><td>${allx}/${ally} (${allz}%)</td><td>${unx}/${uny} (${unz}%)</td></tr>" >> $output
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0
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273 fi
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274 done < $outdir/data_${func}.txt
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275
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276 else
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3
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277 tmp=`cat $outdir/all_${func}_n.txt`
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0
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278 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
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279
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5
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280 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
|
|
0
|
281 do
|
|
|
282 if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] ; then #meh
|
|
3
|
283 echo "<tr><td>$name</td><td>${allx}/${ally}</td></tr>" >> $output
|
|
0
|
284 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
|
|
3
|
285 echo "<tr><td>$name</td><td>${allz}%</td></tr>" >> $output
|
|
0
|
286 else
|
|
3
|
287 echo "<tr><td>$name</td><td>${allx}/${ally} (${allz}%)</td></tr>" >> $output
|
|
0
|
288 fi
|
|
|
289 done < $outdir/data_${func}.txt
|
|
|
290
|
|
|
291 fi
|
|
|
292 echo "</table>" >> $output
|
|
|
293 #echo "<a href='data_${func}.txt'>Download data</a>" >> $output
|
|
|
294 done
|
|
|
295
|
|
|
296 echo "<img src='plot1.png' /><br />" >> $output
|
|
|
297 echo "<img src='plot2.png' /><br />" >> $output
|
|
|
298 echo "<img src='plot3.png' /><br />" >> $output
|
|
|
299
|
|
|
300 echo "</div>" >> $output #SHM overview tab end
|
|
|
301
|
|
|
302 echo "---------------- images ----------------"
|
|
|
303 echo "---------------- images ----------------<br />" >> $log
|
|
|
304
|
|
23
|
305 echo "<div class='tabbertab' title='SHM Frequency' style='width: 3000px;'>" >> $output
|
|
0
|
306
|
|
|
307 if [ -a $outdir/scatter.png ]
|
|
|
308 then
|
|
|
309 echo "<img src='scatter.png'/><br />" >> $output
|
|
|
310 fi
|
|
|
311 if [ -a $outdir/frequency_ranges.png ]
|
|
|
312 then
|
|
|
313 echo "<img src='frequency_ranges.png'/><br />" >> $output
|
|
|
314 fi
|
|
|
315
|
|
|
316 echo "</div>" >> $output #SHM frequency tab end
|
|
|
317
|
|
23
|
318 echo "<div class='tabbertab' title='Transition tables' style='width: 3000px;'>" >> $output
|
|
0
|
319
|
|
|
320 echo "<table border='0'>" >> $output
|
|
|
321
|
|
|
322 for gene in ${genes[@]}
|
|
|
323 do
|
|
|
324 echo "<tr>" >> $output
|
|
|
325 echo "<td><h1>${gene}</h1></td>" >> $output
|
|
23
|
326
|
|
|
327 if [ -e $outdir/transitions_heatmap_${gene}.png ]
|
|
|
328 then
|
|
|
329 echo "<td><img src='transitions_heatmap_${gene}.png' /></td>" >> $output
|
|
|
330 else
|
|
|
331 echo "<td></td>" >> $output
|
|
|
332 fi
|
|
|
333
|
|
|
334 if [ -e $outdir/transitions_stacked_${gene}.png ]
|
|
|
335 then
|
|
|
336 echo "<td><img src='transitions_stacked_${gene}.png' /></td>" >> $output
|
|
|
337 else
|
|
|
338 echo "<td></td>" >> $output
|
|
|
339 fi
|
|
|
340
|
|
0
|
341 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
|
|
|
342 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
|
|
|
343 first="true"
|
|
|
344 while IFS=, read from a c g t
|
|
|
345 do
|
|
|
346 if [ "$first" == "true" ] ; then
|
|
|
347 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
|
|
|
348 first="false"
|
|
|
349 else
|
|
|
350 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
|
|
|
351 fi
|
|
|
352 done < $outdir/transitions_${gene}_sum.txt
|
|
|
353 echo "</table></td>" >> $output
|
|
|
354
|
|
|
355 echo "</tr>" >> $output
|
|
|
356 done
|
|
|
357
|
|
|
358 echo "<tr>" >> $output
|
|
|
359 echo "<td><h1>All</h1></td>" >> $output
|
|
|
360 echo "<td><img src='transitions_heatmap_all.png' /></td>" >> $output
|
|
|
361 echo "<td><img src='transitions_stacked_all.png' /></td>" >> $output
|
|
|
362 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
|
|
|
363 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
|
|
|
364 first="true"
|
|
|
365 while IFS=, read from a c g t
|
|
|
366 do
|
|
|
367 if [ "$first" == "true" ] ; then
|
|
|
368 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
|
|
|
369 first="false"
|
|
|
370 else
|
|
|
371 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
|
|
|
372 fi
|
|
|
373 done < $outdir/transitions_all_sum.txt
|
|
|
374 echo "</table></td>" >> $output
|
|
|
375
|
|
|
376 echo "</tr>" >> $output
|
|
|
377
|
|
|
378 echo "</table>" >> $output
|
|
|
379
|
|
|
380 echo "</div>" >> $output #transition tables tab end
|
|
|
381
|
|
|
382 echo "<div class='tabbertab' title='Antigen Selection'>" >> $output
|
|
|
383
|
|
23
|
384 if [ -e $outdir/aa_histogram.png ]
|
|
0
|
385 then
|
|
|
386 echo "<img src='aa_histogram.png'/><br />" >> $output
|
|
23
|
387 fi
|
|
|
388
|
|
|
389 if [ -e $outdir/aa_histogram_IGA.png ]
|
|
|
390 then
|
|
0
|
391 echo "<img src='aa_histogram_IGA.png'/><br />" >> $output
|
|
23
|
392 fi
|
|
|
393
|
|
|
394 if [ -e $outdir/aa_histogram_IGG.png ]
|
|
|
395 then
|
|
0
|
396 echo "<img src='aa_histogram_IGG.png'/><br />" >> $output
|
|
23
|
397 fi
|
|
|
398
|
|
|
399 if [ -e $outdir/aa_histogram_IGM.png ]
|
|
|
400 then
|
|
0
|
401 echo "<img src='aa_histogram_IGM.png'/><br />" >> $output
|
|
23
|
402 fi
|
|
|
403
|
|
|
404 if [ -e $outdir/aa_histogram_IGE.png ]
|
|
|
405 then
|
|
6
|
406 echo "<img src='aa_histogram_IGE.png'/><br />" >> $output
|
|
0
|
407 fi
|
|
|
408
|
|
23
|
409
|
|
|
410 if [ -e $outdir/baseline.png ]
|
|
|
411 then
|
|
|
412 echo "<embed src='baseline.pdf' width='700px' height='1000px'>" >> $output
|
|
|
413 fi
|
|
|
414
|
|
|
415 if [ -e $outdir/baseline_IGA.png ]
|
|
|
416 then
|
|
|
417 echo "<embed src='baseline_IGA.pdf' width='700px' height='1000px'>" >> $output
|
|
|
418 fi
|
|
|
419
|
|
|
420 if [ -e $outdir/baseline_IGG.png ]
|
|
|
421 then
|
|
|
422 echo "<embed src='baseline_IGG.pdf' width='700px' height='1000px'>" >> $output
|
|
|
423 fi
|
|
|
424
|
|
|
425 if [ -e $outdir/baseline_IGM.png ]
|
|
|
426 then
|
|
|
427 echo "<embed src='baseline_IGM.pdf' width='700px' height='1000px'>" >> $output
|
|
|
428 fi
|
|
|
429
|
|
|
430 if [ -e $outdir/baseline_IGE.png ]
|
|
|
431 then
|
|
|
432 echo "<embed src='baseline_IGE.pdf' width='700px' height='1000px'>" >> $output
|
|
|
433 fi
|
|
0
|
434
|
|
|
435 echo "</div>" >> $output #antigen selection tab end
|
|
|
436
|
|
|
437 echo "<div class='tabbertab' title='CSR'>" >> $output #CSR tab
|
|
|
438
|
|
23
|
439 if [ -e $outdir/IGA.png ]
|
|
0
|
440 then
|
|
|
441 echo "<img src='IGA.png'/><br />" >> $output
|
|
|
442 fi
|
|
23
|
443 if [ -e $outdir/IGG.png ]
|
|
0
|
444 then
|
|
|
445 echo "<img src='IGG.png'/><br />" >> $output
|
|
|
446 fi
|
|
|
447
|
|
|
448 echo "</div>" >> $output #CSR tab end
|
|
|
449
|
|
5
|
450 if [[ "$fast" == "no" ]] ; then
|
|
|
451
|
|
|
452 echo "---------------- change-o MakeDB ----------------"
|
|
0
|
453
|
|
5
|
454 mkdir $outdir/change_o
|
|
0
|
455
|
|
5
|
456 tmp="$PWD"
|
|
0
|
457
|
|
5
|
458 cd $outdir/change_o
|
|
0
|
459
|
|
5
|
460 bash $dir/change_o/makedb.sh $outdir/new_IMGT.txz false false false $outdir/change_o/change-o-db.txt
|
|
|
461 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
|
462
|
|
5
|
463 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
|
464
|
|
5
|
465 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
|
466
|
|
5
|
467 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
|
|
|
468 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGA.txz false false false $outdir/change_o/change-o-db-IGA.txt
|
|
|
469 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 $outdir/change_o/change-o-defined_clones-summary-IGA.txt
|
|
|
470 else
|
|
|
471 echo "No IGA sequences" > "$outdir/change_o/change-o-db-defined_clones-IGA.txt"
|
|
|
472 echo "No IGA sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGA.txt"
|
|
|
473 fi
|
|
0
|
474
|
|
5
|
475 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
|
|
|
476 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGG.txz false false false $outdir/change_o/change-o-db-IGG.txt
|
|
|
477 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 $outdir/change_o/change-o-defined_clones-summary-IGG.txt
|
|
|
478 else
|
|
|
479 echo "No IGG sequences" > "$outdir/change_o/change-o-db-defined_clones-IGG.txt"
|
|
|
480 echo "No IGG sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGG.txt"
|
|
|
481 fi
|
|
0
|
482
|
|
5
|
483 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
|
|
|
484 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGM.txz false false false $outdir/change_o/change-o-db-IGM.txt
|
|
|
485 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 $outdir/change_o/change-o-defined_clones-summary-IGM.txt
|
|
|
486 else
|
|
|
487 echo "No IGM sequences" > "$outdir/change_o/change-o-db-defined_clones-IGM.txt"
|
|
|
488 echo "No IGM sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGM.txt"
|
|
|
489 fi
|
|
0
|
490
|
|
6
|
491 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
|
|
|
492 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGE.txz false false false $outdir/change_o/change-o-db-IGE.txt
|
|
|
493 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 $outdir/change_o/change-o-defined_clones-summary-IGE.txt
|
|
|
494 else
|
|
|
495 echo "No IGE sequences" > "$outdir/change_o/change-o-db-defined_clones-IGE.txt"
|
|
|
496 echo "No IGE sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGE.txt"
|
|
|
497 fi
|
|
|
498
|
|
5
|
499 PWD="$tmp"
|
|
0
|
500
|
|
16
|
501 echo "<div class='tabbertab' title='Clonality'>" >> $output #clonality tab
|
|
0
|
502
|
|
16
|
503 function clonality_table {
|
|
|
504 local infile=$1
|
|
|
505 local outfile=$2
|
|
|
506
|
|
|
507 echo "<table class='pure-table pure-table-striped'>" >> $outfile
|
|
|
508 echo "<thead><tr><th>Clone size</th><th>Nr of clones</th><th>Nr of sequences</th></tr></thead>" >> $outfile
|
|
|
509
|
|
|
510 first='true'
|
|
|
511
|
|
|
512 while read size clones seqs
|
|
|
513 do
|
|
|
514 if [[ "$first" == "true" ]]; then
|
|
|
515 first="false"
|
|
|
516 continue
|
|
|
517 fi
|
|
|
518 echo "<tr><td>$size</td><td>$clones</td><td>$seqs</td></tr>" >> $outfile
|
|
|
519 done < $infile
|
|
|
520
|
|
|
521 echo "</table>" >> $outfile
|
|
|
522 }
|
|
|
523 echo "<div class='tabber'>" >> $output
|
|
0
|
524
|
|
16
|
525 echo "<div class='tabbertab' title='All'>" >> $output
|
|
|
526 clonality_table $outdir/change_o/change-o-defined_clones-summary.txt $output
|
|
|
527 echo "</div>" >> $output
|
|
0
|
528
|
|
16
|
529 echo "<div class='tabbertab' title='IGA'>" >> $output
|
|
|
530 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGA.txt $output
|
|
|
531 echo "</div>" >> $output
|
|
0
|
532
|
|
16
|
533 echo "<div class='tabbertab' title='IGG'>" >> $output
|
|
|
534 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGG.txt $output
|
|
|
535 echo "</div>" >> $output
|
|
0
|
536
|
|
16
|
537 echo "<div class='tabbertab' title='IGM'>" >> $output
|
|
|
538 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
|
|
|
539 echo "</div>" >> $output
|
|
6
|
540
|
|
16
|
541 echo "<div class='tabbertab' title='IGE'>" >> $output
|
|
|
542 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
|
|
|
543 echo "</div>" >> $output
|
|
0
|
544
|
|
23
|
545 echo "<div class='tabbertab' title='Overlap'>" >> $output
|
|
16
|
546 cat "$outdir/sequence_overview/index.html" >> $output
|
|
|
547 echo "</div>" >> $output
|
|
0
|
548
|
|
|
549
|
|
16
|
550 echo "</div>" >> $output #clonality tabber end
|
|
0
|
551
|
|
16
|
552 echo "</div>" >> $output #clonality tab end
|
|
0
|
553
|
|
5
|
554 fi
|
|
|
555
|
|
0
|
556 echo "<div class='tabbertab' title='Downloads'>" >> $output
|
|
|
557
|
|
|
558 echo "<table class='pure-table pure-table-striped'>" >> $output
|
|
|
559 echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output
|
|
|
560 echo "<tr><td>The complete dataset</td><td><a href='merged.txt' download='merged.txt' >Download</a></td></tr>" >> $output
|
|
|
561 echo "<tr><td>The filtered dataset</td><td><a href='filtered.txt' download='filtered.txt' >Download</a></td></tr>" >> $output
|
|
|
562 echo "<tr><td>The alignment info on the unmatched sequences</td><td><a href='unmatched.txt' download='unmatched.txt' >Download</a></td></tr>" >> $output
|
|
|
563
|
|
2
|
564 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Overview</td></tr>" >> $output
|
|
23
|
565 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
|
566 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
|
|
|
567 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
|
|
|
568 echo "<tr><td>Base count for every sequence</td><td><a href='base_overview.html'>View</a></td></tr>" >> $output
|
|
|
569 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
|
|
|
570 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
|
|
|
571 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
|
|
|
572
|
|
|
573 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Frequency</td></tr>" >> $output
|
|
0
|
574 echo "<tr><td>The data generate the frequency scatter plot</td><td><a href='scatter.txt' download='scatter.txt' >Download</a></td></tr>" >> $output
|
|
|
575 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
|
|
|
576 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
|
|
|
577
|
|
2
|
578 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Transition Tables</td></tr>" >> $output
|
|
23
|
579 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
|
|
|
580 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
|
|
|
581 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
|
|
26
|
582 echo "<tr><td>The data for the 'IGA1' transition plot</td><td><a href='transitions_IGA2_sum.txt' download='transitions_IGA2_sum.txt' >Download</a></td></tr>" >> $output
|
|
23
|
583 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
|
|
|
584 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
|
|
|
585 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
|
|
|
586 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
|
|
|
587 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
|
|
|
588 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
|
|
|
589 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
|
590
|
|
2
|
591 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Antigen Selection</td></tr>" >> $output
|
|
0
|
592 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
|
|
|
593 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
|
|
|
594
|
|
|
595 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
|
|
|
596 echo "<tr><td>Baseline data</td><td><a href='baseline.txt' download='baseline.txt' >Download</a></td></tr>" >> $output
|
|
|
597 echo "<tr><td>Baseline IGA PDF</td><td><a href='baseline_IGA.pdf' download='baseline_IGA.pdf' >Download</a></td></tr>" >> $output
|
|
|
598 echo "<tr><td>Baseline IGA data</td><td><a href='baseline_IGA.txt' download='baseline_IGA.txt' >Download</a></td></tr>" >> $output
|
|
|
599 echo "<tr><td>Baseline IGG PDF</td><td><a href='baseline_IGG.pdf' download='baseline_IGG.pdf' >Download</a></td></tr>" >> $output
|
|
|
600 echo "<tr><td>Baseline IGG data</td><td><a href='baseline_IGG.txt' download='baseline_IGG.txt' >Download</a></td></tr>" >> $output
|
|
|
601 echo "<tr><td>Baseline IGM PDF</td><td><a href='baseline_IGM.pdf' download='baseline_IGM.pdf' >Download</a></td></tr>" >> $output
|
|
|
602 echo "<tr><td>Baseline IGM data</td><td><a href='baseline_IGM.txt' download='baseline_IGM.txt' >Download</a></td></tr>" >> $output
|
|
6
|
603 echo "<tr><td>Baseline IGE data</td><td><a href='baseline_IGE.txt' download='baseline_IGE.txt' >Download</a></td></tr>" >> $output
|
|
0
|
604
|
|
2
|
605 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>CSR</td></tr>" >> $output
|
|
|
606 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
|
|
|
607 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
|
|
|
608
|
|
|
609 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Clonality</td></tr>" >> $output
|
|
|
610 echo "<tr><td>Sequence overlap between subclasses</td><td><a href='sequence_overview/index.html'>View</a></td></tr>" >> $output
|
|
|
611 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
|
|
|
612 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
|
|
|
613 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
|
|
|
614 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
|
|
|
615 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
|
|
|
616 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
|
|
|
617 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
|
|
|
618 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
|
619 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
|
|
|
620 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
|
621
|
|
|
622 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Filtered IMGT output files</td></tr>" >> $output
|
|
0
|
623 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
|
|
|
624 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
|
|
|
625 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
|
|
|
626 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
|
|
|
627 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
|
|
|
628 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
|
|
|
629 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
|
|
|
630 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
|
|
|
631 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
|
|
|
632 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
|
|
6
|
633 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_IGM.txz' >Download</a></td></tr>" >> $output
|
|
0
|
634
|
|
|
635 echo "</table>" >> $output
|
|
|
636
|
|
|
637 echo "</div>" >> $output #downloads tab end
|
|
|
638
|
|
|
639 echo "</div>" >> $output #tabs end
|
|
|
640
|
|
|
641 echo "</html>" >> $output
|
|
|
642
|
|
5
|
643
|
|
|
644 if [[ "$fast" == "no" ]] ; then
|
|
0
|
645
|
|
5
|
646 echo "---------------- baseline ----------------"
|
|
|
647 echo "---------------- baseline ----------------<br />" >> $log
|
|
|
648 tmp="$PWD"
|
|
|
649
|
|
|
650 mkdir $outdir/baseline
|
|
0
|
651
|
|
|
652
|
|
5
|
653 mkdir $outdir/baseline/IGA_IGG_IGM
|
|
|
654 if [[ $(wc -l < $outdir/new_IMGT/1_Summary.txt) -gt "1" ]]; then
|
|
|
655 cd $outdir/baseline/IGA_IGG_IGM
|
|
|
656 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"
|
|
|
657 else
|
|
|
658 echo "No sequences" > "$outdir/baseline.txt"
|
|
|
659 fi
|
|
0
|
660
|
|
5
|
661 mkdir $outdir/baseline/IGA
|
|
|
662 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
|
|
|
663 cd $outdir/baseline/IGA
|
|
|
664 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"
|
|
|
665 else
|
|
|
666 echo "No IGA sequences" > "$outdir/baseline_IGA.txt"
|
|
|
667 fi
|
|
0
|
668
|
|
5
|
669 mkdir $outdir/baseline/IGG
|
|
|
670 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
|
|
|
671 cd $outdir/baseline/IGG
|
|
|
672 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"
|
|
|
673 else
|
|
|
674 echo "No IGG sequences" > "$outdir/baseline_IGG.txt"
|
|
|
675 fi
|
|
0
|
676
|
|
5
|
677 mkdir $outdir/baseline/IGM
|
|
|
678 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
|
|
|
679 cd $outdir/baseline/IGM
|
|
|
680 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"
|
|
|
681 else
|
|
|
682 echo "No IGM sequences" > "$outdir/baseline_IGM.txt"
|
|
|
683 fi
|
|
|
684
|
|
6
|
685 mkdir $outdir/baseline/IGE
|
|
|
686 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
|
|
|
687 cd $outdir/baseline/IGE
|
|
|
688 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGE.txz "IGE" "$dir/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_IGE.pdf" "Sequence.ID" "$outdir/baseline_IGE.txt"
|
|
|
689 else
|
|
|
690 echo "No IGE sequences" > "$outdir/baseline_IGE.txt"
|
|
|
691 fi
|
|
|
692
|
|
5
|
693 cd $tmp
|
|
|
694
|
|
|
695 echo "Cleaning up *.RData files"
|
|
|
696 find $outdir/baseline -name "*.RData" -type f -delete
|
|
|
697
|
|
0
|
698 fi
|
|
|
699
|
|
|
700 echo "---------------- naive_output.r ----------------"
|
|
|
701 echo "---------------- naive_output.r ----------------<br />" >> $log
|
|
|
702
|
|
5
|
703 if [[ "$naive_output" == "yes" ]]
|
|
0
|
704 then
|
|
28
|
705 echo "output naive output"
|
|
18
|
706 if [[ "${class_filter}" == "101_101" ]]
|
|
|
707 then
|
|
28
|
708 echo "copy new_IMGT.txz to ${naive_output_all}"
|
|
21
|
709 cp $outdir/new_IMGT.txz ${naive_output_all}
|
|
18
|
710 else
|
|
28
|
711 echo "copy for classes"
|
|
18
|
712 cp $outdir/new_IMGT_IGA.txz ${naive_output_ca}
|
|
|
713 cp $outdir/new_IMGT_IGG.txz ${naive_output_cg}
|
|
|
714 cp $outdir/new_IMGT_IGM.txz ${naive_output_cm}
|
|
|
715 cp $outdir/new_IMGT_IGE.txz ${naive_output_ce}
|
|
|
716 fi
|
|
0
|
717 fi
|
|
|
718
|
|
|
719 echo "</table>" >> $outdir/base_overview.html
|
|
|
720
|
|
|
721 mv $log $outdir/log.html
|
|
|
722
|
|
|
723 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
|
|
|
724 echo "<table border = 1>" >> $log
|
|
|
725 echo "<thead><tr><th>Info</th><th>Sequences</th><th>Percentage</th></tr></thead>" >> $log
|
|
|
726 tIFS="$TMP"
|
|
|
727 IFS=$'\t'
|
|
|
728 while read step seq perc
|
|
|
729 do
|
|
|
730 echo "<tr>" >> $log
|
|
|
731 echo "<td>$step</td>" >> $log
|
|
|
732 echo "<td>$seq</td>" >> $log
|
|
|
733 echo "<td>${perc}%</td>" >> $log
|
|
|
734 echo "</tr>" >> $log
|
|
|
735 done < $outdir/filtering_steps.txt
|
|
|
736 echo "</table border></center></html>" >> $log
|
|
|
737
|
|
|
738 IFS="$tIFS"
|
|
|
739
|
|
|
740
|
|
|
741 echo "---------------- Done! ----------------"
|
|
|
742 echo "---------------- Done! ----------------<br />" >> $outdir/log.html
|
|
|
743
|
|
|
744
|
|
|
745
|
|
|
746
|
|
|
747
|
|
|
748
|
|
|
749
|
|
|
750
|
|
|
751
|
|
|
752
|
|
|
753
|
|
|
754
|
|
|
755
|
|
|
756
|
|
|
757
|
|
|
758
|
|
|
759
|
|
|
760
|
|
|
761
|
|
|
762
|
|
|
763
|
