annotate wrapper.sh @ 87:64bbc6734ec7 draft

"planemo upload commit 0dcc3e4e47a066373ff0bd56f16536298f8ac2a0"
author rhpvorderman
date Wed, 27 Oct 2021 11:30:25 +0000
parents 4db34e32dd47
children 3c9d4d976c47
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1 #!/usr/bin/env bash
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2 set -e -o pipefail
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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=$9
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14 naive_output_ca=${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=${15}
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20 filter_unique_count=${16}
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21 class_filter=${17}
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22 empty_region_filter=${18}
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23 fast=${19}
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24
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25 #exec 5> debug_output.txt
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26 #BASH_XTRACEFD="5"
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27 #PS4='$(date +%s.%N) $LINENO: '
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28 #set -x
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29
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30 mkdir -p $outdir
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31
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32 tar -xzf $dir/style.tar.gz -C $outdir
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33
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34 echo "---------------- read parameters ----------------"
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35 echo "---------------- read parameters ----------------<br />" > $log
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36
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37 echo "unpacking IMGT file"
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38
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39 type="`file $input`"
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40 if [[ "$type" == *"Zip archive"* ]] ; then
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41 echo "Zip archive"
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42 echo "unzip $input -d $PWD/files/"
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43 unzip $input -d $PWD/files/
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44 elif [[ "$type" == *"XZ compressed data"* ]] ; then
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45 echo "ZX archive"
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46 echo "tar -xJf $input -C $PWD/files/"
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47 mkdir -p "$PWD/files/$title"
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48 tar -xJf $input -C "$PWD/files/$title"
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49 else
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50 echo "Unrecognized format $type"
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51 echo "Unrecognized format $type" > $log
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52 exit 1
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53 fi
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54
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55 cat "`find $PWD/files/ -name "1_*"`" > $PWD/summary.txt
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56 cat "`find $PWD/files/ -name "2_*"`" > $PWD/gapped_nt.txt
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57 cat "`find $PWD/files/ -name "3_*"`" > $PWD/sequences.txt
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58 cat "`find $PWD/files/ -name "4_*"`" > $PWD/gapped_aa.txt
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59 cat "`find $PWD/files/ -name "5_*"`" > $PWD/aa.txt
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60 cat "`find $PWD/files/ -name "6_*"`" > $PWD/junction.txt
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61 cat "`find $PWD/files/ -name "7_*"`" > $PWD/mutationanalysis.txt
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62 cat "`find $PWD/files/ -name "8_*"`" > $PWD/mutationstats.txt
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63 cat "`find $PWD/files/ -name "9_*"`" > $PWD/aa_change_stats.txt
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64 cat "`find $PWD/files/ -name "10_*"`" > $PWD/hotspots.txt
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65
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66 echo "---------------- unique id check ----------------"
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67
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68 Rscript $dir/check_unique_id.r $PWD/summary.txt $PWD/gapped_nt.txt $PWD/sequences.txt $PWD/gapped_aa.txt $PWD/aa.txt $PWD/junction.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/aa_change_stats.txt $PWD/hotspots.txt
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69
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70 if [[ ${#BLASTN_DIR} -ge 5 ]] ; then
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71 echo "On server, using BLASTN_DIR env: ${BLASTN_DIR}"
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72 else
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73 BLASTN_DIR="/home/galaxy/Downloads/ncbi-blast-2.4.0+/bin"
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74 echo "Dev Galaxy set BLASTN_DIR to: ${BLASTN_DIR}"
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75 fi
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76
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77 echo "---------------- class identification ----------------"
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78 echo "---------------- class identification ----------------<br />" >> $log
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79
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80 python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt
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81
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82 echo "---------------- merge_and_filter.r ----------------"
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83 echo "---------------- merge_and_filter.r ----------------<br />" >> $log
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84
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85 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt "$PWD/gapped_aa.txt" $outdir/identified_genes.txt $outdir/merged.txt $outdir/before_unique_filter.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${filter_unique_count} ${class_filter} ${empty_region_filter} 2>&1
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86
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87 if [[ "${naive_output}" == "yes" ]] || [[ "$fast" == "no" ]] ; then
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88
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89 echo "---------------- creating new IMGT zips ----------------"
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90 echo "---------------- creating new IMGT zips ----------------<br />" >> $log
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91
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92 mkdir $outdir/new_IMGT
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93
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94 cp $PWD/summary.txt "$outdir/new_IMGT/1_Summary.txt"
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95 cp $PWD/gapped_nt.txt "$outdir/new_IMGT/2_IMGT-gapped-nt-sequences.txt"
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96 cp $PWD/sequences.txt "$outdir/new_IMGT/3_Nt-sequences.txt"
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97 cp $PWD/gapped_aa.txt "$outdir/new_IMGT/4_IMGT-gapped-AA-sequences.txt"
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98 cp $PWD/aa.txt "$outdir/new_IMGT/5_AA-sequences.txt"
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99 cp $PWD/junction.txt "$outdir/new_IMGT/6_Junction.txt"
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100 cp $PWD/mutationanalysis.txt "$outdir/new_IMGT/7_V-REGION-mutation-and-AA-change-table.txt"
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101 cp $PWD/mutationstats.txt "$outdir/new_IMGT/8_V-REGION-nt-mutation-statistics.txt"
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102 cp $PWD/aa_change_stats.txt "$outdir/new_IMGT/9_V-REGION-AA-change-statistics.txt"
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103 cp $PWD/hotspots.txt "$outdir/new_IMGT/10_V-REGION-mutation-hotspots.txt"
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104
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105 mkdir $outdir/new_IMGT_IGA
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106 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA
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107
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108 mkdir $outdir/new_IMGT_IGA1
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109 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA1
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110
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111 mkdir $outdir/new_IMGT_IGA2
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112 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA2
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113
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114 mkdir $outdir/new_IMGT_IGG
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115 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG
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116
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117 mkdir $outdir/new_IMGT_IGG1
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118 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG1
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119
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120 mkdir $outdir/new_IMGT_IGG2
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121 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG2
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122
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123 mkdir $outdir/new_IMGT_IGG3
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124 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG3
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125
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126 mkdir $outdir/new_IMGT_IGG4
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127 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG4
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128
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129 mkdir $outdir/new_IMGT_IGM
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130 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGM
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131
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132 mkdir $outdir/new_IMGT_IGE
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133 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGE
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134
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135 Rscript $dir/new_imgt.r $outdir/new_IMGT/ $outdir/merged.txt "-" 2>&1
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136
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137 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA/ $outdir/merged.txt "IGA" 2>&1
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138 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA1/ $outdir/merged.txt "IGA1" 2>&1
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139 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA2/ $outdir/merged.txt "IGA2" 2>&1
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140
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141 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG/ $outdir/merged.txt "IGG" 2>&1
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142 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG1/ $outdir/merged.txt "IGG1" 2>&1
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143 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG2/ $outdir/merged.txt "IGG2" 2>&1
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144 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG3/ $outdir/merged.txt "IGG3" 2>&1
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145 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG4/ $outdir/merged.txt "IGG4" 2>&1
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146
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147 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGM/ $outdir/merged.txt "IGM" 2>&1
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148
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149 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGE/ $outdir/merged.txt "IGE" 2>&1
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150
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151
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152 tmp="$PWD"
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153 cd $outdir/new_IMGT/ #tar weirdness...
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154 tar -cJf ../new_IMGT.txz *
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155
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156 cd $outdir/new_IMGT_IGA/
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157 tar -cJf ../new_IMGT_IGA.txz *
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158
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159 cd $outdir/new_IMGT_IGA1/
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160 tar -cJf ../new_IMGT_IGA1.txz *
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161
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162 cd $outdir/new_IMGT_IGA2/
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163 tar -cJf ../new_IMGT_IGA2.txz *
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164
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165 cd $outdir/new_IMGT_IGG/
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166 tar -cJf ../new_IMGT_IGG.txz *
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167
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168 cd $outdir/new_IMGT_IGG1/
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169 tar -cJf ../new_IMGT_IGG1.txz *
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170
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171 cd $outdir/new_IMGT_IGG2/
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davidvanzessen
parents:
diff changeset
172 tar -cJf ../new_IMGT_IGG2.txz *
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davidvanzessen
parents:
diff changeset
173
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davidvanzessen
parents:
diff changeset
174 cd $outdir/new_IMGT_IGG3/
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davidvanzessen
parents:
diff changeset
175 tar -cJf ../new_IMGT_IGG3.txz *
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davidvanzessen
parents:
diff changeset
176
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davidvanzessen
parents:
diff changeset
177 cd $outdir/new_IMGT_IGG4/
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davidvanzessen
parents:
diff changeset
178 tar -cJf ../new_IMGT_IGG4.txz *
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davidvanzessen
parents:
diff changeset
179
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davidvanzessen
parents:
diff changeset
180 cd $outdir/new_IMGT_IGM/
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davidvanzessen
parents:
diff changeset
181 tar -cJf ../new_IMGT_IGM.txz *
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davidvanzessen
parents:
diff changeset
182
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davidvanzessen
parents:
diff changeset
183 cd $outdir/new_IMGT_IGE/
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davidvanzessen
parents:
diff changeset
184 tar -cJf ../new_IMGT_IGE.txz *
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davidvanzessen
parents:
diff changeset
185
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davidvanzessen
parents:
diff changeset
186 cd $tmp
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davidvanzessen
parents:
diff changeset
187 fi
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davidvanzessen
parents:
diff changeset
188
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davidvanzessen
parents:
diff changeset
189 echo "---------------- shm_csr.r ----------------"
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davidvanzessen
parents:
diff changeset
190 echo "---------------- shm_csr.r ----------------<br />" >> $log
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davidvanzessen
parents:
diff changeset
191
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davidvanzessen
parents:
diff changeset
192 classes="IGA,IGA1,IGA2,IGG,IGG1,IGG2,IGG3,IGG4,IGM,IGE,unmatched"
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davidvanzessen
parents:
diff changeset
193 echo "R mutation analysis"
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davidvanzessen
parents:
diff changeset
194 Rscript $dir/shm_csr.r $outdir/merged.txt $classes $outdir ${empty_region_filter} 2>&1
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davidvanzessen
parents:
diff changeset
195
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davidvanzessen
parents:
diff changeset
196 echo "---------------- plot_pdfs.r ----------------"
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davidvanzessen
parents:
diff changeset
197 echo "---------------- plot_pdfs.r ----------------<br />" >> $log
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davidvanzessen
parents:
diff changeset
198
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davidvanzessen
parents:
diff changeset
199 echo "Rscript $dir/shm_csr.r $outdir/pdfplots.RData $outdir 2>&1"
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davidvanzessen
parents:
diff changeset
200
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davidvanzessen
parents:
diff changeset
201 Rscript $dir/plot_pdf.r "$outdir/pdfplots.RData" "$outdir" 2>&1
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davidvanzessen
parents:
diff changeset
202
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davidvanzessen
parents:
diff changeset
203 echo "---------------- shm_csr.py ----------------"
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davidvanzessen
parents:
diff changeset
204 echo "---------------- shm_csr.py ----------------<br />" >> $log
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davidvanzessen
parents:
diff changeset
205
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davidvanzessen
parents:
diff changeset
206 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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davidvanzessen
parents:
diff changeset
207
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davidvanzessen
parents:
diff changeset
208 echo "---------------- aa_histogram.r ----------------"
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davidvanzessen
parents:
diff changeset
209 echo "---------------- aa_histogram.r ----------------<br />" >> $log
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davidvanzessen
parents:
diff changeset
210
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davidvanzessen
parents:
diff changeset
211 Rscript $dir/aa_histogram.r $outdir/aa_id_mutations.txt $outdir/absent_aa_id.txt "IGA,IGG,IGM,IGE" $outdir/ 2>&1
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davidvanzessen
parents:
diff changeset
212 if [ -e "$outdir/aa_histogram_.png" ]; then
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davidvanzessen
parents:
diff changeset
213 mv $outdir/aa_histogram_.png $outdir/aa_histogram.png
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davidvanzessen
parents:
diff changeset
214 mv $outdir/aa_histogram_.pdf $outdir/aa_histogram.pdf
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davidvanzessen
parents:
diff changeset
215 mv $outdir/aa_histogram_.txt $outdir/aa_histogram.txt
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davidvanzessen
parents:
diff changeset
216 mv $outdir/aa_histogram_absent_.txt $outdir/aa_histogram_absent.txt
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davidvanzessen
parents:
diff changeset
217 mv $outdir/aa_histogram_count_.txt $outdir/aa_histogram_count.txt
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davidvanzessen
parents:
diff changeset
218 mv $outdir/aa_histogram_sum_.txt $outdir/aa_histogram_sum.txt
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davidvanzessen
parents:
diff changeset
219 fi
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davidvanzessen
parents:
diff changeset
220
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davidvanzessen
parents:
diff changeset
221 genes=(IGA IGA1 IGA2 IGG IGG1 IGG2 IGG3 IGG4 IGM IGE)
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davidvanzessen
parents:
diff changeset
222
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davidvanzessen
parents:
diff changeset
223 funcs=(sum mean median)
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davidvanzessen
parents:
diff changeset
224 funcs=(sum)
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davidvanzessen
parents:
diff changeset
225
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davidvanzessen
parents:
diff changeset
226 echo "---------------- sequence_overview.r ----------------"
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davidvanzessen
parents:
diff changeset
227 echo "---------------- sequence_overview.r ----------------<br />" >> $log
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davidvanzessen
parents:
diff changeset
228
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davidvanzessen
parents:
diff changeset
229 mkdir $outdir/sequence_overview
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davidvanzessen
parents:
diff changeset
230
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davidvanzessen
parents:
diff changeset
231 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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davidvanzessen
parents:
diff changeset
232
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davidvanzessen
parents:
diff changeset
233 echo "<table border='1'>" > $outdir/base_overview.html
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davidvanzessen
parents:
diff changeset
234
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davidvanzessen
parents:
diff changeset
235 while IFS=$'\t' read ID class seq A C G T
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davidvanzessen
parents:
diff changeset
236 do
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davidvanzessen
parents:
diff changeset
237 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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davidvanzessen
parents:
diff changeset
238 done < $outdir/sequence_overview/ntoverview.txt
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davidvanzessen
parents:
diff changeset
239
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davidvanzessen
parents:
diff changeset
240 echo "<html><center><h1>$title</h1></center>" > $output
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davidvanzessen
parents:
diff changeset
241 echo "<meta name='viewport' content='width=device-width, initial-scale=1'>" >> $output
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davidvanzessen
parents:
diff changeset
242 echo "<script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $output
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davidvanzessen
parents:
diff changeset
243 echo "<script type='text/javascript' src='tabber.js'></script>" >> $output
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davidvanzessen
parents:
diff changeset
244 echo "<script type='text/javascript' src='script.js'></script>" >> $output
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davidvanzessen
parents:
diff changeset
245 echo "<link rel='stylesheet' type='text/css' href='style.css'>" >> $output
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davidvanzessen
parents:
diff changeset
246 echo "<link rel='stylesheet' type='text/css' href='pure-min.css'>" >> $output
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davidvanzessen
parents:
diff changeset
247
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davidvanzessen
parents:
diff changeset
248 matched_count="`cat $outdir/merged.txt | grep -v 'unmatched' | tail -n +2 | wc -l`"
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davidvanzessen
parents:
diff changeset
249 unmatched_count="`cat $outdir/unmatched.txt | tail -n +2 | wc -l`"
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davidvanzessen
parents:
diff changeset
250 total_count=$((matched_count + unmatched_count))
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davidvanzessen
parents:
diff changeset
251 perc_count=$((unmatched_count / total_count * 100))
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davidvanzessen
parents:
diff changeset
252 perc_count=`bc -l <<< "scale=2; ${unmatched_count} / ${total_count} * 100"`
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davidvanzessen
parents:
diff changeset
253 perc_count=`bc -l <<< "scale=2; (${unmatched_count} / ${total_count} * 100 ) / 1"`
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davidvanzessen
parents:
diff changeset
254
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davidvanzessen
parents:
diff changeset
255 echo "<center><h2>Total: ${total_count}</h2></center>" >> $output
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davidvanzessen
parents:
diff changeset
256 echo "<center><h2>Matched: ${matched_count} Unmatched: ${unmatched_count}</h2></center>" >> $output
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davidvanzessen
parents:
diff changeset
257 echo "<center><h2>Percentage unmatched: ${perc_count}</h2></center>" >> $output
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davidvanzessen
parents:
diff changeset
258
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davidvanzessen
parents:
diff changeset
259 echo "---------------- main tables ----------------"
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davidvanzessen
parents:
diff changeset
260 echo "---------------- main tables ----------------<br />" >> $log
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davidvanzessen
parents:
diff changeset
261
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davidvanzessen
parents:
diff changeset
262 echo "<div class='tabber'>" >> $output
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davidvanzessen
parents:
diff changeset
263 echo "<div class='tabbertab' title='SHM Overview' style='width: 3000px;'>" >> $output
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davidvanzessen
parents:
diff changeset
264
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davidvanzessen
parents:
diff changeset
265 for func in ${funcs[@]}
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davidvanzessen
parents:
diff changeset
266 do
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davidvanzessen
parents:
diff changeset
267
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davidvanzessen
parents:
diff changeset
268 echo "---------------- $func table ----------------"
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davidvanzessen
parents:
diff changeset
269 echo "---------------- $func table ----------------<br />" >> $log
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davidvanzessen
parents:
diff changeset
270
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davidvanzessen
parents:
diff changeset
271 cat $outdir/mutations_${func}.txt $outdir/shm_overview_tandem_row.txt $outdir/hotspot_analysis_${func}.txt > $outdir/data_${func}.txt
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davidvanzessen
parents:
diff changeset
272
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davidvanzessen
parents:
diff changeset
273 echo "---------------- pattern_plots.r ----------------"
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davidvanzessen
parents:
diff changeset
274 echo "---------------- pattern_plots.r ----------------<br />" >> $log
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davidvanzessen
parents:
diff changeset
275
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davidvanzessen
parents:
diff changeset
276 Rscript $dir/pattern_plots.r $outdir/data_${func}.txt $outdir/aid_motives $outdir/relative_mutations $outdir/absolute_mutations $outdir/shm_overview.txt 2>&1
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davidvanzessen
parents:
diff changeset
277
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davidvanzessen
parents:
diff changeset
278 echo "<table class='pure-table pure-table-striped'>" >> $output
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davidvanzessen
parents:
diff changeset
279 echo "<thead><tr><th>info</th>" >> $output
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davidvanzessen
parents:
diff changeset
280
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davidvanzessen
parents:
diff changeset
281 if [ "${class_filter}" != "101_101" ] ; then
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davidvanzessen
parents:
diff changeset
282
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davidvanzessen
parents:
diff changeset
283 for gene in ${genes[@]}
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davidvanzessen
parents:
diff changeset
284 do
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davidvanzessen
parents:
diff changeset
285 tmp=`cat $outdir/${gene}_${func}_n.txt`
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davidvanzessen
parents:
diff changeset
286 echo "<th><a href='matched_${gene}_${func}.txt'>${gene} (N = $tmp)</a></th>" >> $output
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davidvanzessen
parents:
diff changeset
287 done
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davidvanzessen
parents:
diff changeset
288
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davidvanzessen
parents:
diff changeset
289 tmp=`cat $outdir/all_${func}_n.txt`
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davidvanzessen
parents:
diff changeset
290 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
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davidvanzessen
parents:
diff changeset
291 tmp=`cat $outdir/unmatched_${func}_n.txt`
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davidvanzessen
parents:
diff changeset
292 echo "<th><a href='unmatched.txt'>unmatched (N = ${unmatched_count})</a></th><tr></thead>" >> $output
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davidvanzessen
parents:
diff changeset
293
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davidvanzessen
parents:
diff changeset
294 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
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davidvanzessen
parents:
diff changeset
295 do
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davidvanzessen
parents:
diff changeset
296 if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] || [ "$name" == "Tandems/Expected (ratio)" ] ; then #meh
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davidvanzessen
parents:
diff changeset
297 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>" >> $output
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davidvanzessen
parents:
diff changeset
298 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
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davidvanzessen
parents:
diff changeset
299 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>" >> $output
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davidvanzessen
parents:
diff changeset
300 else
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davidvanzessen
parents:
diff changeset
301 echo "<tr><td>$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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davidvanzessen
parents:
diff changeset
302 fi
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davidvanzessen
parents:
diff changeset
303 done < $outdir/data_${func}.txt
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
304
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davidvanzessen
parents:
diff changeset
305 else
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davidvanzessen
parents:
diff changeset
306 tmp=`cat $outdir/all_${func}_n.txt`
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davidvanzessen
parents:
diff changeset
307 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
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davidvanzessen
parents:
diff changeset
308
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davidvanzessen
parents:
diff changeset
309 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
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davidvanzessen
parents:
diff changeset
310 do
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davidvanzessen
parents:
diff changeset
311 if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] ; then #meh
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davidvanzessen
parents:
diff changeset
312 echo "<tr><td>$name</td><td>${allx}/${ally}</td></tr>" >> $output
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davidvanzessen
parents:
diff changeset
313 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
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davidvanzessen
parents:
diff changeset
314 echo "<tr><td>$name</td><td>${allz}%</td></tr>" >> $output
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davidvanzessen
parents:
diff changeset
315 else
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davidvanzessen
parents:
diff changeset
316 echo "<tr><td>$name</td><td>${allx}/${ally} (${allz}%)</td></tr>" >> $output
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davidvanzessen
parents:
diff changeset
317 fi
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davidvanzessen
parents:
diff changeset
318 done < $outdir/data_${func}.txt
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davidvanzessen
parents:
diff changeset
319
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davidvanzessen
parents:
diff changeset
320 fi
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davidvanzessen
parents:
diff changeset
321 echo "</table>" >> $output
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davidvanzessen
parents:
diff changeset
322 #echo "<a href='data_${func}.txt'>Download data</a>" >> $output
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davidvanzessen
parents:
diff changeset
323 done
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davidvanzessen
parents:
diff changeset
324
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davidvanzessen
parents:
diff changeset
325 echo "<a href='aid_motives.pdf'><img src='aid_motives.png' /></a><br />" >> $output
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davidvanzessen
parents:
diff changeset
326 echo "<a href='relative_mutations.pdf'><img src='relative_mutations.png' /></a><br />" >> $output
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davidvanzessen
parents:
diff changeset
327 echo "<a href='absolute_mutations.pdf'><img src='absolute_mutations.png' /></a><br />" >> $output
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davidvanzessen
parents:
diff changeset
328 echo "<br />" >> $output
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davidvanzessen
parents:
diff changeset
329 cat $dir/shm_overview.htm >> $output
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davidvanzessen
parents:
diff changeset
330 echo "</div>" >> $output #SHM overview tab end
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davidvanzessen
parents:
diff changeset
331
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
332 echo "---------------- images ----------------"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
333 echo "---------------- images ----------------<br />" >> $log
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
334
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
335 echo "<div class='tabbertab' title='SHM Frequency' style='width: 3000px;'></a>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
336
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
337 if [ -a $outdir/scatter.png ]
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
338 then
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
339 echo "<a href='scatter.pdf'><img src='scatter.png'/><br />" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
340 fi
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
341 if [ -a $outdir/frequency_ranges.png ]
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
342 then
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
343 echo "<a href='frequency_ranges.pdf'><img src='frequency_ranges.png'/></a><br />" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
344 fi
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
345
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
346 echo "<br />" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
347 cat $dir/shm_frequency.htm >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
348
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
349 echo "</div>" >> $output #SHM frequency tab end
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
350
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
351 echo "<div class='tabbertab' title='Transition tables' style='width: 3000px;'>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
352
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
353 echo "<table border='0'>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
354
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
355 for gene in ${genes[@]}
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
356 do
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
357 echo "<tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
358 echo "<td><h1>${gene}</h1></td>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
359
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
360 if [ -e $outdir/transitions_heatmap_${gene}.png ]
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
361 then
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
362 echo "<td><a href='transitions_heatmap_${gene}.pdf'><img src='transitions_heatmap_${gene}.png' /></a></td>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
363 else
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
364 echo "<td></td>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
365 fi
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
366
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
367 if [ -e $outdir/transitions_stacked_${gene}.png ]
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
368 then
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
369 echo "<td><a href='transitions_stacked_${gene}.pdf'><img src='transitions_stacked_${gene}.png' /></a></td>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
370 else
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
371 echo "<td></td>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
372 fi
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
373
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
374 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
375 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
376 first="true"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
377 while IFS=, read from a c g t
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
378 do
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
379 if [ "$first" == "true" ] ; then
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
380 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
381 first="false"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
382 else
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
383 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
384 fi
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
385 done < $outdir/transitions_${gene}_sum.txt
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
386 echo "</table></td>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
387
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
388 echo "</tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
389 done
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
390
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
391 echo "<tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
392 echo "<td><h1>All</h1></td>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
393 echo "<td><a href='transitions_heatmap_all.pdf'><img src='transitions_heatmap_all.png' /></a></td>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
394 echo "<td><a href='transitions_stacked_all.pdf'><img src='transitions_stacked_all.png' /></a></td>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
395 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
396 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
397 first="true"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
398 while IFS=, read from a c g t
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
399 do
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
400 if [ "$first" == "true" ] ; then
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
401 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
402 first="false"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
403 else
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
404 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
405 fi
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
406 done < $outdir/transitions_all_sum.txt
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
407 echo "</table></td>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
408
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
409 echo "</tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
410
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
411 echo "</table>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
412
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
413 echo "<br />" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
414 cat $dir/shm_transition.htm >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
415
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
416 echo "</div>" >> $output #transition tables tab end
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
417
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
418 echo "<div class='tabbertab' title='Antigen Selection'>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
419
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
420 if [ -e $outdir/aa_histogram.png ]
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
421 then
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
422 echo "<a href='aa_histogram.pdf'><img src='aa_histogram.png'/></a><br />" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
423 fi
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
424
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
425 if [ -e $outdir/aa_histogram_IGA.png ]
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
426 then
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
427 echo "<a href='aa_histogram_IGA.pdf'><img src='aa_histogram_IGA.png'/></a><br />" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
428 fi
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
429
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
430 if [ -e $outdir/aa_histogram_IGG.png ]
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
431 then
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
432 echo "<a href='aa_histogram_IGG.pdf'><img src='aa_histogram_IGG.png'/></a><br />" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
433 fi
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
434
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
435 if [ -e $outdir/aa_histogram_IGM.png ]
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
436 then
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
437 echo "<a href='aa_histogram_IGM.pdf'><img src='aa_histogram_IGM.png'/></a><br />" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
438 fi
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
439
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
440 if [ -e $outdir/aa_histogram_IGE.png ]
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
441 then
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
442 echo "<a href='aa_histogram_IGE.pdf'><img src='aa_histogram_IGE.png'/></a><br />" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
443 fi
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
444
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
445
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
446
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
447 if [[ "$fast" == "no" ]] ; then
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
448
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
449
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
450
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
451 echo "---------------- baseline ----------------"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
452 echo "---------------- baseline ----------------<br />" >> $log
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
453 tmp="$PWD"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
454
83
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
455 mkdir -p $outdir/baseline
81
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
456
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
457 echo "<center><h1>BASELINe</h1>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
458 header_substring="Based on CDR1, FR2, CDR2, FR3 (27:27:38:55:65:104:-)"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
459
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
460 baseline_boundaries="27:27:38:55:65:104:-"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
461
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
462 if [[ "${empty_region_filter}" == "leader" ]] ; then
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
463 baseline_boundaries="1:26:38:55:65:104:-"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
464 header_substring="Based on FR1, CDR1, FR2, CDR2, FR3 (1:26:38:55:65:104,-)"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
465 fi
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
466
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
467 echo "<p>${header_substring}</p></center>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
468
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
469 mkdir $outdir/baseline/IGA_IGG_IGM
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
470 if [[ $(wc -l < $outdir/new_IMGT/1_Summary.txt) -gt "1" ]]; then
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
471 cd $outdir/baseline/IGA_IGG_IGM
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
472 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT.txz "IGA_IGG_IGM_IGE" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
473 else
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
474 echo "No sequences" > "$outdir/baseline.txt"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
475 fi
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
476
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
477 mkdir $outdir/baseline/IGA
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
478 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
479 cd $outdir/baseline/IGA
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
480 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT_IGA.txz "IGA" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGA.pdf" "Sequence.ID" "$outdir/baseline_IGA.txt"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
481 else
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
482 echo "No IGA sequences" > "$outdir/baseline_IGA.txt"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
483 fi
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
484
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
485 mkdir $outdir/baseline/IGG
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
486 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
487 cd $outdir/baseline/IGG
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
488 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT_IGG.txz "IGG" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGG.pdf" "Sequence.ID" "$outdir/baseline_IGG.txt"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
489 else
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
490 echo "No IGG sequences" > "$outdir/baseline_IGG.txt"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
491 fi
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
492
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
493 mkdir $outdir/baseline/IGM
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
494 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
495 cd $outdir/baseline/IGM
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
496 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT_IGM.txz "IGM" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGM.pdf" "Sequence.ID" "$outdir/baseline_IGM.txt"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
497 else
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
498 echo "No IGM sequences" > "$outdir/baseline_IGM.txt"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
499 fi
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
500
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
501 mkdir $outdir/baseline/IGE
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
502 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
503 cd $outdir/baseline/IGE
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
504 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT_IGE.txz "IGE" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGE.pdf" "Sequence.ID" "$outdir/baseline_IGE.txt"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
505 else
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
506 echo "No IGE sequences" > "$outdir/baseline_IGE.txt"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
507 fi
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
508
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
509 cd $tmp
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
510
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
511 echo "Cleaning up *.RData files"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
512 find $outdir/baseline -name "*.RData" -type f -delete
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
513
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
514 if [ -e $outdir/baseline.pdf ]
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
515 then
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
516 echo "<embed src='baseline.pdf' width='700px' height='1000px'>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
517 fi
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
518
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
519 if [ -e $outdir/baseline_IGA.pdf ]
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
520 then
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
521 echo "<embed src='baseline_IGA.pdf' width='700px' height='1000px'>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
522 fi
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
523
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
524 if [ -e $outdir/baseline_IGG.pdf ]
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
525 then
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
526 echo "<embed src='baseline_IGG.pdf' width='700px' height='1000px'>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
527 fi
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
528
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
529 if [ -e $outdir/baseline_IGM.pdf ]
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
530 then
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
531 echo "<embed src='baseline_IGM.pdf' width='700px' height='1000px'>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
532 fi
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
533
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
534 if [ -e $outdir/baseline_IGE.pdf ]
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
535 then
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
536 echo "<embed src='baseline_IGE.pdf' width='700px' height='1000px'>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
537 fi
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
538 fi
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
539
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
540 echo "<br />" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
541 cat $dir/shm_selection.htm >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
542
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
543 echo "</div>" >> $output #antigen selection tab end
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
544
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
545 echo "<div class='tabbertab' title='CSR'>" >> $output #CSR tab
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
546
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
547 if [ -e $outdir/IGA.png ]
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
548 then
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
549 echo "<a href='IGA.pdf'><img src='IGA.png'/></a><br />" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
550 fi
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
551 if [ -e $outdir/IGG.png ]
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
552 then
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
553 echo "<a href='IGG.pdf'><img src='IGG.png'/></a><br />" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
554 fi
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
555
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
556 echo "<br />" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
557 cat $dir/shm_csr.htm >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
558
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
559 echo "</div>" >> $output #CSR tab end
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
560
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
561 if [[ "$fast" == "no" ]] ; then
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
562
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
563 echo "---------------- change-o MakeDB ----------------"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
564
83
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
565 mkdir -p $outdir/change_o
81
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
566
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
567 tmp="$PWD"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
568
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
569 cd $outdir/change_o
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
570
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
571 bash $dir/change_o/makedb.sh $outdir/new_IMGT.txz false false false $outdir/change_o/change-o-db.txt
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
572 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
573 Rscript $dir/change_o/select_first_in_clone.r $outdir/change_o/change-o-db-defined_clones.txt $outdir/change_o/change-o-db-defined_first_clones.txt 2>&1
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
574
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
575 mkdir $outdir/new_IMGT_changeo
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
576 cp $outdir/new_IMGT/* $outdir/new_IMGT_changeo
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
577
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
578 Rscript $dir/new_imgt.r $outdir/new_IMGT_changeo $outdir/change_o/change-o-db-defined_first_clones.txt "-" 2>&1
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
579
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
580 cd $outdir/new_IMGT_changeo
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
581 tar -cJf ../new_IMGT_first_seq_of_clone.txz *
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
582 cd $outdir/change_o
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
583
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
584 rm -rf $outdir/new_IMGT_changeo
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
585
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
586 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
587 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"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
588
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
589 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
590 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGA.txz false false false $outdir/change_o/change-o-db-IGA.txt
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
591 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
592 Rscript $dir/change_o/select_first_in_clone.r $outdir/change_o/change-o-db-defined_clones-IGA.txt $outdir/change_o/change-o-db-defined_first_clones-IGA.txt 2>&1
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
593
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
594 mkdir $outdir/new_IMGT_IGA_changeo
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
595 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA_changeo
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
596
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
597 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA_changeo $outdir/change_o/change-o-db-defined_first_clones-IGA.txt "-" 2>&1
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
598
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
599 cd $outdir/new_IMGT_IGA_changeo
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
600 tar -cJf ../new_IMGT_IGA_first_seq_of_clone.txz *
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
601
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
602 rm -rf $outdir/new_IMGT_IGA_changeo
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
603
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
604 cd $outdir/change_o
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
605 else
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
606 echo "No IGA sequences" > "$outdir/change_o/change-o-db-defined_clones-IGA.txt"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
607 echo "No IGA sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGA.txt"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
608 fi
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
609
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
610 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
611 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGG.txz false false false $outdir/change_o/change-o-db-IGG.txt
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
612 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
613 Rscript $dir/change_o/select_first_in_clone.r $outdir/change_o/change-o-db-defined_clones-IGG.txt $outdir/change_o/change-o-db-defined_first_clones-IGG.txt 2>&1
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
614
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
615 mkdir $outdir/new_IMGT_IGG_changeo
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
616 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG_changeo
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
617
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
618 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG_changeo $outdir/change_o/change-o-db-defined_first_clones-IGG.txt "-" 2>&1
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
619
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
620 cd $outdir/new_IMGT_IGG_changeo
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
621 tar -cJf ../new_IMGT_IGG_first_seq_of_clone.txz *
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
622 rm -rf $outdir/new_IMGT_IGG_changeo
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
623
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
624 cd $outdir/change_o
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
625 else
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
626 echo "No IGG sequences" > "$outdir/change_o/change-o-db-defined_clones-IGG.txt"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
627 echo "No IGG sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGG.txt"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
628 fi
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
629
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
630 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
631 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGM.txz false false false $outdir/change_o/change-o-db-IGM.txt
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
632 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
633 Rscript $dir/change_o/select_first_in_clone.r $outdir/change_o/change-o-db-defined_clones-IGM.txt $outdir/change_o/change-o-db-defined_first_clones-IGM.txt 2>&1
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
634
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
635 mkdir $outdir/new_IMGT_IGM_changeo
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
636 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGM_changeo
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
637
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
638 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGM_changeo $outdir/change_o/change-o-db-defined_first_clones-IGM.txt "-" 2>&1
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
639
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
640 cd $outdir/new_IMGT_IGM_changeo
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
641 tar -cJf ../new_IMGT_IGM_first_seq_of_clone.txz *
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
642
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
643 rm -rf $outdir/new_IMGT_IGM_changeo
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
644
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
645 cd $outdir/change_o
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
646 else
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
647 echo "No IGM sequences" > "$outdir/change_o/change-o-db-defined_clones-IGM.txt"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
648 echo "No IGM sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGM.txt"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
649 fi
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
650
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
651 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
652 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGE.txz false false false $outdir/change_o/change-o-db-IGE.txt
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
653 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
654 Rscript $dir/change_o/select_first_in_clone.r $outdir/change_o/change-o-db-defined_clones-IGE.txt $outdir/change_o/change-o-db-defined_first_clones-IGE.txt 2>&1
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
655
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
656 mkdir $outdir/new_IMGT_IGE_changeo
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
657 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGE_changeo
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
658
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
659 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGE_changeo $outdir/change_o/change-o-db-defined_first_clones-IGE.txt "-" 2>&1
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
660
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
661 cd $outdir/new_IMGT_IGE_changeo
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
662 tar -cJf ../new_IMGT_IGE_first_seq_of_clone.txz *
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
663
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
664 rm -rf $outdir/new_IMGT_IGE_changeo
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
665
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
666 cd $outdir/change_o
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
667 else
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
668 echo "No IGE sequences" > "$outdir/change_o/change-o-db-defined_clones-IGE.txt"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
669 echo "No IGE sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGE.txt"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
670 fi
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
671
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
672 cd "$tmp"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
673
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
674 rm -rf $outdir/new_IMGT
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
675 rm -rf $outdir/new_IMGT_IGA/
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
676 rm -rf $outdir/new_IMGT_IGA1/
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
677 rm -rf $outdir/new_IMGT_IGA2/
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
678 rm -rf $outdir/new_IMGT_IGG/
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
679 rm -rf $outdir/new_IMGT_IGG1/
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
680 rm -rf $outdir/new_IMGT_IGG2/
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
681 rm -rf $outdir/new_IMGT_IGG3/
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
682 rm -rf $outdir/new_IMGT_IGG4/
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
683 rm -rf $outdir/new_IMGT_IGM/
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
684 rm -rf $outdir/new_IMGT_IGE/
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
685
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
686 echo "<div class='tabbertab' title='Clonal Relation' style='width: 7000px;'>" >> $output #clonality tab
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
687
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
688 function clonality_table {
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
689 local infile=$1
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
690 local outfile=$2
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
691
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
692 echo "<table class='pure-table pure-table-striped'>" >> $outfile
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
693 echo "<thead><tr><th>Clone size</th><th>Nr of clones</th><th>Nr of sequences</th></tr></thead>" >> $outfile
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
694
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
695 first='true'
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
696
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
697 while read size clones seqs
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
698 do
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
699 if [[ "$first" == "true" ]]; then
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
700 first="false"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
701 continue
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
702 fi
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
703 echo "<tr><td>$size</td><td>$clones</td><td>$seqs</td></tr>" >> $outfile
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
704 done < $infile
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
705
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
706 echo "</table>" >> $outfile
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
707 }
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
708 echo "<div class='tabber'>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
709
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
710 echo "<div class='tabbertab' title='All'>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
711 clonality_table $outdir/change_o/change-o-defined_clones-summary.txt $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
712 echo "</div>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
713
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
714 echo "<div class='tabbertab' title='IGA'>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
715 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGA.txt $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
716 echo "</div>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
717
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
718 echo "<div class='tabbertab' title='IGG'>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
719 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGG.txt $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
720 echo "</div>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
721
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
722 echo "<div class='tabbertab' title='IGM'>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
723 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
724 echo "</div>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
725
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
726 echo "<div class='tabbertab' title='IGE'>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
727 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
728 echo "</div>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
729
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
730 echo "<div class='tabbertab' title='Overlap' style='width: 7000px;'>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
731 cat "$outdir/sequence_overview/index.html" | sed -e 's:</td>:</td>\n:g' | sed "s:href='\(.*\).html:href='sequence_overview/\1.html:g" >> $output # rewrite href to 'sequence_overview/..."
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
732 echo "</div>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
733
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
734 echo "</div>" >> $output #clonality tabber end
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
735
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
736 echo "<br />" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
737 cat $dir/shm_clonality.htm >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
738
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
739 echo "</div>" >> $output #clonality tab end
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
740
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
741 fi
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
742
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
743 echo "<div class='tabbertab' title='Downloads'>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
744
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
745 echo "<table class='pure-table pure-table-striped'>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
746 echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
747 echo "<tr><td>The complete dataset</td><td><a href='merged.txt' download='merged.txt' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
748 echo "<tr><td>The filtered dataset</td><td><a href='filtered.txt' download='filtered.txt' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
749 echo "<tr><td>The alignment info on the unmatched sequences</td><td><a href='unmatched.txt' download='unmatched.txt' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
750
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
751 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Overview</td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
752 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
753 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
754 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
755 echo "<tr><td>Base count for every sequence</td><td><a href='base_overview.html'>View</a></td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
756 echo "<tr><td>The data used to generate the percentage of mutations in AID and pol eta motives plot</td><td><a href='aid_motives.txt' download='aid_motives.txt' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
757 echo "<tr><td>The data used to generate the relative mutation patterns plot</td><td><a href='relative_mutations.txt' download='relative_mutations.txt' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
758 echo "<tr><td>The data used to generate the absolute mutation patterns plot</td><td><a href='absolute_mutations.txt' download='absolute_mutations.txt' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
759 echo "<tr><td>Data about tandem mutations by ID</td><td><a href='tandems_by_id.txt' download='tandems_by_id.txt' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
760
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
761 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Frequency</td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
762 echo "<tr><td>The data generate the frequency scatter plot</td><td><a href='scatter.txt' download='scatter.txt' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
763 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
764 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
765
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
766 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Transition Tables</td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
767 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
768 echo "<tr><td>The data for the 'IGA' transition plot</td><td><a href='transitions_IGA_sum.txt' download='transitions_IGA_sum.txt' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
769 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
770 echo "<tr><td>The data for the 'IGA2' transition plot</td><td><a href='transitions_IGA2_sum.txt' download='transitions_IGA2_sum.txt' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
771 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
772 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
773 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
774 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
775 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
776 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
777 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
778
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
779 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Antigen Selection</td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
780 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
781 echo "<tr><td>Presence of AA per sequence ID</td><td><a href='absent_aa_id.txt' download='absent_aa_id.txt' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
782
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
783 echo "<tr><td>The data used to generate the aa mutation frequency plot</td><td><a href='aa_histogram_sum.txt' download='aa_histogram_sum.txt' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
784 echo "<tr><td>The data used to generate the aa mutation frequency plot for IGA</td><td><a href='aa_histogram_sum_IGA.txt' download='aa_histogram_sum_IGA.txt' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
785 echo "<tr><td>The data used to generate the aa mutation frequency plot for IGG</td><td><a href='aa_histogram_sum_IGG.txt' download='aa_histogram_sum_IGG.txt' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
786 echo "<tr><td>The data used to generate the aa mutation frequency plot for IGM</td><td><a href='aa_histogram_sum_IGM.txt' download='aa_histogram_sum_IGM.txt' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
787 echo "<tr><td>The data used to generate the aa mutation frequency plot for IGE</td><td><a href='aa_histogram_sum_IGE.txt' download='aa_histogram_sum_IGE.txt' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
788
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
789 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
790 echo "<tr><td>Baseline data</td><td><a href='baseline.txt' download='baseline.txt' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
791 echo "<tr><td>Baseline IGA PDF</td><td><a href='baseline_IGA.pdf' download='baseline_IGA.pdf' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
792 echo "<tr><td>Baseline IGA data</td><td><a href='baseline_IGA.txt' download='baseline_IGA.txt' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
793 echo "<tr><td>Baseline IGG PDF</td><td><a href='baseline_IGG.pdf' download='baseline_IGG.pdf' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
794 echo "<tr><td>Baseline IGG data</td><td><a href='baseline_IGG.txt' download='baseline_IGG.txt' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
795 echo "<tr><td>Baseline IGM PDF</td><td><a href='baseline_IGM.pdf' download='baseline_IGM.pdf' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
796 echo "<tr><td>Baseline IGM data</td><td><a href='baseline_IGM.txt' download='baseline_IGM.txt' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
797 echo "<tr><td>Baseline IGE PDF</td><td><a href='baseline_IGE.pdf' download='baseline_IGE.pdf' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
798 echo "<tr><td>Baseline IGE data</td><td><a href='baseline_IGE.txt' download='baseline_IGE.txt' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
799
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
800 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>CSR</td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
801 echo "<tr><td>The data for the IGA subclass distribution plot</td><td><a href='IGA_pie.txt' download='IGA_pie.txt' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
802 echo "<tr><td>The data for the IGG subclass distribution plot</td><td><a href='IGG_pie.txt' download='IGG_pie.txt' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
803
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
804
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
805 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Clonal Relation</td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
806 echo "<tr><td>Sequence overlap between subclasses</td><td><a href='sequence_overview/index.html'>View</a></td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
807 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
808 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
809 echo "<tr><td>An IMGT archive with just just the first sequence of a clone</td><td><a href='new_IMGT_first_seq_of_clone.txz' download='new_IMGT_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
810
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
811 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
812 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
813 echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGA)</td><td><a href='new_IMGT_IGA_first_seq_of_clone.txz' download='new_IMGT_IGA_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
814
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
815 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
816 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
817 echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGG)</td><td><a href='new_IMGT_IGG_first_seq_of_clone.txz' download='new_IMGT_IGG_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
818
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
819 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
820 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
821 echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGM)</td><td><a href='new_IMGT_IGM_first_seq_of_clone.txz' download='new_IMGT_IGM_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
822
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
823 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
824 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
825 echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGE)</td><td><a href='new_IMGT_IGE_first_seq_of_clone.txz' download='new_IMGT_IGE_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
826
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
827 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Filtered IMGT output files</td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
828 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
829 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
830 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
831 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
832 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
833 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
834 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
835 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
836 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
837 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
838 echo "<tr><td>An IMGT archive with just the matched and filtered IGE sequences</td><td><a href='new_IMGT_IGE.txz' download='new_IMGT_IGE.txz' >Download</a></td></tr>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
839
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
840 echo "</table>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
841
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
842 echo "<br />" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
843 cat $dir/shm_downloads.htm >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
844
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
845 echo "</div>" >> $output #downloads tab end
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
846
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
847 echo "</div>" >> $output #tabs end
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
848
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
849 echo "</html>" >> $output
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
850
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
851
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
852 echo "---------------- naive_output.r ----------------"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
853 echo "---------------- naive_output.r ----------------<br />" >> $log
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
854
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
855 if [[ "$naive_output" == "yes" ]]
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
856 then
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
857 echo "output naive output"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
858 if [[ "${class_filter}" == "101_101" ]]
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
859 then
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
860 echo "copy new_IMGT.txz to ${naive_output_all}"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
861 cp $outdir/new_IMGT.txz ${naive_output_all}
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
862 else
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
863 echo "copy for classes"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
864 cp $outdir/new_IMGT_IGA.txz ${naive_output_ca}
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
865 cp $outdir/new_IMGT_IGG.txz ${naive_output_cg}
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
866 cp $outdir/new_IMGT_IGM.txz ${naive_output_cm}
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
867 cp $outdir/new_IMGT_IGE.txz ${naive_output_ce}
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
868 fi
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
869 fi
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
870
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
871 echo "</table>" >> $outdir/base_overview.html
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
872
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
873 mv $log $outdir/log.html
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
874
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
875 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
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
876 echo "<table border = 1>" >> $log
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
877 echo "<thead><tr><th>Info</th><th>Sequences</th><th>Percentage</th></tr></thead>" >> $log
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
878 tIFS="$TMP"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
879 IFS=$'\t'
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
880 while read step seq perc
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
881 do
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
882 echo "<tr>" >> $log
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
883 echo "<td>$step</td>" >> $log
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
884 echo "<td>$seq</td>" >> $log
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
885 echo "<td>${perc}%</td>" >> $log
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
886 echo "</tr>" >> $log
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
887 done < $outdir/filtering_steps.txt
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
888 echo "</table>" >> $log
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
889 echo "<br />" >> $log
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
890 cat $dir/shm_first.htm >> $log
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
891 echo "</center></html>" >> $log
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
892
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
893 IFS="$tIFS"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
894
84
4db34e32dd47 "planemo upload commit 78ace939ed7437b8b360588032449a99aad949eb"
rhpvorderman
parents: 83
diff changeset
895 echo "---------------- remove_files----------------"
4db34e32dd47 "planemo upload commit 78ace939ed7437b8b360588032449a99aad949eb"
rhpvorderman
parents: 83
diff changeset
896 echo "---------------- remove_files----------------<br />" >> $log
4db34e32dd47 "planemo upload commit 78ace939ed7437b8b360588032449a99aad949eb"
rhpvorderman
parents: 83
diff changeset
897
4db34e32dd47 "planemo upload commit 78ace939ed7437b8b360588032449a99aad949eb"
rhpvorderman
parents: 83
diff changeset
898 rm -r -v results/baseline
4db34e32dd47 "planemo upload commit 78ace939ed7437b8b360588032449a99aad949eb"
rhpvorderman
parents: 83
diff changeset
899 rm -r -v files
4db34e32dd47 "planemo upload commit 78ace939ed7437b8b360588032449a99aad949eb"
rhpvorderman
parents: 83
diff changeset
900 filename='remove_files.txt'
4db34e32dd47 "planemo upload commit 78ace939ed7437b8b360588032449a99aad949eb"
rhpvorderman
parents: 83
diff changeset
901
4db34e32dd47 "planemo upload commit 78ace939ed7437b8b360588032449a99aad949eb"
rhpvorderman
parents: 83
diff changeset
902 while read file; do
4db34e32dd47 "planemo upload commit 78ace939ed7437b8b360588032449a99aad949eb"
rhpvorderman
parents: 83
diff changeset
903 rm -v $file
4db34e32dd47 "planemo upload commit 78ace939ed7437b8b360588032449a99aad949eb"
rhpvorderman
parents: 83
diff changeset
904 done < "$filename"
4db34e32dd47 "planemo upload commit 78ace939ed7437b8b360588032449a99aad949eb"
rhpvorderman
parents: 83
diff changeset
905
81
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
906
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
907 echo "---------------- Done! ----------------"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
908 echo "---------------- Done! ----------------<br />" >> $outdir/log.html
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
909
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
910
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
911
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
912
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
913
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
914