annotate wrapper.sh @ 37:767dd9327009 draft

Uploaded
author davidvanzessen
date Fri, 16 Dec 2016 10:17:16 -0500
parents 43d182135230
children a24f8c93583a
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1 #!/bin/bash
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2 #set -e
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3 dir="$(cd "$(dirname "$0")" && pwd)"
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4 input=$1
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5 method=$2
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6 log=$3 #becomes the main html page at the end
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7 outdir=$4
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8 output="$outdir/index.html" #copied to $log location at the end
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9 title="$5"
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10 include_fr1=$6
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11 functionality=$7
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12 unique=$8
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13 naive_output=$9
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14 naive_output_ca=${10}
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15 naive_output_cg=${11}
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16 naive_output_cm=${12}
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17 naive_output_ce=${13}
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18 naive_output_all=${14}
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19 filter_unique=${15}
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20 class_filter=${16}
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21 empty_region_filter=${17}
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22 fast=${18}
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23 mkdir $outdir
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24
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25 tar -xzf $dir/style.tar.gz -C $outdir
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26
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27 echo "---------------- read parameters ----------------"
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28 echo "---------------- read parameters ----------------<br />" > $log
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29
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30 echo "unpacking IMGT file"
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31
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32 type="`file $input`"
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33 if [[ "$type" == *"Zip archive"* ]] ; then
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34 echo "Zip archive"
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35 echo "unzip $input -d $PWD/files/"
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36 unzip $input -d $PWD/files/
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37 elif [[ "$type" == *"XZ compressed data"* ]] ; then
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38 echo "ZX archive"
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39 echo "tar -xJf $input -C $PWD/files/"
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40 mkdir -p "$PWD/files/$title"
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41 tar -xJf $input -C "$PWD/files/$title"
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42 fi
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43
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44 cat "`find $PWD/files/ -name "1_*"`" > $PWD/summary.txt
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45 cat "`find $PWD/files/ -name "3_*"`" > $PWD/sequences.txt
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46 cat "`find $PWD/files/ -name "5_*"`" > $PWD/aa.txt
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47 cat "`find $PWD/files/ -name "6_*"`" > $PWD/junction.txt
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48 cat "`find $PWD/files/ -name "7_*"`" > $PWD/mutationanalysis.txt
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49 cat "`find $PWD/files/ -name "8_*"`" > $PWD/mutationstats.txt
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50 cat "`find $PWD/files/ -name "10_*"`" > $PWD/hotspots.txt
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51
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52 if [[ ${#BLASTN_DIR} -ge 5 ]] ; then
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53 echo "On server, using BLASTN_DIR env: ${BLASTN_DIR}"
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54 else
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55 BLASTN_DIR="/home/galaxy/Downloads/ncbi-blast-2.4.0+/bin"
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56 echo "Dev Galaxy set BLASTN_DIR to: ${BLASTN_DIR}"
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57 fi
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58
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59 echo "---------------- class identification ----------------"
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60 echo "---------------- class identification ----------------<br />" >> $log
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61
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62 python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt
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63
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64 echo "---------------- merge_and_filter.r ----------------"
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65 echo "---------------- merge_and_filter.r ----------------<br />" >> $log
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66
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67 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $PWD/aa.txt $outdir/identified_genes.txt $outdir/merged.txt $outdir/before_unique_filter.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${class_filter} ${empty_region_filter} 2>&1
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69 if [[ "$fast" == "no" ]] ; then
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71 echo "---------------- creating new IMGT zips ----------------"
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72 echo "---------------- creating new IMGT zips ----------------<br />" >> $log
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73
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74 mkdir $outdir/new_IMGT
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75
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76 cat "`find $PWD/files/ -name "1_*"`" > "$outdir/new_IMGT/1_Summary.txt"
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77 cat "`find $PWD/files/ -name "2_*"`" > "$outdir/new_IMGT/2_IMGT-gapped-nt-sequences.txt"
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78 cat "`find $PWD/files/ -name "3_*"`" > "$outdir/new_IMGT/3_Nt-sequences.txt"
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79 cat "`find $PWD/files/ -name "4_*"`" > "$outdir/new_IMGT/4_IMGT-gapped-AA-sequences.txt"
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80 cat "`find $PWD/files/ -name "5_*"`" > "$outdir/new_IMGT/5_AA-sequences.txt"
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81 cat "`find $PWD/files/ -name "6_*"`" > "$outdir/new_IMGT/6_Junction.txt"
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82 cat "`find $PWD/files/ -name "7_*"`" > "$outdir/new_IMGT/7_V-REGION-mutation-and-AA-change-table.txt"
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83 cat "`find $PWD/files/ -name "8_*"`" > "$outdir/new_IMGT/8_V-REGION-nt-mutation-statistics.txt"
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84 cat "`find $PWD/files/ -name "9_*"`" > "$outdir/new_IMGT/9_V-REGION-AA-change-statistics.txt"
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85 cat "`find $PWD/files/ -name "10_*"`" > "$outdir/new_IMGT/10_V-REGION-mutation-hotspots.txt"
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87 mkdir $outdir/new_IMGT_IGA
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88 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA
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90 mkdir $outdir/new_IMGT_IGA1
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91 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA1
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93 mkdir $outdir/new_IMGT_IGA2
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94 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA2
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96 mkdir $outdir/new_IMGT_IGG
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97 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG
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99 mkdir $outdir/new_IMGT_IGG1
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100 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG1
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102 mkdir $outdir/new_IMGT_IGG2
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103 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG2
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105 mkdir $outdir/new_IMGT_IGG3
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106 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG3
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108 mkdir $outdir/new_IMGT_IGG4
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109 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG4
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111 mkdir $outdir/new_IMGT_IGM
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112 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGM
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114 mkdir $outdir/new_IMGT_IGE
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115 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGE
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117 Rscript $dir/new_imgt.r $outdir/new_IMGT/ $outdir/merged.txt "-" 2>&1
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118
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119 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA/ $outdir/merged.txt "IGA" 2>&1
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120 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA1/ $outdir/merged.txt "IGA1" 2>&1
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121 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA2/ $outdir/merged.txt "IGA2" 2>&1
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122
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123 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG/ $outdir/merged.txt "IGG" 2>&1
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124 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG1/ $outdir/merged.txt "IGG1" 2>&1
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125 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG2/ $outdir/merged.txt "IGG2" 2>&1
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126 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG3/ $outdir/merged.txt "IGG3" 2>&1
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127 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG4/ $outdir/merged.txt "IGG4" 2>&1
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128
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129 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGM/ $outdir/merged.txt "IGM" 2>&1
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131 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGE/ $outdir/merged.txt "IGE" 2>&1
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134 tmp="$PWD"
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135 cd $outdir/new_IMGT/ #tar weirdness...
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136 tar -cJf ../new_IMGT.txz *
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137
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138 cd $outdir/new_IMGT_IGA/
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139 tar -cJf ../new_IMGT_IGA.txz *
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140
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141 cd $outdir/new_IMGT_IGA1/
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142 tar -cJf ../new_IMGT_IGA1.txz *
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144 cd $outdir/new_IMGT_IGA2/
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145 tar -cJf ../new_IMGT_IGA2.txz *
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147 cd $outdir/new_IMGT_IGG/
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148 tar -cJf ../new_IMGT_IGG.txz *
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150 cd $outdir/new_IMGT_IGG1/
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151 tar -cJf ../new_IMGT_IGG1.txz *
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153 cd $outdir/new_IMGT_IGG2/
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154 tar -cJf ../new_IMGT_IGG2.txz *
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155
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156 cd $outdir/new_IMGT_IGG3/
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157 tar -cJf ../new_IMGT_IGG3.txz *
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158
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159 cd $outdir/new_IMGT_IGG4/
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160 tar -cJf ../new_IMGT_IGG4.txz *
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161
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162 cd $outdir/new_IMGT_IGM/
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163 tar -cJf ../new_IMGT_IGM.txz *
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164
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165 cd $outdir/new_IMGT_IGE/
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166 tar -cJf ../new_IMGT_IGE.txz *
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167
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168 cd $tmp
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169 fi
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170
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171 echo "---------------- shm_csr.r ----------------"
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172 echo "---------------- shm_csr.r ----------------<br />" >> $log
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davidvanzessen
parents:
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173
5
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davidvanzessen
parents: 4
diff changeset
174 classes="IGA,IGA1,IGA2,IGG,IGG1,IGG2,IGG3,IGG4,IGM,IGE,unmatched"
0
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davidvanzessen
parents:
diff changeset
175 echo "R mutation analysis"
1
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davidvanzessen
parents: 0
diff changeset
176 Rscript $dir/shm_csr.r $outdir/merged.txt $classes $outdir ${empty_region_filter} 2>&1
0
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davidvanzessen
parents:
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177
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davidvanzessen
parents:
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178 echo "---------------- shm_csr.py ----------------"
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davidvanzessen
parents:
diff changeset
179 echo "---------------- shm_csr.py ----------------<br />" >> $log
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davidvanzessen
parents:
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180
1
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davidvanzessen
parents: 0
diff changeset
181 python $dir/shm_csr.py --input $outdir/merged.txt --genes $classes --empty_region_filter "${empty_region_filter}" --output $outdir/hotspot_analysis.txt
0
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davidvanzessen
parents:
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182
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davidvanzessen
parents:
diff changeset
183 echo "---------------- aa_histogram.r ----------------"
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davidvanzessen
parents:
diff changeset
184 echo "---------------- aa_histogram.r ----------------<br />" >> $log
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davidvanzessen
parents:
diff changeset
185
5
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davidvanzessen
parents: 4
diff changeset
186 Rscript $dir/aa_histogram.r $outdir/aa_id_mutations.txt $outdir/absent_aa_id.txt "IGA,IGG,IGM,IGE" $outdir/ 2>&1
0
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davidvanzessen
parents:
diff changeset
187 if [ -e "$outdir/aa_histogram_.png" ]; then
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davidvanzessen
parents:
diff changeset
188 mv $outdir/aa_histogram_.png $outdir/aa_histogram.png
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davidvanzessen
parents:
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189 mv $outdir/aa_histogram_.txt $outdir/aa_histogram.txt
29
80c4eebf7bc9 Uploaded
davidvanzessen
parents: 28
diff changeset
190 mv $outdir/aa_histogram_absent_.txt $outdir/aa_histogram_absent.txt
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davidvanzessen
parents: 28
diff changeset
191 mv $outdir/aa_histogram_count_.txt $outdir/aa_histogram_count.txt
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davidvanzessen
parents: 28
diff changeset
192 mv $outdir/aa_histogram_sum_.txt $outdir/aa_histogram_sum.txt
0
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davidvanzessen
parents:
diff changeset
193 fi
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davidvanzessen
parents:
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194
5
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parents: 4
diff changeset
195 genes=(IGA IGA1 IGA2 IGG IGG1 IGG2 IGG3 IGG4 IGM IGE)
0
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davidvanzessen
parents:
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196
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davidvanzessen
parents:
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197 funcs=(sum mean median)
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davidvanzessen
parents:
diff changeset
198 funcs=(sum)
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davidvanzessen
parents:
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199
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davidvanzessen
parents:
diff changeset
200 echo "---------------- sequence_overview.r ----------------"
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davidvanzessen
parents:
diff changeset
201 echo "---------------- sequence_overview.r ----------------<br />" >> $log
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davidvanzessen
parents:
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202
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davidvanzessen
parents:
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203 mkdir $outdir/sequence_overview
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davidvanzessen
parents:
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204
7
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parents: 6
diff changeset
205 Rscript $dir/sequence_overview.r $outdir/before_unique_filter.txt $outdir/merged.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt ${empty_region_filter} 2>&1
0
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davidvanzessen
parents:
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206
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davidvanzessen
parents:
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207 echo "<table border='1'>" > $outdir/base_overview.html
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davidvanzessen
parents:
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208
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davidvanzessen
parents:
diff changeset
209 while IFS=$'\t' read ID class seq A C G T
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davidvanzessen
parents:
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210 do
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parents:
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211 echo "<tr><td>$ID</td><td>$seq</td><td>$class</td><td>$A</td><td>$C</td><td>$G</td><td>$T</td></tr>" >> $outdir/base_overview.html
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davidvanzessen
parents:
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212 done < $outdir/sequence_overview/ntoverview.txt
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davidvanzessen
parents:
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213
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davidvanzessen
parents:
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214 echo "<html><center><h1>$title</h1></center>" > $output
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davidvanzessen
parents:
diff changeset
215 echo "<meta name='viewport' content='width=device-width, initial-scale=1'>" >> $output
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davidvanzessen
parents:
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216 echo "<script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $output
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davidvanzessen
parents:
diff changeset
217 echo "<script type='text/javascript' src='tabber.js'></script>" >> $output
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davidvanzessen
parents:
diff changeset
218 echo "<script type='text/javascript' src='script.js'></script>" >> $output
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davidvanzessen
parents:
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219 echo "<link rel='stylesheet' type='text/css' href='style.css'>" >> $output
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davidvanzessen
parents:
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220 echo "<link rel='stylesheet' type='text/css' href='pure-min.css'>" >> $output
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davidvanzessen
parents:
diff changeset
221
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davidvanzessen
parents:
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222 matched_count="`cat $outdir/merged.txt | grep -v 'unmatched' | tail -n +2 | wc -l`"
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davidvanzessen
parents:
diff changeset
223 unmatched_count="`cat $outdir/unmatched.txt | tail -n +2 | wc -l`"
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davidvanzessen
parents:
diff changeset
224 total_count=$((matched_count + unmatched_count))
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davidvanzessen
parents:
diff changeset
225 perc_count=$((unmatched_count / total_count * 100))
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davidvanzessen
parents:
diff changeset
226 perc_count=`bc -l <<< "scale=2; ${unmatched_count} / ${total_count} * 100"`
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davidvanzessen
parents:
diff changeset
227 perc_count=`bc -l <<< "scale=2; (${unmatched_count} / ${total_count} * 100 ) / 1"`
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davidvanzessen
parents:
diff changeset
228
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davidvanzessen
parents:
diff changeset
229 echo "<center><h2>Total: ${total_count}</h2></center>" >> $output
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davidvanzessen
parents:
diff changeset
230 echo "<center><h2>Matched: ${matched_count} Unmatched: ${unmatched_count}</h2></center>" >> $output
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davidvanzessen
parents:
diff changeset
231 echo "<center><h2>Percentage unmatched: ${perc_count}</h2></center>" >> $output
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davidvanzessen
parents:
diff changeset
232
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davidvanzessen
parents:
diff changeset
233 echo "---------------- main tables ----------------"
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davidvanzessen
parents:
diff changeset
234 echo "---------------- main tables ----------------<br />" >> $log
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davidvanzessen
parents:
diff changeset
235
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davidvanzessen
parents:
diff changeset
236 echo "<div class='tabber'>" >> $output
23
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davidvanzessen
parents: 21
diff changeset
237 echo "<div class='tabbertab' title='SHM Overview' style='width: 3000px;'>" >> $output
0
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davidvanzessen
parents:
diff changeset
238
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davidvanzessen
parents:
diff changeset
239 for func in ${funcs[@]}
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davidvanzessen
parents:
diff changeset
240 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
241
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davidvanzessen
parents:
diff changeset
242 echo "---------------- $func table ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
243 echo "---------------- $func table ----------------<br />" >> $log
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davidvanzessen
parents:
diff changeset
244
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davidvanzessen
parents:
diff changeset
245 cat $outdir/mutations_${func}.txt $outdir/hotspot_analysis_${func}.txt > $outdir/data_${func}.txt
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davidvanzessen
parents:
diff changeset
246
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davidvanzessen
parents:
diff changeset
247 echo "---------------- pattern_plots.r ----------------"
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davidvanzessen
parents:
diff changeset
248 echo "---------------- pattern_plots.r ----------------<br />" >> $log
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davidvanzessen
parents:
diff changeset
249
23
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parents: 21
diff changeset
250 Rscript $dir/pattern_plots.r $outdir/data_${func}.txt $outdir/plot1 $outdir/plot2 $outdir/plot3 $outdir/shm_overview.txt 2>&1
0
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davidvanzessen
parents:
diff changeset
251
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davidvanzessen
parents:
diff changeset
252 echo "<table class='pure-table pure-table-striped'>" >> $output
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davidvanzessen
parents:
diff changeset
253 echo "<thead><tr><th>info</th>" >> $output
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davidvanzessen
parents:
diff changeset
254
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davidvanzessen
parents:
diff changeset
255 if [ "${class_filter}" != "101_101" ] ; then
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davidvanzessen
parents:
diff changeset
256
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davidvanzessen
parents:
diff changeset
257 for gene in ${genes[@]}
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davidvanzessen
parents:
diff changeset
258 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
259 tmp=`cat $outdir/${gene}_${func}_n.txt`
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davidvanzessen
parents:
diff changeset
260 echo "<th><a href='matched_${gene}_${func}.txt'>${gene} (N = $tmp)</a></th>" >> $output
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davidvanzessen
parents:
diff changeset
261 done
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davidvanzessen
parents:
diff changeset
262
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davidvanzessen
parents:
diff changeset
263 tmp=`cat $outdir/all_${func}_n.txt`
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davidvanzessen
parents:
diff changeset
264 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
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davidvanzessen
parents:
diff changeset
265 tmp=`cat $outdir/unmatched_${func}_n.txt`
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davidvanzessen
parents:
diff changeset
266 echo "<th><a href='unmatched.txt'>unmatched (N = ${unmatched_count})</a></th><tr></thead>" >> $output
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davidvanzessen
parents:
diff changeset
267
5
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davidvanzessen
parents: 4
diff changeset
268 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
0
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davidvanzessen
parents:
diff changeset
269 do
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davidvanzessen
parents:
diff changeset
270 if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] ; then #meh
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
271 echo "<tr><td>$name</td><td>${cax}/${cay} (${caz})</td><td>${ca1x}/${ca1y} (${ca1z})</td><td>${ca2x}/${ca2y} (${ca2z})</td><td>${cgx}/${cgy} (${cgz})</td><td>${cg1x}/${cg1y} (${cg1z})</td><td>${cg2x}/${cg2y} (${cg2z})</td><td>${cg3x}/${cg3y} (${cg3z})</td><td>${cg4x}/${cg4y} (${cg4z})</td><td>${cmx}/${cmy} (${cmz})</td><td>${cex}/${cey} (${cez})</td><td>${allx}/${ally} (${allz})</td><td>${unx}/${uny} (${unz})</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
272 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
273 echo "<tr><td>$name</td><td>${caz}%</td><td>${ca1z}%</td><td>${ca2z}%</td><td>${cgz}%</td><td>${cg1z}%</td><td>${cg2z}%</td><td>${cg3z}%</td><td>${cg4z}%</td><td>${cmz}%</td><td>${cez}%</td><td>${allz}%</td><td>${unz}%</td></tr>" >> $output
0
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davidvanzessen
parents:
diff changeset
274 else
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
275 echo "<tr><td>$name</td><td>${cax}/${cay} (${caz}%)</td><td>${ca1x}/${ca1y} (${ca1z}%)</td><td>${ca2x}/${ca2y} (${ca2z}%)</td><td>${cgx}/${cgy} (${cgz}%)</td><td>${cg1x}/${cg1y} (${cg1z}%)</td><td>${cg2x}/${cg2y} (${cg2z}%)</td><td>${cg3x}/${cg3y} (${cg3z}%)</td><td>${cg4x}/${cg4y} (${cg4z}%)</td><td>${cmx}/${cmy} (${cmz}%)</td><td>${cex}/${cey} (${cez}%)</td><td>${allx}/${ally} (${allz}%)</td><td>${unx}/${uny} (${unz}%)</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
276 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
277 done < $outdir/data_${func}.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
278
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
279 else
3
275ab5175fd6 Uploaded
davidvanzessen
parents: 2
diff changeset
280 tmp=`cat $outdir/all_${func}_n.txt`
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
281 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
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davidvanzessen
parents:
diff changeset
282
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
283 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
284 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
285 if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] ; then #meh
3
275ab5175fd6 Uploaded
davidvanzessen
parents: 2
diff changeset
286 echo "<tr><td>$name</td><td>${allx}/${ally}</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
287 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
3
275ab5175fd6 Uploaded
davidvanzessen
parents: 2
diff changeset
288 echo "<tr><td>$name</td><td>${allz}%</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
289 else
3
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davidvanzessen
parents: 2
diff changeset
290 echo "<tr><td>$name</td><td>${allx}/${ally} (${allz}%)</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
291 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
292 done < $outdir/data_${func}.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
293
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
294 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
295 echo "</table>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
296 #echo "<a href='data_${func}.txt'>Download data</a>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
297 done
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
298
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davidvanzessen
parents:
diff changeset
299 echo "<img src='plot1.png' /><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
300 echo "<img src='plot2.png' /><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
301 echo "<img src='plot3.png' /><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
302
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davidvanzessen
parents:
diff changeset
303 echo "</div>" >> $output #SHM overview tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
304
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davidvanzessen
parents:
diff changeset
305 echo "---------------- images ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
306 echo "---------------- images ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
307
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
308 echo "<div class='tabbertab' title='SHM Frequency' style='width: 3000px;'>" >> $output
0
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davidvanzessen
parents:
diff changeset
309
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davidvanzessen
parents:
diff changeset
310 if [ -a $outdir/scatter.png ]
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
311 then
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davidvanzessen
parents:
diff changeset
312 echo "<img src='scatter.png'/><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
313 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
314 if [ -a $outdir/frequency_ranges.png ]
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davidvanzessen
parents:
diff changeset
315 then
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davidvanzessen
parents:
diff changeset
316 echo "<img src='frequency_ranges.png'/><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
317 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
318
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
319 echo "</div>" >> $output #SHM frequency tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
320
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
321 echo "<div class='tabbertab' title='Transition tables' style='width: 3000px;'>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
322
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
323 echo "<table border='0'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
324
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
325 for gene in ${genes[@]}
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
326 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
327 echo "<tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
328 echo "<td><h1>${gene}</h1></td>" >> $output
23
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davidvanzessen
parents: 21
diff changeset
329
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davidvanzessen
parents: 21
diff changeset
330 if [ -e $outdir/transitions_heatmap_${gene}.png ]
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davidvanzessen
parents: 21
diff changeset
331 then
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
332 echo "<td><img src='transitions_heatmap_${gene}.png' /></td>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
333 else
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
334 echo "<td></td>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
335 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
336
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
337 if [ -e $outdir/transitions_stacked_${gene}.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
338 then
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
339 echo "<td><img src='transitions_stacked_${gene}.png' /></td>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
340 else
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
341 echo "<td></td>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
342 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
343
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
344 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
345 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
346 first="true"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
347 while IFS=, read from a c g t
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
348 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
349 if [ "$first" == "true" ] ; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
350 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
351 first="false"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
352 else
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
353 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
354 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
355 done < $outdir/transitions_${gene}_sum.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
356 echo "</table></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
357
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
358 echo "</tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
359 done
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
360
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
361 echo "<tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
362 echo "<td><h1>All</h1></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
363 echo "<td><img src='transitions_heatmap_all.png' /></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
364 echo "<td><img src='transitions_stacked_all.png' /></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
365 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
366 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
367 first="true"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
368 while IFS=, read from a c g t
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
369 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
370 if [ "$first" == "true" ] ; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
371 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
372 first="false"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
373 else
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
374 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
375 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
376 done < $outdir/transitions_all_sum.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
377 echo "</table></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
378
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
379 echo "</tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
380
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
381 echo "</table>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
382
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
383 echo "</div>" >> $output #transition tables tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
384
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
385 echo "<div class='tabbertab' title='Antigen Selection'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
386
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
387 if [ -e $outdir/aa_histogram.png ]
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
388 then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
389 echo "<img src='aa_histogram.png'/><br />" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
390 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
391
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
392 if [ -e $outdir/aa_histogram_IGA.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
393 then
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
394 echo "<img src='aa_histogram_IGA.png'/><br />" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
395 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
396
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
397 if [ -e $outdir/aa_histogram_IGG.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
398 then
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
399 echo "<img src='aa_histogram_IGG.png'/><br />" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
400 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
401
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
402 if [ -e $outdir/aa_histogram_IGM.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
403 then
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
404 echo "<img src='aa_histogram_IGM.png'/><br />" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
405 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
406
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
407 if [ -e $outdir/aa_histogram_IGE.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
408 then
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
409 echo "<img src='aa_histogram_IGE.png'/><br />" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
410 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
411
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
412
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
413
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
414 if [[ "$fast" == "no" ]] ; then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
415
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
416 echo "---------------- baseline ----------------"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
417 echo "---------------- baseline ----------------<br />" >> $log
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
418 tmp="$PWD"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
419
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
420 mkdir $outdir/baseline
37
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
421
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
422 baseline_boundaries="27:27:38:55:65:104:-"
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
423
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
424 if [[ "${empty_region_filter}" == "leader" ]] ; then
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
425 baseline_boundaries="1:26:38:55:65:104:-"
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
426 fi
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
427
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
428 mkdir $outdir/baseline/IGA_IGG_IGM
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
429 if [[ $(wc -l < $outdir/new_IMGT/1_Summary.txt) -gt "1" ]]; then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
430 cd $outdir/baseline/IGA_IGG_IGM
37
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
431 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT.txz "IGA_IGG_IGM" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt"
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
432 else
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
433 echo "No sequences" > "$outdir/baseline.txt"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
434 fi
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
435
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
436 mkdir $outdir/baseline/IGA
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
437 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
438 cd $outdir/baseline/IGA
37
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
439 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT_IGA.txz "IGA" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGA.pdf" "Sequence.ID" "$outdir/baseline_IGA.txt"
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
440 else
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
441 echo "No IGA sequences" > "$outdir/baseline_IGA.txt"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
442 fi
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
443
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
444 mkdir $outdir/baseline/IGG
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
445 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
446 cd $outdir/baseline/IGG
37
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
447 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT_IGG.txz "IGG" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGG.pdf" "Sequence.ID" "$outdir/baseline_IGG.txt"
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
448 else
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
449 echo "No IGG sequences" > "$outdir/baseline_IGG.txt"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
450 fi
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
451
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
452 mkdir $outdir/baseline/IGM
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
453 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
454 cd $outdir/baseline/IGM
37
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
455 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT_IGM.txz "IGM" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGM.pdf" "Sequence.ID" "$outdir/baseline_IGM.txt"
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
456 else
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
457 echo "No IGM sequences" > "$outdir/baseline_IGM.txt"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
458 fi
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
459
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
460 mkdir $outdir/baseline/IGE
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
461 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
462 cd $outdir/baseline/IGE
37
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
463 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT_IGE.txz "IGE" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGE.pdf" "Sequence.ID" "$outdir/baseline_IGE.txt"
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
464 else
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
465 echo "No IGE sequences" > "$outdir/baseline_IGE.txt"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
466 fi
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
467
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
468 cd $tmp
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
469
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
470 echo "Cleaning up *.RData files"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
471 find $outdir/baseline -name "*.RData" -type f -delete
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
472
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
473 if [ -e $outdir/baseline.pdf ]
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
474 then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
475 echo "<embed src='baseline.pdf' width='700px' height='1000px'>" >> $output
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
476 fi
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
477
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
478 if [ -e $outdir/baseline_IGA.pdf ]
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
479 then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
480 echo "<embed src='baseline_IGA.pdf' width='700px' height='1000px'>" >> $output
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
481 fi
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
482
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
483 if [ -e $outdir/baseline_IGG.pdf ]
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
484 then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
485 echo "<embed src='baseline_IGG.pdf' width='700px' height='1000px'>" >> $output
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
486 fi
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
487
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
488 if [ -e $outdir/baseline_IGM.pdf ]
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
489 then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
490 echo "<embed src='baseline_IGM.pdf' width='700px' height='1000px'>" >> $output
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
491 fi
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
492
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
493 if [ -e $outdir/baseline_IGE.pdf ]
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
494 then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
495 echo "<embed src='baseline_IGE.pdf' width='700px' height='1000px'>" >> $output
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
496 fi
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
497 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
498
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
499 echo "</div>" >> $output #antigen selection tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
500
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
501 echo "<div class='tabbertab' title='CSR'>" >> $output #CSR tab
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
502
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
503 if [ -e $outdir/IGA.png ]
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
504 then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
505 echo "<img src='IGA.png'/><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
506 fi
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
507 if [ -e $outdir/IGG.png ]
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
508 then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
509 echo "<img src='IGG.png'/><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
510 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
511
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
512 echo "</div>" >> $output #CSR tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
513
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
514 if [[ "$fast" == "no" ]] ; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
515
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
516 echo "---------------- change-o MakeDB ----------------"
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
517
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
518 mkdir $outdir/change_o
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
519
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
520 tmp="$PWD"
0
c33d93683a09 Uploaded
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parents:
diff changeset
521
5
012a738edf5a Uploaded
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parents: 4
diff changeset
522 cd $outdir/change_o
0
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parents:
diff changeset
523
5
012a738edf5a Uploaded
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parents: 4
diff changeset
524 bash $dir/change_o/makedb.sh $outdir/new_IMGT.txz false false false $outdir/change_o/change-o-db.txt
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
525 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones.txt $outdir/change_o/change-o-defined_clones-summary.txt
0
c33d93683a09 Uploaded
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parents:
diff changeset
526
5
012a738edf5a Uploaded
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parents: 4
diff changeset
527 Rscript $dir/merge.r $outdir/change_o/change-o-db-defined_clones.txt $outdir/merged.txt "all" "Sequence.ID,best_match" "SEQUENCE_ID" "Sequence.ID" $outdir/change_o/change-o-db-defined_clones.txt 2>&1
0
c33d93683a09 Uploaded
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parents:
diff changeset
528
5
012a738edf5a Uploaded
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parents: 4
diff changeset
529 echo "Rscript $dir/merge.r $outdir/change_o/change-o-db-defined_clones.txt $outdir/$outdir/merged.txt 'all' 'Sequence.ID,best_match' 'Sequence.ID' 'Sequence.ID' '\t' $outdir/change_o/change-o-db-defined_clones.txt 2>&1"
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
530
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
531 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
532 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGA.txz false false false $outdir/change_o/change-o-db-IGA.txt
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
533 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 $outdir/change_o/change-o-defined_clones-summary-IGA.txt
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
534 else
012a738edf5a Uploaded
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parents: 4
diff changeset
535 echo "No IGA sequences" > "$outdir/change_o/change-o-db-defined_clones-IGA.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
536 echo "No IGA sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGA.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
537 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
538
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
539 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
540 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGG.txz false false false $outdir/change_o/change-o-db-IGG.txt
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
541 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 $outdir/change_o/change-o-defined_clones-summary-IGG.txt
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
542 else
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
543 echo "No IGG sequences" > "$outdir/change_o/change-o-db-defined_clones-IGG.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
544 echo "No IGG sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGG.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
545 fi
0
c33d93683a09 Uploaded
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parents:
diff changeset
546
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
547 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
548 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGM.txz false false false $outdir/change_o/change-o-db-IGM.txt
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
549 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 $outdir/change_o/change-o-defined_clones-summary-IGM.txt
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
550 else
012a738edf5a Uploaded
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parents: 4
diff changeset
551 echo "No IGM sequences" > "$outdir/change_o/change-o-db-defined_clones-IGM.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
552 echo "No IGM sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGM.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
553 fi
0
c33d93683a09 Uploaded
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parents:
diff changeset
554
6
2ddb9a21f635 Uploaded
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parents: 5
diff changeset
555 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
556 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGE.txz false false false $outdir/change_o/change-o-db-IGE.txt
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
557 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 $outdir/change_o/change-o-defined_clones-summary-IGE.txt
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
558 else
2ddb9a21f635 Uploaded
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parents: 5
diff changeset
559 echo "No IGE sequences" > "$outdir/change_o/change-o-db-defined_clones-IGE.txt"
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
560 echo "No IGE sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGE.txt"
2ddb9a21f635 Uploaded
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parents: 5
diff changeset
561 fi
2ddb9a21f635 Uploaded
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parents: 5
diff changeset
562
5
012a738edf5a Uploaded
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parents: 4
diff changeset
563 PWD="$tmp"
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
564
16
4e596473c25c Uploaded
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parents: 14
diff changeset
565 echo "<div class='tabbertab' title='Clonality'>" >> $output #clonality tab
0
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davidvanzessen
parents:
diff changeset
566
16
4e596473c25c Uploaded
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parents: 14
diff changeset
567 function clonality_table {
4e596473c25c Uploaded
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parents: 14
diff changeset
568 local infile=$1
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
569 local outfile=$2
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
570
4e596473c25c Uploaded
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parents: 14
diff changeset
571 echo "<table class='pure-table pure-table-striped'>" >> $outfile
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
572 echo "<thead><tr><th>Clone size</th><th>Nr of clones</th><th>Nr of sequences</th></tr></thead>" >> $outfile
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
573
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
574 first='true'
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
575
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
576 while read size clones seqs
4e596473c25c Uploaded
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parents: 14
diff changeset
577 do
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
578 if [[ "$first" == "true" ]]; then
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
579 first="false"
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
580 continue
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
581 fi
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
582 echo "<tr><td>$size</td><td>$clones</td><td>$seqs</td></tr>" >> $outfile
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
583 done < $infile
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
584
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
585 echo "</table>" >> $outfile
4e596473c25c Uploaded
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parents: 14
diff changeset
586 }
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
587 echo "<div class='tabber'>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
588
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
589 echo "<div class='tabbertab' title='All'>" >> $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
590 clonality_table $outdir/change_o/change-o-defined_clones-summary.txt $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
591 echo "</div>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
592
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
593 echo "<div class='tabbertab' title='IGA'>" >> $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
594 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGA.txt $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
595 echo "</div>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
596
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
597 echo "<div class='tabbertab' title='IGG'>" >> $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
598 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGG.txt $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
599 echo "</div>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
600
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
601 echo "<div class='tabbertab' title='IGM'>" >> $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
602 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
603 echo "</div>" >> $output
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
604
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
605 echo "<div class='tabbertab' title='IGE'>" >> $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
606 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
607 echo "</div>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
608
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
609 echo "<div class='tabbertab' title='Overlap'>" >> $output
31
fe44a905aee9 Uploaded
davidvanzessen
parents: 30
diff changeset
610 cat "$outdir/sequence_overview/index.html" | sed "s%href='\(.*\).html%href='sequence_overview/\1.html%g" >> $output # rewrite href to 'sequence_overview/..."
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
611 echo "</div>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
612
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
613
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
614 echo "</div>" >> $output #clonality tabber end
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
615
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
616 echo "</div>" >> $output #clonality tab end
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
617
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
618 fi
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
619
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
620 echo "<div class='tabbertab' title='Downloads'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
621
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
622 echo "<table class='pure-table pure-table-striped'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
623 echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
624 echo "<tr><td>The complete dataset</td><td><a href='merged.txt' download='merged.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
625 echo "<tr><td>The filtered dataset</td><td><a href='filtered.txt' download='filtered.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
626 echo "<tr><td>The alignment info on the unmatched sequences</td><td><a href='unmatched.txt' download='unmatched.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
627
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
628 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Overview</td></tr>" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
629 echo "<tr><td>The SHM Overview table as a dataset</td><td><a href='shm_overview.txt' download='shm_overview.txt' >Download</a></td></tr>" >> $output
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
630 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
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
631 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
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
632 echo "<tr><td>Base count for every sequence</td><td><a href='base_overview.html'>View</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
633 echo "<tr><td>The data used to generate the RGYW/WRCY and TW/WA plot</td><td><a href='plot1.txt' download='plot1.txt' >Download</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
634 echo "<tr><td>The data used to generate the relative transition and transversion plot</td><td><a href='plot2.txt' download='plot2.txt' >Download</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
635 echo "<tr><td>The data used to generate the absolute transition and transversion plot</td><td><a href='plot3.txt' download='plot3.txt' >Download</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
636
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
637 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Frequency</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
638 echo "<tr><td>The data generate the frequency scatter plot</td><td><a href='scatter.txt' download='scatter.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
639 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
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
640 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
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
641
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
642 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Transition Tables</td></tr>" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
643 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
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
644 echo "<tr><td>The data for the 'IGA' transition plot</td><td><a href='transitions_IGA_sum.txt' download='transitions_all_sum.txt' >Download</a></td></tr>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
645 echo "<tr><td>The data for the 'IGA1' transition plot</td><td><a href='transitions_IGA1_sum.txt' download='transitions_IGA1_sum.txt' >Download</a></td></tr>" >> $output
30
33a7c49d48a7 Uploaded
davidvanzessen
parents: 29
diff changeset
646 echo "<tr><td>The data for the 'IGA2' transition plot</td><td><a href='transitions_IGA2_sum.txt' download='transitions_IGA2_sum.txt' >Download</a></td></tr>" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
647 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
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
648 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
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
649 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
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
650 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
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
651 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
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
652 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
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
653 echo "<tr><td>The data for the 'IGE' transition plot</td><td><a href='transitions_IGE_sum.txt' download='transitions_IGE_sum.txt' >Download</a></td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
654
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
655 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Antigen Selection</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
656 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
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
657 echo "<tr><td>Absent AA location data per sequence ID</td><td><a href='absent_aa_id.txt' download='absent_aa_id.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
658
29
80c4eebf7bc9 Uploaded
davidvanzessen
parents: 28
diff changeset
659 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
80c4eebf7bc9 Uploaded
davidvanzessen
parents: 28
diff changeset
660 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
80c4eebf7bc9 Uploaded
davidvanzessen
parents: 28
diff changeset
661 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
80c4eebf7bc9 Uploaded
davidvanzessen
parents: 28
diff changeset
662 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
80c4eebf7bc9 Uploaded
davidvanzessen
parents: 28
diff changeset
663 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
80c4eebf7bc9 Uploaded
davidvanzessen
parents: 28
diff changeset
664
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
665 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
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
666 echo "<tr><td>Baseline data</td><td><a href='baseline.txt' download='baseline.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
667 echo "<tr><td>Baseline IGA PDF</td><td><a href='baseline_IGA.pdf' download='baseline_IGA.pdf' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
668 echo "<tr><td>Baseline IGA data</td><td><a href='baseline_IGA.txt' download='baseline_IGA.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
669 echo "<tr><td>Baseline IGG PDF</td><td><a href='baseline_IGG.pdf' download='baseline_IGG.pdf' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
670 echo "<tr><td>Baseline IGG data</td><td><a href='baseline_IGG.txt' download='baseline_IGG.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
671 echo "<tr><td>Baseline IGM PDF</td><td><a href='baseline_IGM.pdf' download='baseline_IGM.pdf' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
672 echo "<tr><td>Baseline IGM data</td><td><a href='baseline_IGM.txt' download='baseline_IGM.txt' >Download</a></td></tr>" >> $output
31
fe44a905aee9 Uploaded
davidvanzessen
parents: 30
diff changeset
673 echo "<tr><td>Baseline IGE PDF</td><td><a href='baseline_IGE.pdf' download='baseline_IGE.pdf' >Download</a></td></tr>" >> $output
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
674 echo "<tr><td>Baseline IGE data</td><td><a href='baseline_IGE.txt' download='baseline_IGE.txt' >Download</a></td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
675
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
676 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>CSR</td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
677 echo "<tr><td>The data for the CSR IGA pie plot</td><td><a href='IGA_pie.txt' download='IGA_pie.txt' >Download</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
678 echo "<tr><td>The data for the CSR IGG pie plot</td><td><a href='IGG_pie.txt' download='IGG_pie.txt' >Download</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
679
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
680 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Clonality</td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
681 echo "<tr><td>Sequence overlap between subclasses</td><td><a href='sequence_overview/index.html'>View</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
682 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
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
683 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
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
684 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
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
685 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
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
686 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
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
687 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
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
688 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
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
689 echo "<tr><td>The Change-O DB defined clones summary file of IGM</td><td><a href='change_o/change-o-defined_clones-summary-IGM.txt' download='change_o/change-o-defined_clones-summary-IGM.txt' >Download</a></td></tr>" >> $output
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
690 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
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
691 echo "<tr><td>The Change-O DB defined clones summary file of IGE</td><td><a href='change_o/change-o-defined_clones-summary-IGE.txt' download='change_o/change-o-defined_clones-summary-IGE.txt' >Download</a></td></tr>" >> $output
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
692
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
693 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Filtered IMGT output files</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
694 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
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
695 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
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
696 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
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
697 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
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
698 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
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
699 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
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
700 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
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
701 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
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
702 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
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
703 echo "<tr><td>An IMGT archive with just the matched and filtered IGM sequences</td><td><a href='new_IMGT_IGM.txz' download='new_IMGT_IGM.txz' >Download</a></td></tr>" >> $output
31
fe44a905aee9 Uploaded
davidvanzessen
parents: 30
diff changeset
704 echo "<tr><td>An IMGT archive with just the matched and filtered IGE sequences</td><td><a href='new_IMGT_IGE.txz' download='new_IMGT_IGE.txz' >Download</a></td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
705
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
706 echo "</table>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
707
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
708 echo "</div>" >> $output #downloads tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
709
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
710 echo "</div>" >> $output #tabs end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
711
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
712 echo "</html>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
713
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
714
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
715 echo "---------------- naive_output.r ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
716 echo "---------------- naive_output.r ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
717
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
718 if [[ "$naive_output" == "yes" ]]
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
719 then
28
c0ecc31829bd Uploaded
davidvanzessen
parents: 26
diff changeset
720 echo "output naive output"
18
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
721 if [[ "${class_filter}" == "101_101" ]]
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
722 then
28
c0ecc31829bd Uploaded
davidvanzessen
parents: 26
diff changeset
723 echo "copy new_IMGT.txz to ${naive_output_all}"
21
c281993e515b Uploaded
davidvanzessen
parents: 20
diff changeset
724 cp $outdir/new_IMGT.txz ${naive_output_all}
18
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
725 else
28
c0ecc31829bd Uploaded
davidvanzessen
parents: 26
diff changeset
726 echo "copy for classes"
18
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
727 cp $outdir/new_IMGT_IGA.txz ${naive_output_ca}
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
728 cp $outdir/new_IMGT_IGG.txz ${naive_output_cg}
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
729 cp $outdir/new_IMGT_IGM.txz ${naive_output_cm}
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
730 cp $outdir/new_IMGT_IGE.txz ${naive_output_ce}
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
731 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
732 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
733
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
734 echo "</table>" >> $outdir/base_overview.html
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
735
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
736 mv $log $outdir/log.html
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
737
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
738 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
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
739 echo "<table border = 1>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
740 echo "<thead><tr><th>Info</th><th>Sequences</th><th>Percentage</th></tr></thead>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
741 tIFS="$TMP"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
742 IFS=$'\t'
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
743 while read step seq perc
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
744 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
745 echo "<tr>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
746 echo "<td>$step</td>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
747 echo "<td>$seq</td>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
748 echo "<td>${perc}%</td>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
749 echo "</tr>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
750 done < $outdir/filtering_steps.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
751 echo "</table border></center></html>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
752
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
753 IFS="$tIFS"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
754
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
755
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
756 echo "---------------- Done! ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
757 echo "---------------- Done! ----------------<br />" >> $outdir/log.html
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
758
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
759
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
760
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
761
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
762
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
763
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
764
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
765
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
766
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
767
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
768
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
769
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
770
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
771
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
772
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
773
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
774
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
775
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
776
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
777
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
778