annotate wrapper.sh @ 29:80c4eebf7bc9 draft

Uploaded
author davidvanzessen
date Thu, 08 Dec 2016 04:51:09 -0500
parents c0ecc31829bd
children 33a7c49d48a7
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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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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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130
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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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143
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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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parents:
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173
5
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parents: 4
diff changeset
174 classes="IGA,IGA1,IGA2,IGG,IGG1,IGG2,IGG3,IGG4,IGM,IGE,unmatched"
0
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davidvanzessen
parents:
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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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parents:
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178 echo "---------------- shm_csr.py ----------------"
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davidvanzessen
parents:
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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:
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183 echo "---------------- aa_histogram.r ----------------"
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davidvanzessen
parents:
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184 echo "---------------- aa_histogram.r ----------------<br />" >> $log
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davidvanzessen
parents:
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185
5
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parents: 4
diff changeset
186 Rscript $dir/aa_histogram.r $outdir/aa_id_mutations.txt $outdir/absent_aa_id.txt "IGA,IGG,IGM,IGE" $outdir/ 2>&1
0
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davidvanzessen
parents:
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187 if [ -e "$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
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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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parents:
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193 fi
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parents:
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194
5
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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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parents:
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198 funcs=(sum)
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parents:
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199
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davidvanzessen
parents:
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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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203 mkdir $outdir/sequence_overview
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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'>" > $outdir/base_overview.html
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davidvanzessen
parents:
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208
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davidvanzessen
parents:
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209 while IFS=$'\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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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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parents:
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212 done < $outdir/sequence_overview/ntoverview.txt
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davidvanzessen
parents:
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213
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parents:
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214 echo "<html><center><h1>$title</h1></center>" > $output
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davidvanzessen
parents:
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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:
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217 echo "<script type='text/javascript' src='tabber.js'></script>" >> $output
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parents:
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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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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
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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:
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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:
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226 perc_count=`bc -l <<< "scale=2; ${unmatched_count} / ${total_count} * 100"`
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davidvanzessen
parents:
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227 perc_count=`bc -l <<< "scale=2; (${unmatched_count} / ${total_count} * 100 ) / 1"`
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parents:
diff changeset
228
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229 echo "<center><h2>Total: ${total_count}</h2></center>" >> $output
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davidvanzessen
parents:
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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:
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232
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davidvanzessen
parents:
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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
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davidvanzessen
parents:
diff changeset
241
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davidvanzessen
parents:
diff changeset
242 echo "---------------- $func table ----------------"
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davidvanzessen
parents:
diff changeset
243 echo "---------------- $func table ----------------<br />" >> $log
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davidvanzessen
parents:
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244
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parents:
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245 cat $outdir/mutations_${func}.txt $outdir/hotspot_analysis_${func}.txt > $outdir/data_${func}.txt
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parents:
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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
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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
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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>" >> $output
0
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davidvanzessen
parents:
diff changeset
272 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
5
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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>" >> $output
0
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davidvanzessen
parents:
diff changeset
274 else
5
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davidvanzessen
parents: 4
diff changeset
275 echo "<tr><td>$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
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davidvanzessen
parents:
diff changeset
276 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
277 done < $outdir/data_${func}.txt
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davidvanzessen
parents:
diff changeset
278
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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>" >> $output
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davidvanzessen
parents:
diff changeset
282
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
283 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
284 do
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davidvanzessen
parents:
diff changeset
285 if [ "$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>" >> $output
0
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davidvanzessen
parents:
diff changeset
287 elif [ "$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>" >> $output
0
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davidvanzessen
parents:
diff changeset
289 else
3
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davidvanzessen
parents: 2
diff changeset
290 echo "<tr><td>$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
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davidvanzessen
parents:
diff changeset
294 fi
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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
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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
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davidvanzessen
parents:
diff changeset
300 echo "<img src='plot2.png' /><br />" >> $output
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davidvanzessen
parents:
diff changeset
301 echo "<img src='plot3.png' /><br />" >> $output
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davidvanzessen
parents:
diff changeset
302
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davidvanzessen
parents:
diff changeset
303 echo "</div>" >> $output #SHM overview tab end
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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
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davidvanzessen
parents:
diff changeset
307
23
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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 ]
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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
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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
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davidvanzessen
parents:
diff changeset
319 echo "</div>" >> $output #SHM frequency tab end
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davidvanzessen
parents:
diff changeset
320
23
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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
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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>" >> $output
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davidvanzessen
parents:
diff changeset
328 echo "<td><h1>${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
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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
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
413 if [ -e $outdir/baseline.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
414 then
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
415 echo "<embed src='baseline.pdf' width='700px' height='1000px'>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
416 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
417
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
418 if [ -e $outdir/baseline_IGA.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
419 then
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
420 echo "<embed src='baseline_IGA.pdf' width='700px' height='1000px'>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
421 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
422
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
423 if [ -e $outdir/baseline_IGG.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
424 then
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
425 echo "<embed src='baseline_IGG.pdf' width='700px' height='1000px'>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
426 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
427
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
428 if [ -e $outdir/baseline_IGM.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
429 then
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
430 echo "<embed src='baseline_IGM.pdf' width='700px' height='1000px'>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
431 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
432
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
433 if [ -e $outdir/baseline_IGE.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
434 then
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
435 echo "<embed src='baseline_IGE.pdf' width='700px' height='1000px'>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
436 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
437
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
438 echo "</div>" >> $output #antigen selection tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
439
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
440 echo "<div class='tabbertab' title='CSR'>" >> $output #CSR tab
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
441
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
442 if [ -e $outdir/IGA.png ]
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
443 then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
444 echo "<img src='IGA.png'/><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
445 fi
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
446 if [ -e $outdir/IGG.png ]
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
447 then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
448 echo "<img src='IGG.png'/><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
449 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
450
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
451 echo "</div>" >> $output #CSR tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
452
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
453 if [[ "$fast" == "no" ]] ; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
454
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
455 echo "---------------- change-o MakeDB ----------------"
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
456
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
457 mkdir $outdir/change_o
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
458
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
459 tmp="$PWD"
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
460
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
461 cd $outdir/change_o
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
462
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
463 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
464 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
davidvanzessen
parents:
diff changeset
465
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
466 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
davidvanzessen
parents:
diff changeset
467
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
468 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
469
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
470 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
471 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
472 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 $outdir/change_o/change-o-defined_clones-summary-IGA.txt
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
473 else
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
474 echo "No IGA sequences" > "$outdir/change_o/change-o-db-defined_clones-IGA.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
475 echo "No IGA sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGA.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
476 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
477
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
478 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
479 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
480 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 $outdir/change_o/change-o-defined_clones-summary-IGG.txt
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
481 else
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
482 echo "No IGG sequences" > "$outdir/change_o/change-o-db-defined_clones-IGG.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
483 echo "No IGG sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGG.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
484 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
485
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
486 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
487 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
488 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 $outdir/change_o/change-o-defined_clones-summary-IGM.txt
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
489 else
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
490 echo "No IGM sequences" > "$outdir/change_o/change-o-db-defined_clones-IGM.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
491 echo "No IGM sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGM.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
492 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
493
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
494 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
495 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
496 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 $outdir/change_o/change-o-defined_clones-summary-IGE.txt
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
497 else
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
498 echo "No IGE sequences" > "$outdir/change_o/change-o-db-defined_clones-IGE.txt"
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
499 echo "No IGE sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGE.txt"
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
500 fi
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
501
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
502 PWD="$tmp"
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
503
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
504 echo "<div class='tabbertab' title='Clonality'>" >> $output #clonality tab
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
505
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
506 function clonality_table {
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parents: 14
diff changeset
507 local infile=$1
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davidvanzessen
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diff changeset
508 local outfile=$2
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diff changeset
509
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parents: 14
diff changeset
510 echo "<table class='pure-table pure-table-striped'>" >> $outfile
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davidvanzessen
parents: 14
diff changeset
511 echo "<thead><tr><th>Clone size</th><th>Nr of clones</th><th>Nr of sequences</th></tr></thead>" >> $outfile
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davidvanzessen
parents: 14
diff changeset
512
4e596473c25c Uploaded
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diff changeset
513 first='true'
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
514
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davidvanzessen
parents: 14
diff changeset
515 while read size clones seqs
4e596473c25c Uploaded
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diff changeset
516 do
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diff changeset
517 if [[ "$first" == "true" ]]; then
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davidvanzessen
parents: 14
diff changeset
518 first="false"
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davidvanzessen
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diff changeset
519 continue
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
520 fi
4e596473c25c Uploaded
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parents: 14
diff changeset
521 echo "<tr><td>$size</td><td>$clones</td><td>$seqs</td></tr>" >> $outfile
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diff changeset
522 done < $infile
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
523
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parents: 14
diff changeset
524 echo "</table>" >> $outfile
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parents: 14
diff changeset
525 }
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
526 echo "<div class='tabber'>" >> $output
0
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davidvanzessen
parents:
diff changeset
527
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
528 echo "<div class='tabbertab' title='All'>" >> $output
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davidvanzessen
parents: 14
diff changeset
529 clonality_table $outdir/change_o/change-o-defined_clones-summary.txt $output
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davidvanzessen
parents: 14
diff changeset
530 echo "</div>" >> $output
0
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davidvanzessen
parents:
diff changeset
531
16
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davidvanzessen
parents: 14
diff changeset
532 echo "<div class='tabbertab' title='IGA'>" >> $output
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davidvanzessen
parents: 14
diff changeset
533 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGA.txt $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
534 echo "</div>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
535
16
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davidvanzessen
parents: 14
diff changeset
536 echo "<div class='tabbertab' title='IGG'>" >> $output
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davidvanzessen
parents: 14
diff changeset
537 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGG.txt $output
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davidvanzessen
parents: 14
diff changeset
538 echo "</div>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
539
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
540 echo "<div class='tabbertab' title='IGM'>" >> $output
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davidvanzessen
parents: 14
diff changeset
541 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
542 echo "</div>" >> $output
6
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davidvanzessen
parents: 5
diff changeset
543
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
544 echo "<div class='tabbertab' title='IGE'>" >> $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
545 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
546 echo "</div>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
547
23
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parents: 21
diff changeset
548 echo "<div class='tabbertab' title='Overlap'>" >> $output
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
549 cat "$outdir/sequence_overview/index.html" >> $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
550 echo "</div>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
551
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
552
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
553 echo "</div>" >> $output #clonality tabber end
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
554
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
555 echo "</div>" >> $output #clonality tab end
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
556
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
557 fi
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
558
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
559 echo "<div class='tabbertab' title='Downloads'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
560
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
561 echo "<table class='pure-table pure-table-striped'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
562 echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
563 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
564 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
565 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
566
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
567 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Overview</td></tr>" >> $output
23
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davidvanzessen
parents: 21
diff changeset
568 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
569 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
570 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
571 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
572 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
573 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
574 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
575
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
576 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Frequency</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
577 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
578 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
579 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
580
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
581 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Transition Tables</td></tr>" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
582 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
583 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
584 echo "<tr><td>The data for the 'IGA1' transition plot</td><td><a href='transitions_IGA1_sum.txt' download='transitions_IGA1_sum.txt' >Download</a></td></tr>" >> $output
26
ce25fb581ca3 Uploaded
davidvanzessen
parents: 23
diff changeset
585 echo "<tr><td>The data for the 'IGA1' transition plot</td><td><a href='transitions_IGA2_sum.txt' download='transitions_IGA2_sum.txt' >Download</a></td></tr>" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
586 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
587 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
588 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
589 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
590 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
591 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
592 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
593
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
594 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Antigen Selection</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
595 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
596 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
597
29
80c4eebf7bc9 Uploaded
davidvanzessen
parents: 28
diff changeset
598 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
599 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
600 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
601 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
602 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
603
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
604 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
605 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
606 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
607 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
608 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
609 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
610 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
611 echo "<tr><td>Baseline IGM data</td><td><a href='baseline_IGM.txt' download='baseline_IGM.txt' >Download</a></td></tr>" >> $output
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
612 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
613
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
614 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>CSR</td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
615 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
616 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
617
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
618 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Clonality</td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
619 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
620 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
621 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
622 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
623 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
624 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
625 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
626 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
627 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
628 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
629 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
630
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
631 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Filtered IMGT output files</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
632 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
633 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
634 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
635 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
636 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
637 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
638 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
639 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
640 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
641 echo "<tr><td>An IMGT archive with just the matched and filtered IGM sequences</td><td><a href='new_IMGT_IGM.txz' download='new_IMGT_IGM.txz' >Download</a></td></tr>" >> $output
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
642 echo "<tr><td>An IMGT archive with just the matched and filtered IGE sequences</td><td><a href='new_IMGT_IGE.txz' download='new_IMGT_IGM.txz' >Download</a></td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
643
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
644 echo "</table>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
645
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
646 echo "</div>" >> $output #downloads tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
647
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
648 echo "</div>" >> $output #tabs end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
649
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
650 echo "</html>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
651
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
652
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
653 if [[ "$fast" == "no" ]] ; then
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
654
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
655 echo "---------------- baseline ----------------"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
656 echo "---------------- baseline ----------------<br />" >> $log
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
657 tmp="$PWD"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
658
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
659 mkdir $outdir/baseline
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
660
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
661
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
662 mkdir $outdir/baseline/IGA_IGG_IGM
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
663 if [[ $(wc -l < $outdir/new_IMGT/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
664 cd $outdir/baseline/IGA_IGG_IGM
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
665 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT.txz "IGA_IGG_IGM" "$dir/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
666 else
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
667 echo "No sequences" > "$outdir/baseline.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
668 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
669
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
670 mkdir $outdir/baseline/IGA
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
671 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
672 cd $outdir/baseline/IGA
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
673 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGA.txz "IGA" "$dir/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_IGA.pdf" "Sequence.ID" "$outdir/baseline_IGA.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
674 else
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
675 echo "No IGA sequences" > "$outdir/baseline_IGA.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
676 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
677
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
678 mkdir $outdir/baseline/IGG
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
679 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
680 cd $outdir/baseline/IGG
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
681 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGG.txz "cg" "$dir/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_IGG.pdf" "Sequence.ID" "$outdir/baseline_IGG.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
682 else
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
683 echo "No IGG sequences" > "$outdir/baseline_IGG.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
684 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
685
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
686 mkdir $outdir/baseline/IGM
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
687 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
688 cd $outdir/baseline/IGM
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
689 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGM.txz "IGM" "$dir/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_IGM.pdf" "Sequence.ID" "$outdir/baseline_IGM.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
690 else
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
691 echo "No IGM sequences" > "$outdir/baseline_IGM.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
692 fi
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
693
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
694 mkdir $outdir/baseline/IGE
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
695 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
696 cd $outdir/baseline/IGE
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
697 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGE.txz "IGE" "$dir/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_IGE.pdf" "Sequence.ID" "$outdir/baseline_IGE.txt"
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
698 else
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
699 echo "No IGE sequences" > "$outdir/baseline_IGE.txt"
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
700 fi
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
701
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
702 cd $tmp
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
703
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
704 echo "Cleaning up *.RData files"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
705 find $outdir/baseline -name "*.RData" -type f -delete
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
706
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
707 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
708
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
709 echo "---------------- naive_output.r ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
710 echo "---------------- naive_output.r ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
711
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
712 if [[ "$naive_output" == "yes" ]]
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
713 then
28
c0ecc31829bd Uploaded
davidvanzessen
parents: 26
diff changeset
714 echo "output naive output"
18
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
715 if [[ "${class_filter}" == "101_101" ]]
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
716 then
28
c0ecc31829bd Uploaded
davidvanzessen
parents: 26
diff changeset
717 echo "copy new_IMGT.txz to ${naive_output_all}"
21
c281993e515b Uploaded
davidvanzessen
parents: 20
diff changeset
718 cp $outdir/new_IMGT.txz ${naive_output_all}
18
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
719 else
28
c0ecc31829bd Uploaded
davidvanzessen
parents: 26
diff changeset
720 echo "copy for classes"
18
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
721 cp $outdir/new_IMGT_IGA.txz ${naive_output_ca}
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
722 cp $outdir/new_IMGT_IGG.txz ${naive_output_cg}
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
723 cp $outdir/new_IMGT_IGM.txz ${naive_output_cm}
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
724 cp $outdir/new_IMGT_IGE.txz ${naive_output_ce}
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
725 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
726 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
727
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
728 echo "</table>" >> $outdir/base_overview.html
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
729
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
730 mv $log $outdir/log.html
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
731
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
732 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
733 echo "<table border = 1>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
734 echo "<thead><tr><th>Info</th><th>Sequences</th><th>Percentage</th></tr></thead>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
735 tIFS="$TMP"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
736 IFS=$'\t'
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
737 while read step seq perc
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
738 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
739 echo "<tr>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
740 echo "<td>$step</td>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
741 echo "<td>$seq</td>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
742 echo "<td>${perc}%</td>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
743 echo "</tr>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
744 done < $outdir/filtering_steps.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
745 echo "</table border></center></html>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
746
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
747 IFS="$tIFS"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
748
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
749
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
750 echo "---------------- Done! ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
751 echo "---------------- Done! ----------------<br />" >> $outdir/log.html
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
752
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
753
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
754
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
755
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
756
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
757
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