annotate wrapper.sh @ 43:77a7ac76c7b9 draft

Uploaded
author davidvanzessen
date Tue, 11 Apr 2017 08:02:17 -0400
parents 1cf60ae234b4
children b66e8946ba75
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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 "4_*"`" > $PWD/gapped_aa.txt
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47 cat "`find $PWD/files/ -name "5_*"`" > $PWD/aa.txt
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48 cat "`find $PWD/files/ -name "6_*"`" > $PWD/junction.txt
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49 cat "`find $PWD/files/ -name "7_*"`" > $PWD/mutationanalysis.txt
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50 cat "`find $PWD/files/ -name "8_*"`" > $PWD/mutationstats.txt
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51 cat "`find $PWD/files/ -name "10_*"`" > $PWD/hotspots.txt
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52
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53 if [[ ${#BLASTN_DIR} -ge 5 ]] ; then
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54 echo "On server, using BLASTN_DIR env: ${BLASTN_DIR}"
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55 else
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56 BLASTN_DIR="/home/galaxy/Downloads/ncbi-blast-2.4.0+/bin"
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57 echo "Dev Galaxy set BLASTN_DIR to: ${BLASTN_DIR}"
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58 fi
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59
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60 echo "---------------- class identification ----------------"
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61 echo "---------------- class identification ----------------<br />" >> $log
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62
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63 python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt
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64
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65 echo "---------------- merge_and_filter.r ----------------"
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66 echo "---------------- merge_and_filter.r ----------------<br />" >> $log
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67
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68 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt "$PWD/gapped_aa.txt" $outdir/identified_genes.txt $outdir/merged.txt $outdir/before_unique_filter.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${class_filter} ${empty_region_filter} 2>&1
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70 if [[ "$fast" == "no" ]] ; then
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71
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72 echo "---------------- creating new IMGT zips ----------------"
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73 echo "---------------- creating new IMGT zips ----------------<br />" >> $log
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74
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75 mkdir $outdir/new_IMGT
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77 cat "`find $PWD/files/ -name "1_*"`" > "$outdir/new_IMGT/1_Summary.txt"
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78 cat "`find $PWD/files/ -name "2_*"`" > "$outdir/new_IMGT/2_IMGT-gapped-nt-sequences.txt"
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79 cat "`find $PWD/files/ -name "3_*"`" > "$outdir/new_IMGT/3_Nt-sequences.txt"
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80 cat "`find $PWD/files/ -name "4_*"`" > "$outdir/new_IMGT/4_IMGT-gapped-AA-sequences.txt"
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81 cat "`find $PWD/files/ -name "5_*"`" > "$outdir/new_IMGT/5_AA-sequences.txt"
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82 cat "`find $PWD/files/ -name "6_*"`" > "$outdir/new_IMGT/6_Junction.txt"
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83 cat "`find $PWD/files/ -name "7_*"`" > "$outdir/new_IMGT/7_V-REGION-mutation-and-AA-change-table.txt"
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84 cat "`find $PWD/files/ -name "8_*"`" > "$outdir/new_IMGT/8_V-REGION-nt-mutation-statistics.txt"
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85 cat "`find $PWD/files/ -name "9_*"`" > "$outdir/new_IMGT/9_V-REGION-AA-change-statistics.txt"
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86 cat "`find $PWD/files/ -name "10_*"`" > "$outdir/new_IMGT/10_V-REGION-mutation-hotspots.txt"
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88 mkdir $outdir/new_IMGT_IGA
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89 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA
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91 mkdir $outdir/new_IMGT_IGA1
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92 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA1
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94 mkdir $outdir/new_IMGT_IGA2
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95 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA2
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97 mkdir $outdir/new_IMGT_IGG
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98 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG
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100 mkdir $outdir/new_IMGT_IGG1
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101 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG1
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103 mkdir $outdir/new_IMGT_IGG2
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104 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG2
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106 mkdir $outdir/new_IMGT_IGG3
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107 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG3
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109 mkdir $outdir/new_IMGT_IGG4
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110 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG4
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112 mkdir $outdir/new_IMGT_IGM
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113 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGM
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115 mkdir $outdir/new_IMGT_IGE
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116 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGE
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118 Rscript $dir/new_imgt.r $outdir/new_IMGT/ $outdir/merged.txt "-" 2>&1
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119
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120 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA/ $outdir/merged.txt "IGA" 2>&1
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121 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA1/ $outdir/merged.txt "IGA1" 2>&1
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122 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA2/ $outdir/merged.txt "IGA2" 2>&1
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124 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG/ $outdir/merged.txt "IGG" 2>&1
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125 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG1/ $outdir/merged.txt "IGG1" 2>&1
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126 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG2/ $outdir/merged.txt "IGG2" 2>&1
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127 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG3/ $outdir/merged.txt "IGG3" 2>&1
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128 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG4/ $outdir/merged.txt "IGG4" 2>&1
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129
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130 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGM/ $outdir/merged.txt "IGM" 2>&1
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132 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGE/ $outdir/merged.txt "IGE" 2>&1
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135 tmp="$PWD"
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136 cd $outdir/new_IMGT/ #tar weirdness...
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137 tar -cJf ../new_IMGT.txz *
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138
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139 cd $outdir/new_IMGT_IGA/
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140 tar -cJf ../new_IMGT_IGA.txz *
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141
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142 cd $outdir/new_IMGT_IGA1/
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143 tar -cJf ../new_IMGT_IGA1.txz *
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145 cd $outdir/new_IMGT_IGA2/
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146 tar -cJf ../new_IMGT_IGA2.txz *
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148 cd $outdir/new_IMGT_IGG/
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149 tar -cJf ../new_IMGT_IGG.txz *
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151 cd $outdir/new_IMGT_IGG1/
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152 tar -cJf ../new_IMGT_IGG1.txz *
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154 cd $outdir/new_IMGT_IGG2/
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155 tar -cJf ../new_IMGT_IGG2.txz *
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156
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157 cd $outdir/new_IMGT_IGG3/
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158 tar -cJf ../new_IMGT_IGG3.txz *
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159
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160 cd $outdir/new_IMGT_IGG4/
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161 tar -cJf ../new_IMGT_IGG4.txz *
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162
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163 cd $outdir/new_IMGT_IGM/
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164 tar -cJf ../new_IMGT_IGM.txz *
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166 cd $outdir/new_IMGT_IGE/
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167 tar -cJf ../new_IMGT_IGE.txz *
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169 cd $tmp
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170 fi
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171
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davidvanzessen
parents:
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172 echo "---------------- shm_csr.r ----------------"
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davidvanzessen
parents:
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173 echo "---------------- shm_csr.r ----------------<br />" >> $log
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davidvanzessen
parents:
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174
5
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davidvanzessen
parents: 4
diff changeset
175 classes="IGA,IGA1,IGA2,IGG,IGG1,IGG2,IGG3,IGG4,IGM,IGE,unmatched"
0
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davidvanzessen
parents:
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176 echo "R mutation analysis"
1
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davidvanzessen
parents: 0
diff changeset
177 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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178
43
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davidvanzessen
parents: 42
diff changeset
179 echo "---------------- plot_pdfs.r ----------------"
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davidvanzessen
parents: 42
diff changeset
180 echo "---------------- plot_pdfs.r ----------------<br />" >> $log
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davidvanzessen
parents: 42
diff changeset
181
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davidvanzessen
parents: 42
diff changeset
182 echo "Rscript $dir/shm_csr.r $outdir/pdfplots.RData $outdir 2>&1"
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davidvanzessen
parents: 42
diff changeset
183
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davidvanzessen
parents: 42
diff changeset
184 Rscript $dir/plot_pdf.r "$outdir/pdfplots.RData" "$outdir" 2>&1
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davidvanzessen
parents: 42
diff changeset
185
0
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davidvanzessen
parents:
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186 echo "---------------- shm_csr.py ----------------"
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davidvanzessen
parents:
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187 echo "---------------- shm_csr.py ----------------<br />" >> $log
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davidvanzessen
parents:
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188
1
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davidvanzessen
parents: 0
diff changeset
189 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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190
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davidvanzessen
parents:
diff changeset
191 echo "---------------- aa_histogram.r ----------------"
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davidvanzessen
parents:
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192 echo "---------------- aa_histogram.r ----------------<br />" >> $log
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davidvanzessen
parents:
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193
5
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davidvanzessen
parents: 4
diff changeset
194 Rscript $dir/aa_histogram.r $outdir/aa_id_mutations.txt $outdir/absent_aa_id.txt "IGA,IGG,IGM,IGE" $outdir/ 2>&1
0
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davidvanzessen
parents:
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195 if [ -e "$outdir/aa_histogram_.png" ]; then
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davidvanzessen
parents:
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196 mv $outdir/aa_histogram_.png $outdir/aa_histogram.png
42
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davidvanzessen
parents: 41
diff changeset
197 mv $outdir/aa_histogram_.pdf $outdir/aa_histogram.pdf
0
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davidvanzessen
parents:
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198 mv $outdir/aa_histogram_.txt $outdir/aa_histogram.txt
29
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davidvanzessen
parents: 28
diff changeset
199 mv $outdir/aa_histogram_absent_.txt $outdir/aa_histogram_absent.txt
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davidvanzessen
parents: 28
diff changeset
200 mv $outdir/aa_histogram_count_.txt $outdir/aa_histogram_count.txt
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davidvanzessen
parents: 28
diff changeset
201 mv $outdir/aa_histogram_sum_.txt $outdir/aa_histogram_sum.txt
0
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davidvanzessen
parents:
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202 fi
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davidvanzessen
parents:
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203
5
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davidvanzessen
parents: 4
diff changeset
204 genes=(IGA IGA1 IGA2 IGG IGG1 IGG2 IGG3 IGG4 IGM IGE)
0
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davidvanzessen
parents:
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205
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davidvanzessen
parents:
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206 funcs=(sum mean median)
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davidvanzessen
parents:
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207 funcs=(sum)
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davidvanzessen
parents:
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208
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davidvanzessen
parents:
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209 echo "---------------- sequence_overview.r ----------------"
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davidvanzessen
parents:
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210 echo "---------------- sequence_overview.r ----------------<br />" >> $log
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davidvanzessen
parents:
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211
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davidvanzessen
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212 mkdir $outdir/sequence_overview
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213
7
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diff changeset
214 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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215
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davidvanzessen
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216 echo "<table border='1'>" > $outdir/base_overview.html
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davidvanzessen
parents:
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217
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davidvanzessen
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218 while IFS=$'\t' read ID class seq A C G T
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davidvanzessen
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219 do
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220 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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221 done < $outdir/sequence_overview/ntoverview.txt
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davidvanzessen
parents:
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222
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davidvanzessen
parents:
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223 echo "<html><center><h1>$title</h1></center>" > $output
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davidvanzessen
parents:
diff changeset
224 echo "<meta name='viewport' content='width=device-width, initial-scale=1'>" >> $output
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davidvanzessen
parents:
diff changeset
225 echo "<script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $output
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davidvanzessen
parents:
diff changeset
226 echo "<script type='text/javascript' src='tabber.js'></script>" >> $output
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davidvanzessen
parents:
diff changeset
227 echo "<script type='text/javascript' src='script.js'></script>" >> $output
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davidvanzessen
parents:
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228 echo "<link rel='stylesheet' type='text/css' href='style.css'>" >> $output
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davidvanzessen
parents:
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229 echo "<link rel='stylesheet' type='text/css' href='pure-min.css'>" >> $output
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davidvanzessen
parents:
diff changeset
230
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davidvanzessen
parents:
diff changeset
231 matched_count="`cat $outdir/merged.txt | grep -v 'unmatched' | tail -n +2 | wc -l`"
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davidvanzessen
parents:
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232 unmatched_count="`cat $outdir/unmatched.txt | tail -n +2 | wc -l`"
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davidvanzessen
parents:
diff changeset
233 total_count=$((matched_count + unmatched_count))
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davidvanzessen
parents:
diff changeset
234 perc_count=$((unmatched_count / total_count * 100))
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davidvanzessen
parents:
diff changeset
235 perc_count=`bc -l <<< "scale=2; ${unmatched_count} / ${total_count} * 100"`
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davidvanzessen
parents:
diff changeset
236 perc_count=`bc -l <<< "scale=2; (${unmatched_count} / ${total_count} * 100 ) / 1"`
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davidvanzessen
parents:
diff changeset
237
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davidvanzessen
parents:
diff changeset
238 echo "<center><h2>Total: ${total_count}</h2></center>" >> $output
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davidvanzessen
parents:
diff changeset
239 echo "<center><h2>Matched: ${matched_count} Unmatched: ${unmatched_count}</h2></center>" >> $output
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davidvanzessen
parents:
diff changeset
240 echo "<center><h2>Percentage unmatched: ${perc_count}</h2></center>" >> $output
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davidvanzessen
parents:
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241
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davidvanzessen
parents:
diff changeset
242 echo "---------------- main tables ----------------"
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davidvanzessen
parents:
diff changeset
243 echo "---------------- main tables ----------------<br />" >> $log
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davidvanzessen
parents:
diff changeset
244
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davidvanzessen
parents:
diff changeset
245 echo "<div class='tabber'>" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
246 echo "<div class='tabbertab' title='SHM Overview' style='width: 3000px;'>" >> $output
0
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davidvanzessen
parents:
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247
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davidvanzessen
parents:
diff changeset
248 for func in ${funcs[@]}
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davidvanzessen
parents:
diff changeset
249 do
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davidvanzessen
parents:
diff changeset
250
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davidvanzessen
parents:
diff changeset
251 echo "---------------- $func table ----------------"
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davidvanzessen
parents:
diff changeset
252 echo "---------------- $func table ----------------<br />" >> $log
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davidvanzessen
parents:
diff changeset
253
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davidvanzessen
parents:
diff changeset
254 cat $outdir/mutations_${func}.txt $outdir/hotspot_analysis_${func}.txt > $outdir/data_${func}.txt
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davidvanzessen
parents:
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255
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davidvanzessen
parents:
diff changeset
256 echo "---------------- pattern_plots.r ----------------"
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davidvanzessen
parents:
diff changeset
257 echo "---------------- pattern_plots.r ----------------<br />" >> $log
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davidvanzessen
parents:
diff changeset
258
43
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davidvanzessen
parents: 42
diff changeset
259 Rscript $dir/pattern_plots.r $outdir/data_${func}.txt $outdir/aid_motives $outdir/relative_mutations $outdir/absolute_mutations $outdir/shm_overview.txt 2>&1
0
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davidvanzessen
parents:
diff changeset
260
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davidvanzessen
parents:
diff changeset
261 echo "<table class='pure-table pure-table-striped'>" >> $output
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davidvanzessen
parents:
diff changeset
262 echo "<thead><tr><th>info</th>" >> $output
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davidvanzessen
parents:
diff changeset
263
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davidvanzessen
parents:
diff changeset
264 if [ "${class_filter}" != "101_101" ] ; then
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davidvanzessen
parents:
diff changeset
265
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davidvanzessen
parents:
diff changeset
266 for gene in ${genes[@]}
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davidvanzessen
parents:
diff changeset
267 do
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davidvanzessen
parents:
diff changeset
268 tmp=`cat $outdir/${gene}_${func}_n.txt`
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davidvanzessen
parents:
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269 echo "<th><a href='matched_${gene}_${func}.txt'>${gene} (N = $tmp)</a></th>" >> $output
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davidvanzessen
parents:
diff changeset
270 done
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davidvanzessen
parents:
diff changeset
271
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davidvanzessen
parents:
diff changeset
272 tmp=`cat $outdir/all_${func}_n.txt`
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davidvanzessen
parents:
diff changeset
273 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
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davidvanzessen
parents:
diff changeset
274 tmp=`cat $outdir/unmatched_${func}_n.txt`
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davidvanzessen
parents:
diff changeset
275 echo "<th><a href='unmatched.txt'>unmatched (N = ${unmatched_count})</a></th><tr></thead>" >> $output
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davidvanzessen
parents:
diff changeset
276
5
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davidvanzessen
parents: 4
diff changeset
277 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
0
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davidvanzessen
parents:
diff changeset
278 do
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davidvanzessen
parents:
diff changeset
279 if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] ; then #meh
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
280 echo "<tr><td>$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>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
281 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
282 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>" >> $output
0
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davidvanzessen
parents:
diff changeset
283 else
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
284 echo "<tr><td>$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
285 fi
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davidvanzessen
parents:
diff changeset
286 done < $outdir/data_${func}.txt
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davidvanzessen
parents:
diff changeset
287
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davidvanzessen
parents:
diff changeset
288 else
3
275ab5175fd6 Uploaded
davidvanzessen
parents: 2
diff changeset
289 tmp=`cat $outdir/all_${func}_n.txt`
0
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davidvanzessen
parents:
diff changeset
290 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
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davidvanzessen
parents:
diff changeset
291
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
292 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
0
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davidvanzessen
parents:
diff changeset
293 do
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davidvanzessen
parents:
diff changeset
294 if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] ; then #meh
3
275ab5175fd6 Uploaded
davidvanzessen
parents: 2
diff changeset
295 echo "<tr><td>$name</td><td>${allx}/${ally}</td></tr>" >> $output
0
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davidvanzessen
parents:
diff changeset
296 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
3
275ab5175fd6 Uploaded
davidvanzessen
parents: 2
diff changeset
297 echo "<tr><td>$name</td><td>${allz}%</td></tr>" >> $output
0
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davidvanzessen
parents:
diff changeset
298 else
3
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davidvanzessen
parents: 2
diff changeset
299 echo "<tr><td>$name</td><td>${allx}/${ally} (${allz}%)</td></tr>" >> $output
0
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davidvanzessen
parents:
diff changeset
300 fi
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davidvanzessen
parents:
diff changeset
301 done < $outdir/data_${func}.txt
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davidvanzessen
parents:
diff changeset
302
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davidvanzessen
parents:
diff changeset
303 fi
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davidvanzessen
parents:
diff changeset
304 echo "</table>" >> $output
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davidvanzessen
parents:
diff changeset
305 #echo "<a href='data_${func}.txt'>Download data</a>" >> $output
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davidvanzessen
parents:
diff changeset
306 done
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davidvanzessen
parents:
diff changeset
307
42
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davidvanzessen
parents: 41
diff changeset
308 echo "<a href='aid_motives.pdf'><img src='aid_motives.png' /></a><br />" >> $output
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davidvanzessen
parents: 41
diff changeset
309 echo "<a href='relative_mutations.pdf'><img src='relative_mutations.png' /></a><br />" >> $output
43
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davidvanzessen
parents: 42
diff changeset
310 echo "<a href='absolute_mutations.pdf'><img src='absolute_mutations.png' /></a><br />" >> $output
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
311 echo "<br />" >> $output
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davidvanzessen
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diff changeset
312 cat $dir/shm_overview.htm >> $output
0
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davidvanzessen
parents:
diff changeset
313 echo "</div>" >> $output #SHM overview tab end
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davidvanzessen
parents:
diff changeset
314
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davidvanzessen
parents:
diff changeset
315 echo "---------------- images ----------------"
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davidvanzessen
parents:
diff changeset
316 echo "---------------- images ----------------<br />" >> $log
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davidvanzessen
parents:
diff changeset
317
42
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davidvanzessen
parents: 41
diff changeset
318 echo "<div class='tabbertab' title='SHM Frequency' style='width: 3000px;'></a>" >> $output
0
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davidvanzessen
parents:
diff changeset
319
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davidvanzessen
parents:
diff changeset
320 if [ -a $outdir/scatter.png ]
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davidvanzessen
parents:
diff changeset
321 then
42
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davidvanzessen
parents: 41
diff changeset
322 echo "<a href='scatter.pdf'><img src='scatter.png'/><br />" >> $output
0
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davidvanzessen
parents:
diff changeset
323 fi
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davidvanzessen
parents:
diff changeset
324 if [ -a $outdir/frequency_ranges.png ]
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davidvanzessen
parents:
diff changeset
325 then
42
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davidvanzessen
parents: 41
diff changeset
326 echo "<a href='frequency_ranges.pdf'><img src='frequency_ranges.png'/></a><br />" >> $output
0
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davidvanzessen
parents:
diff changeset
327 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
328
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
329 echo "<br />" >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
330 cat $dir/shm_frequency.htm >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
331
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
332 echo "</div>" >> $output #SHM frequency tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
333
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
334 echo "<div class='tabbertab' title='Transition tables' style='width: 3000px;'>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
335
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
336 echo "<table border='0'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
337
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
338 for gene in ${genes[@]}
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
339 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
340 echo "<tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
341 echo "<td><h1>${gene}</h1></td>" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
342
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
343 if [ -e $outdir/transitions_heatmap_${gene}.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
344 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
345 echo "<td><a href='transitions_heatmap_${gene}.pdf'><img src='transitions_heatmap_${gene}.png' /></a></td>" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
346 else
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
347 echo "<td></td>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
348 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
349
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
350 if [ -e $outdir/transitions_stacked_${gene}.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
351 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
352 echo "<td><a href='transitions_stacked_${gene}.pdf'><img src='transitions_stacked_${gene}.png' /></a></td>" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
353 else
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
354 echo "<td></td>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
355 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
356
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
357 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
358 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
359 first="true"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
360 while IFS=, read from a c g t
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
361 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
362 if [ "$first" == "true" ] ; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
363 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
364 first="false"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
365 else
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
366 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
367 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
368 done < $outdir/transitions_${gene}_sum.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
369 echo "</table></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
370
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
371 echo "</tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
372 done
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
373
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
374 echo "<tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
375 echo "<td><h1>All</h1></td>" >> $output
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
376 echo "<td><a href='transitions_heatmap_all.pdf'><img src='transitions_heatmap_all.png' /></a></td>" >> $output
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
377 echo "<td><a href='transitions_stacked_all.pdf'><img src='transitions_stacked_all.png' /></a></td>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
378 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
379 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
380 first="true"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
381 while IFS=, read from a c g t
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
382 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
383 if [ "$first" == "true" ] ; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
384 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
385 first="false"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
386 else
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
387 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
388 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
389 done < $outdir/transitions_all_sum.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
390 echo "</table></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
391
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
392 echo "</tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
393
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
394 echo "</table>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
395
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
396 echo "<br />" >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
397 cat $dir/shm_transition.htm >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
398
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
399 echo "</div>" >> $output #transition tables tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
400
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
401 echo "<div class='tabbertab' title='Antigen Selection'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
402
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
403 if [ -e $outdir/aa_histogram.png ]
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
404 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
405 echo "<a href='aa_histogram.pdf'><img src='aa_histogram.png'/></a><br />" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
406 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
407
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
408 if [ -e $outdir/aa_histogram_IGA.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
409 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
410 echo "<a href='aa_histogram_IGA.pdf'><img src='aa_histogram_IGA.png'/></a><br />" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
411 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
412
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
413 if [ -e $outdir/aa_histogram_IGG.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
414 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
415 echo "<a href='aa_histogram_IGG.pdf'><img src='aa_histogram_IGG.png'/></a><br />" >> $output
23
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/aa_histogram_IGM.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
419 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
420 echo "<a href='aa_histogram_IGM.pdf'><img src='aa_histogram_IGM.png'/></a><br />" >> $output
23
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/aa_histogram_IGE.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
424 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
425 echo "<a href='aa_histogram_IGE.pdf'><img src='aa_histogram_IGE.png'/></a><br />" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
426 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
427
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
428
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
429
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
430 if [[ "$fast" == "no" ]] ; then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
431
41
b8ac74723ab0 Uploaded
davidvanzessen
parents: 40
diff changeset
432
b8ac74723ab0 Uploaded
davidvanzessen
parents: 40
diff changeset
433
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
434 echo "---------------- baseline ----------------"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
435 echo "---------------- baseline ----------------<br />" >> $log
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
436 tmp="$PWD"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
437
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
438 mkdir $outdir/baseline
37
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
439
41
b8ac74723ab0 Uploaded
davidvanzessen
parents: 40
diff changeset
440 echo "<center><h1>BASELINe</h1>" >> $output
b8ac74723ab0 Uploaded
davidvanzessen
parents: 40
diff changeset
441 header_substring="Based on CDR1, FR2, CDR2, FR3 (27:27:38:55:65:104:-)"
b8ac74723ab0 Uploaded
davidvanzessen
parents: 40
diff changeset
442
37
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
443 baseline_boundaries="27:27:38:55:65:104:-"
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
444
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
445 if [[ "${empty_region_filter}" == "leader" ]] ; then
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
446 baseline_boundaries="1:26:38:55:65:104:-"
41
b8ac74723ab0 Uploaded
davidvanzessen
parents: 40
diff changeset
447 header_substring="Based on FR1, CDR1, FR2, CDR2, FR3 (1:26:38:55:65:104,-)"
37
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
448 fi
41
b8ac74723ab0 Uploaded
davidvanzessen
parents: 40
diff changeset
449
b8ac74723ab0 Uploaded
davidvanzessen
parents: 40
diff changeset
450 echo "<p>${header_substring}</p></center>" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
451
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
452 mkdir $outdir/baseline/IGA_IGG_IGM
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
453 if [[ $(wc -l < $outdir/new_IMGT/1_Summary.txt) -gt "1" ]]; then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
454 cd $outdir/baseline/IGA_IGG_IGM
41
b8ac74723ab0 Uploaded
davidvanzessen
parents: 40
diff changeset
455 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT.txz "IGA_IGG_IGM_IGE" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt"
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
456 else
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
457 echo "No sequences" > "$outdir/baseline.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/IGA
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
461 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
462 cd $outdir/baseline/IGA
37
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
463 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT_IGA.txz "IGA" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGA.pdf" "Sequence.ID" "$outdir/baseline_IGA.txt"
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
464 else
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
465 echo "No IGA sequences" > "$outdir/baseline_IGA.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 mkdir $outdir/baseline/IGG
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
469 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
470 cd $outdir/baseline/IGG
37
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
471 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
472 else
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
473 echo "No IGG sequences" > "$outdir/baseline_IGG.txt"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
474 fi
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
475
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
476 mkdir $outdir/baseline/IGM
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
477 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
478 cd $outdir/baseline/IGM
37
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
479 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
480 else
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
481 echo "No IGM sequences" > "$outdir/baseline_IGM.txt"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
482 fi
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
483
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
484 mkdir $outdir/baseline/IGE
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
485 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
486 cd $outdir/baseline/IGE
37
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
487 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
488 else
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
489 echo "No IGE sequences" > "$outdir/baseline_IGE.txt"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
490 fi
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
491
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
492 cd $tmp
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
493
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
494 echo "Cleaning up *.RData files"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
495 find $outdir/baseline -name "*.RData" -type f -delete
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
496
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
497 if [ -e $outdir/baseline.pdf ]
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
498 then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
499 echo "<embed src='baseline.pdf' width='700px' height='1000px'>" >> $output
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
500 fi
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
501
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
502 if [ -e $outdir/baseline_IGA.pdf ]
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
503 then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
504 echo "<embed src='baseline_IGA.pdf' width='700px' height='1000px'>" >> $output
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
505 fi
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
506
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
507 if [ -e $outdir/baseline_IGG.pdf ]
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
508 then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
509 echo "<embed src='baseline_IGG.pdf' width='700px' height='1000px'>" >> $output
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
510 fi
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
511
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
512 if [ -e $outdir/baseline_IGM.pdf ]
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
513 then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
514 echo "<embed src='baseline_IGM.pdf' width='700px' height='1000px'>" >> $output
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
515 fi
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
516
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
517 if [ -e $outdir/baseline_IGE.pdf ]
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
518 then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
519 echo "<embed src='baseline_IGE.pdf' width='700px' height='1000px'>" >> $output
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
520 fi
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
521 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
522
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
523 echo "<br />" >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
524 cat $dir/shm_selection.htm >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
525
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
526 echo "</div>" >> $output #antigen selection tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
527
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
528 echo "<div class='tabbertab' title='CSR'>" >> $output #CSR tab
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
529
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
530 if [ -e $outdir/IGA.png ]
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
531 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
532 echo "<a href='IGA.pdf'><img src='IGA.png'/></a><br />" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
533 fi
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
534 if [ -e $outdir/IGG.png ]
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
535 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
536 echo "<a href='IGG.pdf'><img src='IGG.png'/></a><br />" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
537 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
538
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
539 echo "<br />" >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
540 cat $dir/shm_csr.htm >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
541
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
542 echo "</div>" >> $output #CSR tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
543
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
544 if [[ "$fast" == "no" ]] ; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
545
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
546 echo "---------------- change-o MakeDB ----------------"
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
547
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
548 mkdir $outdir/change_o
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
549
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
550 tmp="$PWD"
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
551
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
552 cd $outdir/change_o
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
553
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
554 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
555 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
556
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
557 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
558
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
559 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
560
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
561 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
562 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
563 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 $outdir/change_o/change-o-defined_clones-summary-IGA.txt
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
564 else
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
565 echo "No IGA sequences" > "$outdir/change_o/change-o-db-defined_clones-IGA.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
566 echo "No IGA sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGA.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
567 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
568
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
569 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
570 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
571 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 $outdir/change_o/change-o-defined_clones-summary-IGG.txt
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
572 else
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
573 echo "No IGG sequences" > "$outdir/change_o/change-o-db-defined_clones-IGG.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
574 echo "No IGG sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGG.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
575 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
576
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
577 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
578 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
579 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 $outdir/change_o/change-o-defined_clones-summary-IGM.txt
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
580 else
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
581 echo "No IGM sequences" > "$outdir/change_o/change-o-db-defined_clones-IGM.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
582 echo "No IGM sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGM.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
583 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
584
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
585 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
586 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
587 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 $outdir/change_o/change-o-defined_clones-summary-IGE.txt
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
588 else
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
589 echo "No IGE sequences" > "$outdir/change_o/change-o-db-defined_clones-IGE.txt"
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
590 echo "No IGE sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGE.txt"
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
591 fi
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
592
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
593 PWD="$tmp"
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
594
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
595 echo "<div class='tabbertab' title='Clonal Relation' style='width: 7000px;'>" >> $output #clonality tab
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
596
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
597 function clonality_table {
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
598 local infile=$1
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
599 local outfile=$2
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
600
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
601 echo "<table class='pure-table pure-table-striped'>" >> $outfile
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
602 echo "<thead><tr><th>Clone size</th><th>Nr of clones</th><th>Nr of sequences</th></tr></thead>" >> $outfile
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
603
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
604 first='true'
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
605
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
606 while read size clones seqs
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
607 do
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
608 if [[ "$first" == "true" ]]; then
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
609 first="false"
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
610 continue
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
611 fi
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
612 echo "<tr><td>$size</td><td>$clones</td><td>$seqs</td></tr>" >> $outfile
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
613 done < $infile
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
614
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
615 echo "</table>" >> $outfile
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
616 }
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
617 echo "<div class='tabber'>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
618
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
619 echo "<div class='tabbertab' title='All'>" >> $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
620 clonality_table $outdir/change_o/change-o-defined_clones-summary.txt $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
621 echo "</div>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
622
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
623 echo "<div class='tabbertab' title='IGA'>" >> $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
624 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGA.txt $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
625 echo "</div>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
626
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
627 echo "<div class='tabbertab' title='IGG'>" >> $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
628 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGG.txt $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
629 echo "</div>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
630
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
631 echo "<div class='tabbertab' title='IGM'>" >> $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
632 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
633 echo "</div>" >> $output
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
634
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
635 echo "<div class='tabbertab' title='IGE'>" >> $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
636 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
637 echo "</div>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
638
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
639 echo "<div class='tabbertab' title='Overlap' style='width: 7000px;'>" >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
640 cat "$outdir/sequence_overview/index.html" | sed -e 's:</td>:</td>\n:g' | sed "s:href='\(.*\).html:href='sequence_overview/\1.html:g" >> $output # rewrite href to 'sequence_overview/..."
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
641 echo "</div>" >> $output
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
642
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
643 echo "</div>" >> $output #clonality tabber end
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
644
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
645 echo "<br />" >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
646 cat $dir/shm_clonality.htm >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
647
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
648 echo "</div>" >> $output #clonality tab end
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
649
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
650 fi
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
651
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
652 echo "<div class='tabbertab' title='Downloads'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
653
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
654 echo "<table class='pure-table pure-table-striped'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
655 echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
656 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
657 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
658 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
659
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
660 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Overview</td></tr>" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
661 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
662 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
663 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
664 echo "<tr><td>Base count for every sequence</td><td><a href='base_overview.html'>View</a></td></tr>" >> $output
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
665 echo "<tr><td>The data used to generate the percentage of mutations in AID and pol eta motives plot</td><td><a href='aid_motives.txt' download='aid_motives.txt' >Download</a></td></tr>" >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
666 echo "<tr><td>The data used to generate the relative mutation patterns plot</td><td><a href='relative_mutations.txt' download='relative_mutations.txt' >Download</a></td></tr>" >> $output
43
77a7ac76c7b9 Uploaded
davidvanzessen
parents: 42
diff changeset
667 echo "<tr><td>The data used to generate the absolute mutation patterns plot</td><td><a href='absolute_mutations.txt' download='absolute_mutations.txt' >Download</a></td></tr>" >> $output
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
668
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
669 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Frequency</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
670 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
671 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
672 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
673
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
674 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Transition Tables</td></tr>" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
675 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
676 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
677 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
678 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
679 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
680 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
681 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
682 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
683 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
684 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
685 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
686
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
687 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Antigen Selection</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
688 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
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
689 echo "<tr><td>Presence of AA per sequence ID</td><td><a href='absent_aa_id.txt' download='absent_aa_id.txt' >Download</a></td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
690
29
80c4eebf7bc9 Uploaded
davidvanzessen
parents: 28
diff changeset
691 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
692 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
693 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
694 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
695 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
696
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
697 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
698 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
699 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
700 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
701 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
702 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
703 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
704 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
705 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
706 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
707
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
708 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>CSR</td></tr>" >> $output
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
709 echo "<tr><td>The data for the IGA subclass distribution plot</td><td><a href='IGA_pie.txt' download='IGA_pie.txt' >Download</a></td></tr>" >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
710 echo "<tr><td>The data for the IGG subclass distribution plot</td><td><a href='IGG_pie.txt' download='IGG_pie.txt' >Download</a></td></tr>" >> $output
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
711
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
712 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Clonal Relation</td></tr>" >> $output
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
713 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
714 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
715 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
716 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
717 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
718 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
719 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
720 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
721 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
722 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
723 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
724
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
725 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Filtered IMGT output files</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
726 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
727 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
728 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
729 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
730 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
731 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
732 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
733 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
734 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
735 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
736 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
737
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
738 echo "</table>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
739
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
740 echo "<br />" >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
741 cat $dir/shm_downloads.htm >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
742
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
743 echo "</div>" >> $output #downloads tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
744
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
745 echo "</div>" >> $output #tabs end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
746
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
747 echo "</html>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
748
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
749
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
750 echo "---------------- naive_output.r ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
751 echo "---------------- naive_output.r ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
752
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
753 if [[ "$naive_output" == "yes" ]]
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
754 then
28
c0ecc31829bd Uploaded
davidvanzessen
parents: 26
diff changeset
755 echo "output naive output"
18
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
756 if [[ "${class_filter}" == "101_101" ]]
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
757 then
28
c0ecc31829bd Uploaded
davidvanzessen
parents: 26
diff changeset
758 echo "copy new_IMGT.txz to ${naive_output_all}"
21
c281993e515b Uploaded
davidvanzessen
parents: 20
diff changeset
759 cp $outdir/new_IMGT.txz ${naive_output_all}
18
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
760 else
28
c0ecc31829bd Uploaded
davidvanzessen
parents: 26
diff changeset
761 echo "copy for classes"
18
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
762 cp $outdir/new_IMGT_IGA.txz ${naive_output_ca}
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
763 cp $outdir/new_IMGT_IGG.txz ${naive_output_cg}
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
764 cp $outdir/new_IMGT_IGM.txz ${naive_output_cm}
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
765 cp $outdir/new_IMGT_IGE.txz ${naive_output_ce}
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
766 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
767 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
768
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
769 echo "</table>" >> $outdir/base_overview.html
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
770
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
771 mv $log $outdir/log.html
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
772
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
773 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
774 echo "<table border = 1>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
775 echo "<thead><tr><th>Info</th><th>Sequences</th><th>Percentage</th></tr></thead>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
776 tIFS="$TMP"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
777 IFS=$'\t'
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
778 while read step seq perc
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
779 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
780 echo "<tr>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
781 echo "<td>$step</td>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
782 echo "<td>$seq</td>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
783 echo "<td>${perc}%</td>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
784 echo "</tr>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
785 done < $outdir/filtering_steps.txt
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
786 echo "</table>" >> $log
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
787 echo "<br />" >> $log
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
788 cat $dir/shm_first.htm >> $log
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
789 echo "</center></html>" >> $log
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
790
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
791 IFS="$tIFS"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
792
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
793
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
794 echo "---------------- Done! ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
795 echo "---------------- Done! ----------------<br />" >> $outdir/log.html
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
796
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
797
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
798
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
799
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
800
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
801
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
802
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
803
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
804
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
805
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
806
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
807
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
808
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
809
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
810
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
811
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
812
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
813
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
814
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
815
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
816