annotate wrapper.sh @ 53:3be28ac82909 draft

Uploaded
author davidvanzessen
date Wed, 24 May 2017 04:26:04 -0400
parents f5fe63533c58
children 6cd12c71c3d3
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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=${15}
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20 filter_unique_count=${16}
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21 class_filter=${17}
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22 empty_region_filter=${18}
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23 fast=${19}
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24
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25 mkdir $outdir
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26
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27 tar -xzf $dir/style.tar.gz -C $outdir
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28
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29 echo "---------------- read parameters ----------------"
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30 echo "---------------- read parameters ----------------<br />" > $log
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31
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32 echo "unpacking IMGT file"
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33
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34 type="`file $input`"
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35 if [[ "$type" == *"Zip archive"* ]] ; then
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36 echo "Zip archive"
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37 echo "unzip $input -d $PWD/files/"
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38 unzip $input -d $PWD/files/
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39 elif [[ "$type" == *"XZ compressed data"* ]] ; then
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40 echo "ZX archive"
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41 echo "tar -xJf $input -C $PWD/files/"
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42 mkdir -p "$PWD/files/$title"
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43 tar -xJf $input -C "$PWD/files/$title"
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44 fi
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45
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46 cat "`find $PWD/files/ -name "1_*"`" > $PWD/summary.txt
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47 cat "`find $PWD/files/ -name "3_*"`" > $PWD/sequences.txt
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48 cat "`find $PWD/files/ -name "4_*"`" > $PWD/gapped_aa.txt
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49 cat "`find $PWD/files/ -name "5_*"`" > $PWD/aa.txt
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50 cat "`find $PWD/files/ -name "6_*"`" > $PWD/junction.txt
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51 cat "`find $PWD/files/ -name "7_*"`" > $PWD/mutationanalysis.txt
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52 cat "`find $PWD/files/ -name "8_*"`" > $PWD/mutationstats.txt
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53 cat "`find $PWD/files/ -name "10_*"`" > $PWD/hotspots.txt
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54
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55 if [[ ${#BLASTN_DIR} -ge 5 ]] ; then
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56 echo "On server, using BLASTN_DIR env: ${BLASTN_DIR}"
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57 else
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58 BLASTN_DIR="/home/galaxy/Downloads/ncbi-blast-2.4.0+/bin"
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59 echo "Dev Galaxy set BLASTN_DIR to: ${BLASTN_DIR}"
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60 fi
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61
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62 echo "---------------- class identification ----------------"
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63 echo "---------------- class identification ----------------<br />" >> $log
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64
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65 python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt
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67 echo "---------------- merge_and_filter.r ----------------"
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68 echo "---------------- merge_and_filter.r ----------------<br />" >> $log
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69
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70 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt "$PWD/gapped_aa.txt" $outdir/identified_genes.txt $outdir/merged.txt $outdir/before_unique_filter.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${filter_unique_count} ${class_filter} ${empty_region_filter} 2>&1
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72 if [[ "$fast" == "no" ]] ; then
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73
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74 echo "---------------- creating new IMGT zips ----------------"
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75 echo "---------------- creating new IMGT zips ----------------<br />" >> $log
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77 mkdir $outdir/new_IMGT
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79 cat "`find $PWD/files/ -name "1_*"`" > "$outdir/new_IMGT/1_Summary.txt"
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80 cat "`find $PWD/files/ -name "2_*"`" > "$outdir/new_IMGT/2_IMGT-gapped-nt-sequences.txt"
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81 cat "`find $PWD/files/ -name "3_*"`" > "$outdir/new_IMGT/3_Nt-sequences.txt"
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82 cat "`find $PWD/files/ -name "4_*"`" > "$outdir/new_IMGT/4_IMGT-gapped-AA-sequences.txt"
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83 cat "`find $PWD/files/ -name "5_*"`" > "$outdir/new_IMGT/5_AA-sequences.txt"
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84 cat "`find $PWD/files/ -name "6_*"`" > "$outdir/new_IMGT/6_Junction.txt"
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85 cat "`find $PWD/files/ -name "7_*"`" > "$outdir/new_IMGT/7_V-REGION-mutation-and-AA-change-table.txt"
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86 cat "`find $PWD/files/ -name "8_*"`" > "$outdir/new_IMGT/8_V-REGION-nt-mutation-statistics.txt"
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87 cat "`find $PWD/files/ -name "9_*"`" > "$outdir/new_IMGT/9_V-REGION-AA-change-statistics.txt"
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88 cat "`find $PWD/files/ -name "10_*"`" > "$outdir/new_IMGT/10_V-REGION-mutation-hotspots.txt"
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90 mkdir $outdir/new_IMGT_IGA
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91 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA
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93 mkdir $outdir/new_IMGT_IGA1
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94 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA1
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96 mkdir $outdir/new_IMGT_IGA2
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97 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA2
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99 mkdir $outdir/new_IMGT_IGG
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100 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG
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102 mkdir $outdir/new_IMGT_IGG1
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103 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG1
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105 mkdir $outdir/new_IMGT_IGG2
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106 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG2
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108 mkdir $outdir/new_IMGT_IGG3
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109 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG3
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111 mkdir $outdir/new_IMGT_IGG4
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112 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG4
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114 mkdir $outdir/new_IMGT_IGM
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115 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGM
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117 mkdir $outdir/new_IMGT_IGE
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118 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGE
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120 Rscript $dir/new_imgt.r $outdir/new_IMGT/ $outdir/merged.txt "-" 2>&1
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122 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA/ $outdir/merged.txt "IGA" 2>&1
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123 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA1/ $outdir/merged.txt "IGA1" 2>&1
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124 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA2/ $outdir/merged.txt "IGA2" 2>&1
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126 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG/ $outdir/merged.txt "IGG" 2>&1
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127 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG1/ $outdir/merged.txt "IGG1" 2>&1
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128 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG2/ $outdir/merged.txt "IGG2" 2>&1
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129 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG3/ $outdir/merged.txt "IGG3" 2>&1
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130 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG4/ $outdir/merged.txt "IGG4" 2>&1
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131
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132 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGM/ $outdir/merged.txt "IGM" 2>&1
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133
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134 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGE/ $outdir/merged.txt "IGE" 2>&1
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137 tmp="$PWD"
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138 cd $outdir/new_IMGT/ #tar weirdness...
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139 tar -cJf ../new_IMGT.txz *
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141 cd $outdir/new_IMGT_IGA/
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142 tar -cJf ../new_IMGT_IGA.txz *
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144 cd $outdir/new_IMGT_IGA1/
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145 tar -cJf ../new_IMGT_IGA1.txz *
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147 cd $outdir/new_IMGT_IGA2/
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148 tar -cJf ../new_IMGT_IGA2.txz *
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150 cd $outdir/new_IMGT_IGG/
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151 tar -cJf ../new_IMGT_IGG.txz *
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153 cd $outdir/new_IMGT_IGG1/
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154 tar -cJf ../new_IMGT_IGG1.txz *
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156 cd $outdir/new_IMGT_IGG2/
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157 tar -cJf ../new_IMGT_IGG2.txz *
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158
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159 cd $outdir/new_IMGT_IGG3/
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160 tar -cJf ../new_IMGT_IGG3.txz *
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161
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162 cd $outdir/new_IMGT_IGG4/
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163 tar -cJf ../new_IMGT_IGG4.txz *
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164
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165 cd $outdir/new_IMGT_IGM/
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166 tar -cJf ../new_IMGT_IGM.txz *
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168 cd $outdir/new_IMGT_IGE/
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169 tar -cJf ../new_IMGT_IGE.txz *
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diff changeset
171 cd $tmp
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parents: 4
diff changeset
172 fi
0
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parents:
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173
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davidvanzessen
parents:
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174 echo "---------------- shm_csr.r ----------------"
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davidvanzessen
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175 echo "---------------- shm_csr.r ----------------<br />" >> $log
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davidvanzessen
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176
5
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diff changeset
177 classes="IGA,IGA1,IGA2,IGG,IGG1,IGG2,IGG3,IGG4,IGM,IGE,unmatched"
0
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178 echo "R mutation analysis"
1
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davidvanzessen
parents: 0
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179 Rscript $dir/shm_csr.r $outdir/merged.txt $classes $outdir ${empty_region_filter} 2>&1
0
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180
43
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parents: 42
diff changeset
181 echo "---------------- plot_pdfs.r ----------------"
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parents: 42
diff changeset
182 echo "---------------- plot_pdfs.r ----------------<br />" >> $log
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davidvanzessen
parents: 42
diff changeset
183
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davidvanzessen
parents: 42
diff changeset
184 echo "Rscript $dir/shm_csr.r $outdir/pdfplots.RData $outdir 2>&1"
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davidvanzessen
parents: 42
diff changeset
185
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davidvanzessen
parents: 42
diff changeset
186 Rscript $dir/plot_pdf.r "$outdir/pdfplots.RData" "$outdir" 2>&1
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davidvanzessen
parents: 42
diff changeset
187
0
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davidvanzessen
parents:
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188 echo "---------------- shm_csr.py ----------------"
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davidvanzessen
parents:
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189 echo "---------------- shm_csr.py ----------------<br />" >> $log
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davidvanzessen
parents:
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190
1
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parents: 0
diff changeset
191 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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parents:
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192
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davidvanzessen
parents:
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193 echo "---------------- aa_histogram.r ----------------"
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davidvanzessen
parents:
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194 echo "---------------- aa_histogram.r ----------------<br />" >> $log
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195
5
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diff changeset
196 Rscript $dir/aa_histogram.r $outdir/aa_id_mutations.txt $outdir/absent_aa_id.txt "IGA,IGG,IGM,IGE" $outdir/ 2>&1
0
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parents:
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197 if [ -e "$outdir/aa_histogram_.png" ]; then
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parents:
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198 mv $outdir/aa_histogram_.png $outdir/aa_histogram.png
42
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199 mv $outdir/aa_histogram_.pdf $outdir/aa_histogram.pdf
0
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parents:
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200 mv $outdir/aa_histogram_.txt $outdir/aa_histogram.txt
29
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davidvanzessen
parents: 28
diff changeset
201 mv $outdir/aa_histogram_absent_.txt $outdir/aa_histogram_absent.txt
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davidvanzessen
parents: 28
diff changeset
202 mv $outdir/aa_histogram_count_.txt $outdir/aa_histogram_count.txt
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diff changeset
203 mv $outdir/aa_histogram_sum_.txt $outdir/aa_histogram_sum.txt
0
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parents:
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204 fi
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205
5
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diff changeset
206 genes=(IGA IGA1 IGA2 IGG IGG1 IGG2 IGG3 IGG4 IGM IGE)
0
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davidvanzessen
parents:
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207
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davidvanzessen
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208 funcs=(sum mean median)
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davidvanzessen
parents:
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209 funcs=(sum)
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davidvanzessen
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210
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211 echo "---------------- sequence_overview.r ----------------"
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davidvanzessen
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212 echo "---------------- sequence_overview.r ----------------<br />" >> $log
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davidvanzessen
parents:
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213
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214 mkdir $outdir/sequence_overview
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215
7
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diff changeset
216 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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217
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218 echo "<table border='1'>" > $outdir/base_overview.html
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219
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220 while IFS=$'\t' read ID class seq A C G T
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davidvanzessen
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221 do
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222 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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223 done < $outdir/sequence_overview/ntoverview.txt
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davidvanzessen
parents:
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224
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davidvanzessen
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225 echo "<html><center><h1>$title</h1></center>" > $output
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davidvanzessen
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226 echo "<meta name='viewport' content='width=device-width, initial-scale=1'>" >> $output
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davidvanzessen
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227 echo "<script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $output
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davidvanzessen
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diff changeset
228 echo "<script type='text/javascript' src='tabber.js'></script>" >> $output
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davidvanzessen
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229 echo "<script type='text/javascript' src='script.js'></script>" >> $output
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davidvanzessen
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230 echo "<link rel='stylesheet' type='text/css' href='style.css'>" >> $output
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davidvanzessen
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231 echo "<link rel='stylesheet' type='text/css' href='pure-min.css'>" >> $output
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davidvanzessen
parents:
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232
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davidvanzessen
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233 matched_count="`cat $outdir/merged.txt | grep -v 'unmatched' | tail -n +2 | wc -l`"
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davidvanzessen
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234 unmatched_count="`cat $outdir/unmatched.txt | tail -n +2 | wc -l`"
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davidvanzessen
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diff changeset
235 total_count=$((matched_count + unmatched_count))
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davidvanzessen
parents:
diff changeset
236 perc_count=$((unmatched_count / total_count * 100))
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davidvanzessen
parents:
diff changeset
237 perc_count=`bc -l <<< "scale=2; ${unmatched_count} / ${total_count} * 100"`
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davidvanzessen
parents:
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238 perc_count=`bc -l <<< "scale=2; (${unmatched_count} / ${total_count} * 100 ) / 1"`
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davidvanzessen
parents:
diff changeset
239
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davidvanzessen
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diff changeset
240 echo "<center><h2>Total: ${total_count}</h2></center>" >> $output
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davidvanzessen
parents:
diff changeset
241 echo "<center><h2>Matched: ${matched_count} Unmatched: ${unmatched_count}</h2></center>" >> $output
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davidvanzessen
parents:
diff changeset
242 echo "<center><h2>Percentage unmatched: ${perc_count}</h2></center>" >> $output
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davidvanzessen
parents:
diff changeset
243
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davidvanzessen
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244 echo "---------------- main tables ----------------"
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parents:
diff changeset
245 echo "---------------- main tables ----------------<br />" >> $log
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davidvanzessen
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diff changeset
246
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davidvanzessen
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247 echo "<div class='tabber'>" >> $output
23
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davidvanzessen
parents: 21
diff changeset
248 echo "<div class='tabbertab' title='SHM Overview' style='width: 3000px;'>" >> $output
0
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davidvanzessen
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249
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davidvanzessen
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diff changeset
250 for func in ${funcs[@]}
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davidvanzessen
parents:
diff changeset
251 do
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davidvanzessen
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diff changeset
252
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davidvanzessen
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diff changeset
253 echo "---------------- $func table ----------------"
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diff changeset
254 echo "---------------- $func table ----------------<br />" >> $log
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davidvanzessen
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diff changeset
255
47
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diff changeset
256 cat $outdir/mutations_${func}.txt $outdir/shm_overview_tandem_row.txt $outdir/hotspot_analysis_${func}.txt > $outdir/data_${func}.txt
0
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davidvanzessen
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257
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diff changeset
258 echo "---------------- pattern_plots.r ----------------"
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davidvanzessen
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diff changeset
259 echo "---------------- pattern_plots.r ----------------<br />" >> $log
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davidvanzessen
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diff changeset
260
43
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diff changeset
261 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
262
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davidvanzessen
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diff changeset
263 echo "<table class='pure-table pure-table-striped'>" >> $output
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davidvanzessen
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diff changeset
264 echo "<thead><tr><th>info</th>" >> $output
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davidvanzessen
parents:
diff changeset
265
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davidvanzessen
parents:
diff changeset
266 if [ "${class_filter}" != "101_101" ] ; then
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davidvanzessen
parents:
diff changeset
267
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davidvanzessen
parents:
diff changeset
268 for gene in ${genes[@]}
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davidvanzessen
parents:
diff changeset
269 do
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davidvanzessen
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diff changeset
270 tmp=`cat $outdir/${gene}_${func}_n.txt`
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davidvanzessen
parents:
diff changeset
271 echo "<th><a href='matched_${gene}_${func}.txt'>${gene} (N = $tmp)</a></th>" >> $output
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davidvanzessen
parents:
diff changeset
272 done
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davidvanzessen
parents:
diff changeset
273
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davidvanzessen
parents:
diff changeset
274 tmp=`cat $outdir/all_${func}_n.txt`
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davidvanzessen
parents:
diff changeset
275 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
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davidvanzessen
parents:
diff changeset
276 tmp=`cat $outdir/unmatched_${func}_n.txt`
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davidvanzessen
parents:
diff changeset
277 echo "<th><a href='unmatched.txt'>unmatched (N = ${unmatched_count})</a></th><tr></thead>" >> $output
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davidvanzessen
parents:
diff changeset
278
5
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davidvanzessen
parents: 4
diff changeset
279 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
0
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davidvanzessen
parents:
diff changeset
280 do
47
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davidvanzessen
parents: 45
diff changeset
281 if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] || [ "$name" == "Tandems/Expected (ratio)" ] ; then #meh
5
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davidvanzessen
parents: 4
diff changeset
282 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>" >> $output
0
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davidvanzessen
parents:
diff changeset
283 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
5
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davidvanzessen
parents: 4
diff changeset
284 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>" >> $output
0
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davidvanzessen
parents:
diff changeset
285 else
5
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davidvanzessen
parents: 4
diff changeset
286 echo "<tr><td>$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
287 fi
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davidvanzessen
parents:
diff changeset
288 done < $outdir/data_${func}.txt
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davidvanzessen
parents:
diff changeset
289
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davidvanzessen
parents:
diff changeset
290 else
3
275ab5175fd6 Uploaded
davidvanzessen
parents: 2
diff changeset
291 tmp=`cat $outdir/all_${func}_n.txt`
0
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davidvanzessen
parents:
diff changeset
292 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
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davidvanzessen
parents:
diff changeset
293
5
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davidvanzessen
parents: 4
diff changeset
294 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
0
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davidvanzessen
parents:
diff changeset
295 do
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davidvanzessen
parents:
diff changeset
296 if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] ; then #meh
3
275ab5175fd6 Uploaded
davidvanzessen
parents: 2
diff changeset
297 echo "<tr><td>$name</td><td>${allx}/${ally}</td></tr>" >> $output
0
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davidvanzessen
parents:
diff changeset
298 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
3
275ab5175fd6 Uploaded
davidvanzessen
parents: 2
diff changeset
299 echo "<tr><td>$name</td><td>${allz}%</td></tr>" >> $output
0
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davidvanzessen
parents:
diff changeset
300 else
3
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davidvanzessen
parents: 2
diff changeset
301 echo "<tr><td>$name</td><td>${allx}/${ally} (${allz}%)</td></tr>" >> $output
0
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davidvanzessen
parents:
diff changeset
302 fi
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davidvanzessen
parents:
diff changeset
303 done < $outdir/data_${func}.txt
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davidvanzessen
parents:
diff changeset
304
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davidvanzessen
parents:
diff changeset
305 fi
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davidvanzessen
parents:
diff changeset
306 echo "</table>" >> $output
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davidvanzessen
parents:
diff changeset
307 #echo "<a href='data_${func}.txt'>Download data</a>" >> $output
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davidvanzessen
parents:
diff changeset
308 done
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davidvanzessen
parents:
diff changeset
309
42
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davidvanzessen
parents: 41
diff changeset
310 echo "<a href='aid_motives.pdf'><img src='aid_motives.png' /></a><br />" >> $output
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davidvanzessen
parents: 41
diff changeset
311 echo "<a href='relative_mutations.pdf'><img src='relative_mutations.png' /></a><br />" >> $output
43
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davidvanzessen
parents: 42
diff changeset
312 echo "<a href='absolute_mutations.pdf'><img src='absolute_mutations.png' /></a><br />" >> $output
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
313 echo "<br />" >> $output
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davidvanzessen
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diff changeset
314 cat $dir/shm_overview.htm >> $output
0
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davidvanzessen
parents:
diff changeset
315 echo "</div>" >> $output #SHM overview tab end
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davidvanzessen
parents:
diff changeset
316
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davidvanzessen
parents:
diff changeset
317 echo "---------------- images ----------------"
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davidvanzessen
parents:
diff changeset
318 echo "---------------- images ----------------<br />" >> $log
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davidvanzessen
parents:
diff changeset
319
42
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davidvanzessen
parents: 41
diff changeset
320 echo "<div class='tabbertab' title='SHM Frequency' style='width: 3000px;'></a>" >> $output
0
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davidvanzessen
parents:
diff changeset
321
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davidvanzessen
parents:
diff changeset
322 if [ -a $outdir/scatter.png ]
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davidvanzessen
parents:
diff changeset
323 then
42
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davidvanzessen
parents: 41
diff changeset
324 echo "<a href='scatter.pdf'><img src='scatter.png'/><br />" >> $output
0
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davidvanzessen
parents:
diff changeset
325 fi
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davidvanzessen
parents:
diff changeset
326 if [ -a $outdir/frequency_ranges.png ]
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davidvanzessen
parents:
diff changeset
327 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
328 echo "<a href='frequency_ranges.pdf'><img src='frequency_ranges.png'/></a><br />" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
329 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
330
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
331 echo "<br />" >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
332 cat $dir/shm_frequency.htm >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
333
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
334 echo "</div>" >> $output #SHM frequency tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
335
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
336 echo "<div class='tabbertab' title='Transition tables' style='width: 3000px;'>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
337
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
338 echo "<table border='0'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
339
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
340 for gene in ${genes[@]}
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
341 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
342 echo "<tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
343 echo "<td><h1>${gene}</h1></td>" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
344
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
345 if [ -e $outdir/transitions_heatmap_${gene}.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
346 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
347 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
348 else
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
349 echo "<td></td>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
350 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
351
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
352 if [ -e $outdir/transitions_stacked_${gene}.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
353 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
354 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
355 else
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
356 echo "<td></td>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
357 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
358
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
359 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
360 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
361 first="true"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
362 while IFS=, read from a c g t
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
363 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
364 if [ "$first" == "true" ] ; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
365 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
366 first="false"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
367 else
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
368 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
369 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
370 done < $outdir/transitions_${gene}_sum.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
371 echo "</table></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
372
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
373 echo "</tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
374 done
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
375
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
376 echo "<tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
377 echo "<td><h1>All</h1></td>" >> $output
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
378 echo "<td><a href='transitions_heatmap_all.pdf'><img src='transitions_heatmap_all.png' /></a></td>" >> $output
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
379 echo "<td><a href='transitions_stacked_all.pdf'><img src='transitions_stacked_all.png' /></a></td>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
380 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
381 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
382 first="true"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
383 while IFS=, read from a c g t
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
384 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
385 if [ "$first" == "true" ] ; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
386 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
387 first="false"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
388 else
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
389 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
390 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
391 done < $outdir/transitions_all_sum.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
392 echo "</table></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
393
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
394 echo "</tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
395
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
396 echo "</table>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
397
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
398 echo "<br />" >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
399 cat $dir/shm_transition.htm >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
400
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
401 echo "</div>" >> $output #transition tables tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
402
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
403 echo "<div class='tabbertab' title='Antigen Selection'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
404
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
405 if [ -e $outdir/aa_histogram.png ]
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
406 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
407 echo "<a href='aa_histogram.pdf'><img src='aa_histogram.png'/></a><br />" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
408 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
409
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
410 if [ -e $outdir/aa_histogram_IGA.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
411 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
412 echo "<a href='aa_histogram_IGA.pdf'><img src='aa_histogram_IGA.png'/></a><br />" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
413 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
414
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
415 if [ -e $outdir/aa_histogram_IGG.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
416 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
417 echo "<a href='aa_histogram_IGG.pdf'><img src='aa_histogram_IGG.png'/></a><br />" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
418 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
419
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
420 if [ -e $outdir/aa_histogram_IGM.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
421 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
422 echo "<a href='aa_histogram_IGM.pdf'><img src='aa_histogram_IGM.png'/></a><br />" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
423 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
424
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
425 if [ -e $outdir/aa_histogram_IGE.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
426 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
427 echo "<a href='aa_histogram_IGE.pdf'><img src='aa_histogram_IGE.png'/></a><br />" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
428 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
429
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
430
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
431
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
432 if [[ "$fast" == "no" ]] ; then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
433
41
b8ac74723ab0 Uploaded
davidvanzessen
parents: 40
diff changeset
434
b8ac74723ab0 Uploaded
davidvanzessen
parents: 40
diff changeset
435
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
436 echo "---------------- baseline ----------------"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
437 echo "---------------- baseline ----------------<br />" >> $log
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
438 tmp="$PWD"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
439
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
440 mkdir $outdir/baseline
37
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
441
41
b8ac74723ab0 Uploaded
davidvanzessen
parents: 40
diff changeset
442 echo "<center><h1>BASELINe</h1>" >> $output
b8ac74723ab0 Uploaded
davidvanzessen
parents: 40
diff changeset
443 header_substring="Based on CDR1, FR2, CDR2, FR3 (27:27:38:55:65:104:-)"
b8ac74723ab0 Uploaded
davidvanzessen
parents: 40
diff changeset
444
37
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
445 baseline_boundaries="27:27:38:55:65:104:-"
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
446
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
447 if [[ "${empty_region_filter}" == "leader" ]] ; then
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
448 baseline_boundaries="1:26:38:55:65:104:-"
41
b8ac74723ab0 Uploaded
davidvanzessen
parents: 40
diff changeset
449 header_substring="Based on FR1, CDR1, FR2, CDR2, FR3 (1:26:38:55:65:104,-)"
37
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
450 fi
41
b8ac74723ab0 Uploaded
davidvanzessen
parents: 40
diff changeset
451
b8ac74723ab0 Uploaded
davidvanzessen
parents: 40
diff changeset
452 echo "<p>${header_substring}</p></center>" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
453
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
454 mkdir $outdir/baseline/IGA_IGG_IGM
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
455 if [[ $(wc -l < $outdir/new_IMGT/1_Summary.txt) -gt "1" ]]; then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
456 cd $outdir/baseline/IGA_IGG_IGM
41
b8ac74723ab0 Uploaded
davidvanzessen
parents: 40
diff changeset
457 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
458 else
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
459 echo "No sequences" > "$outdir/baseline.txt"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
460 fi
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
461
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
462 mkdir $outdir/baseline/IGA
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
463 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
464 cd $outdir/baseline/IGA
37
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
465 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
466 else
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
467 echo "No IGA sequences" > "$outdir/baseline_IGA.txt"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
468 fi
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
469
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
470 mkdir $outdir/baseline/IGG
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
471 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
472 cd $outdir/baseline/IGG
37
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
473 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
474 else
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
475 echo "No IGG sequences" > "$outdir/baseline_IGG.txt"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
476 fi
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
477
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
478 mkdir $outdir/baseline/IGM
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
479 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
480 cd $outdir/baseline/IGM
37
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
481 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
482 else
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
483 echo "No IGM sequences" > "$outdir/baseline_IGM.txt"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
484 fi
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
485
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
486 mkdir $outdir/baseline/IGE
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
487 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
488 cd $outdir/baseline/IGE
37
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
489 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
490 else
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
491 echo "No IGE sequences" > "$outdir/baseline_IGE.txt"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
492 fi
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
493
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
494 cd $tmp
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
495
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
496 echo "Cleaning up *.RData files"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
497 find $outdir/baseline -name "*.RData" -type f -delete
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
498
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
499 if [ -e $outdir/baseline.pdf ]
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
500 then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
501 echo "<embed src='baseline.pdf' width='700px' height='1000px'>" >> $output
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
502 fi
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
503
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
504 if [ -e $outdir/baseline_IGA.pdf ]
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
505 then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
506 echo "<embed src='baseline_IGA.pdf' width='700px' height='1000px'>" >> $output
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
507 fi
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
508
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
509 if [ -e $outdir/baseline_IGG.pdf ]
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
510 then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
511 echo "<embed src='baseline_IGG.pdf' width='700px' height='1000px'>" >> $output
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
512 fi
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
513
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
514 if [ -e $outdir/baseline_IGM.pdf ]
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
515 then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
516 echo "<embed src='baseline_IGM.pdf' width='700px' height='1000px'>" >> $output
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
517 fi
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
518
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
519 if [ -e $outdir/baseline_IGE.pdf ]
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
520 then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
521 echo "<embed src='baseline_IGE.pdf' width='700px' height='1000px'>" >> $output
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
522 fi
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
523 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
524
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
525 echo "<br />" >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
526 cat $dir/shm_selection.htm >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
527
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
528 echo "</div>" >> $output #antigen selection tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
529
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
530 echo "<div class='tabbertab' title='CSR'>" >> $output #CSR tab
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
531
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
532 if [ -e $outdir/IGA.png ]
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
533 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
534 echo "<a href='IGA.pdf'><img src='IGA.png'/></a><br />" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
535 fi
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
536 if [ -e $outdir/IGG.png ]
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
537 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
538 echo "<a href='IGG.pdf'><img src='IGG.png'/></a><br />" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
539 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
540
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
541 echo "<br />" >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
542 cat $dir/shm_csr.htm >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
543
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
544 echo "</div>" >> $output #CSR tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
545
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
546 if [[ "$fast" == "no" ]] ; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
547
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
548 echo "---------------- change-o MakeDB ----------------"
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
549
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
550 mkdir $outdir/change_o
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
551
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
552 tmp="$PWD"
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
553
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
554 cd $outdir/change_o
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
555
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
556 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
557 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
558
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
559 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
560
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
561 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
562
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
563 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
564 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
565 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 $outdir/change_o/change-o-defined_clones-summary-IGA.txt
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
566 else
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
567 echo "No IGA sequences" > "$outdir/change_o/change-o-db-defined_clones-IGA.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
568 echo "No IGA sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGA.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
569 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
570
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
571 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
572 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
573 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 $outdir/change_o/change-o-defined_clones-summary-IGG.txt
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
574 else
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
575 echo "No IGG sequences" > "$outdir/change_o/change-o-db-defined_clones-IGG.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
576 echo "No IGG sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGG.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
577 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
578
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
579 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
580 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
581 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 $outdir/change_o/change-o-defined_clones-summary-IGM.txt
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
582 else
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
583 echo "No IGM sequences" > "$outdir/change_o/change-o-db-defined_clones-IGM.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
584 echo "No IGM sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGM.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
585 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
586
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
587 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
588 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
589 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 $outdir/change_o/change-o-defined_clones-summary-IGE.txt
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
590 else
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
591 echo "No IGE sequences" > "$outdir/change_o/change-o-db-defined_clones-IGE.txt"
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
592 echo "No IGE sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGE.txt"
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
593 fi
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
594
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
595 PWD="$tmp"
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
596
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
597 echo "<div class='tabbertab' title='Clonal Relation' style='width: 7000px;'>" >> $output #clonality tab
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
598
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
599 function clonality_table {
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
600 local infile=$1
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
601 local outfile=$2
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
602
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
603 echo "<table class='pure-table pure-table-striped'>" >> $outfile
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
604 echo "<thead><tr><th>Clone size</th><th>Nr of clones</th><th>Nr of sequences</th></tr></thead>" >> $outfile
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
605
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
606 first='true'
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
607
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
608 while read size clones seqs
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
609 do
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
610 if [[ "$first" == "true" ]]; then
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
611 first="false"
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
612 continue
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
613 fi
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
614 echo "<tr><td>$size</td><td>$clones</td><td>$seqs</td></tr>" >> $outfile
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
615 done < $infile
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
616
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
617 echo "</table>" >> $outfile
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
618 }
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
619 echo "<div class='tabber'>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
620
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
621 echo "<div class='tabbertab' title='All'>" >> $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
622 clonality_table $outdir/change_o/change-o-defined_clones-summary.txt $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
623 echo "</div>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
624
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
625 echo "<div class='tabbertab' title='IGA'>" >> $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
626 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGA.txt $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
627 echo "</div>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
628
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
629 echo "<div class='tabbertab' title='IGG'>" >> $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
630 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGG.txt $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
631 echo "</div>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
632
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
633 echo "<div class='tabbertab' title='IGM'>" >> $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
634 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
635 echo "</div>" >> $output
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
636
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
637 echo "<div class='tabbertab' title='IGE'>" >> $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
638 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
639 echo "</div>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
640
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
641 echo "<div class='tabbertab' title='Overlap' style='width: 7000px;'>" >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
642 cat "$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
643 echo "</div>" >> $output
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
644
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
645 echo "</div>" >> $output #clonality tabber end
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
646
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
647 echo "<br />" >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
648 cat $dir/shm_clonality.htm >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
649
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
650 echo "</div>" >> $output #clonality tab end
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
651
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
652 fi
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
653
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
654 echo "<div class='tabbertab' title='Downloads'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
655
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
656 echo "<table class='pure-table pure-table-striped'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
657 echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
658 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
659 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
660 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
661
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
662 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Overview</td></tr>" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
663 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
664 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
665 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
666 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
667 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
668 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
669 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
47
64711f461c8e Uploaded
davidvanzessen
parents: 45
diff changeset
670 echo "<tr><td>Data about tandem mutations by ID</td><td><a href='tandems_by_id.txt' download='tandems_by_id.txt' >Download</a></td></tr>" >> $output
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
671
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
672 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Frequency</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
673 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
674 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
675 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
676
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
677 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Transition Tables</td></tr>" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
678 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
45
b66e8946ba75 Uploaded
davidvanzessen
parents: 43
diff changeset
679 echo "<tr><td>The data for the 'IGA' transition plot</td><td><a href='transitions_IGA_sum.txt' download='transitions_IGA_sum.txt' >Download</a></td></tr>" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
680 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
681 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
682 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
683 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
684 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
685 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
686 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
687 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
688 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
689
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
690 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Antigen Selection</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
691 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
692 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
693
29
80c4eebf7bc9 Uploaded
davidvanzessen
parents: 28
diff changeset
694 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
695 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
696 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
697 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
698 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
699
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
700 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
701 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
702 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
703 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
704 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
705 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
706 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
707 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
708 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
709 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
710
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
711 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>CSR</td></tr>" >> $output
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
712 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
713 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
714
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
715 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Clonal Relation</td></tr>" >> $output
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
716 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
717 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
718 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
719 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
720 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
721 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
722 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
723 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
724 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
725 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
726 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
727
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
728 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Filtered IMGT output files</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
729 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
730 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
731 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
732 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
733 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
734 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
735 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
736 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
737 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
738 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
739 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
740
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
741 echo "</table>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
742
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
743 echo "<br />" >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
744 cat $dir/shm_downloads.htm >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
745
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
746 echo "</div>" >> $output #downloads tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
747
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
748 echo "</div>" >> $output #tabs end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
749
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
750 echo "</html>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
751
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
752
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
753 echo "---------------- naive_output.r ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
754 echo "---------------- naive_output.r ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
755
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
756 if [[ "$naive_output" == "yes" ]]
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
757 then
28
c0ecc31829bd Uploaded
davidvanzessen
parents: 26
diff changeset
758 echo "output naive output"
18
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
759 if [[ "${class_filter}" == "101_101" ]]
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
760 then
28
c0ecc31829bd Uploaded
davidvanzessen
parents: 26
diff changeset
761 echo "copy new_IMGT.txz to ${naive_output_all}"
21
c281993e515b Uploaded
davidvanzessen
parents: 20
diff changeset
762 cp $outdir/new_IMGT.txz ${naive_output_all}
18
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
763 else
28
c0ecc31829bd Uploaded
davidvanzessen
parents: 26
diff changeset
764 echo "copy for classes"
18
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
765 cp $outdir/new_IMGT_IGA.txz ${naive_output_ca}
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
766 cp $outdir/new_IMGT_IGG.txz ${naive_output_cg}
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
767 cp $outdir/new_IMGT_IGM.txz ${naive_output_cm}
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
768 cp $outdir/new_IMGT_IGE.txz ${naive_output_ce}
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
769 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
770 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
771
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
772 echo "</table>" >> $outdir/base_overview.html
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
773
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
774 mv $log $outdir/log.html
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
775
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
776 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
777 echo "<table border = 1>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
778 echo "<thead><tr><th>Info</th><th>Sequences</th><th>Percentage</th></tr></thead>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
779 tIFS="$TMP"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
780 IFS=$'\t'
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
781 while read step seq perc
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
782 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
783 echo "<tr>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
784 echo "<td>$step</td>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
785 echo "<td>$seq</td>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
786 echo "<td>${perc}%</td>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
787 echo "</tr>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
788 done < $outdir/filtering_steps.txt
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
789 echo "</table>" >> $log
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
790 echo "<br />" >> $log
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
791 cat $dir/shm_first.htm >> $log
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
792 echo "</center></html>" >> $log
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
793
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
794 IFS="$tIFS"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
795
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
796
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
797 echo "---------------- Done! ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
798 echo "---------------- Done! ----------------<br />" >> $outdir/log.html
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
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
817
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
818
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
819