annotate wrapper.sh @ 58:1a8e1dd21b16 draft

Uploaded
author davidvanzessen
date Tue, 18 Jul 2017 04:58:22 -0400
parents cb779a45537b
children 7b9481fa4a70
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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 else
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45 echo "Unrecognized format $type"
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46 echo "Unrecognized format $type" > $log
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47 exit 1
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48 fi
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49
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50 cat "`find $PWD/files/ -name "1_*"`" > $PWD/summary.txt
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51 cat "`find $PWD/files/ -name "2_*"`" > $PWD/gapped_nt.txt
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52 cat "`find $PWD/files/ -name "3_*"`" > $PWD/sequences.txt
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53 cat "`find $PWD/files/ -name "4_*"`" > $PWD/gapped_aa.txt
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54 cat "`find $PWD/files/ -name "5_*"`" > $PWD/aa.txt
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55 cat "`find $PWD/files/ -name "6_*"`" > $PWD/junction.txt
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56 cat "`find $PWD/files/ -name "7_*"`" > $PWD/mutationanalysis.txt
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57 cat "`find $PWD/files/ -name "8_*"`" > $PWD/mutationstats.txt
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58 cat "`find $PWD/files/ -name "9_*"`" > $PWD/aa_change_stats.txt
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59 cat "`find $PWD/files/ -name "10_*"`" > $PWD/hotspots.txt
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60
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61 echo "---------------- unique id check ----------------"
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62
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63 Rscript $dir/check_unique_id.r $PWD/summary.txt $PWD/gapped_nt.txt $PWD/sequences.txt $PWD/gapped_aa.txt $PWD/aa.txt $PWD/junction.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/aa_change_stats.txt $PWD/hotspots.txt
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64
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65 if [[ ${#BLASTN_DIR} -ge 5 ]] ; then
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66 echo "On server, using BLASTN_DIR env: ${BLASTN_DIR}"
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67 else
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68 BLASTN_DIR="/home/galaxy/Downloads/ncbi-blast-2.4.0+/bin"
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69 echo "Dev Galaxy set BLASTN_DIR to: ${BLASTN_DIR}"
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70 fi
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71
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72 echo "---------------- class identification ----------------"
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73 echo "---------------- class identification ----------------<br />" >> $log
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74
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75 python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt
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77 echo "---------------- merge_and_filter.r ----------------"
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78 echo "---------------- merge_and_filter.r ----------------<br />" >> $log
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79
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80 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} ${empty_region_filter} 2>&1
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81
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82 if [[ "${naive_output}" == "yes" ]] || [[ "$fast" == "no" ]] ; then
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83
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84 echo "---------------- creating new IMGT zips ----------------"
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85 echo "---------------- creating new IMGT zips ----------------<br />" >> $log
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87 mkdir $outdir/new_IMGT
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88
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89 cp $PWD/summary.txt "$outdir/new_IMGT/1_Summary.txt"
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90 cp $PWD/gapped_nt.txt "$outdir/new_IMGT/2_IMGT-gapped-nt-sequences.txt"
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91 cp $PWD/sequences.txt "$outdir/new_IMGT/3_Nt-sequences.txt"
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92 cp $PWD/gapped_aa.txt "$outdir/new_IMGT/4_IMGT-gapped-AA-sequences.txt"
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93 cp $PWD/aa.txt "$outdir/new_IMGT/5_AA-sequences.txt"
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94 cp $PWD/junction.txt "$outdir/new_IMGT/6_Junction.txt"
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95 cp $PWD/mutationanalysis.txt "$outdir/new_IMGT/7_V-REGION-mutation-and-AA-change-table.txt"
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96 cp $PWD/mutationstats.txt "$outdir/new_IMGT/8_V-REGION-nt-mutation-statistics.txt"
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97 cp $PWD/aa_change_stats.txt "$outdir/new_IMGT/9_V-REGION-AA-change-statistics.txt"
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98 cp $PWD/hotspots.txt "$outdir/new_IMGT/10_V-REGION-mutation-hotspots.txt"
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100 mkdir $outdir/new_IMGT_IGA
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101 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA
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102
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103 mkdir $outdir/new_IMGT_IGA1
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104 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA1
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106 mkdir $outdir/new_IMGT_IGA2
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107 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA2
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109 mkdir $outdir/new_IMGT_IGG
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110 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG
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112 mkdir $outdir/new_IMGT_IGG1
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113 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG1
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115 mkdir $outdir/new_IMGT_IGG2
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116 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG2
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118 mkdir $outdir/new_IMGT_IGG3
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119 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG3
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121 mkdir $outdir/new_IMGT_IGG4
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122 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG4
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124 mkdir $outdir/new_IMGT_IGM
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125 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGM
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126
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127 mkdir $outdir/new_IMGT_IGE
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128 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGE
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129
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130 Rscript $dir/new_imgt.r $outdir/new_IMGT/ $outdir/merged.txt "-" 2>&1
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131
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132 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA/ $outdir/merged.txt "IGA" 2>&1
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133 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA1/ $outdir/merged.txt "IGA1" 2>&1
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134 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA2/ $outdir/merged.txt "IGA2" 2>&1
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135
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136 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG/ $outdir/merged.txt "IGG" 2>&1
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137 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG1/ $outdir/merged.txt "IGG1" 2>&1
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138 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG2/ $outdir/merged.txt "IGG2" 2>&1
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139 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG3/ $outdir/merged.txt "IGG3" 2>&1
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140 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG4/ $outdir/merged.txt "IGG4" 2>&1
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141
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142 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGM/ $outdir/merged.txt "IGM" 2>&1
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143
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144 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGE/ $outdir/merged.txt "IGE" 2>&1
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147 tmp="$PWD"
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148 cd $outdir/new_IMGT/ #tar weirdness...
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149 tar -cJf ../new_IMGT.txz *
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150
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151 cd $outdir/new_IMGT_IGA/
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152 tar -cJf ../new_IMGT_IGA.txz *
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154 cd $outdir/new_IMGT_IGA1/
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155 tar -cJf ../new_IMGT_IGA1.txz *
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156
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157 cd $outdir/new_IMGT_IGA2/
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158 tar -cJf ../new_IMGT_IGA2.txz *
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159
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160 cd $outdir/new_IMGT_IGG/
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161 tar -cJf ../new_IMGT_IGG.txz *
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162
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163 cd $outdir/new_IMGT_IGG1/
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164 tar -cJf ../new_IMGT_IGG1.txz *
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166 cd $outdir/new_IMGT_IGG2/
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167 tar -cJf ../new_IMGT_IGG2.txz *
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168
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169 cd $outdir/new_IMGT_IGG3/
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170 tar -cJf ../new_IMGT_IGG3.txz *
0
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171
5
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diff changeset
172 cd $outdir/new_IMGT_IGG4/
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diff changeset
173 tar -cJf ../new_IMGT_IGG4.txz *
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parents: 4
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174
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diff changeset
175 cd $outdir/new_IMGT_IGM/
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diff changeset
176 tar -cJf ../new_IMGT_IGM.txz *
0
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177
5
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diff changeset
178 cd $outdir/new_IMGT_IGE/
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179 tar -cJf ../new_IMGT_IGE.txz *
0
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180
5
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181 cd $tmp
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182 fi
0
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183
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parents:
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184 echo "---------------- shm_csr.r ----------------"
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davidvanzessen
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185 echo "---------------- shm_csr.r ----------------<br />" >> $log
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186
5
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187 classes="IGA,IGA1,IGA2,IGG,IGG1,IGG2,IGG3,IGG4,IGM,IGE,unmatched"
0
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188 echo "R mutation analysis"
1
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189 Rscript $dir/shm_csr.r $outdir/merged.txt $classes $outdir ${empty_region_filter} 2>&1
0
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190
43
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parents: 42
diff changeset
191 echo "---------------- plot_pdfs.r ----------------"
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parents: 42
diff changeset
192 echo "---------------- plot_pdfs.r ----------------<br />" >> $log
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parents: 42
diff changeset
193
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parents: 42
diff changeset
194 echo "Rscript $dir/shm_csr.r $outdir/pdfplots.RData $outdir 2>&1"
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davidvanzessen
parents: 42
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195
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diff changeset
196 Rscript $dir/plot_pdf.r "$outdir/pdfplots.RData" "$outdir" 2>&1
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parents: 42
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197
0
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198 echo "---------------- shm_csr.py ----------------"
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199 echo "---------------- shm_csr.py ----------------<br />" >> $log
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200
1
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201 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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202
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203 echo "---------------- aa_histogram.r ----------------"
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davidvanzessen
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204 echo "---------------- aa_histogram.r ----------------<br />" >> $log
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205
5
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diff changeset
206 Rscript $dir/aa_histogram.r $outdir/aa_id_mutations.txt $outdir/absent_aa_id.txt "IGA,IGG,IGM,IGE" $outdir/ 2>&1
0
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207 if [ -e "$outdir/aa_histogram_.png" ]; then
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208 mv $outdir/aa_histogram_.png $outdir/aa_histogram.png
42
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209 mv $outdir/aa_histogram_.pdf $outdir/aa_histogram.pdf
0
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210 mv $outdir/aa_histogram_.txt $outdir/aa_histogram.txt
29
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diff changeset
211 mv $outdir/aa_histogram_absent_.txt $outdir/aa_histogram_absent.txt
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diff changeset
212 mv $outdir/aa_histogram_count_.txt $outdir/aa_histogram_count.txt
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213 mv $outdir/aa_histogram_sum_.txt $outdir/aa_histogram_sum.txt
0
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214 fi
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215
5
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diff changeset
216 genes=(IGA IGA1 IGA2 IGG IGG1 IGG2 IGG3 IGG4 IGM IGE)
0
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217
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218 funcs=(sum mean median)
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219 funcs=(sum)
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220
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221 echo "---------------- sequence_overview.r ----------------"
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222 echo "---------------- sequence_overview.r ----------------<br />" >> $log
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223
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224 mkdir $outdir/sequence_overview
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225
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diff changeset
226 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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parents:
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227
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228 echo "<table border='1'>" > $outdir/base_overview.html
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229
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230 while IFS=$'\t' read ID class seq A C G T
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231 do
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232 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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233 done < $outdir/sequence_overview/ntoverview.txt
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234
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235 echo "<html><center><h1>$title</h1></center>" > $output
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236 echo "<meta name='viewport' content='width=device-width, initial-scale=1'>" >> $output
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davidvanzessen
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237 echo "<script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $output
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davidvanzessen
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238 echo "<script type='text/javascript' src='tabber.js'></script>" >> $output
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239 echo "<script type='text/javascript' src='script.js'></script>" >> $output
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davidvanzessen
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240 echo "<link rel='stylesheet' type='text/css' href='style.css'>" >> $output
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davidvanzessen
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241 echo "<link rel='stylesheet' type='text/css' href='pure-min.css'>" >> $output
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242
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243 matched_count="`cat $outdir/merged.txt | grep -v 'unmatched' | tail -n +2 | wc -l`"
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244 unmatched_count="`cat $outdir/unmatched.txt | tail -n +2 | wc -l`"
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davidvanzessen
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diff changeset
245 total_count=$((matched_count + unmatched_count))
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davidvanzessen
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246 perc_count=$((unmatched_count / total_count * 100))
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davidvanzessen
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247 perc_count=`bc -l <<< "scale=2; ${unmatched_count} / ${total_count} * 100"`
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davidvanzessen
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248 perc_count=`bc -l <<< "scale=2; (${unmatched_count} / ${total_count} * 100 ) / 1"`
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249
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250 echo "<center><h2>Total: ${total_count}</h2></center>" >> $output
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davidvanzessen
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diff changeset
251 echo "<center><h2>Matched: ${matched_count} Unmatched: ${unmatched_count}</h2></center>" >> $output
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davidvanzessen
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252 echo "<center><h2>Percentage unmatched: ${perc_count}</h2></center>" >> $output
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253
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254 echo "---------------- main tables ----------------"
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255 echo "---------------- main tables ----------------<br />" >> $log
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256
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257 echo "<div class='tabber'>" >> $output
23
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diff changeset
258 echo "<div class='tabbertab' title='SHM Overview' style='width: 3000px;'>" >> $output
0
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259
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davidvanzessen
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diff changeset
260 for func in ${funcs[@]}
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davidvanzessen
parents:
diff changeset
261 do
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davidvanzessen
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262
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263 echo "---------------- $func table ----------------"
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264 echo "---------------- $func table ----------------<br />" >> $log
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265
47
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diff changeset
266 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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267
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268 echo "---------------- pattern_plots.r ----------------"
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269 echo "---------------- pattern_plots.r ----------------<br />" >> $log
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270
43
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diff changeset
271 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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272
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273 echo "<table class='pure-table pure-table-striped'>" >> $output
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davidvanzessen
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274 echo "<thead><tr><th>info</th>" >> $output
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davidvanzessen
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275
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davidvanzessen
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276 if [ "${class_filter}" != "101_101" ] ; then
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davidvanzessen
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277
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davidvanzessen
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diff changeset
278 for gene in ${genes[@]}
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davidvanzessen
parents:
diff changeset
279 do
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davidvanzessen
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diff changeset
280 tmp=`cat $outdir/${gene}_${func}_n.txt`
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281 echo "<th><a href='matched_${gene}_${func}.txt'>${gene} (N = $tmp)</a></th>" >> $output
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davidvanzessen
parents:
diff changeset
282 done
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davidvanzessen
parents:
diff changeset
283
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davidvanzessen
parents:
diff changeset
284 tmp=`cat $outdir/all_${func}_n.txt`
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davidvanzessen
parents:
diff changeset
285 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
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davidvanzessen
parents:
diff changeset
286 tmp=`cat $outdir/unmatched_${func}_n.txt`
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davidvanzessen
parents:
diff changeset
287 echo "<th><a href='unmatched.txt'>unmatched (N = ${unmatched_count})</a></th><tr></thead>" >> $output
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davidvanzessen
parents:
diff changeset
288
5
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davidvanzessen
parents: 4
diff changeset
289 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
0
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davidvanzessen
parents:
diff changeset
290 do
47
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davidvanzessen
parents: 45
diff changeset
291 if [ "$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
292 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>" >> $output
0
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davidvanzessen
parents:
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293 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
5
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diff changeset
294 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>" >> $output
0
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davidvanzessen
parents:
diff changeset
295 else
5
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davidvanzessen
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diff changeset
296 echo "<tr><td>$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:
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297 fi
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davidvanzessen
parents:
diff changeset
298 done < $outdir/data_${func}.txt
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davidvanzessen
parents:
diff changeset
299
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davidvanzessen
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diff changeset
300 else
3
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davidvanzessen
parents: 2
diff changeset
301 tmp=`cat $outdir/all_${func}_n.txt`
0
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davidvanzessen
parents:
diff changeset
302 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
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davidvanzessen
parents:
diff changeset
303
5
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davidvanzessen
parents: 4
diff changeset
304 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
0
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davidvanzessen
parents:
diff changeset
305 do
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davidvanzessen
parents:
diff changeset
306 if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] ; then #meh
3
275ab5175fd6 Uploaded
davidvanzessen
parents: 2
diff changeset
307 echo "<tr><td>$name</td><td>${allx}/${ally}</td></tr>" >> $output
0
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davidvanzessen
parents:
diff changeset
308 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
3
275ab5175fd6 Uploaded
davidvanzessen
parents: 2
diff changeset
309 echo "<tr><td>$name</td><td>${allz}%</td></tr>" >> $output
0
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davidvanzessen
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diff changeset
310 else
3
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davidvanzessen
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diff changeset
311 echo "<tr><td>$name</td><td>${allx}/${ally} (${allz}%)</td></tr>" >> $output
0
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davidvanzessen
parents:
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312 fi
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davidvanzessen
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diff changeset
313 done < $outdir/data_${func}.txt
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davidvanzessen
parents:
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314
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davidvanzessen
parents:
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315 fi
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davidvanzessen
parents:
diff changeset
316 echo "</table>" >> $output
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davidvanzessen
parents:
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317 #echo "<a href='data_${func}.txt'>Download data</a>" >> $output
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davidvanzessen
parents:
diff changeset
318 done
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davidvanzessen
parents:
diff changeset
319
42
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davidvanzessen
parents: 41
diff changeset
320 echo "<a href='aid_motives.pdf'><img src='aid_motives.png' /></a><br />" >> $output
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davidvanzessen
parents: 41
diff changeset
321 echo "<a href='relative_mutations.pdf'><img src='relative_mutations.png' /></a><br />" >> $output
43
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davidvanzessen
parents: 42
diff changeset
322 echo "<a href='absolute_mutations.pdf'><img src='absolute_mutations.png' /></a><br />" >> $output
39
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davidvanzessen
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diff changeset
323 echo "<br />" >> $output
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davidvanzessen
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diff changeset
324 cat $dir/shm_overview.htm >> $output
0
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davidvanzessen
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diff changeset
325 echo "</div>" >> $output #SHM overview tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
326
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
327 echo "---------------- images ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
328 echo "---------------- images ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
329
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
330 echo "<div class='tabbertab' title='SHM Frequency' style='width: 3000px;'></a>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
331
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
332 if [ -a $outdir/scatter.png ]
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
333 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
334 echo "<a href='scatter.pdf'><img src='scatter.png'/><br />" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
335 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
336 if [ -a $outdir/frequency_ranges.png ]
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
337 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
338 echo "<a href='frequency_ranges.pdf'><img src='frequency_ranges.png'/></a><br />" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
339 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
340
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
341 echo "<br />" >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
342 cat $dir/shm_frequency.htm >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
343
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
344 echo "</div>" >> $output #SHM frequency tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
345
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
346 echo "<div class='tabbertab' title='Transition tables' style='width: 3000px;'>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
347
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
348 echo "<table border='0'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
349
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
350 for gene in ${genes[@]}
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
351 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
352 echo "<tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
353 echo "<td><h1>${gene}</h1></td>" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
354
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
355 if [ -e $outdir/transitions_heatmap_${gene}.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
356 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
357 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
358 else
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
359 echo "<td></td>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
360 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
361
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
362 if [ -e $outdir/transitions_stacked_${gene}.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
363 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
364 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
365 else
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
366 echo "<td></td>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
367 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
368
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
369 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
370 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
371 first="true"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
372 while IFS=, read from a c g t
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
373 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
374 if [ "$first" == "true" ] ; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
375 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
376 first="false"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
377 else
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
378 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
379 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
380 done < $outdir/transitions_${gene}_sum.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
381 echo "</table></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
382
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
383 echo "</tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
384 done
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
385
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
386 echo "<tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
387 echo "<td><h1>All</h1></td>" >> $output
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
388 echo "<td><a href='transitions_heatmap_all.pdf'><img src='transitions_heatmap_all.png' /></a></td>" >> $output
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
389 echo "<td><a href='transitions_stacked_all.pdf'><img src='transitions_stacked_all.png' /></a></td>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
390 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
391 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
392 first="true"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
393 while IFS=, read from a c g t
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
394 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
395 if [ "$first" == "true" ] ; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
396 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
397 first="false"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
398 else
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
399 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
400 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
401 done < $outdir/transitions_all_sum.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
402 echo "</table></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
403
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
404 echo "</tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
405
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
406 echo "</table>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
407
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
408 echo "<br />" >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
409 cat $dir/shm_transition.htm >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
410
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
411 echo "</div>" >> $output #transition tables tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
412
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
413 echo "<div class='tabbertab' title='Antigen Selection'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
414
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
415 if [ -e $outdir/aa_histogram.png ]
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
416 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
417 echo "<a href='aa_histogram.pdf'><img src='aa_histogram.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_IGA.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
421 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
422 echo "<a href='aa_histogram_IGA.pdf'><img src='aa_histogram_IGA.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_IGG.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
426 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
427 echo "<a href='aa_histogram_IGG.pdf'><img src='aa_histogram_IGG.png'/></a><br />" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
428 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
429
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
430 if [ -e $outdir/aa_histogram_IGM.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
431 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
432 echo "<a href='aa_histogram_IGM.pdf'><img src='aa_histogram_IGM.png'/></a><br />" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
433 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
434
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
435 if [ -e $outdir/aa_histogram_IGE.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
436 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
437 echo "<a href='aa_histogram_IGE.pdf'><img src='aa_histogram_IGE.png'/></a><br />" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
438 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
439
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
440
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
441
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
442 if [[ "$fast" == "no" ]] ; then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
443
41
b8ac74723ab0 Uploaded
davidvanzessen
parents: 40
diff changeset
444
b8ac74723ab0 Uploaded
davidvanzessen
parents: 40
diff changeset
445
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
446 echo "---------------- baseline ----------------"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
447 echo "---------------- baseline ----------------<br />" >> $log
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
448 tmp="$PWD"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
449
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
450 mkdir $outdir/baseline
37
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
451
41
b8ac74723ab0 Uploaded
davidvanzessen
parents: 40
diff changeset
452 echo "<center><h1>BASELINe</h1>" >> $output
b8ac74723ab0 Uploaded
davidvanzessen
parents: 40
diff changeset
453 header_substring="Based on CDR1, FR2, CDR2, FR3 (27:27:38:55:65:104:-)"
b8ac74723ab0 Uploaded
davidvanzessen
parents: 40
diff changeset
454
37
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
455 baseline_boundaries="27:27:38:55:65:104:-"
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
456
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
457 if [[ "${empty_region_filter}" == "leader" ]] ; then
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
458 baseline_boundaries="1:26:38:55:65:104:-"
41
b8ac74723ab0 Uploaded
davidvanzessen
parents: 40
diff changeset
459 header_substring="Based on FR1, CDR1, FR2, CDR2, FR3 (1:26:38:55:65:104,-)"
37
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
460 fi
41
b8ac74723ab0 Uploaded
davidvanzessen
parents: 40
diff changeset
461
b8ac74723ab0 Uploaded
davidvanzessen
parents: 40
diff changeset
462 echo "<p>${header_substring}</p></center>" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
463
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
464 mkdir $outdir/baseline/IGA_IGG_IGM
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
465 if [[ $(wc -l < $outdir/new_IMGT/1_Summary.txt) -gt "1" ]]; then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
466 cd $outdir/baseline/IGA_IGG_IGM
41
b8ac74723ab0 Uploaded
davidvanzessen
parents: 40
diff changeset
467 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
468 else
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
469 echo "No sequences" > "$outdir/baseline.txt"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
470 fi
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
471
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
472 mkdir $outdir/baseline/IGA
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
473 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
474 cd $outdir/baseline/IGA
37
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
475 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
476 else
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
477 echo "No IGA sequences" > "$outdir/baseline_IGA.txt"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
478 fi
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
479
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
480 mkdir $outdir/baseline/IGG
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
481 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
482 cd $outdir/baseline/IGG
37
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
483 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
484 else
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
485 echo "No IGG sequences" > "$outdir/baseline_IGG.txt"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
486 fi
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
487
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
488 mkdir $outdir/baseline/IGM
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
489 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
490 cd $outdir/baseline/IGM
37
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
491 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
492 else
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
493 echo "No IGM sequences" > "$outdir/baseline_IGM.txt"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
494 fi
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
495
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
496 mkdir $outdir/baseline/IGE
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
497 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
498 cd $outdir/baseline/IGE
37
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
499 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
500 else
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
501 echo "No IGE sequences" > "$outdir/baseline_IGE.txt"
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 cd $tmp
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
505
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
506 echo "Cleaning up *.RData files"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
507 find $outdir/baseline -name "*.RData" -type f -delete
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
508
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
509 if [ -e $outdir/baseline.pdf ]
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
510 then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
511 echo "<embed src='baseline.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_IGA.pdf ]
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
515 then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
516 echo "<embed src='baseline_IGA.pdf' width='700px' height='1000px'>" >> $output
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
517 fi
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
518
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
519 if [ -e $outdir/baseline_IGG.pdf ]
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
520 then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
521 echo "<embed src='baseline_IGG.pdf' width='700px' height='1000px'>" >> $output
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
522 fi
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
523
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
524 if [ -e $outdir/baseline_IGM.pdf ]
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
525 then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
526 echo "<embed src='baseline_IGM.pdf' width='700px' height='1000px'>" >> $output
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
527 fi
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
528
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
529 if [ -e $outdir/baseline_IGE.pdf ]
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
530 then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
531 echo "<embed src='baseline_IGE.pdf' width='700px' height='1000px'>" >> $output
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
532 fi
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
533 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
534
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
535 echo "<br />" >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
536 cat $dir/shm_selection.htm >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
537
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
538 echo "</div>" >> $output #antigen selection tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
539
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
540 echo "<div class='tabbertab' title='CSR'>" >> $output #CSR tab
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
541
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
542 if [ -e $outdir/IGA.png ]
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
543 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
544 echo "<a href='IGA.pdf'><img src='IGA.png'/></a><br />" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
545 fi
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
546 if [ -e $outdir/IGG.png ]
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
547 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
548 echo "<a href='IGG.pdf'><img src='IGG.png'/></a><br />" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
549 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
550
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
551 echo "<br />" >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
552 cat $dir/shm_csr.htm >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
553
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
554 echo "</div>" >> $output #CSR tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
555
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
556 if [[ "$fast" == "no" ]] ; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
557
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
558 echo "---------------- change-o MakeDB ----------------"
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
559
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
560 mkdir $outdir/change_o
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
561
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
562 tmp="$PWD"
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
563
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
564 cd $outdir/change_o
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
565
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
566 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
567 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
55
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
568 Rscript $dir/change_o/select_first_in_clone.r $outdir/change_o/change-o-db-defined_clones.txt $outdir/change_o/change-o-db-defined_first_clones.txt 2>&1
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
569
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
570 mkdir $outdir/new_IMGT_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
571 cp $outdir/new_IMGT/* $outdir/new_IMGT_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
572
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
573 Rscript $dir/new_imgt.r $outdir/new_IMGT_changeo $outdir/change_o/change-o-db-defined_first_clones.txt "-" 2>&1
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
574
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
575 cd $outdir/new_IMGT_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
576 tar -cJf ../new_IMGT_first_seq_of_clone.txz *
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
577 cd $outdir/change_o
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
578
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
579 rm -rf $outdir/new_IMGT_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
580
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
581 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
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
582 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"
55
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
583
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
584 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
585 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
586 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
55
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
587 Rscript $dir/change_o/select_first_in_clone.r $outdir/change_o/change-o-db-defined_clones-IGA.txt $outdir/change_o/change-o-db-defined_first_clones-IGA.txt 2>&1
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
588
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
589 mkdir $outdir/new_IMGT_IGA_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
590 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
591
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
592 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA_changeo $outdir/change_o/change-o-db-defined_first_clones-IGA.txt "-" 2>&1
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
593
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
594 cd $outdir/new_IMGT_IGA_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
595 tar -cJf ../new_IMGT_IGA_first_seq_of_clone.txz *
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
596
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
597 rm -rf $outdir/new_IMGT_IGA_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
598
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
599 cd $outdir/change_o
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
600 else
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
601 echo "No IGA sequences" > "$outdir/change_o/change-o-db-defined_clones-IGA.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
602 echo "No IGA sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGA.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
603 fi
55
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
604
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
605 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
606 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
607 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
55
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
608 Rscript $dir/change_o/select_first_in_clone.r $outdir/change_o/change-o-db-defined_clones-IGG.txt $outdir/change_o/change-o-db-defined_first_clones-IGG.txt 2>&1
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
609
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
610 mkdir $outdir/new_IMGT_IGG_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
611 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
612
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
613 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG_changeo $outdir/change_o/change-o-db-defined_first_clones-IGG.txt "-" 2>&1
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
614
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
615 cd $outdir/new_IMGT_IGG_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
616 tar -cJf ../new_IMGT_IGG_first_seq_of_clone.txz *
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
617 rm -rf $outdir/new_IMGT_IGG_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
618
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
619 cd $outdir/change_o
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
620 else
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
621 echo "No IGG sequences" > "$outdir/change_o/change-o-db-defined_clones-IGG.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
622 echo "No IGG sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGG.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
623 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
624
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
625 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
626 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
627 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
55
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
628 Rscript $dir/change_o/select_first_in_clone.r $outdir/change_o/change-o-db-defined_clones-IGM.txt $outdir/change_o/change-o-db-defined_first_clones-IGM.txt 2>&1
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
629
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
630 mkdir $outdir/new_IMGT_IGM_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
631 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGM_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
632
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
633 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGM_changeo $outdir/change_o/change-o-db-defined_first_clones-IGM.txt "-" 2>&1
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
634
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
635 cd $outdir/new_IMGT_IGM_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
636 tar -cJf ../new_IMGT_IGM_first_seq_of_clone.txz *
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
637
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
638 rm -rf $outdir/new_IMGT_IGM_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
639
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
640 cd $outdir/change_o
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
641 else
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
642 echo "No IGM sequences" > "$outdir/change_o/change-o-db-defined_clones-IGM.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
643 echo "No IGM sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGM.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
644 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
645
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
646 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
647 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
648 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
55
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
649 Rscript $dir/change_o/select_first_in_clone.r $outdir/change_o/change-o-db-defined_clones-IGE.txt $outdir/change_o/change-o-db-defined_first_clones-IGE.txt 2>&1
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
650
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
651 mkdir $outdir/new_IMGT_IGE_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
652 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGE_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
653
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
654 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGE_changeo $outdir/change_o/change-o-db-defined_first_clones-IGE.txt "-" 2>&1
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
655
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
656 cd $outdir/new_IMGT_IGE_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
657 tar -cJf ../new_IMGT_IGE_first_seq_of_clone.txz *
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
658
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
659 rm -rf $outdir/new_IMGT_IGE_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
660
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
661 cd $outdir/change_o
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
662 else
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
663 echo "No IGE sequences" > "$outdir/change_o/change-o-db-defined_clones-IGE.txt"
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
664 echo "No IGE sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGE.txt"
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
665 fi
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
666
55
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
667 cd "$tmp"
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
668
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
669 rm -rf $outdir/new_IMGT
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
670 rm -rf $outdir/new_IMGT_IGA/
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
671 rm -rf $outdir/new_IMGT_IGA1/
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
672 rm -rf $outdir/new_IMGT_IGA2/
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
673 rm -rf $outdir/new_IMGT_IGG/
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
674 rm -rf $outdir/new_IMGT_IGG1/
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
675 rm -rf $outdir/new_IMGT_IGG2/
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
676 rm -rf $outdir/new_IMGT_IGG3/
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
677 rm -rf $outdir/new_IMGT_IGG4/
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
678 rm -rf $outdir/new_IMGT_IGM/
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
679 rm -rf $outdir/new_IMGT_IGE/
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
680
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
681 echo "<div class='tabbertab' title='Clonal Relation' style='width: 7000px;'>" >> $output #clonality tab
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
682
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
683 function clonality_table {
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
684 local infile=$1
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
685 local outfile=$2
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
686
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
687 echo "<table class='pure-table pure-table-striped'>" >> $outfile
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
688 echo "<thead><tr><th>Clone size</th><th>Nr of clones</th><th>Nr of sequences</th></tr></thead>" >> $outfile
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
689
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
690 first='true'
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
691
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
692 while read size clones seqs
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
693 do
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
694 if [[ "$first" == "true" ]]; then
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
695 first="false"
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
696 continue
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
697 fi
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
698 echo "<tr><td>$size</td><td>$clones</td><td>$seqs</td></tr>" >> $outfile
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
699 done < $infile
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
700
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
701 echo "</table>" >> $outfile
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
702 }
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
703 echo "<div class='tabber'>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
704
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
705 echo "<div class='tabbertab' title='All'>" >> $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
706 clonality_table $outdir/change_o/change-o-defined_clones-summary.txt $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
707 echo "</div>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
708
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
709 echo "<div class='tabbertab' title='IGA'>" >> $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
710 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGA.txt $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
711 echo "</div>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
712
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
713 echo "<div class='tabbertab' title='IGG'>" >> $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
714 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGG.txt $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
715 echo "</div>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
716
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
717 echo "<div class='tabbertab' title='IGM'>" >> $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
718 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
719 echo "</div>" >> $output
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
720
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
721 echo "<div class='tabbertab' title='IGE'>" >> $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
722 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
723 echo "</div>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
724
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
725 echo "<div class='tabbertab' title='Overlap' style='width: 7000px;'>" >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
726 cat "$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
727 echo "</div>" >> $output
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
728
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
729 echo "</div>" >> $output #clonality tabber end
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
730
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
731 echo "<br />" >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
732 cat $dir/shm_clonality.htm >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
733
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
734 echo "</div>" >> $output #clonality tab end
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
735
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
736 fi
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
737
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
738 echo "<div class='tabbertab' title='Downloads'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
739
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
740 echo "<table class='pure-table pure-table-striped'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
741 echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
742 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
743 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
744 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
745
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
746 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Overview</td></tr>" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
747 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
748 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
749 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
750 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
751 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
752 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
753 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
754 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
755
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
756 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Frequency</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
757 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
758 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
759 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
760
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
761 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Transition Tables</td></tr>" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
762 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
763 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
764 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
765 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
766 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
767 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
768 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
769 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
770 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
771 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
772 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
773
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
774 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Antigen Selection</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
775 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
776 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
777
29
80c4eebf7bc9 Uploaded
davidvanzessen
parents: 28
diff changeset
778 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
779 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
780 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
781 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
782 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
783
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
784 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
785 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
786 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
787 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
788 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
789 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
790 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
791 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
792 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
793 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
794
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
795 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>CSR</td></tr>" >> $output
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
796 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
797 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
798
55
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
799
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
800 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Clonal Relation</td></tr>" >> $output
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
801 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
802 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
803 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
55
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
804 echo "<tr><td>An IMGT archive with just just the first sequence of a clone</td><td><a href='new_IMGT_first_seq_of_clone.txz' download='new_IMGT_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
805
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
806 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
807 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
55
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
808 echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGA)</td><td><a href='new_IMGT_IGA_first_seq_of_clone.txz' download='new_IMGT_IGA_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
809
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
810 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
811 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
55
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
812 echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGG)</td><td><a href='new_IMGT_IGG_first_seq_of_clone.txz' download='new_IMGT_IGG_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
813
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
814 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
815 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
55
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
816 echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGM)</td><td><a href='new_IMGT_IGM_first_seq_of_clone.txz' download='new_IMGT_IGM_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
817
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
818 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
819 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
55
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
820 echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGE)</td><td><a href='new_IMGT_IGE_first_seq_of_clone.txz' download='new_IMGT_IGE_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
821
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
822 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Filtered IMGT output files</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
823 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
824 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
825 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
826 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
827 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
828 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
829 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
830 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
831 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
832 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
833 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
834
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
835 echo "</table>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
836
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
837 echo "<br />" >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
838 cat $dir/shm_downloads.htm >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
839
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
840 echo "</div>" >> $output #downloads tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
841
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
842 echo "</div>" >> $output #tabs end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
843
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
844 echo "</html>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
845
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
846
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
847 echo "---------------- naive_output.r ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
848 echo "---------------- naive_output.r ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
849
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
850 if [[ "$naive_output" == "yes" ]]
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
851 then
28
c0ecc31829bd Uploaded
davidvanzessen
parents: 26
diff changeset
852 echo "output naive output"
18
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
853 if [[ "${class_filter}" == "101_101" ]]
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
854 then
28
c0ecc31829bd Uploaded
davidvanzessen
parents: 26
diff changeset
855 echo "copy new_IMGT.txz to ${naive_output_all}"
21
c281993e515b Uploaded
davidvanzessen
parents: 20
diff changeset
856 cp $outdir/new_IMGT.txz ${naive_output_all}
18
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
857 else
28
c0ecc31829bd Uploaded
davidvanzessen
parents: 26
diff changeset
858 echo "copy for classes"
18
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
859 cp $outdir/new_IMGT_IGA.txz ${naive_output_ca}
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
860 cp $outdir/new_IMGT_IGG.txz ${naive_output_cg}
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
861 cp $outdir/new_IMGT_IGM.txz ${naive_output_cm}
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
862 cp $outdir/new_IMGT_IGE.txz ${naive_output_ce}
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
863 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
864 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
865
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
866 echo "</table>" >> $outdir/base_overview.html
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
867
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
868 mv $log $outdir/log.html
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
869
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
870 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
871 echo "<table border = 1>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
872 echo "<thead><tr><th>Info</th><th>Sequences</th><th>Percentage</th></tr></thead>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
873 tIFS="$TMP"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
874 IFS=$'\t'
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
875 while read step seq perc
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
876 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
877 echo "<tr>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
878 echo "<td>$step</td>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
879 echo "<td>$seq</td>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
880 echo "<td>${perc}%</td>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
881 echo "</tr>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
882 done < $outdir/filtering_steps.txt
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
883 echo "</table>" >> $log
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
884 echo "<br />" >> $log
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
885 cat $dir/shm_first.htm >> $log
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
886 echo "</center></html>" >> $log
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
887
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
888 IFS="$tIFS"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
889
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
890
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
891 echo "---------------- Done! ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
892 echo "---------------- Done! ----------------<br />" >> $outdir/log.html
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
893
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
894
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
895
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
896
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
897
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
898
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
899
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
900
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
901
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
902
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
903
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
904
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
905
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
906
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
907
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
908
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
909
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
910
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
911
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
912
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
913