annotate wrapper.sh @ 23:81453585dfc3 draft

Uploaded
author davidvanzessen
date Thu, 01 Dec 2016 09:32:06 -0500
parents c281993e515b
children ce25fb581ca3
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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_ca=$9
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14 naive_output_cg=${10}
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15 naive_output_cm=${11}
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16 naive_output_ce=${12}
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17 naive_output_all=${13}
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18 filter_unique=${14}
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19 class_filter=${15}
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20 empty_region_filter=${16}
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21 fast=${17}
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22 mkdir $outdir
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23
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24 tar -xzf $dir/style.tar.gz -C $outdir
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25
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26 echo "---------------- read parameters ----------------"
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27 echo "---------------- read parameters ----------------<br />" > $log
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28
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29 echo "unpacking IMGT file"
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30
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31 type="`file $input`"
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32 if [[ "$type" == *"Zip archive"* ]] ; then
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33 echo "Zip archive"
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34 echo "unzip $input -d $PWD/files/"
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35 unzip $input -d $PWD/files/
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36 elif [[ "$type" == *"XZ compressed data"* ]] ; then
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37 echo "ZX archive"
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38 echo "tar -xJf $input -C $PWD/files/"
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39 mkdir -p $PWD/files/$title
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40 tar -xJf $input -C $PWD/files/$title
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41 fi
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42
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43 cat `find $PWD/files/ -name "1_*"` > $PWD/summary.txt
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44 cat `find $PWD/files/ -name "3_*"` > $PWD/sequences.txt
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45 cat `find $PWD/files/ -name "5_*"` > $PWD/aa.txt
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46 cat `find $PWD/files/ -name "6_*"` > $PWD/junction.txt
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47 cat `find $PWD/files/ -name "7_*"` > $PWD/mutationanalysis.txt
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48 cat `find $PWD/files/ -name "8_*"` > $PWD/mutationstats.txt
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49 cat `find $PWD/files/ -name "10_*"` > $PWD/hotspots.txt
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50
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51 if [[ ${#BLASTN_DIR} -ge 5 ]] ; then
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52 echo "On server, using BLASTN_DIR env: ${BLASTN_DIR}"
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53 else
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54 BLASTN_DIR="/home/galaxy/Downloads/ncbi-blast-2.4.0+/bin"
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55 echo "Dev Galaxy set BLASTN_DIR to: ${BLASTN_DIR}"
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56 fi
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57
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58 echo "---------------- class identification ----------------"
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59 echo "---------------- class identification ----------------<br />" >> $log
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60
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61 python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt
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62
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63 echo "---------------- merge_and_filter.r ----------------"
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64 echo "---------------- merge_and_filter.r ----------------<br />" >> $log
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65
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66 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $PWD/aa.txt $outdir/identified_genes.txt $outdir/merged.txt $outdir/before_unique_filter.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${class_filter} ${empty_region_filter} 2>&1
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68 if [[ "$fast" == "no" ]] ; then
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69
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70 echo "---------------- creating new IMGT zips ----------------"
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71 echo "---------------- creating new IMGT zips ----------------<br />" >> $log
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72
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73 mkdir $outdir/new_IMGT
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74
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75 cat `find $PWD/files/ -name "1_*"` > "$outdir/new_IMGT/1_Summary.txt"
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76 cat `find $PWD/files/ -name "2_*"` > "$outdir/new_IMGT/2_IMGT-gapped-nt-sequences.txt"
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77 cat `find $PWD/files/ -name "3_*"` > "$outdir/new_IMGT/3_Nt-sequences.txt"
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78 cat `find $PWD/files/ -name "4_*"` > "$outdir/new_IMGT/4_IMGT-gapped-AA-sequences.txt"
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79 cat `find $PWD/files/ -name "5_*"` > "$outdir/new_IMGT/5_AA-sequences.txt"
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80 cat `find $PWD/files/ -name "6_*"` > "$outdir/new_IMGT/6_Junction.txt"
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81 cat `find $PWD/files/ -name "7_*"` > "$outdir/new_IMGT/7_V-REGION-mutation-and-AA-change-table.txt"
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82 cat `find $PWD/files/ -name "8_*"` > "$outdir/new_IMGT/8_V-REGION-nt-mutation-statistics.txt"
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83 cat `find $PWD/files/ -name "9_*"` > "$outdir/new_IMGT/9_V-REGION-AA-change-statistics.txt"
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84 cat `find $PWD/files/ -name "10_*"` > "$outdir/new_IMGT/10_V-REGION-mutation-hotspots.txt"
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86 mkdir $outdir/new_IMGT_IGA
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87 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA
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89 mkdir $outdir/new_IMGT_IGA1
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90 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA1
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92 mkdir $outdir/new_IMGT_IGA2
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93 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA2
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95 mkdir $outdir/new_IMGT_IGG
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96 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG
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98 mkdir $outdir/new_IMGT_IGG1
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99 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG1
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101 mkdir $outdir/new_IMGT_IGG2
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102 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG2
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104 mkdir $outdir/new_IMGT_IGG3
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105 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG3
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107 mkdir $outdir/new_IMGT_IGG4
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108 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG4
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110 mkdir $outdir/new_IMGT_IGM
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111 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGM
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113 mkdir $outdir/new_IMGT_IGE
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114 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGE
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115
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116 Rscript $dir/new_imgt.r $outdir/new_IMGT/ $outdir/merged.txt "-" 2>&1
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117
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118 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA/ $outdir/merged.txt "IGA" 2>&1
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119 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA1/ $outdir/merged.txt "IGA1" 2>&1
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120 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA2/ $outdir/merged.txt "IGA2" 2>&1
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121
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122 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG/ $outdir/merged.txt "IGG" 2>&1
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123 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG1/ $outdir/merged.txt "IGG1" 2>&1
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124 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG2/ $outdir/merged.txt "IGG2" 2>&1
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125 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG3/ $outdir/merged.txt "IGG3" 2>&1
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126 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG4/ $outdir/merged.txt "IGG4" 2>&1
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127
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128 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGM/ $outdir/merged.txt "IGM" 2>&1
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129
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130 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGE/ $outdir/merged.txt "IGE" 2>&1
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133 tmp="$PWD"
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134 cd $outdir/new_IMGT/ #tar weirdness...
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135 tar -cJf ../new_IMGT.txz *
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136
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137 cd $outdir/new_IMGT_IGA/
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138 tar -cJf ../new_IMGT_IGA.txz *
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139
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140 cd $outdir/new_IMGT_IGA1/
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141 tar -cJf ../new_IMGT_IGA1.txz *
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142
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143 cd $outdir/new_IMGT_IGA2/
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144 tar -cJf ../new_IMGT_IGA2.txz *
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146 cd $outdir/new_IMGT_IGG/
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147 tar -cJf ../new_IMGT_IGG.txz *
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148
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149 cd $outdir/new_IMGT_IGG1/
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150 tar -cJf ../new_IMGT_IGG1.txz *
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151
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152 cd $outdir/new_IMGT_IGG2/
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153 tar -cJf ../new_IMGT_IGG2.txz *
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154
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155 cd $outdir/new_IMGT_IGG3/
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156 tar -cJf ../new_IMGT_IGG3.txz *
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157
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158 cd $outdir/new_IMGT_IGG4/
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159 tar -cJf ../new_IMGT_IGG4.txz *
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160
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161 cd $outdir/new_IMGT_IGM/
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162 tar -cJf ../new_IMGT_IGM.txz *
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163
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164 cd $outdir/new_IMGT_IGE/
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165 tar -cJf ../new_IMGT_IGE.txz *
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167 cd $tmp
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168 fi
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169
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170 echo "---------------- shm_csr.r ----------------"
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171 echo "---------------- shm_csr.r ----------------<br />" >> $log
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172
5
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parents: 4
diff changeset
173 classes="IGA,IGA1,IGA2,IGG,IGG1,IGG2,IGG3,IGG4,IGM,IGE,unmatched"
0
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davidvanzessen
parents:
diff changeset
174 echo "R mutation analysis"
1
faae21ba5c63 Uploaded
davidvanzessen
parents: 0
diff changeset
175 Rscript $dir/shm_csr.r $outdir/merged.txt $classes $outdir ${empty_region_filter} 2>&1
0
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davidvanzessen
parents:
diff changeset
176
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davidvanzessen
parents:
diff changeset
177 echo "---------------- shm_csr.py ----------------"
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davidvanzessen
parents:
diff changeset
178 echo "---------------- shm_csr.py ----------------<br />" >> $log
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davidvanzessen
parents:
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179
1
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davidvanzessen
parents: 0
diff changeset
180 python $dir/shm_csr.py --input $outdir/merged.txt --genes $classes --empty_region_filter "${empty_region_filter}" --output $outdir/hotspot_analysis.txt
0
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davidvanzessen
parents:
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181
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davidvanzessen
parents:
diff changeset
182 echo "---------------- aa_histogram.r ----------------"
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davidvanzessen
parents:
diff changeset
183 echo "---------------- aa_histogram.r ----------------<br />" >> $log
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davidvanzessen
parents:
diff changeset
184
5
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davidvanzessen
parents: 4
diff changeset
185 Rscript $dir/aa_histogram.r $outdir/aa_id_mutations.txt $outdir/absent_aa_id.txt "IGA,IGG,IGM,IGE" $outdir/ 2>&1
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
186 if [ -e "$outdir/aa_histogram_.png" ]; then
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davidvanzessen
parents:
diff changeset
187 mv $outdir/aa_histogram_.png $outdir/aa_histogram.png
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davidvanzessen
parents:
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188 mv $outdir/aa_histogram_.txt $outdir/aa_histogram.txt
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davidvanzessen
parents:
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189 fi
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davidvanzessen
parents:
diff changeset
190
5
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parents: 4
diff changeset
191 genes=(IGA IGA1 IGA2 IGG IGG1 IGG2 IGG3 IGG4 IGM IGE)
0
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davidvanzessen
parents:
diff changeset
192
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davidvanzessen
parents:
diff changeset
193 funcs=(sum mean median)
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davidvanzessen
parents:
diff changeset
194 funcs=(sum)
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davidvanzessen
parents:
diff changeset
195
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davidvanzessen
parents:
diff changeset
196 echo "---------------- sequence_overview.r ----------------"
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davidvanzessen
parents:
diff changeset
197 echo "---------------- sequence_overview.r ----------------<br />" >> $log
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davidvanzessen
parents:
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198
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parents:
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199 mkdir $outdir/sequence_overview
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parents:
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200
7
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parents: 6
diff changeset
201 Rscript $dir/sequence_overview.r $outdir/before_unique_filter.txt $outdir/merged.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt ${empty_region_filter} 2>&1
0
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davidvanzessen
parents:
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202
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davidvanzessen
parents:
diff changeset
203 echo "<table border='1'>" > $outdir/base_overview.html
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davidvanzessen
parents:
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204
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davidvanzessen
parents:
diff changeset
205 while IFS=$'\t' read ID class seq A C G T
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davidvanzessen
parents:
diff changeset
206 do
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davidvanzessen
parents:
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207 echo "<tr><td>$ID</td><td>$seq</td><td>$class</td><td>$A</td><td>$C</td><td>$G</td><td>$T</td></tr>" >> $outdir/base_overview.html
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davidvanzessen
parents:
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208 done < $outdir/sequence_overview/ntoverview.txt
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davidvanzessen
parents:
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209
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davidvanzessen
parents:
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210 echo "<html><center><h1>$title</h1></center>" > $output
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davidvanzessen
parents:
diff changeset
211 echo "<meta name='viewport' content='width=device-width, initial-scale=1'>" >> $output
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davidvanzessen
parents:
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212 echo "<script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $output
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davidvanzessen
parents:
diff changeset
213 echo "<script type='text/javascript' src='tabber.js'></script>" >> $output
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davidvanzessen
parents:
diff changeset
214 echo "<script type='text/javascript' src='script.js'></script>" >> $output
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davidvanzessen
parents:
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215 echo "<link rel='stylesheet' type='text/css' href='style.css'>" >> $output
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davidvanzessen
parents:
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216 echo "<link rel='stylesheet' type='text/css' href='pure-min.css'>" >> $output
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davidvanzessen
parents:
diff changeset
217
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davidvanzessen
parents:
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218 matched_count="`cat $outdir/merged.txt | grep -v 'unmatched' | tail -n +2 | wc -l`"
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davidvanzessen
parents:
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219 unmatched_count="`cat $outdir/unmatched.txt | tail -n +2 | wc -l`"
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davidvanzessen
parents:
diff changeset
220 total_count=$((matched_count + unmatched_count))
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davidvanzessen
parents:
diff changeset
221 perc_count=$((unmatched_count / total_count * 100))
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davidvanzessen
parents:
diff changeset
222 perc_count=`bc -l <<< "scale=2; ${unmatched_count} / ${total_count} * 100"`
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davidvanzessen
parents:
diff changeset
223 perc_count=`bc -l <<< "scale=2; (${unmatched_count} / ${total_count} * 100 ) / 1"`
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davidvanzessen
parents:
diff changeset
224
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davidvanzessen
parents:
diff changeset
225 echo "<center><h2>Total: ${total_count}</h2></center>" >> $output
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davidvanzessen
parents:
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226 echo "<center><h2>Matched: ${matched_count} Unmatched: ${unmatched_count}</h2></center>" >> $output
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davidvanzessen
parents:
diff changeset
227 echo "<center><h2>Percentage unmatched: ${perc_count}</h2></center>" >> $output
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davidvanzessen
parents:
diff changeset
228
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davidvanzessen
parents:
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229 echo "---------------- main tables ----------------"
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parents:
diff changeset
230 echo "---------------- main tables ----------------<br />" >> $log
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davidvanzessen
parents:
diff changeset
231
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parents:
diff changeset
232 echo "<div class='tabber'>" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
233 echo "<div class='tabbertab' title='SHM Overview' style='width: 3000px;'>" >> $output
0
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davidvanzessen
parents:
diff changeset
234
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davidvanzessen
parents:
diff changeset
235 for func in ${funcs[@]}
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davidvanzessen
parents:
diff changeset
236 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
237
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davidvanzessen
parents:
diff changeset
238 echo "---------------- $func table ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
239 echo "---------------- $func table ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
240
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davidvanzessen
parents:
diff changeset
241 cat $outdir/mutations_${func}.txt $outdir/hotspot_analysis_${func}.txt > $outdir/data_${func}.txt
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parents:
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242
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davidvanzessen
parents:
diff changeset
243 echo "---------------- pattern_plots.r ----------------"
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davidvanzessen
parents:
diff changeset
244 echo "---------------- pattern_plots.r ----------------<br />" >> $log
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davidvanzessen
parents:
diff changeset
245
23
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parents: 21
diff changeset
246 Rscript $dir/pattern_plots.r $outdir/data_${func}.txt $outdir/plot1 $outdir/plot2 $outdir/plot3 $outdir/shm_overview.txt 2>&1
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
247
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davidvanzessen
parents:
diff changeset
248 echo "<table class='pure-table pure-table-striped'>" >> $output
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davidvanzessen
parents:
diff changeset
249 echo "<thead><tr><th>info</th>" >> $output
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davidvanzessen
parents:
diff changeset
250
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davidvanzessen
parents:
diff changeset
251 if [ "${class_filter}" != "101_101" ] ; then
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davidvanzessen
parents:
diff changeset
252
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davidvanzessen
parents:
diff changeset
253 for gene in ${genes[@]}
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davidvanzessen
parents:
diff changeset
254 do
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davidvanzessen
parents:
diff changeset
255 tmp=`cat $outdir/${gene}_${func}_n.txt`
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davidvanzessen
parents:
diff changeset
256 echo "<th><a href='matched_${gene}_${func}.txt'>${gene} (N = $tmp)</a></th>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
257 done
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
258
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davidvanzessen
parents:
diff changeset
259 tmp=`cat $outdir/all_${func}_n.txt`
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davidvanzessen
parents:
diff changeset
260 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
261 tmp=`cat $outdir/unmatched_${func}_n.txt`
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davidvanzessen
parents:
diff changeset
262 echo "<th><a href='unmatched.txt'>unmatched (N = ${unmatched_count})</a></th><tr></thead>" >> $output
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davidvanzessen
parents:
diff changeset
263
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
264 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
0
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davidvanzessen
parents:
diff changeset
265 do
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davidvanzessen
parents:
diff changeset
266 if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] ; then #meh
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
267 echo "<tr><td>$name</td><td>${cax}/${cay} (${caz})</td><td>${ca1x}/${ca1y} (${ca1z})</td><td>${ca2x}/${ca2y} (${ca2z})</td><td>${cgx}/${cgy} (${cgz})</td><td>${cg1x}/${cg1y} (${cg1z})</td><td>${cg2x}/${cg2y} (${cg2z})</td><td>${cg3x}/${cg3y} (${cg3z})</td><td>${cg4x}/${cg4y} (${cg4z})</td><td>${cmx}/${cmy} (${cmz})</td><td>${cex}/${cey} (${cez})</td><td>${allx}/${ally} (${allz})</td><td>${unx}/${uny} (${unz})</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
268 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
269 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>" >> $output
0
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davidvanzessen
parents:
diff changeset
270 else
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
271 echo "<tr><td>$name</td><td>${cax}/${cay} (${caz}%)</td><td>${ca1x}/${ca1y} (${ca1z}%)</td><td>${ca2x}/${ca2y} (${ca2z}%)</td><td>${cgx}/${cgy} (${cgz}%)</td><td>${cg1x}/${cg1y} (${cg1z}%)</td><td>${cg2x}/${cg2y} (${cg2z}%)</td><td>${cg3x}/${cg3y} (${cg3z}%)</td><td>${cg4x}/${cg4y} (${cg4z}%)</td><td>${cmx}/${cmy} (${cmz}%)</td><td>${cex}/${cey} (${cez}%)</td><td>${allx}/${ally} (${allz}%)</td><td>${unx}/${uny} (${unz}%)</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
272 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
273 done < $outdir/data_${func}.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
274
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
275 else
3
275ab5175fd6 Uploaded
davidvanzessen
parents: 2
diff changeset
276 tmp=`cat $outdir/all_${func}_n.txt`
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
277 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
278
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
279 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
280 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
281 if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] ; then #meh
3
275ab5175fd6 Uploaded
davidvanzessen
parents: 2
diff changeset
282 echo "<tr><td>$name</td><td>${allx}/${ally}</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
283 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
3
275ab5175fd6 Uploaded
davidvanzessen
parents: 2
diff changeset
284 echo "<tr><td>$name</td><td>${allz}%</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
285 else
3
275ab5175fd6 Uploaded
davidvanzessen
parents: 2
diff changeset
286 echo "<tr><td>$name</td><td>${allx}/${ally} (${allz}%)</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
287 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
288 done < $outdir/data_${func}.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
289
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
290 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
291 echo "</table>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
292 #echo "<a href='data_${func}.txt'>Download data</a>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
293 done
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
294
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
295 echo "<img src='plot1.png' /><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
296 echo "<img src='plot2.png' /><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
297 echo "<img src='plot3.png' /><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
298
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davidvanzessen
parents:
diff changeset
299 echo "</div>" >> $output #SHM overview tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
300
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
301 echo "---------------- images ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
302 echo "---------------- images ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
303
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
304 echo "<div class='tabbertab' title='SHM Frequency' style='width: 3000px;'>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
305
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
306 if [ -a $outdir/scatter.png ]
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
307 then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
308 echo "<img src='scatter.png'/><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
309 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
310 if [ -a $outdir/frequency_ranges.png ]
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
311 then
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davidvanzessen
parents:
diff changeset
312 echo "<img src='frequency_ranges.png'/><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
313 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
314
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davidvanzessen
parents:
diff changeset
315 echo "</div>" >> $output #SHM frequency tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
316
23
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davidvanzessen
parents: 21
diff changeset
317 echo "<div class='tabbertab' title='Transition tables' style='width: 3000px;'>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
318
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
319 echo "<table border='0'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
320
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
321 for gene in ${genes[@]}
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
322 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
323 echo "<tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
324 echo "<td><h1>${gene}</h1></td>" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
325
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davidvanzessen
parents: 21
diff changeset
326 if [ -e $outdir/transitions_heatmap_${gene}.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
327 then
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
328 echo "<td><img src='transitions_heatmap_${gene}.png' /></td>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
329 else
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davidvanzessen
parents: 21
diff changeset
330 echo "<td></td>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
331 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
332
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
333 if [ -e $outdir/transitions_stacked_${gene}.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
334 then
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
335 echo "<td><img src='transitions_stacked_${gene}.png' /></td>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
336 else
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
337 echo "<td></td>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
338 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
339
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
340 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
341 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
342 first="true"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
343 while IFS=, read from a c g t
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
344 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
345 if [ "$first" == "true" ] ; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
346 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
347 first="false"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
348 else
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
349 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
350 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
351 done < $outdir/transitions_${gene}_sum.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
352 echo "</table></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
353
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
354 echo "</tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
355 done
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
356
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
357 echo "<tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
358 echo "<td><h1>All</h1></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
359 echo "<td><img src='transitions_heatmap_all.png' /></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
360 echo "<td><img src='transitions_stacked_all.png' /></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
361 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
362 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
363 first="true"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
364 while IFS=, read from a c g t
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
365 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
366 if [ "$first" == "true" ] ; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
367 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
368 first="false"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
369 else
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
370 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
371 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
372 done < $outdir/transitions_all_sum.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
373 echo "</table></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
374
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
375 echo "</tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
376
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
377 echo "</table>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
378
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
379 echo "</div>" >> $output #transition tables tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
380
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
381 echo "<div class='tabbertab' title='Antigen Selection'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
382
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
383 if [ -e $outdir/aa_histogram.png ]
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
384 then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
385 echo "<img src='aa_histogram.png'/><br />" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
386 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
387
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
388 if [ -e $outdir/aa_histogram_IGA.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
389 then
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
390 echo "<img src='aa_histogram_IGA.png'/><br />" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
391 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
392
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
393 if [ -e $outdir/aa_histogram_IGG.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
394 then
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
395 echo "<img src='aa_histogram_IGG.png'/><br />" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
396 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
397
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
398 if [ -e $outdir/aa_histogram_IGM.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
399 then
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
400 echo "<img src='aa_histogram_IGM.png'/><br />" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
401 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
402
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
403 if [ -e $outdir/aa_histogram_IGE.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
404 then
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
405 echo "<img src='aa_histogram_IGE.png'/><br />" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
406 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
407
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
408
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
409 if [ -e $outdir/baseline.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
410 then
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
411 echo "<embed src='baseline.pdf' width='700px' height='1000px'>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
412 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
413
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
414 if [ -e $outdir/baseline_IGA.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
415 then
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
416 echo "<embed src='baseline_IGA.pdf' width='700px' height='1000px'>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
417 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
418
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
419 if [ -e $outdir/baseline_IGG.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
420 then
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
421 echo "<embed src='baseline_IGG.pdf' width='700px' height='1000px'>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
422 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
423
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
424 if [ -e $outdir/baseline_IGM.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
425 then
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
426 echo "<embed src='baseline_IGM.pdf' width='700px' height='1000px'>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
427 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
428
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
429 if [ -e $outdir/baseline_IGE.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
430 then
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
431 echo "<embed src='baseline_IGE.pdf' width='700px' height='1000px'>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
432 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
433
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
434 echo "</div>" >> $output #antigen selection tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
435
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
436 echo "<div class='tabbertab' title='CSR'>" >> $output #CSR tab
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
437
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
438 if [ -e $outdir/IGA.png ]
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
439 then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
440 echo "<img src='IGA.png'/><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
441 fi
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
442 if [ -e $outdir/IGG.png ]
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
443 then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
444 echo "<img src='IGG.png'/><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
445 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
446
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
447 echo "</div>" >> $output #CSR tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
448
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
449 if [[ "$fast" == "no" ]] ; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
450
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
451 echo "---------------- change-o MakeDB ----------------"
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
452
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
453 mkdir $outdir/change_o
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
454
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
455 tmp="$PWD"
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
456
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
457 cd $outdir/change_o
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
458
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
459 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
460 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones.txt $outdir/change_o/change-o-defined_clones-summary.txt
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
461
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
462 Rscript $dir/merge.r $outdir/change_o/change-o-db-defined_clones.txt $outdir/merged.txt "all" "Sequence.ID,best_match" "SEQUENCE_ID" "Sequence.ID" $outdir/change_o/change-o-db-defined_clones.txt 2>&1
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
463
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
464 echo "Rscript $dir/merge.r $outdir/change_o/change-o-db-defined_clones.txt $outdir/$outdir/merged.txt 'all' 'Sequence.ID,best_match' 'Sequence.ID' 'Sequence.ID' '\t' $outdir/change_o/change-o-db-defined_clones.txt 2>&1"
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
465
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
466 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
467 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
468 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGA.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGA.txt $outdir/change_o/change-o-defined_clones-summary-IGA.txt
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
469 else
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
470 echo "No IGA sequences" > "$outdir/change_o/change-o-db-defined_clones-IGA.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
471 echo "No IGA sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGA.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
472 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
473
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
474 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
475 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
476 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGG.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGG.txt $outdir/change_o/change-o-defined_clones-summary-IGG.txt
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
477 else
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
478 echo "No IGG sequences" > "$outdir/change_o/change-o-db-defined_clones-IGG.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
479 echo "No IGG sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGG.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
480 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
481
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
482 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
483 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
484 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGM.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGM.txt $outdir/change_o/change-o-defined_clones-summary-IGM.txt
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
485 else
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
486 echo "No IGM sequences" > "$outdir/change_o/change-o-db-defined_clones-IGM.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
487 echo "No IGM sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGM.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
488 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
489
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
490 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
491 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
492 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGE.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGE.txt $outdir/change_o/change-o-defined_clones-summary-IGE.txt
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
493 else
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
494 echo "No IGE sequences" > "$outdir/change_o/change-o-db-defined_clones-IGE.txt"
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
495 echo "No IGE sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGE.txt"
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
496 fi
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
497
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
498 PWD="$tmp"
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
499
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
500 echo "<div class='tabbertab' title='Clonality'>" >> $output #clonality tab
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
501
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
502 function clonality_table {
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
503 local infile=$1
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
504 local outfile=$2
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
505
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
506 echo "<table class='pure-table pure-table-striped'>" >> $outfile
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
507 echo "<thead><tr><th>Clone size</th><th>Nr of clones</th><th>Nr of sequences</th></tr></thead>" >> $outfile
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
508
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
509 first='true'
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
510
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
511 while read size clones seqs
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
512 do
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
513 if [[ "$first" == "true" ]]; then
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
514 first="false"
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
515 continue
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
516 fi
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
517 echo "<tr><td>$size</td><td>$clones</td><td>$seqs</td></tr>" >> $outfile
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
518 done < $infile
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
519
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
520 echo "</table>" >> $outfile
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
521 }
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
522 echo "<div class='tabber'>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
523
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
524 echo "<div class='tabbertab' title='All'>" >> $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
525 clonality_table $outdir/change_o/change-o-defined_clones-summary.txt $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
526 echo "</div>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
527
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
528 echo "<div class='tabbertab' title='IGA'>" >> $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
529 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGA.txt $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
530 echo "</div>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
531
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
532 echo "<div class='tabbertab' title='IGG'>" >> $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
533 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGG.txt $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
534 echo "</div>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
535
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
536 echo "<div class='tabbertab' title='IGM'>" >> $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
537 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
538 echo "</div>" >> $output
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
539
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
540 echo "<div class='tabbertab' title='IGE'>" >> $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
541 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
542 echo "</div>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
543
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
544 echo "<div class='tabbertab' title='Overlap'>" >> $output
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
545 cat "$outdir/sequence_overview/index.html" >> $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
546 echo "</div>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
547
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
548
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
549 echo "</div>" >> $output #clonality tabber end
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
550
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
551 echo "</div>" >> $output #clonality tab end
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
552
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
553 fi
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
554
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
555 echo "<div class='tabbertab' title='Downloads'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
556
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
557 echo "<table class='pure-table pure-table-striped'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
558 echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
559 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
560 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
561 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
562
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
563 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Overview</td></tr>" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
564 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
565 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
566 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
567 echo "<tr><td>Base count for every sequence</td><td><a href='base_overview.html'>View</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
568 echo "<tr><td>The data used to generate the RGYW/WRCY and TW/WA plot</td><td><a href='plot1.txt' download='plot1.txt' >Download</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
569 echo "<tr><td>The data used to generate the relative transition and transversion plot</td><td><a href='plot2.txt' download='plot2.txt' >Download</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
570 echo "<tr><td>The data used to generate the absolute transition and transversion plot</td><td><a href='plot3.txt' download='plot3.txt' >Download</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
571
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
572 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Frequency</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
573 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
574 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
575 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
576
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
577 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Transition Tables</td></tr>" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
578 echo "<tr><td>The data for the 'all' transition plot</td><td><a href='transitions_all_sum.txt' download='transitions_all_sum.txt' >Download</a></td></tr>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
579 echo "<tr><td>The data for the 'IGA' transition plot</td><td><a href='transitions_IGA_sum.txt' download='transitions_all_sum.txt' >Download</a></td></tr>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
580 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
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
581 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
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
582 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
583 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
584 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
585 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
586 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
587 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
588 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
589
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
590 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Antigen Selection</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
591 echo "<tr><td>AA mutation data per sequence ID</td><td><a href='aa_id_mutations.txt' download='aa_id_mutations.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
592 echo "<tr><td>Absent AA location data per sequence ID</td><td><a href='absent_aa_id.txt' download='absent_aa_id.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
593
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
594 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
595 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
596 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
597 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
598 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
599 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
600 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
601 echo "<tr><td>Baseline IGM data</td><td><a href='baseline_IGM.txt' download='baseline_IGM.txt' >Download</a></td></tr>" >> $output
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
602 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
603
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
604 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>CSR</td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
605 echo "<tr><td>The data for the CSR IGA pie plot</td><td><a href='IGA_pie.txt' download='IGA_pie.txt' >Download</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
606 echo "<tr><td>The data for the CSR IGG pie plot</td><td><a href='IGG_pie.txt' download='IGG_pie.txt' >Download</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
607
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
608 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Clonality</td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
609 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
610 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
611 echo "<tr><td>The Change-O DB defined clones summary file</td><td><a href='change_o/change-o-defined_clones-summary.txt' download='change_o/change-o-defined_clones-summary.txt' >Download</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
612 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
613 echo "<tr><td>The Change-O DB defined clones summary file of IGA</td><td><a href='change_o/change-o-defined_clones-summary-IGA.txt' download='change_o/change-o-defined_clones-summary-IGA.txt' >Download</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
614 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
615 echo "<tr><td>The Change-O DB defined clones summary file of IGG</td><td><a href='change_o/change-o-defined_clones-summary-IGG.txt' download='change_o/change-o-defined_clones-summary-IGG.txt' >Download</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
616 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
617 echo "<tr><td>The Change-O DB defined clones summary file of IGM</td><td><a href='change_o/change-o-defined_clones-summary-IGM.txt' download='change_o/change-o-defined_clones-summary-IGM.txt' >Download</a></td></tr>" >> $output
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
618 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
619 echo "<tr><td>The Change-O DB defined clones summary file of IGE</td><td><a href='change_o/change-o-defined_clones-summary-IGE.txt' download='change_o/change-o-defined_clones-summary-IGE.txt' >Download</a></td></tr>" >> $output
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
620
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
621 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Filtered IMGT output files</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
622 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
623 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
624 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
625 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
626 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
627 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
628 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
629 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
630 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
631 echo "<tr><td>An IMGT archive with just the matched and filtered IGM sequences</td><td><a href='new_IMGT_IGM.txz' download='new_IMGT_IGM.txz' >Download</a></td></tr>" >> $output
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
632 echo "<tr><td>An IMGT archive with just the matched and filtered IGE sequences</td><td><a href='new_IMGT_IGE.txz' download='new_IMGT_IGM.txz' >Download</a></td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
633
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
634 echo "</table>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
635
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
636 echo "</div>" >> $output #downloads tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
637
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
638 echo "</div>" >> $output #tabs end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
639
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
640 echo "</html>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
641
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
642
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
643 if [[ "$fast" == "no" ]] ; then
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
644
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
645 echo "---------------- baseline ----------------"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
646 echo "---------------- baseline ----------------<br />" >> $log
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
647 tmp="$PWD"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
648
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
649 mkdir $outdir/baseline
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
650
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
651
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
652 mkdir $outdir/baseline/IGA_IGG_IGM
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
653 if [[ $(wc -l < $outdir/new_IMGT/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
654 cd $outdir/baseline/IGA_IGG_IGM
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
655 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT.txz "IGA_IGG_IGM" "$dir/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
656 else
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
657 echo "No sequences" > "$outdir/baseline.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
658 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
659
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
660 mkdir $outdir/baseline/IGA
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
661 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
662 cd $outdir/baseline/IGA
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
663 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGA.txz "IGA" "$dir/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_IGA.pdf" "Sequence.ID" "$outdir/baseline_IGA.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
664 else
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
665 echo "No IGA sequences" > "$outdir/baseline_IGA.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
666 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
667
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
668 mkdir $outdir/baseline/IGG
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
669 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
670 cd $outdir/baseline/IGG
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
671 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGG.txz "cg" "$dir/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_IGG.pdf" "Sequence.ID" "$outdir/baseline_IGG.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
672 else
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
673 echo "No IGG sequences" > "$outdir/baseline_IGG.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
674 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
675
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
676 mkdir $outdir/baseline/IGM
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
677 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
678 cd $outdir/baseline/IGM
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
679 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGM.txz "IGM" "$dir/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_IGM.pdf" "Sequence.ID" "$outdir/baseline_IGM.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
680 else
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
681 echo "No IGM sequences" > "$outdir/baseline_IGM.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
682 fi
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
683
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
684 mkdir $outdir/baseline/IGE
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
685 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
686 cd $outdir/baseline/IGE
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
687 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGE.txz "IGE" "$dir/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_IGE.pdf" "Sequence.ID" "$outdir/baseline_IGE.txt"
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
688 else
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
689 echo "No IGE sequences" > "$outdir/baseline_IGE.txt"
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
690 fi
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
691
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
692 cd $tmp
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
693
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
694 echo "Cleaning up *.RData files"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
695 find $outdir/baseline -name "*.RData" -type f -delete
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
696
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
697 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
698
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
699 echo "---------------- naive_output.r ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
700 echo "---------------- naive_output.r ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
701
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
702 if [[ "$naive_output" == "yes" ]]
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
703 then
18
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
704 if [[ "${class_filter}" == "101_101" ]]
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
705 then
21
c281993e515b Uploaded
davidvanzessen
parents: 20
diff changeset
706 cp $outdir/new_IMGT.txz ${naive_output_all}
18
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
707 else
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
708 cp $outdir/new_IMGT_IGA.txz ${naive_output_ca}
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
709 cp $outdir/new_IMGT_IGG.txz ${naive_output_cg}
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
710 cp $outdir/new_IMGT_IGM.txz ${naive_output_cm}
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
711 cp $outdir/new_IMGT_IGE.txz ${naive_output_ce}
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
712 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
713 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
714
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
715 echo "</table>" >> $outdir/base_overview.html
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
716
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
717 mv $log $outdir/log.html
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
718
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
719 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
720 echo "<table border = 1>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
721 echo "<thead><tr><th>Info</th><th>Sequences</th><th>Percentage</th></tr></thead>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
722 tIFS="$TMP"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
723 IFS=$'\t'
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
724 while read step seq perc
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
725 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
726 echo "<tr>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
727 echo "<td>$step</td>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
728 echo "<td>$seq</td>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
729 echo "<td>${perc}%</td>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
730 echo "</tr>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
731 done < $outdir/filtering_steps.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
732 echo "</table border></center></html>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
733
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
734 IFS="$tIFS"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
735
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
736
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
737 echo "---------------- Done! ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
738 echo "---------------- Done! ----------------<br />" >> $outdir/log.html
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
739
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
740
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
741
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
742
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
743
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
744
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
745
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
746
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
747
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
748
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
749
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
750
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
751
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
752
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
753
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
754
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
755
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
756
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
757
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
758
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
759