annotate wrapper.sh @ 7:ad9be244b104 draft

Uploaded
author davidvanzessen
date Mon, 07 Nov 2016 03:04:07 -0500
parents 2ddb9a21f635
children 59765d2c8890
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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 filter_unique=${13}
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18 class_filter=${14}
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19 empty_region_filter=${15}
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20 fast=${16}
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21 mkdir $outdir
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22
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23 tar -xzf $dir/style.tar.gz -C $outdir
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24
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25 echo "---------------- read parameters ----------------"
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26 echo "---------------- read parameters ----------------<br />" > $log
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27
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28 echo "unpacking IMGT file"
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29
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30 type="`file $input`"
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31 if [[ "$type" == *"Zip archive"* ]] ; then
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32 echo "Zip archive"
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33 echo "unzip $input -d $PWD/files/"
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34 unzip $input -d $PWD/files/
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35 elif [[ "$type" == *"XZ compressed data"* ]] ; then
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36 echo "ZX archive"
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37 echo "tar -xJf $input -C $PWD/files/"
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38 mkdir -p $PWD/files/$title
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39 tar -xJf $input -C $PWD/files/$title
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40 fi
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41
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42 cat `find $PWD/files/ -name "1_*"` > $PWD/summary.txt
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43 cat `find $PWD/files/ -name "3_*"` > $PWD/sequences.txt
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44 cat `find $PWD/files/ -name "5_*"` > $PWD/aa.txt
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45 cat `find $PWD/files/ -name "6_*"` > $PWD/junction.txt
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46 cat `find $PWD/files/ -name "7_*"` > $PWD/mutationanalysis.txt
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47 cat `find $PWD/files/ -name "8_*"` > $PWD/mutationstats.txt
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48 cat `find $PWD/files/ -name "10_*"` > $PWD/hotspots.txt
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49
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50 if [[ ${#BLASTN_DIR} -ge 5 ]] ; then
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51 echo "On server, using BLASTN_DIR env: ${BLASTN_DIR}"
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52 else
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53 BLASTN_DIR="/home/galaxy/Downloads/ncbi-blast-2.4.0+/bin"
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54 echo "Dev Galaxy set BLASTN_DIR to: ${BLASTN_DIR}"
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55 fi
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56
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57 echo "---------------- class identification ----------------"
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58 echo "---------------- class identification ----------------<br />" >> $log
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59
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60 python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt
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61
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62 echo "---------------- merge_and_filter.r ----------------"
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63 echo "---------------- merge_and_filter.r ----------------<br />" >> $log
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64
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65 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $outdir/identified_genes.txt $outdir/merged.txt $outdir/before_unique_filter.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${class_filter} ${empty_region_filter} 2>&1
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66
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67 if [[ "$fast" == "no" ]] ; then
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68
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69 echo "---------------- creating new IMGT zips ----------------"
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70 echo "---------------- creating new IMGT zips ----------------<br />" >> $log
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71
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72 mkdir $outdir/new_IMGT
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73
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74 cat `find $PWD/files/ -name "1_*"` > "$outdir/new_IMGT/1_Summary.txt"
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75 cat `find $PWD/files/ -name "2_*"` > "$outdir/new_IMGT/2_IMGT-gapped-nt-sequences.txt"
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76 cat `find $PWD/files/ -name "3_*"` > "$outdir/new_IMGT/3_Nt-sequences.txt"
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77 cat `find $PWD/files/ -name "4_*"` > "$outdir/new_IMGT/4_IMGT-gapped-AA-sequences.txt"
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78 cat `find $PWD/files/ -name "5_*"` > "$outdir/new_IMGT/5_AA-sequences.txt"
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79 cat `find $PWD/files/ -name "6_*"` > "$outdir/new_IMGT/6_Junction.txt"
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80 cat `find $PWD/files/ -name "7_*"` > "$outdir/new_IMGT/7_V-REGION-mutation-and-AA-change-table.txt"
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81 cat `find $PWD/files/ -name "8_*"` > "$outdir/new_IMGT/8_V-REGION-nt-mutation-statistics.txt"
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82 cat `find $PWD/files/ -name "9_*"` > "$outdir/new_IMGT/9_V-REGION-AA-change-statistics.txt"
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83 cat `find $PWD/files/ -name "10_*"` > "$outdir/new_IMGT/10_V-REGION-mutation-hotspots.txt"
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85 mkdir $outdir/new_IMGT_IGA
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86 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA
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88 mkdir $outdir/new_IMGT_IGA1
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89 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA1
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91 mkdir $outdir/new_IMGT_IGA2
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92 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA2
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94 mkdir $outdir/new_IMGT_IGG
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95 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG
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97 mkdir $outdir/new_IMGT_IGG1
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98 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG1
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100 mkdir $outdir/new_IMGT_IGG2
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101 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG2
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103 mkdir $outdir/new_IMGT_IGG3
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104 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG3
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106 mkdir $outdir/new_IMGT_IGG4
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107 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG4
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108
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109 mkdir $outdir/new_IMGT_IGM
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110 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGM
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112 mkdir $outdir/new_IMGT_IGE
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113 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGE
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114
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115 Rscript $dir/new_imgt.r $outdir/new_IMGT/ $outdir/merged.txt "-" 2>&1
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116
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117 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA/ $outdir/merged.txt "IGA" 2>&1
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118 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA1/ $outdir/merged.txt "IGA1" 2>&1
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119 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA2/ $outdir/merged.txt "IGA2" 2>&1
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120
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121 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG/ $outdir/merged.txt "IGG" 2>&1
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122 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG1/ $outdir/merged.txt "IGG1" 2>&1
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123 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG2/ $outdir/merged.txt "IGG2" 2>&1
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124 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG3/ $outdir/merged.txt "IGG3" 2>&1
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125 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG4/ $outdir/merged.txt "IGG4" 2>&1
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126
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127 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGM/ $outdir/merged.txt "IGM" 2>&1
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128
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129 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGE/ $outdir/merged.txt "IGE" 2>&1
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131
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132 tmp="$PWD"
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133 cd $outdir/new_IMGT/ #tar weirdness...
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134 tar -cJf ../new_IMGT.txz *
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135
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136 cd $outdir/new_IMGT_IGA/
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137 tar -cJf ../new_IMGT_IGA.txz *
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138
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139 cd $outdir/new_IMGT_IGA1/
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140 tar -cJf ../new_IMGT_IGA1.txz *
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141
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142 cd $outdir/new_IMGT_IGA2/
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143 tar -cJf ../new_IMGT_IGA2.txz *
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145 cd $outdir/new_IMGT_IGG/
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146 tar -cJf ../new_IMGT_IGG.txz *
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147
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148 cd $outdir/new_IMGT_IGG1/
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149 tar -cJf ../new_IMGT_IGG1.txz *
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151 cd $outdir/new_IMGT_IGG2/
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152 tar -cJf ../new_IMGT_IGG2.txz *
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153
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154 cd $outdir/new_IMGT_IGG3/
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155 tar -cJf ../new_IMGT_IGG3.txz *
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156
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157 cd $outdir/new_IMGT_IGG4/
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158 tar -cJf ../new_IMGT_IGG4.txz *
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159
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160 cd $outdir/new_IMGT_IGM/
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161 tar -cJf ../new_IMGT_IGM.txz *
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162
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163 cd $outdir/new_IMGT_IGE/
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164 tar -cJf ../new_IMGT_IGE.txz *
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165
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166 cd $tmp
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167 fi
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168
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169 echo "---------------- shm_csr.r ----------------"
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170 echo "---------------- shm_csr.r ----------------<br />" >> $log
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171
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172 classes="IGA,IGA1,IGA2,IGG,IGG1,IGG2,IGG3,IGG4,IGM,IGE,unmatched"
0
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davidvanzessen
parents:
diff changeset
173 echo "R mutation analysis"
1
faae21ba5c63 Uploaded
davidvanzessen
parents: 0
diff changeset
174 Rscript $dir/shm_csr.r $outdir/merged.txt $classes $outdir ${empty_region_filter} 2>&1
0
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davidvanzessen
parents:
diff changeset
175
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davidvanzessen
parents:
diff changeset
176 echo "---------------- shm_csr.py ----------------"
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davidvanzessen
parents:
diff changeset
177 echo "---------------- shm_csr.py ----------------<br />" >> $log
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davidvanzessen
parents:
diff changeset
178
1
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davidvanzessen
parents: 0
diff changeset
179 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:
diff changeset
180
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davidvanzessen
parents:
diff changeset
181 echo "---------------- aa_histogram.r ----------------"
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davidvanzessen
parents:
diff changeset
182 echo "---------------- aa_histogram.r ----------------<br />" >> $log
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davidvanzessen
parents:
diff changeset
183
5
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davidvanzessen
parents: 4
diff changeset
184 Rscript $dir/aa_histogram.r $outdir/aa_id_mutations.txt $outdir/absent_aa_id.txt "IGA,IGG,IGM,IGE" $outdir/ 2>&1
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
185 if [ -e "$outdir/aa_histogram_.png" ]; then
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davidvanzessen
parents:
diff changeset
186 mv $outdir/aa_histogram_.png $outdir/aa_histogram.png
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davidvanzessen
parents:
diff changeset
187 mv $outdir/aa_histogram_.txt $outdir/aa_histogram.txt
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davidvanzessen
parents:
diff changeset
188 fi
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davidvanzessen
parents:
diff changeset
189
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
190 genes=(IGA IGA1 IGA2 IGG IGG1 IGG2 IGG3 IGG4 IGM IGE)
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
191
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davidvanzessen
parents:
diff changeset
192 funcs=(sum mean median)
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davidvanzessen
parents:
diff changeset
193 funcs=(sum)
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davidvanzessen
parents:
diff changeset
194
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davidvanzessen
parents:
diff changeset
195 echo "---------------- sequence_overview.r ----------------"
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davidvanzessen
parents:
diff changeset
196 echo "---------------- sequence_overview.r ----------------<br />" >> $log
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davidvanzessen
parents:
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197
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davidvanzessen
parents:
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198 mkdir $outdir/sequence_overview
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davidvanzessen
parents:
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199
7
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davidvanzessen
parents: 6
diff changeset
200 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:
diff changeset
201
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davidvanzessen
parents:
diff changeset
202 echo "<table border='1'>" > $outdir/base_overview.html
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davidvanzessen
parents:
diff changeset
203
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davidvanzessen
parents:
diff changeset
204 while IFS=$'\t' read ID class seq A C G T
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davidvanzessen
parents:
diff changeset
205 do
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davidvanzessen
parents:
diff changeset
206 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:
diff changeset
207 done < $outdir/sequence_overview/ntoverview.txt
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davidvanzessen
parents:
diff changeset
208
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davidvanzessen
parents:
diff changeset
209 echo "<html><center><h1>$title</h1></center>" > $output
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davidvanzessen
parents:
diff changeset
210 echo "<meta name='viewport' content='width=device-width, initial-scale=1'>" >> $output
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davidvanzessen
parents:
diff changeset
211 echo "<script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $output
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davidvanzessen
parents:
diff changeset
212 echo "<script type='text/javascript' src='tabber.js'></script>" >> $output
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davidvanzessen
parents:
diff changeset
213 echo "<script type='text/javascript' src='script.js'></script>" >> $output
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davidvanzessen
parents:
diff changeset
214 echo "<link rel='stylesheet' type='text/css' href='style.css'>" >> $output
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davidvanzessen
parents:
diff changeset
215 echo "<link rel='stylesheet' type='text/css' href='pure-min.css'>" >> $output
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davidvanzessen
parents:
diff changeset
216
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davidvanzessen
parents:
diff changeset
217 matched_count="`cat $outdir/merged.txt | grep -v 'unmatched' | tail -n +2 | wc -l`"
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davidvanzessen
parents:
diff changeset
218 unmatched_count="`cat $outdir/unmatched.txt | tail -n +2 | wc -l`"
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davidvanzessen
parents:
diff changeset
219 total_count=$((matched_count + unmatched_count))
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davidvanzessen
parents:
diff changeset
220 perc_count=$((unmatched_count / total_count * 100))
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davidvanzessen
parents:
diff changeset
221 perc_count=`bc -l <<< "scale=2; ${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 ) / 1"`
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davidvanzessen
parents:
diff changeset
223
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davidvanzessen
parents:
diff changeset
224 echo "<center><h2>Total: ${total_count}</h2></center>" >> $output
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davidvanzessen
parents:
diff changeset
225 echo "<center><h2>Matched: ${matched_count} Unmatched: ${unmatched_count}</h2></center>" >> $output
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davidvanzessen
parents:
diff changeset
226 echo "<center><h2>Percentage unmatched: ${perc_count}</h2></center>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
227
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davidvanzessen
parents:
diff changeset
228 echo "---------------- main tables ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
229 echo "---------------- main tables ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
230
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davidvanzessen
parents:
diff changeset
231 echo "<div class='tabber'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
232 echo "<div class='tabbertab' title='SHM Overview'>" >> $output
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davidvanzessen
parents:
diff changeset
233
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davidvanzessen
parents:
diff changeset
234 for func in ${funcs[@]}
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davidvanzessen
parents:
diff changeset
235 do
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davidvanzessen
parents:
diff changeset
236
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davidvanzessen
parents:
diff changeset
237 echo "---------------- $func table ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
238 echo "---------------- $func table ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
239
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davidvanzessen
parents:
diff changeset
240 cat $outdir/mutations_${func}.txt $outdir/hotspot_analysis_${func}.txt > $outdir/data_${func}.txt
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davidvanzessen
parents:
diff changeset
241
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davidvanzessen
parents:
diff changeset
242 echo "---------------- pattern_plots.r ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
243 echo "---------------- pattern_plots.r ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
244
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davidvanzessen
parents:
diff changeset
245 Rscript $dir/pattern_plots.r $outdir/data_${func}.txt $outdir/plot1 $outdir/plot2 $outdir/plot3 2>&1
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
246
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davidvanzessen
parents:
diff changeset
247 echo "<table class='pure-table pure-table-striped'>" >> $output
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davidvanzessen
parents:
diff changeset
248 echo "<thead><tr><th>info</th>" >> $output
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davidvanzessen
parents:
diff changeset
249
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davidvanzessen
parents:
diff changeset
250 if [ "${class_filter}" != "101_101" ] ; then
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davidvanzessen
parents:
diff changeset
251
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davidvanzessen
parents:
diff changeset
252 for gene in ${genes[@]}
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davidvanzessen
parents:
diff changeset
253 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
254 tmp=`cat $outdir/${gene}_${func}_n.txt`
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davidvanzessen
parents:
diff changeset
255 echo "<th><a href='matched_${gene}_${func}.txt'>${gene} (N = $tmp)</a></th>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
256 done
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davidvanzessen
parents:
diff changeset
257
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davidvanzessen
parents:
diff changeset
258 tmp=`cat $outdir/all_${func}_n.txt`
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
259 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
260 tmp=`cat $outdir/unmatched_${func}_n.txt`
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
261 echo "<th><a href='unmatched.txt'>unmatched (N = ${unmatched_count})</a></th><tr></thead>" >> $output
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davidvanzessen
parents:
diff changeset
262
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
263 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
264 do
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davidvanzessen
parents:
diff changeset
265 if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] ; then #meh
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
266 echo "<tr><td>$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>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
267 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
268 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>" >> $output
0
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davidvanzessen
parents:
diff changeset
269 else
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
270 echo "<tr><td>$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
271 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
272 done < $outdir/data_${func}.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
273
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
274 else
3
275ab5175fd6 Uploaded
davidvanzessen
parents: 2
diff changeset
275 tmp=`cat $outdir/all_${func}_n.txt`
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
276 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
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davidvanzessen
parents:
diff changeset
277
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
278 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
279 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
280 if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] ; then #meh
3
275ab5175fd6 Uploaded
davidvanzessen
parents: 2
diff changeset
281 echo "<tr><td>$name</td><td>${allx}/${ally}</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
282 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
3
275ab5175fd6 Uploaded
davidvanzessen
parents: 2
diff changeset
283 echo "<tr><td>$name</td><td>${allz}%</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
284 else
3
275ab5175fd6 Uploaded
davidvanzessen
parents: 2
diff changeset
285 echo "<tr><td>$name</td><td>${allx}/${ally} (${allz}%)</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
286 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
287 done < $outdir/data_${func}.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
288
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
289 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
290 echo "</table>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
291 #echo "<a href='data_${func}.txt'>Download data</a>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
292 done
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
293
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
294 echo "<img src='plot1.png' /><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
295 echo "<img src='plot2.png' /><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
296 echo "<img src='plot3.png' /><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
297
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
298 echo "</div>" >> $output #SHM overview tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
299
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
300 echo "---------------- images ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
301 echo "---------------- images ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
302
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
303 echo "<div class='tabbertab' title='SHM Frequency'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
304
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
305 if [ -a $outdir/scatter.png ]
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
306 then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
307 echo "<img src='scatter.png'/><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
308 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
309 if [ -a $outdir/frequency_ranges.png ]
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
310 then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
311 echo "<img src='frequency_ranges.png'/><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
312 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
313
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
314 echo "</div>" >> $output #SHM frequency tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
315
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
316 echo "<div class='tabbertab' title='Transition tables'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
317
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
318 echo "<table border='0'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
319
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
320 for gene in ${genes[@]}
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
321 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
322 echo "<tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
323 echo "<td><h1>${gene}</h1></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
324 echo "<td><img src='transitions_heatmap_${gene}.png' /></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
325 echo "<td><img src='transitions_stacked_${gene}.png' /></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
326 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
327 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
328 first="true"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
329 while IFS=, read from a c g t
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
330 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
331 if [ "$first" == "true" ] ; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
332 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
333 first="false"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
334 else
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
335 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
336 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
337 done < $outdir/transitions_${gene}_sum.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
338 echo "</table></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
339
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
340 echo "</tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
341 done
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
342
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
343 echo "<tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
344 echo "<td><h1>All</h1></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
345 echo "<td><img src='transitions_heatmap_all.png' /></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
346 echo "<td><img src='transitions_stacked_all.png' /></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
347 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
348 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
349 first="true"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
350 while IFS=, read from a c g t
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
351 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
352 if [ "$first" == "true" ] ; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
353 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
354 first="false"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
355 else
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
356 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
357 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
358 done < $outdir/transitions_all_sum.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
359 echo "</table></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
360
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
361 echo "</tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
362
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
363 echo "</table>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
364
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
365 echo "</div>" >> $output #transition tables tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
366
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
367 echo "<div class='tabbertab' title='Antigen Selection'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
368
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
369 if [ -a $outdir/aa_histogram.png ]
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
370 then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
371 echo "<img src='aa_histogram.png'/><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
372 echo "<img src='aa_histogram_IGA.png'/><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
373 echo "<img src='aa_histogram_IGG.png'/><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
374 echo "<img src='aa_histogram_IGM.png'/><br />" >> $output
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
375 echo "<img src='aa_histogram_IGE.png'/><br />" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
376 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
377
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
378 echo "<embed src='baseline.pdf' width='700px' height='1000px'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
379 echo "<embed src='baseline_IGA.pdf' width='700px' height='1000px'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
380 echo "<embed src='baseline_IGG.pdf' width='700px' height='1000px'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
381 echo "<embed src='baseline_IGM.pdf' width='700px' height='1000px'>" >> $output
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
382 echo "<embed src='baseline_IGE.pdf' width='700px' height='1000px'>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
383
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
384 echo "</div>" >> $output #antigen selection tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
385
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
386 echo "<div class='tabbertab' title='CSR'>" >> $output #CSR tab
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
387
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
388 if [ -a $outdir/IGA.png ]
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
389 then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
390 echo "<img src='IGA.png'/><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
391 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
392 if [ -a $outdir/IGG.png ]
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
393 then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
394 echo "<img src='IGG.png'/><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
395 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
396
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
397 echo "</div>" >> $output #CSR tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
398
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
399 if [[ "$fast" == "no" ]] ; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
400
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
401 echo "---------------- change-o MakeDB ----------------"
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
402
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
403 mkdir $outdir/change_o
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
404
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
405 tmp="$PWD"
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
406
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
407 cd $outdir/change_o
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
408
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
409 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
410 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
411
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
412 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
413
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
414 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
415
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
416 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
417 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
418 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 $outdir/change_o/change-o-defined_clones-summary-IGA.txt
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
419 else
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
420 echo "No IGA sequences" > "$outdir/change_o/change-o-db-defined_clones-IGA.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
421 echo "No IGA sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGA.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
422 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
423
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
424 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
425 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
426 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 $outdir/change_o/change-o-defined_clones-summary-IGG.txt
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
427 else
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
428 echo "No IGG sequences" > "$outdir/change_o/change-o-db-defined_clones-IGG.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
429 echo "No IGG sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGG.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
430 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
431
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
432 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
433 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
434 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 $outdir/change_o/change-o-defined_clones-summary-IGM.txt
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
435 else
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
436 echo "No IGM sequences" > "$outdir/change_o/change-o-db-defined_clones-IGM.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
437 echo "No IGM sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGM.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
438 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
439
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
440 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
441 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
442 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 $outdir/change_o/change-o-defined_clones-summary-IGE.txt
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
443 else
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
444 echo "No IGE sequences" > "$outdir/change_o/change-o-db-defined_clones-IGE.txt"
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
445 echo "No IGE sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGE.txt"
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
446 fi
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
447
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
448 PWD="$tmp"
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
449
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
450 echo "<div class='tabbertab' title='Clonality'>" >> $output #clonality tab
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
451
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
452 function clonality_table {
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
453 local infile=$1
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
454 local outfile=$2
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
455
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
456 echo "<table class='pure-table pure-table-striped'>" >> $outfile
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
457 echo "<thead><tr><th>Clone size</th><th>Nr of clones</th><th>Nr of sequences</th></tr></thead>" >> $outfile
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
458
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
459 first='true'
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
460
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
461 while read size clones seqs
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
462 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
463 if [[ "$first" == "true" ]]; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
464 first="false"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
465 continue
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
466 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
467 echo "<tr><td>$size</td><td>$clones</td><td>$seqs</td></tr>" >> $outfile
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
468 done < $infile
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
469
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
470 echo "</table>" >> $outfile
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
471 }
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
472 echo "<div class='tabber'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
473
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
474 echo "<div class='tabbertab' title='All'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
475 clonality_table $outdir/change_o/change-o-defined_clones-summary.txt $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
476 echo "</div>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
477
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
478 echo "<div class='tabbertab' title='IGA'>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
479 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGA.txt $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
480 echo "</div>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
481
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
482 echo "<div class='tabbertab' title='IGG'>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
483 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGG.txt $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
484 echo "</div>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
485
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
486 echo "<div class='tabbertab' title='IGM'>" >> $output
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
487 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
488 echo "</div>" >> $output
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
489
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
490 echo "<div class='tabbertab' title='IGE'>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
491 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
492 echo "</div>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
493
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
494 echo "<div class='tabbertab' title='Overview'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
495 cat "$outdir/sequence_overview/index.html" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
496 echo "</div>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
497
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
498
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
499 echo "</div>" >> $output #clonality tabber end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
500
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
501 echo "</div>" >> $output #clonality tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
502
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
503 fi
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
504
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
505 echo "<div class='tabbertab' title='Downloads'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
506
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
507 echo "<table class='pure-table pure-table-striped'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
508 echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
509 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
510 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
511 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
512
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
513 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Overview</td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
514 echo "<tr><td>The SHM Overview table as a dataset</td><td><a href='data_sum.txt' download='data_sum.txt' >Download</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
515 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
516 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
517 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
518 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
519 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
520 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
521
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
522 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Frequency</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
523 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
524 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
525 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
526
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
527 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Transition Tables</td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
528 echo "<tr><td>The data for the 'all' transition plot</td><td><a href='transition_all_sum.txt' download='transition_all_sum.txt' >Download</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
529 echo "<tr><td>The data for the 'IGA' transition plot</td><td><a href='transition_IGA_sum.txt' download='transition_all_sum.txt' >Download</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
530 echo "<tr><td>The data for the 'IGA1' transition plot</td><td><a href='transition_IGA1_sum.txt' download='transition_IGA1_sum.txt' >Download</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
531 echo "<tr><td>The data for the 'IGA1' transition plot</td><td><a href='transition_IGA1_sum.txt' download='transition_IGA1_sum.txt' >Download</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
532 echo "<tr><td>The data for the 'IGG' transition plot</td><td><a href='transition_IGG_sum.txt' download='transition_IGG_sum.txt' >Download</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
533 echo "<tr><td>The data for the 'IGG1' transition plot</td><td><a href='transition_IGG1_sum.txt' download='transition_IGG1_sum.txt' >Download</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
534 echo "<tr><td>The data for the 'IGG2' transition plot</td><td><a href='transition_IGG2_sum.txt' download='transition_IGG2_sum.txt' >Download</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
535 echo "<tr><td>The data for the 'IGG3' transition plot</td><td><a href='transition_IGG3_sum.txt' download='transition_IGG3_sum.txt' >Download</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
536 echo "<tr><td>The data for the 'IGG4' transition plot</td><td><a href='transition_IGG4_sum.txt' download='transition_IGG4_sum.txt' >Download</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
537 echo "<tr><td>The data for the 'IGM' transition plot</td><td><a href='transition_IGM_sum.txt' download='transition_IGM_sum.txt' >Download</a></td></tr>" >> $output
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
538 echo "<tr><td>The data for the 'IGE' transition plot</td><td><a href='transition_IGE_sum.txt' download='transition_IGE_sum.txt' >Download</a></td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
539
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
540 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Antigen Selection</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
541 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
542 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
543
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
544 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
545 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
546 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
547 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
548 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
549 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
550 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
551 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
552 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
553
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
554 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>CSR</td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
555 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
556 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
557
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
558 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Clonality</td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
559 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
560 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
561 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
562 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
563 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
564 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
565 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
566 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
567 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
568 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
569 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
570
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
571 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Filtered IMGT output files</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
572 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
573 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
574 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
575 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
576 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
577 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
578 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
579 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
580 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
581 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
582 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
583
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
584 echo "</table>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
585
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
586 echo "</div>" >> $output #downloads tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
587
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
588 echo "</div>" >> $output #tabs end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
589
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
590 echo "</html>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
591
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
592
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
593 if [[ "$fast" == "no" ]] ; then
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
594
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
595 echo "---------------- baseline ----------------"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
596 echo "---------------- baseline ----------------<br />" >> $log
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
597 tmp="$PWD"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
598
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
599 mkdir $outdir/baseline
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
600
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
601
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
602 mkdir $outdir/baseline/IGA_IGG_IGM
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
603 if [[ $(wc -l < $outdir/new_IMGT/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
604 cd $outdir/baseline/IGA_IGG_IGM
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
605 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
606 else
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
607 echo "No sequences" > "$outdir/baseline.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
608 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
609
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
610 mkdir $outdir/baseline/IGA
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
611 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
612 cd $outdir/baseline/IGA
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
613 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
614 else
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
615 echo "No IGA sequences" > "$outdir/baseline_IGA.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
616 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
617
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
618 mkdir $outdir/baseline/IGG
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
619 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
620 cd $outdir/baseline/IGG
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
621 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
622 else
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
623 echo "No IGG sequences" > "$outdir/baseline_IGG.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
624 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
625
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
626 mkdir $outdir/baseline/IGM
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
627 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
628 cd $outdir/baseline/IGM
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
629 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
630 else
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
631 echo "No IGM sequences" > "$outdir/baseline_IGM.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
632 fi
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
633
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
634 mkdir $outdir/baseline/IGE
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
635 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
636 cd $outdir/baseline/IGE
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
637 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
638 else
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
639 echo "No IGE sequences" > "$outdir/baseline_IGE.txt"
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
640 fi
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
641
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
642 cd $tmp
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
643
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
644 echo "Cleaning up *.RData files"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
645 find $outdir/baseline -name "*.RData" -type f -delete
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
646
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
647 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
648
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
649 echo "---------------- naive_output.r ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
650 echo "---------------- naive_output.r ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
651
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
652 if [[ "$naive_output" == "yes" ]]
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
653 then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
654 cp $outdir/new_IMGT_IGA.txz ${naive_output_ca}
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
655 cp $outdir/new_IMGT_IGG.txz ${naive_output_cg}
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
656 cp $outdir/new_IMGT_IGM.txz ${naive_output_cm}
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
657 cp $outdir/new_IMGT_IGE.txz ${naive_output_ce}
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
658 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
659
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
660 echo "</table>" >> $outdir/base_overview.html
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
661
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
662 mv $log $outdir/log.html
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
663
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
664 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
665 echo "<table border = 1>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
666 echo "<thead><tr><th>Info</th><th>Sequences</th><th>Percentage</th></tr></thead>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
667 tIFS="$TMP"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
668 IFS=$'\t'
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
669 while read step seq perc
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
670 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
671 echo "<tr>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
672 echo "<td>$step</td>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
673 echo "<td>$seq</td>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
674 echo "<td>${perc}%</td>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
675 echo "</tr>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
676 done < $outdir/filtering_steps.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
677 echo "</table border></center></html>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
678
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
679 IFS="$tIFS"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
680
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
681
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
682 echo "---------------- Done! ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
683 echo "---------------- Done! ----------------<br />" >> $outdir/log.html
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
684
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
685
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
686
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
687
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
688
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
689
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
690
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
691
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
692
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
693
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
694
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
695
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
696
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
697
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
698
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
699
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
700
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
701
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
702
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
703
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
704