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0
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1 #!/bin/bash
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110
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2 #set -e
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0
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3 dir="$(cd "$(dirname "$0")" && pwd)"
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4 input=$1
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19
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5 method=$2
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102
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6 log=$3 #becomes the main html page at the end
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19
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7 outdir=$4
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102
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8 output="$outdir/index.html" #copied to $log location at the end
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19
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9 title=$5
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22
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10 include_fr1=$6
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34
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11 functionality=$7
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12 unique=$8
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69
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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=${11}
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16 filter_unique=${12}
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17 class_filter=${13}
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114
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18 empty_region_filter=${14}
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0
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19 mkdir $outdir
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20
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110
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21 tar -xzf $dir/style.tar.gz -C $outdir
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22
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55
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23 echo "---------------- read parameters ----------------"
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102
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24 echo "---------------- read parameters ----------------<br />" > $log
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55
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25
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26 echo "unpacking IMGT file"
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27
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35
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28 type="`file $input`"
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29 if [[ "$type" == *"Zip archive"* ]] ; then
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30 echo "Zip archive"
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31 echo "unzip $input -d $PWD/files/"
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32 unzip $input -d $PWD/files/
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33 elif [[ "$type" == *"XZ compressed data"* ]] ; then
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34 echo "ZX archive"
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35 echo "tar -xJf $input -C $PWD/files/"
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36 mkdir -p $PWD/files/$title
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37 tar -xJf $input -C $PWD/files/$title
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38 fi
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39
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64
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40 cat `find $PWD/files/ -name "1_*"` > $PWD/summary.txt
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41 cat `find $PWD/files/ -name "3_*"` > $PWD/sequences.txt
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42 cat `find $PWD/files/ -name "5_*"` > $PWD/aa.txt
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43 cat `find $PWD/files/ -name "6_*"` > $PWD/junction.txt
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44 cat `find $PWD/files/ -name "7_*"` > $PWD/mutationanalysis.txt
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45 cat `find $PWD/files/ -name "8_*"` > $PWD/mutationstats.txt
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46 cat `find $PWD/files/ -name "10_*"` > $PWD/hotspots.txt
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47
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119
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48 if [[ ${#BLASTN_DIR} -ge 5 ]] ; then
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49 echo "On server, using BLASTN_DIR env: ${BLASTN_DIR}"
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50 else
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51 BLASTN_DIR="/home/galaxy/Downloads/ncbi-blast-2.4.0+/bin"
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52 echo "Dev Galaxy set BLASTN_DIR to: ${BLASTN_DIR}"
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53 fi
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19
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54
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89
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55 echo "---------------- identification ($method) ----------------"
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102
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56 echo "---------------- identification ($method) ----------------<br />" >> $log
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55
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57
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19
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58 if [[ "${method}" == "custom" ]] ; then
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59 python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt
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60 else
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119
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61 echo "---------------- summary_to_fasta.py ----------------"
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62 echo "---------------- summary_to_fasta.py ----------------<br />" >> $log
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110
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63
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119
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64 python $dir/summary_to_fasta.py --input $PWD/summary.txt --fasta $PWD/sequences.fasta
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65
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19
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66 echo -e "qseqid\tsseqid\tpident\tlength\tmismatch\tgapopen\tqstart\tqend\tsstart\tsend\tevalue\tbitscore" > $outdir/identified_genes.txt
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67 ${BLASTN_DIR}/blastn -task blastn -db $dir/subclass_definition.db -query $PWD/sequences.fasta -outfmt 6 >> $outdir/identified_genes.txt
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68 fi
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69
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55
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70 echo "---------------- merge_and_filter.r ----------------"
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102
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71 echo "---------------- merge_and_filter.r ----------------<br />" >> $log
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19
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72
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114
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73 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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0
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74
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98
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75 echo "---------------- creating new IMGT zip ----------------"
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102
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76 echo "---------------- creating new IMGT zip ----------------<br />" >> $log
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95
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77
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78 mkdir $outdir/new_IMGT
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79
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80 cat `find $PWD/files/ -name "1_*"` > "$outdir/new_IMGT/1_Summary.txt"
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81 cat `find $PWD/files/ -name "2_*"` > "$outdir/new_IMGT/2_IMGT-gapped-nt-sequences.txt"
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82 cat `find $PWD/files/ -name "3_*"` > "$outdir/new_IMGT/3_Nt-sequences.txt"
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83 cat `find $PWD/files/ -name "4_*"` > "$outdir/new_IMGT/4_IMGT-gapped-AA-sequences.txt"
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84 cat `find $PWD/files/ -name "5_*"` > "$outdir/new_IMGT/5_AA-sequences.txt"
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85 cat `find $PWD/files/ -name "6_*"` > "$outdir/new_IMGT/6_Junction.txt"
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86 cat `find $PWD/files/ -name "7_*"` > "$outdir/new_IMGT/7_V-REGION-mutation-and-AA-change-table.txt"
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87 cat `find $PWD/files/ -name "8_*"` > "$outdir/new_IMGT/8_V-REGION-nt-mutation-statistics.txt"
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88 cat `find $PWD/files/ -name "9_*"` > "$outdir/new_IMGT/9_V-REGION-AA-change-statistics.txt"
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89 cat `find $PWD/files/ -name "10_*"` > "$outdir/new_IMGT/10_V-REGION-mutation-hotspots.txt"
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90
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99
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91 mkdir $outdir/new_IMGT_ca
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92 cp $outdir/new_IMGT/* $outdir/new_IMGT_ca
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93
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116
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94 mkdir $outdir/new_IMGT_ca1
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95 cp $outdir/new_IMGT/* $outdir/new_IMGT_ca1
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96
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97 mkdir $outdir/new_IMGT_ca2
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98 cp $outdir/new_IMGT/* $outdir/new_IMGT_ca2
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99
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99
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100 mkdir $outdir/new_IMGT_cg
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101 cp $outdir/new_IMGT/* $outdir/new_IMGT_cg
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102
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116
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103 mkdir $outdir/new_IMGT_cg1
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104 cp $outdir/new_IMGT/* $outdir/new_IMGT_cg1
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105
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106 mkdir $outdir/new_IMGT_cg2
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107 cp $outdir/new_IMGT/* $outdir/new_IMGT_cg2
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108
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109 mkdir $outdir/new_IMGT_cg3
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110 cp $outdir/new_IMGT/* $outdir/new_IMGT_cg3
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111
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112 mkdir $outdir/new_IMGT_cg4
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113 cp $outdir/new_IMGT/* $outdir/new_IMGT_cg4
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114
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99
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115 mkdir $outdir/new_IMGT_cm
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116 cp $outdir/new_IMGT/* $outdir/new_IMGT_cm
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117
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114
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118 Rscript $dir/new_imgt.r $outdir/new_IMGT/ $outdir/merged.txt "-" 2>&1
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116
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119
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114
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120 Rscript $dir/new_imgt.r $outdir/new_IMGT_ca/ $outdir/merged.txt "ca" 2>&1
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116
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121 Rscript $dir/new_imgt.r $outdir/new_IMGT_ca1/ $outdir/merged.txt "ca1" 2>&1
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122 Rscript $dir/new_imgt.r $outdir/new_IMGT_ca2/ $outdir/merged.txt "ca2" 2>&1
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123
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114
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124 Rscript $dir/new_imgt.r $outdir/new_IMGT_cg/ $outdir/merged.txt "cg" 2>&1
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116
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125 Rscript $dir/new_imgt.r $outdir/new_IMGT_cg1/ $outdir/merged.txt "cg1" 2>&1
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126 Rscript $dir/new_imgt.r $outdir/new_IMGT_cg2/ $outdir/merged.txt "cg2" 2>&1
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127 Rscript $dir/new_imgt.r $outdir/new_IMGT_cg3/ $outdir/merged.txt "cg3" 2>&1
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128 Rscript $dir/new_imgt.r $outdir/new_IMGT_cg4/ $outdir/merged.txt "cg4" 2>&1
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129
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114
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130 Rscript $dir/new_imgt.r $outdir/new_IMGT_cm/ $outdir/merged.txt "cm" 2>&1
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95
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131
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132
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133 tmp="$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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99
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137 cd $outdir/new_IMGT_ca/
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138 tar -cJf ../new_IMGT_ca.txz *
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139
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117
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140 cd $outdir/new_IMGT_ca1/
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141 tar -cJf ../new_IMGT_ca1.txz *
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142
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143 cd $outdir/new_IMGT_ca2/
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144 tar -cJf ../new_IMGT_ca2.txz *
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145
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99
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146 cd $outdir/new_IMGT_cg/
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147 tar -cJf ../new_IMGT_cg.txz *
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148
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117
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149 cd $outdir/new_IMGT_cg1/
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150 tar -cJf ../new_IMGT_cg1.txz *
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151
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152 cd $outdir/new_IMGT_cg2/
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153 tar -cJf ../new_IMGT_cg2.txz *
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154
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155 cd $outdir/new_IMGT_cg3/
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156 tar -cJf ../new_IMGT_cg3.txz *
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157
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158 cd $outdir/new_IMGT_cg4/
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159 tar -cJf ../new_IMGT_cg4.txz *
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160
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99
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161 cd $outdir/new_IMGT_cm/
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162 tar -cJf ../new_IMGT_cm.txz *
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163
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95
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164 cd $tmp
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165
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55
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166 echo "---------------- mutation_analysis.r ----------------"
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102
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167 echo "---------------- mutation_analysis.r ----------------<br />" >> $log
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55
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168
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82
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169 classes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm,unmatched"
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4
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170 echo "R mutation analysis"
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82
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171 Rscript $dir/mutation_analysis.r $outdir/merged.txt $classes $outdir ${include_fr1} 2>&1
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53
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172
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55
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173
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174 echo "---------------- mutation_analysis.py ----------------"
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102
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175 echo "---------------- mutation_analysis.py ----------------<br />" >> $log
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55
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176
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82
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177 python $dir/mutation_analysis.py --input $outdir/merged.txt --genes $classes --includefr1 "${include_fr1}" --output $outdir/hotspot_analysis.txt
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55
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178
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179 echo "---------------- aa_histogram.r ----------------"
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105
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180 echo "---------------- aa_histogram.r ----------------<br />" >> $log
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55
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181
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107
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182 Rscript $dir/aa_histogram.r $outdir/aa_id_mutations.txt $outdir/absent_aa_id.txt "ca,cg,cm" $outdir/ 2>&1
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110
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183 if [ -e "$outdir/aa_histogram_.png" ]; then
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184 mv $outdir/aa_histogram_.png $outdir/aa_histogram.png
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185 mv $outdir/aa_histogram_.txt $outdir/aa_histogram.txt
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186 fi
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4
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187
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0
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188 genes=(ca ca1 ca2 cg cg1 cg2 cg3 cg4 cm)
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189
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53
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190 funcs=(sum mean median)
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110
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191 funcs=(sum)
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0
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192
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82
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193 echo "---------------- sequence_overview.r ----------------"
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102
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194 echo "---------------- sequence_overview.r ----------------<br />" >> $log
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82
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195
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196 mkdir $outdir/sequence_overview
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197
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100
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198 Rscript $dir/sequence_overview.r $outdir/before_unique_filter.txt $outdir/merged.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt 2>&1
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82
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199
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200 echo "<table border='1'>" > $outdir/base_overview.html
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201
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92
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202 while IFS=$'\t' read ID class seq A C G T
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82
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203 do
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85
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204 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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82
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205 done < $outdir/sequence_overview/ntoverview.txt
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206
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62
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207 echo "<html><center><h1>$title</h1></center>" > $output
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121
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208 echo "<meta name='viewport' content='width=device-width, initial-scale=1'>" >> $output
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110
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209 echo "<script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $output
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210 echo "<script type='text/javascript' src='tabber.js'></script>" >> $output
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211 echo "<script type='text/javascript' src='script.js'></script>" >> $output
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212 echo "<link rel='stylesheet' type='text/css' href='style.css'>" >> $output
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122
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213 echo "<link rel='stylesheet' type='text/css' href='pure-min.css'>" >> $output
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62
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214
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98
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215 matched_count="`cat $outdir/merged.txt | grep -v 'unmatched' | tail -n +2 | wc -l`"
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62
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216 unmatched_count="`cat $outdir/unmatched.txt | tail -n +2 | wc -l`"
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217 total_count=$((matched_count + unmatched_count))
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218 perc_count=$((unmatched_count / total_count * 100))
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219 perc_count=`bc -l <<< "scale=2; ${unmatched_count} / ${total_count} * 100"`
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220 perc_count=`bc -l <<< "scale=2; (${unmatched_count} / ${total_count} * 100 ) / 1"`
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221
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222 echo "<center><h2>Total: ${total_count}</h2></center>" >> $output
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223 echo "<center><h2>Matched: ${matched_count} Unmatched: ${unmatched_count}</h2></center>" >> $output
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224 echo "<center><h2>Percentage unmatched: ${perc_count}</h2></center>" >> $output
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225
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55
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226 echo "---------------- main tables ----------------"
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102
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227 echo "---------------- main tables ----------------<br />" >> $log
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110
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228
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229 echo "<div class='tabber'>" >> $output
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230 echo "<div class='tabbertab' title='SHM Overview'>" >> $output
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231
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53
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232 for func in ${funcs[@]}
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4
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233 do
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55
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234
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235 echo "---------------- $func table ----------------"
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102
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236 echo "---------------- $func table ----------------<br />" >> $log
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55
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237
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94
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238 cat $outdir/mutations_${func}.txt $outdir/hotspot_analysis_${func}.txt > $outdir/data_${func}.txt
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123
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239
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124
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240 echo "---------------- pattern_plots.r ----------------"
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241 echo "---------------- pattern_plots.r ----------------<br />" >> $log
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242
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243 Rscript $dir/pattern_plots.r $outdir/data_${func}.txt $outdir/plot1 $outdir/plot2 $outdir/plot3 2>&1
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244
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121
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245 echo "<table class='pure-table pure-table-striped'>" >> $output
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246 echo "<thead><tr><th>info</th>" >> $output
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53
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247 for gene in ${genes[@]}
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248 do
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249 tmp=`cat $outdir/${gene}_${func}_n.txt`
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250 echo "<th><a href='matched_${gene}_${func}.txt'>${gene} (N = $tmp)</a></th>" >> $output
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251 done
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78
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252
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114
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253 tmp=`cat $outdir/all_${func}_n.txt`
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254 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
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78
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255 tmp=`cat $outdir/unmatched_${func}_n.txt`
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121
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256 echo "<th><a href='unmatched.txt'>unmatched (N = ${unmatched_count})</a></th><tr></thead>" >> $output
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4
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257
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78
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258 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz unx uny unz allx ally allz
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53
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259 do
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260 if [ "$name" == "FR S/R (ratio)" ] || [ "$name" == "CDR S/R (ratio)" ] ; then #meh
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261 echo "<tr><td>$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} (${cmz})</td><td>${allx}/${ally} (${allz})</td></tr>" >> $output
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262 else
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114
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263 echo "<tr><td>$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} (${cmz}%)</td><td>${allx}/${ally} (${allz}%)</td><td>${unx}/${uny} (${unz}%)</td></tr>" >> $output
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53
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264 fi
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94
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265 done < $outdir/data_${func}.txt
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266 echo "</table>" >> $output
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267 #echo "<a href='data_${func}.txt'>Download data</a>" >> $output
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53
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268 done
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269
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124
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270 echo "<img src='plot1.png' /><br />" >> $output
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271 echo "<img src='plot2.png' /><br />" >> $output
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272 echo "<img src='plot3.png' /><br />" >> $output
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273
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110
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274 echo "</div>" >> $output #SHM overview tab end
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275
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276 echo "---------------- images ----------------"
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277 echo "---------------- images ----------------<br />" >> $log
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278
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279 echo "<div class='tabbertab' title='SHM Frequency'>" >> $output
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280
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281 if [ -a $outdir/scatter.png ]
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282 then
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283 echo "<img src='scatter.png'/><br />" >> $output
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284 echo "<a href='scatter.txt'>download data</a><br />" >> $output
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285 fi
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286 if [ -a $outdir/frequency_ranges.png ]
|
|
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287 then
|
|
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288 echo "<img src='frequency_ranges.png'/><br />" >> $output
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289 echo "<a href='frequency_ranges_classes.txt'>download class data</a><br />" >> $output
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290 echo "<a href='frequency_ranges_subclasses.txt'>download subclass data</a><br />" >> $output
|
|
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291 fi
|
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292
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293 echo "</div>" >> $output #SHM frequency tab end
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294
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295 echo "<div class='tabbertab' title='Transition tables'>" >> $output
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296
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114
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297 echo "<table border='0'>" >> $output
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298
|
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110
|
299 for gene in ${genes[@]}
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300 do
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114
|
301 echo "<tr>" >> $output
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302 echo "<td><h1>${gene}</h1></td>" >> $output
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303 echo "<td><img src='transitions_heatmap_${gene}.png' /></td>" >> $output
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304 echo "<td><img src='transitions_stacked_${gene}.png' /></td>" >> $output
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121
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305 echo "<td><table class='pure-table transition-table pure-table-bordered'>" >> $output
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110
|
306 while IFS=, read from a c g t
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307 do
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308 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
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|
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309 done < $outdir/transitions_${gene}_sum.txt
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114
|
310 echo "</table></td>" >> $output
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311
|
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312 echo "</tr>" >> $output
|
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110
|
313 done
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55
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314
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114
|
315 echo "<tr>" >> $output
|
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316 echo "<td><h1>All</h1></td>" >> $output
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317 echo "<td><img src='transitions_heatmap_all.png' /></td>" >> $output
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318 echo "<td><img src='transitions_stacked_all.png' /></td>" >> $output
|
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121
|
319 echo "<td><table class='pure-table transition-table pure-table-bordered'>" >> $output
|
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110
|
320 while IFS=, read from a c g t
|
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321 do
|
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322 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
|
|
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323 done < $outdir/transitions_all_sum.txt
|
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114
|
324 echo "</table></td>" >> $output
|
|
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325
|
|
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326 echo "</tr>" >> $output
|
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327
|
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110
|
328 echo "</table>" >> $output
|
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329
|
|
|
330 echo "</div>" >> $output #transition tables tab end
|
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331
|
|
|
332 echo "<div class='tabbertab' title='Antigen Selection'>" >> $output
|
|
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333
|
|
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334 if [ -a $outdir/aa_histogram.png ]
|
|
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335 then
|
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336 echo "<img src='aa_histogram.png'/><br />" >> $output
|
|
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337 echo "<a href='aa_histogram.txt'>download data</a><br />" >> $output
|
|
|
338 echo "<img src='aa_histogram_ca.png'/><br />" >> $output
|
|
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339 echo "<a href='aa_histogram_ca.txt'>download data</a><br />" >> $output
|
|
|
340 echo "<img src='aa_histogram_cg.png'/><br />" >> $output
|
|
|
341 echo "<a href='aa_histogram_cg.txt'>download data</a><br />" >> $output
|
|
|
342 echo "<img src='aa_histogram_cm.png'/><br />" >> $output
|
|
|
343 echo "<a href='aa_histogram_cm.txt'>download data</a><br />" >> $output
|
|
|
344 fi
|
|
|
345
|
|
|
346 echo "<embed src='baseline_ca.pdf' width='700px' height='1000px'>" >> $output
|
|
|
347 echo "<embed src='baseline_cg.pdf' width='700px' height='1000px'>" >> $output
|
|
|
348 echo "<embed src='baseline_cm.pdf' width='700px' height='1000px'>" >> $output
|
|
|
349
|
|
|
350 echo "</div>" >> $output #antigen selection tab end
|
|
|
351
|
|
|
352 echo "<div class='tabbertab' title='CSR'>" >> $output
|
|
|
353
|
|
|
354 if [ -a $outdir/ca.png ]
|
|
|
355 then
|
|
|
356 echo "<img src='ca.png'/><br />" >> $output
|
|
|
357 echo "<a href='ca.txt'>download data</a><br />" >> $output
|
|
|
358 fi
|
|
|
359 if [ -a $outdir/cg.png ]
|
|
|
360 then
|
|
|
361 echo "<img src='cg.png'/><br />" >> $output
|
|
|
362 echo "<a href='cg.txt'>download data</a><br />" >> $output
|
|
|
363 fi
|
|
|
364
|
|
|
365 echo "</div>" >> $output #CSR tab end
|
|
|
366
|
|
|
367 echo "<div class='tabbertab' title='Downloads'>" >> $output
|
|
94
|
368
|
|
121
|
369 echo "<table class='pure-table pure-table-striped'>" >> $output
|
|
|
370 echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output
|
|
114
|
371 echo "<tr><td>The complete dataset</td><td><a href='merged.txt'>Download</a></td></tr>" >> $output
|
|
123
|
372 echo "<tr><td>The SHM Overview table as a dataset</td><td><a href='data_sum.txt'>Download</a></td></tr>" >> $output
|
|
124
|
373 echo "<tr><td>The data used to generate the first SHM Overview plot</td><td><a href='plot1.txt'>Download</a></td></tr>" >> $output
|
|
|
374 echo "<tr><td>The data used to generate the sexond SHM Overview plot</td><td><a href='plot2.txt'>Download</a></td></tr>" >> $output
|
|
|
375 echo "<tr><td>The data used to generate the third SHM Overview plot</td><td><a href='plot3.txt'>Download</a></td></tr>" >> $output
|
|
114
|
376 echo "<tr><td>The alignment info on the unmatched sequences</td><td><a href='unmatched.txt'>Download</a></td></tr>" >> $output
|
|
|
377 echo "<tr><td>Motif data per sequence ID</td><td><a href='motif_per_seq.txt'>Download</a></td></tr>" >> $output
|
|
|
378 echo "<tr><td>Mutation data per sequence ID</td><td><a href='mutation_by_id.txt'>Download</a></td></tr>" >> $output
|
|
|
379 echo "<tr><td>AA mutation data per sequence ID</td><td><a href='aa_id_mutations.txt'>Download</a></td></tr>" >> $output
|
|
|
380 echo "<tr><td>Absent AA location data per sequence ID</td><td><a href='absent_aa_id.txt'>Download</a></td></tr>" >> $output
|
|
|
381 echo "<tr><td>CDR1+FR2+CDR2+FR3+CDR3 sequences that show up more than once</td><td><a href='sequence_overview/index.html'>Download</a></td></tr>" >> $output
|
|
|
382 echo "<tr><td>Base count for every sequence</td><td><a href='base_overview.html'>Download</a></td></tr>" >> $output
|
|
121
|
383 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</a></td></tr>" >> $output
|
|
114
|
384 echo "<tr><td>Baseline data</td><td><a href='baseline.txt'>Download</a></td></tr>" >> $output
|
|
|
385 echo "<tr><td>Baseline ca PDF</td><td><a href='baseline_ca.pdf'>Download</a></td></tr>" >> $output
|
|
|
386 echo "<tr><td>Baseline ca data</td><td><a href='baseline_ca.txt'>Download</a></td></tr>" >> $output
|
|
|
387 echo "<tr><td>Baseline cg PDF</td><td><a href='baseline_cg.pdf'>Download</a></td></tr>" >> $output
|
|
|
388 echo "<tr><td>Baseline cg data</td><td><a href='baseline_cg.txt'>Download</a></td></tr>" >> $output
|
|
|
389 echo "<tr><td>Baseline cm PDF</td><td><a href='baseline_cm.pdf'>Download</a></td></tr>" >> $output
|
|
|
390 echo "<tr><td>Baseline cm data</td><td><a href='baseline_cm.txt'>Download</a></td></tr>" >> $output
|
|
|
391 echo "<tr><td>An IMGT archive with just the matched and filtered sequences</td><td><a href='new_IMGT.txz'>Download</a></td></tr>" >> $output
|
|
|
392 echo "<tr><td>An IMGT archive with just the matched and filtered ca sequences</td><td><a href='new_IMGT_ca.txz'>Download</a></td></tr>" >> $output
|
|
116
|
393 echo "<tr><td>An IMGT archive with just the matched and filtered ca1 sequences</td><td><a href='new_IMGT_ca1.txz'>Download</a></td></tr>" >> $output
|
|
|
394 echo "<tr><td>An IMGT archive with just the matched and filtered ca2 sequences</td><td><a href='new_IMGT_ca2.txz'>Download</a></td></tr>" >> $output
|
|
114
|
395 echo "<tr><td>An IMGT archive with just the matched and filtered cg sequences</td><td><a href='new_IMGT_cg.txz'>Download</a></td></tr>" >> $output
|
|
116
|
396 echo "<tr><td>An IMGT archive with just the matched and filtered cg1 sequences</td><td><a href='new_IMGT_cg1.txz'>Download</a></td></tr>" >> $output
|
|
|
397 echo "<tr><td>An IMGT archive with just the matched and filtered cg2 sequences</td><td><a href='new_IMGT_cg2.txz'>Download</a></td></tr>" >> $output
|
|
|
398 echo "<tr><td>An IMGT archive with just the matched and filtered cg3 sequences</td><td><a href='new_IMGT_cg3.txz'>Download</a></td></tr>" >> $output
|
|
|
399 echo "<tr><td>An IMGT archive with just the matched and filtered cg4 sequences</td><td><a href='new_IMGT_cg4.txz'>Download</a></td></tr>" >> $output
|
|
114
|
400 echo "<tr><td>An IMGT archive with just the matched and filtered cm sequences</td><td><a href='new_IMGT_cm.txz'>Download</a></td></tr>" >> $output
|
|
120
|
401 echo "<tr><td>The Change-O DB file with defined clones</td><td><a href='change_o/change-o-db-defined_clones.txt'>Download</a></td></tr>" >> $output
|
|
|
402 echo "<tr><td>The Change-O DB defined clones summary file</td><td><a href='change_o/change-o-defined_clones-summary.txt'>Download</a></td></tr>" >> $output
|
|
114
|
403 echo "</table>" >> $output
|
|
99
|
404
|
|
110
|
405 echo "</div>" >> $output #downloads tab end
|
|
55
|
406
|
|
110
|
407 echo "</div>" >> $output #tabs end
|
|
0
|
408
|
|
|
409 echo "</html>" >> $output
|
|
2
|
410
|
|
95
|
411 echo "---------------- baseline ----------------"
|
|
102
|
412 echo "---------------- baseline ----------------<br />" >> $log
|
|
101
|
413 tmp="$PWD"
|
|
|
414
|
|
|
415 mkdir $outdir/baseline
|
|
|
416
|
|
|
417
|
|
|
418 mkdir $outdir/baseline/ca_cg_cm
|
|
102
|
419 if [[ $(wc -l < $outdir/new_IMGT/1_Summary.txt) -gt "1" ]]; then
|
|
|
420 cd $outdir/baseline/ca_cg_cm
|
|
114
|
421 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT.txz "ca_cg_cm" "$dir/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt"
|
|
102
|
422 else
|
|
|
423 echo "No sequences" > "$outdir/baseline.txt"
|
|
|
424 fi
|
|
101
|
425
|
|
|
426 mkdir $outdir/baseline/ca
|
|
102
|
427 if [[ $(wc -l < $outdir/new_IMGT_ca/1_Summary.txt) -gt "1" ]]; then
|
|
|
428 cd $outdir/baseline/ca
|
|
114
|
429 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_ca.txz "ca" "$dir/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_ca.pdf" "Sequence.ID" "$outdir/baseline_ca.txt"
|
|
102
|
430 else
|
|
|
431 echo "No ca sequences" > "$outdir/baseline_ca.txt"
|
|
|
432 fi
|
|
101
|
433
|
|
|
434 mkdir $outdir/baseline/cg
|
|
102
|
435 if [[ $(wc -l < $outdir/new_IMGT_cg/1_Summary.txt) -gt "1" ]]; then
|
|
|
436 cd $outdir/baseline/cg
|
|
114
|
437 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_cg.txz "cg" "$dir/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_cg.pdf" "Sequence.ID" "$outdir/baseline_cg.txt"
|
|
102
|
438 else
|
|
|
439 echo "No cg sequences" > "$outdir/baseline_cg.txt"
|
|
|
440 fi
|
|
101
|
441
|
|
|
442 mkdir $outdir/baseline/cm
|
|
102
|
443 if [[ $(wc -l < $outdir/new_IMGT_cm/1_Summary.txt) -gt "1" ]]; then
|
|
|
444 cd $outdir/baseline/cm
|
|
114
|
445 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_cm.txz "cm" "$dir/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_cm.pdf" "Sequence.ID" "$outdir/baseline_cm.txt"
|
|
102
|
446 else
|
|
|
447 echo "No cm sequences" > "$outdir/baseline_cm.txt"
|
|
|
448 fi
|
|
47
|
449
|
|
101
|
450 cd $tmp
|
|
|
451
|
|
82
|
452 echo "---------------- naive_output.r ----------------"
|
|
102
|
453 echo "---------------- naive_output.r ----------------<br />" >> $log
|
|
55
|
454
|
|
47
|
455 if [[ "$naive_output" != "None" ]]
|
|
|
456 then
|
|
114
|
457 cp $outdir/new_IMGT_ca.txz ${naive_output_ca}
|
|
|
458 cp $outdir/new_IMGT_cg.txz ${naive_output_cg}
|
|
|
459 cp $outdir/new_IMGT_cm.txz ${naive_output_cm}
|
|
47
|
460 fi
|
|
|
461
|
|
81
|
462 echo "</table>" >> $outdir/base_overview.html
|
|
|
463
|
|
120
|
464 echo "---------------- change-o MakeDB ----------------"
|
|
|
465 echo "---------------- change-o MakeDB ----------------<br />" >> $log
|
|
|
466
|
|
|
467 mkdir $outdir/change_o
|
|
|
468
|
|
|
469 tmp="$PWD"
|
|
|
470
|
|
|
471 cd $outdir/change_o
|
|
|
472
|
|
|
473 bash $dir/change_o/makedb.sh $input false false false $outdir/change_o/change-o-db.txt
|
|
|
474
|
|
|
475 echo "---------------- change-o DefineClones ----------------"
|
|
|
476 echo "---------------- change-o DefineClones ----------------<br />" >> $log
|
|
|
477
|
|
|
478 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 $outdir/change_o/change-o-defined_clones-summary.txt
|
|
|
479
|
|
|
480 PWD="$tmp"
|
|
|
481
|
|
105
|
482 mv $log $outdir/log.html
|
|
|
483
|
|
110
|
484 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
|
|
|
485 echo "<table border = 1>" >> $log
|
|
|
486 echo "<thead><tr><th>Info</th><th>Sequences</th><th>Percentage</th></tr></thead>" >> $log
|
|
|
487 tIFS="$TMP"
|
|
|
488 IFS=$'\t'
|
|
|
489 while read step seq perc
|
|
|
490 do
|
|
|
491 echo "<tr>" >> $log
|
|
|
492 echo "<td>$step</td>" >> $log
|
|
|
493 echo "<td>$seq</td>" >> $log
|
|
|
494 echo "<td>${perc}%</td>" >> $log
|
|
|
495 echo "</tr>" >> $log
|
|
|
496 done < $outdir/filtering_steps.txt
|
|
|
497 echo "</table border></center></html>" >> $log
|
|
|
498
|
|
|
499 IFS="$tIFS"
|
|
|
500
|
|
105
|
501
|
|
81
|
502 echo "---------------- Done! ----------------"
|
|
107
|
503 echo "---------------- Done! ----------------<br />" >> $outdir/log.html
|
|
47
|
504
|
|
110
|
505
|
|
|
506
|
|
|
507
|
|
|
508
|
|
|
509
|
|
|
510
|
|
|
511
|
|
|
512
|
|
|
513
|
|
|
514
|
|
|
515
|
|
|
516
|
|
|
517
|
|
|
518
|
|
|
519
|
|
|
520
|
|
|
521
|
|
|
522
|
|
|
523
|
|
|
524
|
