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1 #!/bin/bash
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2 dir="$(cd "$(dirname "$0")" && pwd)"
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3
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4 args=("$@")
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5 output=$1
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6 inputs=("${args[@]:1}")
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7
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8 workdir="$PWD"
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9
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10 echo "Output: $output"
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11 echo "Inputs: ${inputs[@]}"
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12
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13 mkdir "$workdir/output"
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14
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15 function imgt_unpack {
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16 local imgt_zip=$1
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17 local outdir=$2
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18 if [ ! -d "$outdir" ]; then
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19 mkdir "$outdir"
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20 fi
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21 local type="`file $imgt_zip`"
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22 if [[ "$type" == *"Zip archive"* ]] ; then
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23 unzip $imgt_zip -d $outdir
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24 elif [[ "$type" == *"XZ compressed data"* ]] ; then
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25 mkdir -p $outdir
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26 echo "tar -xJf $imgt_zip -C $outdir"
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27 tar -xJf $imgt_zip -C $outdir
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28 fi
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29 }
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30
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31 function concat_imgt_files {
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32 indir=$1
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33 outdir=$2
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34 start_line=$3 #line # to start at, 2 to skip header
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1
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35 id=$4
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2
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36 if [[ "${start_line}" == "1" ]] ; then
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37 cat `find $indir/ -name "1_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>1) {$2=$2id; } print}' >> "$outdir/1_Summary.txt"
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38 cat `find $indir/ -name "2_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>1) {$2=$2id; } print}' >> "$outdir/2_IMGT-gapped-nt-sequences.txt"
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39 cat `find $indir/ -name "3_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>1) {$2=$2id; } print}' >> "$outdir/3_Nt-sequences.txt"
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40 cat `find $indir/ -name "4_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>1) {$2=$2id; } print}' >> "$outdir/4_IMGT-gapped-AA-sequences.txt"
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41 cat `find $indir/ -name "5_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>1) {$2=$2id; } print}' >> "$outdir/5_AA-sequences.txt"
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42 cat `find $indir/ -name "6_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>1) {$2=$2id; } print}' >> "$outdir/6_Junction.txt"
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43 cat `find $indir/ -name "7_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>1) {$2=$2id; } print}' >> "$outdir/7_V-REGION-mutation-and-AA-change-table.txt"
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44 cat `find $indir/ -name "8_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>1) {$2=$2id; } print}' >> "$outdir/8_V-REGION-nt-mutation-statistics.txt"
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45 cat `find $indir/ -name "9_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>1) {$2=$2id; } print}' >> "$outdir/9_V-REGION-AA-change-statistics.txt"
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46 cat `find $indir/ -name "10_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>1) {$2=$2id; } print}' >> "$outdir/10_V-REGION-mutation-hotspots.txt"
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47 else
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48 cat `find $indir/ -name "1_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>0) {$2=$2id; } print}' >> "$outdir/1_Summary.txt"
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49 cat `find $indir/ -name "2_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>0) {$2=$2id; } print}' >> "$outdir/2_IMGT-gapped-nt-sequences.txt"
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50 cat `find $indir/ -name "3_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>0) {$2=$2id; } print}' >> "$outdir/3_Nt-sequences.txt"
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51 cat `find $indir/ -name "4_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>0) {$2=$2id; } print}' >> "$outdir/4_IMGT-gapped-AA-sequences.txt"
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52 cat `find $indir/ -name "5_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>0) {$2=$2id; } print}' >> "$outdir/5_AA-sequences.txt"
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53 cat `find $indir/ -name "6_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>0) {$2=$2id; } print}' >> "$outdir/6_Junction.txt"
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54 cat `find $indir/ -name "7_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>0) {$2=$2id; } print}' >> "$outdir/7_V-REGION-mutation-and-AA-change-table.txt"
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55 cat `find $indir/ -name "8_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>0) {$2=$2id; } print}' >> "$outdir/8_V-REGION-nt-mutation-statistics.txt"
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56 cat `find $indir/ -name "9_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>0) {$2=$2id; } print}' >> "$outdir/9_V-REGION-AA-change-statistics.txt"
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57 cat `find $indir/ -name "10_*"` | tail -n+${start_line} | awk -F $'\t' -v id=$id 'BEGIN {OFS = FS} { if(NR>0) {$2=$2id; } print}' >> "$outdir/10_V-REGION-mutation-hotspots.txt"
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58 fi
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59
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0
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60 }
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61
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62 echo "Unpacking IMGT file 1.."
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63 imgt_unpack ${inputs[0]} "$workdir/input1"
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64
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65 echo "Concatenating IMGT file 1..."
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1
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66 id=${inputs[1]}
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67 concat_imgt_files "$workdir/input1" "$workdir/output" 1 $id
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0
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68
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1
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69 remaining_inputs=("${inputs[@]:2}")
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0
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70
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1
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71 i="0"
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72 while [ $i -lt ${#remaining_inputs[@]} ]; do
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73 j=$((i+1))
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74 input="${remaining_inputs[$i]}"
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75 id="${remaining_inputs[$j]}"
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76
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77 echo "Unpacking IMGT file $j.."
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0
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78 current_dir="$workdir/input${i}"
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79 imgt_unpack "${input}" "${current_dir}"
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80 echo "Concatenating IMGT file $1..."
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1
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81 concat_imgt_files "${current_dir}" "$workdir/output" 2 $id
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82 i=$((i+2))
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0
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83 done
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84
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2
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85 echo "`head $workdir/output/1_Summary.txt`"
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86
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1
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87
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0
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88 echo "Creating new IMGT zip"
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89 cd "$workdir/output"
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90 tar cfJ "$output" *
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91
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92 #awk to fix the sequence numbers repeating?
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93
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94 echo "Done"
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1
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95
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96 exit 0
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97
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98 i="1"
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99 for input in "${remaining_inputs[@]}"
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100 do
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101 echo "Unpacking IMGT file $i.."
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102 current_dir="$workdir/input${i}"
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103 imgt_unpack "${input}" "${current_dir}"
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104 echo "Concatenating IMGT file $1..."
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105 concat_imgt_files "${current_dir}" "$workdir/output" 2 $id
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106 i=$((i+1))
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107 done
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108
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