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0
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1 set -e
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2
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3 dir="$(cd "$(dirname "$0")" && pwd)"
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4
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5 args=($@)
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6 inputs=(${args[@]:1})
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7 output="${args[0]}"
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8 echo "$PWD"
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9
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10 function get_summary_file
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11 {
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12 imgt_zip=$1
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13 summary_file=$2
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14
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15 mkdir ${PWD}/tmp/
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16 type="`file ${imgt_zip}`"
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17 if [[ "$type" == *"Zip archive"* ]] ; then
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18 unzip ${imgt_zip} -d $PWD/tmp/
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19 elif [[ "$type" == *"XZ compressed data"* ]] ; then
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20 mkdir "$PWD/tmp/files"
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21 tar -xJf ${imgt_zip} -C $PWD/tmp/files
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22 fi
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23
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24 cat $PWD/tmp/*/1_* > ${summary_file}
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25 rm -rf $PWD/tmp
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26 }
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27
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28 index=0
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29
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30 echo -e "Patient\tReceptor\tSample\tCell_Count\tClone_Molecule_Count_From_Spikes\tLog10_Frequency\tTotal_Read_Count\tV_Segment_Major_Gene\tJ_Segment_Major_Gene\tClone_Sequence\tCDR3_Sense_Sequence\tRelated_to_leukemia_clone" > "$output"
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31
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32 while true
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33 do
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34 patient="${inputs[$index]}"
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35 index=$((index + 1))
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36 cell_count="${inputs[$index]}"
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37 index=$((index + 1))
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38 receptor="${inputs[$index]}"
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39 index=$((index + 1))
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40 sample_count="${inputs[$index]}"
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41 index=$((index + 1))
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42
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43 sample_name="${inputs[$index]}"
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44 index=$((index + 1))
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45
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46 sample_file="${inputs[$index]}"
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47 index=$((index + 1))
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48
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49 echo "patient: $patient"
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50 echo "cell_count: ${cell_count}"
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51 echo "receptor: $receptor"
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52 echo "sample_count: ${sample_count}"
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53 echo "sample_name: ${sample_name}"
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54 echo "sample_file: ${sample_file}"
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55
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56 get_summary_file ${sample_file} ${PWD}/summ.txt
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57
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58 Rscript --verbose $dir/from_imgt.r ${PWD}/summ.txt ${patient} ${sample_name} ${cell_count} ${receptor} ${PWD}/tmp.txt 2>&1
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59 cat "${PWD}/tmp.txt" >> "$output"
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60
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61 if [[ "${sample_count}" -gt "1" ]]; then
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62 sample_name="${inputs[$index]}"
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63 index=$((index + 1))
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64
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65 sample_file="${inputs[$index]}"
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66 index=$((index + 1))
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67
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68 echo "sample_name: ${sample_name}"
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69 echo "sample_file: ${sample_file}"
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70
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71 get_summary_file ${sample_file} ${PWD}/summ.txt
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72
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73 Rscript --verbose $dir/from_imgt.r ${PWD}/summ.txt ${patient} ${sample_name} ${cell_count} ${receptor} ${PWD}/tmp.txt 2>&1
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74 cat "${PWD}/tmp.txt" >> "$output"
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75 fi
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76
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77 if [[ "${sample_count}" -eq "3" ]]; then
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78 sample_name="${inputs[$index]}"
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79 index=$((index + 1))
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80
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81 sample_file="${inputs[$index]}"
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82 index=$((index + 1))
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83
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84 echo "sample_name: ${sample_name}"
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85 echo "sample_file: ${sample_file}"
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86
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87 get_summary_file ${sample_file} ${PWD}/summ.txt
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88
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89 Rscript --verbose $dir/from_imgt.r ${PWD}/summ.txt ${patient} ${sample_name} ${cell_count} ${receptor} ${PWD}/tmp.txt 2>&1
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90 cat "${PWD}/tmp.txt" >> "$output"
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91 fi
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92 if [[ "${index}" -eq "${#inputs[@]}" ]]; then
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93 exit 0
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94 fi
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95 done
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96
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97
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98
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99
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100
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101
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102
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103
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104
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