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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 action=$1
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5 input=$2
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6 output=$3
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7
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8 cp $input $PWD/input.tab
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9
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10 input="$PWD/input.tab"
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11
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12 mkdir $PWD/outdir
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13
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14 if [ "fasta" == "$action" ] ; then
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15 python3 $dir/ParseDb.py fasta -d $input --outdir $PWD/outdir --outname output
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16 mv $PWD/outdir/output_sequences.fasta $output
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17 elif [ "clip" == "$action" ] ; then
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18 python3 $dir/ParseDb.py clip -d $input --outdir $PWD/outdir --outname output
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19 mv $PWD/outdir/output_sequences.fasta $output
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20 elif [ "split" == "$action" ] ; then
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21 field="`cat $input 2> /dev/null | head -n 1 | cut -f$4 | tr '\n\r' ' '`"
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22 label=$5
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23 mkdir $PWD/split
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24 python3 $dir/ParseDb.py split -d $input --outdir $PWD/split --outname output -f $field
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25 #rename "s/output_${field}/$label/" $PWD/split/*
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26 elif [ "add" == "$action" ] ; then
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27 field="`cat $input 2> /dev/null | head -n 1 | cut -f$4 | tr '\n\r' ' '`"
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28 value=$5
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29 python3 $dir/ParseDb.py add -d $input --outdir $PWD/outdir --outname output -f $field -u $value
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30 mv $PWD/outdir/output_parse-add.tab $output
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31 elif [ "delete" == "$action" ] ; then
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32 field="`cat $input 2> /dev/null | head -n 1 | cut -f$4 | tr '\n\r' ' '`"
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33 value=$5
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34 regex=$6
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35 if [ "true" == "$regex" ] ; then
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36 regex="--regex"
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37 else
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38 regex=""
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39 fi
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40 python3 $dir/ParseDb.py delete -d $input --outdir $PWD/outdir --outname output -f $field -u $value --logic any $regex
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41 mv $PWD/outdir/output_parse-delete.tab $output
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42 elif [ "drop" == "$action" ] ; then
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43 field="`cat $input 2> /dev/null | head -n 1 | cut -f$4 | tr '\n\r' ' '`"
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44 python3 $dir/ParseDb.py drop -d $input --outdir $PWD/outdir --outname output -f $field
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45 mv $PWD/outdir/output_parse-drop.tab $output
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46 elif [ "index" == "$action" ] ; then
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47 field=$4
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48 python3 $dir/ParseDb.py index -d $input --outdir $PWD/outdir --outname output -f $field
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49 mv $PWD/outdir/output_parse-index.tab $output
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50 elif [ "rename" == "$action" ] ; then
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51 field="`cat $input 2> /dev/null | head -n 1 | cut -f$4 | tr '\n\r' ' '`"
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52 newname=$5
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53 python3 $dir/ParseDb.py rename -d $input --outdir $PWD/outdir --outname output -f $field -k $newname
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54 mv $PWD/outdir/output_parse-rename.tab $output
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55 elif [ "select" == "$action" ] ; then
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56 field="`cat $input 2> /dev/null | head -n 1 | cut -f$4 | tr '\n\r' ' '`"
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57 value=$5
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58 regex=$6
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59 if [ "true" == "$regex" ] ; then
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60 regex="--regex"
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61 else
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62 regex=""
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63 fi
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64 python3 $dir/ParseDb.py select -d $input --outdir $PWD/outdir --outname output -f $field -u $value --logic any $regex
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65 mv $PWD/outdir/output_parse-select.tab $output
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66 elif [ "sort" == "$action" ] ; then
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67 field="`cat $input 2> /dev/null | head -n 1 | cut -f$4 | tr '\n\r' ' '`"
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68 num=$5
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69 tmp=""
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70 if [ "true" == "$num" ] ; then
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71 tmp="--num"
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72 fi
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73 desc=$6
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74 if [ "true" == "$desc" ] ; then
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75 tmp="--descend $tmp"
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76 fi
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77 python3 $dir/ParseDb.py sort -d $input --outdir $PWD/outdir --outname output -f $field $tmp
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78 mv $PWD/outdir/output_parse-sort.tab $output
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79 elif [ "update" == "$action" ] ; then
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80 field="`cat $input 2> /dev/null | head -n 1 | cut -f$4 | tr '\n\r' ' '`"
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81 value=$5
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82 replace=$6
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83 regex=$7
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84 if [ "true" == "$regex" ] ; then
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85 regex="--regex"
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86 else
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87 regex=""
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88 fi
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89 python3 $dir/ParseDb.py update -d $input --outdir $PWD/outdir --outname output -f $field -u $value -t $replace $regex
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90 mv $PWD/outdir/output_parse-update.tab $output
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91 fi
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92
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