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1 #!/bin/bash
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2
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3 # Sorting of GFF files.
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4 #
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5 # USAGE: sort_gff.sh [OPTIONS] -i IN.roi -o OUT.roi
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6 #
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7 # Options:
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8 # -r reverse orientation
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9 # -p sort by position (ref, start, end) -- default
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10
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11 # The parameters that we will pass to sort.
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12 SORT_POS_ARGS="-k 1,1 -k 2,2n -k 3,3n"
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13 SORT_POS_ARGS_REV="-k 1,1r -k 2,2nr -k 3,3nr"
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14
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15 # The arguments will go here.
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16 SORT_BY=beginPos
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17 REVERSE=
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18
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19 # Parse option values.
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20 while getopts "pc:i:o:n:r" opt; do
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21 case $opt in
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22 i)
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23 IN_FILE=$OPTARG
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24 ;;
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25 o)
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26 OUT_FILE=$OPTARG
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27 ;;
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28 r)
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29 REVERSE=r
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30 ;;
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31 \?)
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32 echo "Invalid option: -$OPTARG" >&2
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33 exit 1
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34 ;;
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35 esac
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36 done
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37
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38 # Check that -i or -o are given.
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39 if [[ "$IN_FILE" == "" || "$OUT_FILE" == "" ]]; then
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40 echo "Missing option -i or -o" >&2
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41 exit 1
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42 fi
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43
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44 # Setup sort args.
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45 case $SORT_BY in
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46 beginPos)
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47 if [[ "$REVERSE" == "r" ]]; then
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48 SORT_ARGS=${SORT_POS_ARGS_REV}
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49 else
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50 SORT_ARGS=${SORT_POS_ARGS}
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51 fi
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52 ;;
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53 esac
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54
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55 # Execute sorting.
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56 #echo "OUT_FILE=${OUT_FILE}" 2>&2
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57 #echo "SORT_ARGS=${SORT_ARGS}" 1>&2
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58 (
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59 export LC_ALL=C
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60 #echo "sort ${SORT_ARGS} <(grep -v '^#' ${IN_FILE});" 1>&2
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61 sort ${SORT_ARGS} <(grep -v '^#' ${IN_FILE});
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62 ) > ${OUT_FILE}
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63
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64 exit $?
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