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1 #!/bin/sh
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2
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3 # Version 0.1 , 15aug08
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4 # Written by Assaf Gordon (gordon@cshl.edu)
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5 #
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6
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7 LINES="$1"
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8 INFILE="$2"
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9 OUTFILE="$3"
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10
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11 if [ "$LINES" == "" ]; then
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12 cat >&2 <<EOF
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13 Remove Ending Lines
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14
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15 Usage: $0 LINES [INFILE] [OUTFILE]
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16
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17 LINES - number of lines to remove from the end of the file
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18 [INFILE] - input file (if not specified - defaults to STDIN)
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19 [OUTFILE]- output file (if not specified - defaults to STDOUT)
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20
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21 Input Example:
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22
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23 #Chr Start End
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24 chr1 10 15
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25 chr1 40 20
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26 chr1 21 14
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27 total 3 chromosomes
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28
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29 Removing 1 line (the last line) produces:
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30
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31 #Chr Start End
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32 chr1 10 15
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33 chr1 20 40
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34 chr 14 21
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35
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36 Usage Example:
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37
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38 \$ $0 1 < my_input_file.txt > my_output_file.txt
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39
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40 EOF
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41
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42 exit 1
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43 fi
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44
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45 #Validate line argument - remove non-digits characters
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46 LINES=${LINES//[^[:digit:]]/}
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47
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48 #Make sure the line strings isn't empty
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49 #(after the regex above, they will either contains digits or be empty)
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50 if [ -z "$LINES" ]; then
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51 echo "Error: bad line value (must be numeric)" >&2
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52 exit 1
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53 fi
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54
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55 # Use default (stdin/out) values if infile / outfile not specified
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56 [ -z "$INFILE" ] && INFILE="/dev/stdin"
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57 [ -z "$OUTFILE" ] && OUTFILE="/dev/stdout"
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58
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59 #Make sure the input file (if specified) exists.
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60 if [ ! -r "$INFILE" ]; then
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61 echo "Error: input file ($INFILE) not found!" >&2
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62 exit 1
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63 fi
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64
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65
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66 # The "gunzip -f" trick allows
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67 # piping a file (gzip or plain text, real file name or "/dev/stdin") to sed
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68 gunzip -f <"$INFILE" | sed -n -e :a -e "1,${LINES}!{P;N;D;};N;ba" > "$OUTFILE"
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69
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