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1 #!/usr/bin/env perl
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2 use warnings;
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3 use strict;
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4
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5 $, = ' ';
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6 $\ = "\n";
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7 $, = "\t";
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8
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9 my $id = 0;
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10 my $buffer = '';
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11 my $start = 0;
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12 my $end = 0;
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13 my $score = 0;
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14 my $chrom = '';
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15
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16 while (<STDIN>) {
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17 chomp;
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18 next if /^$/;
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19 my @line = split('\s+');
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20 if (/^s\s+$ARGV[0]/) {
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21 $chrom = $line[1];
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22 $chrom =~ s/$ARGV[0]\.//;
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23 $start = $line[2];
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24 $end = $line[2] + $line[3];
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25 s/^s //;
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26 s/ +/:/g;
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27 my $temp = $_;
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28 $buffer = $buffer eq '' ? $temp : "$buffer,$temp";
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29 }
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30 elsif (/^a/) {
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31 $score = +(s/^a score=//);
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32 if($id > 0) {
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33 print $chrom, $start, $end, "$ARGV[0]_$id", $score, $buffer;
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34 }
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35 $id += 1;
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36 $buffer = '';
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37 }
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38
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39 elsif (/^s/) {
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40 s/^s //;
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41 s/ +/:/g;
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42 my $temp = $_;
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43 $buffer = $buffer eq '' ? $temp : "$buffer,$temp";
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44 }
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45 }
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46 print $chrom, $start, $end, "$ARGV[0]_$id", $score, $buffer;
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