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1 #!/usr/bin/perl -w
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2 ###
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3 ###Yufei LUO
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4 ###
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5
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6 use strict;
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7
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8 my $in_file = $ARGV[0];
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9 my $out_file = $ARGV[1];
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10 my $sort_type = $ARGV[2]; # n(umeric) or a(lphanumeric)
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11 my ($line,$ID,$nbOverlaps,%hash);
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12
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13 open(IN, $in_file);
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14 while ($line = <IN>){
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15 chomp($line);
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16 $line=~s/\t/|/g;
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17 my @part=split(/\|/,$line);
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18 my @split=split(";",$part[$#part]);
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19 $split[0] =~ m/^(\w+).+$/;
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20
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21 foreach my $i (@split){
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22 if ($i=~m/nbOverlaps=(.+)/){
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23 $nbOverlaps=$1;
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24 }
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25 if ($i=~m/gene_id=(.+)/){
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26 $ID=$1;
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27 $hash{$ID}=$nbOverlaps;
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28 }
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29 }
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30 }
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31 close(IN);
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32
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33 open(OUT, ">$out_file");
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34 foreach my $key ( sort keys %hash) {
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35 print OUT "$key\t$hash{$key}\n";
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36 }
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37 close(OUT);
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